Talk:Protein/Archive 1

Energy
Would be helpful if the article discussed how proteins can provide energy.

Vegan protein mixing
''Nutritionally, proteins come in two forms: complete proteins contain all eight of the essential amino acids while incomplete protein is missing at least one. The human body requires 14 other amino acids, which it can synthesize from the essential amino acids. Animal-derived foods contain all of those amino acids, while plant sources do not. That is why vegans must mix their protein sources. Ovo-lacto vegetarians usually do not have this problem, since egg's white and cow's milk contain all essential amino acids, as well as soy milk.''
 * If soy contains all esential amino acids, and the 14 other amino acids can be synthesized from the essential amino acids, then why do vegans need to "mix their protein sources?"
 * 68.22.248.146 09:31, 15 Oct 2003 (UTC)
 * Different protein sources contain different mixes of amino acids. A mix of protein sources is the best way to ensure that the body obtains the essential amino acids that it requires, and in sufficient quantity. Non-vegans usually have a sufficient mix without having to worry to much (but see Super Size Me). Physchim62 21:13, 29 May 2005 (UTC)

Molecular weight cap
Capping protein molecular weights at 100,000 is way way underkill. Multisubunit proteins can go a lot higher than that. Polymerized hemoglobin S has an aggregate molecular weight in the millions (I won't even get into such multisubunit freaks as worm oxygen carrying pigments), and what about the molecular weight of a blood clot? -- David M

Genetic and protein engineering
Ok, if protein engineering is the field of playing with proteins after the genetic component, doesn't that lead to confusion with those researchers who were and are involved in de novo protein design, such as the Dickersons of Duke? - Dwmyers

Article appeal to layman, nutrition
This article has a good, systematic description of proteins. However, as this article should be interesting to the layman, we should start by indicating why proteins are important (nutrition and function in biology). I'll get started on this. -adam
 * One can go too far with this kind of thinking. It might be that for most people mustangs are a kind of car, but that's not the subject with which I would want to begin a general article on mustangs. Actually, maybe it's a mistake to try to make an all-purpose protein article. How about a separate one called Protein (nutrition)?168... 19:58 2 Jun 2003 (UTC)
 * I'm going to go ahead and do that (separate the content into two articles, one called Protein (biochemistry) and one called Protein (nutrition)) unless people strenuously object or I hear a good reason why not. 168... 02:46 4 Jun 2003 (UTC)
 * I see there is a nutrition section. It should not be listed first, but we can definately build it up. Science always comes first, as it defines the application. Tyciol 18:28, 1 March 2006 (UTC)
 * I think it's a big mistake to give nutrition equal time with biochemistry and other, more important aspects of proteins discussed in this article. To wit, the discussion in the intro about protein as it relates to nutrition stands out like a sore thumb, and it should be replaced with a disambiguation link. // Internet Esquire 04:19, 23 August 2006 (UTC)

Muscle fibres

 * "For example, muscle is composed of protein fibers, but these fibers have nothing to do with enzymatic reactions."

This is contrary to my understanding of muscle contraction and should be removed. ATP hydrolysis by the myosin, one of the proteins in muscle fibers, is an enzymatic reaction that directly contradicts that above statement. -Barry Hicks
 * You're right, at least so far as the way I use the mushy term "enzymatic." That error was introduced by an unregistered user. I changed it.168... 18:14, 20 Jan 2004 (UTC)
 * The author(s) who originally wrote the sentence or someone else who knows about the topic may not see your note or the mistake. If you know about this, you should feel free to make the necessary corrections. Dori | Talk 17:28, Jan 20, 2004 (UTC)

Title and disambiguation
I think it would be better for the primary article on protein to be the biochemical version (i.e. move protein (biochemistry) back to protein), and we can have a link to protein (nutrition) sense in a disambiguation section. In general if a word has one primary sense, it's best to have to primary article at that word, then then point to other one's in a disambiguation block. This way we would preserve the history of the current article. --Lexor 23:27, 20 Jan 2004 (UTC)


 * Here's the complete and single-sense definition of protein in the American Heritage Dictionary
 * Any of a group of complex organic macromolecules that contain carbon, hydrogen, oxygen, nitrogen, and usually sulfur and are composed of one or more chains of amino acids. Proteins are fundamental components of all living cells and include many substances, such as enzymes, hormones, and antibodies, that are necessary for the proper functioning of an organism. They are essential in the diet of animals for the growth and repair of tissue and can be obtained from foods such as meat, fish, eggs, milk, and legumes.

So, according to the AHD, the primary and only sense of the word includes the significance of protein as a component of nutrition. As a former molecular bioscientist, I like you, think of proteins foremost as molecules and not as something to chew on or digest. But I think we are in the minority, and I don't see on what basis we could argue that what "protein" means to us is more important than what "protein" means to most people. To give over the article title "protein" to just one of its connotations is in effect to assert exactly that. Maybe no nutrio-centrists are complaining now, but we've seen this kind of complaining over Gaia theory, and I'd rather we just do this in a way that doesn't open such cans of worms. Although I had forgotten all about it, I noticed I brought this up in June and nobody had objected since, so I just went ahead with it today. User:Stewartadcock has already been at work chaning "protein" links all over Wikispace to "protein (biochemistry)" links. If we were to decide to undo the change of title, I wouldn't want to be the person to tell him.168... 23:44, 20 Jan 2004 (UTC)


 * Don't worry... it was only about 15 minutes work while I was waiting for some data to be processed. I, basically, just modified the links that went to Proteins a redirect page, rather than Protein -- so they probably needed changing anyway. [User:Stewartadcock|Stewart Adcock]] 18:14, 21 Jan 2004 (UTC)
 * Sorry, I only notice your Talk comment from June 2003 just now, I don't think I had the article on my watchlist back then. It seems to me that protein in the biochemistry sense and the nutrition sense are really talking about the same thing underneath: protein molecules.  Couldn't we simply have a nutrition section within the main protein article on nutrition.  It just doesn't seem that they're different enough concepts to warrant separate articles, unlike, say, law: which has a scientific and a legal meaning?   I suspect most people won't search for the two meanings when they link to protein, and so they'll have to go through another hop to get there, which sort of violates a common Wikipedia principle I've seen invoked: the principle of least surprise (this principle is mentioned in several places, but I'll be darned if I can actually find the link in the Wikipedia: namespace). If we do decide to switch back, I'd be happy to undertake the link switching task. --[User:Lexor|Lexor]] 01:24, 21 Jan 2004 (UTC)
 * I'm attracted by your solution of putting the protein nutrition content into whatever larger article exists on nutrition, but after a moment of teetering I am back to favoring the tack I just took. My reasons are a) I think your proposed solution would require vigilance and enforcement, because the way nutrition info collected in the single protein article was just that people with stuff to say about it liked the thought of sticking it in an article with "protein" in the title, which is liable to happen again and again; and b)there's a lot that can be said about nutrition, and to require that everything nutritional that pertains to protein appears in a single universal nutrition article is in effect to hamper and perhaps limit the growth of both that article and nutrition content generally on Wikipedia. What do you think? Do you disagree? (generous of you to offer to change the links back BTW. Not an antidote to the feeling of wasted effort, but a pill sweetener for sure)168... 02:52, 21 Jan 2004 (UTC)
 * I still think it would be possible to have a protein nutrition section which could be more-or-less for nutrition oriented information, so long as its obvious. I still think that having the main article on protein and a separate protein (nutrition) would be relatively uncontroversial, but I'm happy with having a single article too.  I don't think what's been done is wasted effort either because the hard work of separating the information has already been done. --Lexor 03:31, 21 Jan 2004 (UTC)


 * Also I notice that the current protein (nutrition) article already mentions aspects of the molecular nature of proteins that would make the most sense in the context of a full protein article. If there is a need for a more specialized article on protein in humans, we could create a link to a Main article: protein nutrition in humans or somesuch, and leave a brief summary in the protein article (cf. simulation and computer simulation for an example of this). In fact the more I think about, the more having a single protein article makes sense.  --Lexor 03:35, 21 Jan 2004 (UTC)
 * I'm skeptical, in part because I'm not sure I understand what you have in mind. What would you think of creating a test page? --168...
 * Done, see User:Lexor/Temp/Protein. --Lexor 11:18, 22 Jan 2004 (UTC)

I don't object to an unlimited amount of nutritional info about proteins stuck at the bottom, but what originally got me on this hobby horse was that people were sticking it at the top, right after the intro 'graph. I'm not competent to edit the nutritional info, and with all the fad diets and nutty ideas available for promulgation, I could imagine the section bloating without limit as I stand helpless to edit out the chaff from the gluten and watch what I think of as most important sink lower down the page and away from their pertinent introductory remarks. At first blush, I didn't take to your idea of a protein nutrition in humans article, perhaps because of the title, but I think that could be the answer to my bloat fears. You didn't seem to think so, but I think it would be essential. So if you do go in for the idea of the text page, I'd like to see what you would pick as the minimal nutritional requirement for this article. Assuming it would be brief, I suppose it would be best at the top where there was a section before.168... 04:05, 21 Jan 2004 (UTC)
 * Putting everything regarding nutrition (but with a brief note of nutrition issues in the introduction) at the bottom would be fine with me. I think when it begins to get large or drift from talking about protein into diets and other more nebulous issues, then we could split off that information into another article.  At the moment the information in the current protein (nutrition) would seem to fit comfortably in one article. --Lexor 04:16, 21 Jan 2004 (UTC)

Do you have an answer for the people who wanted that stuff up top, or shall we just hope they never come back again?168... 04:25, 21 Jan 2004 (UTC)
 * I think mention of role of protein in nutrition is entirely appropriate in the intro, just about as much as is included in the dictionary definition you cited should be enough. Where more details can be found will appear in the TOC which will appear immediately after the first 1-2 paras anyway. --Lexor 11:06, 22 Jan 2004 (UTC)
 * O.K., I like that fine (including the test page, which I visited), but remember when the revolution comes I'll be saying this was your idea.168... 04:11, 23 Jan 2004 (UTC)

Merge is complete, I've started switching links back, but got to go offline for a while. The number of links to the main protein article still dwarf the protein (biochemistry), protein (nutrition) ones, however, so it's not so bad. I put editorial comment about possible sub-article protein and nutrition in main article in HTML comment. --Lexor 04:37, 23 Jan 2004 (UTC)
 * There isn't a mention of Protein as a food in the intro at the moment. I think it needs to be there, regardless of the fact that links from nutrition related articles don't point here. How about starting the article "Proteins, one of the major classes of biochemical macromolecules ..." Richard Taylor

Proteins differ from Carbohydrates...
Proteins differ from carbohydrates chiefly in that they contain much nitrogen and a little bit of sulfur, besides carbon, oxygen and hydrogen
 * I'm not sure that I like this sentence. It seems to infer that a protein is a carbohydrate with nitrogen and sulfur in the structure, which is of course patently wrong.  It also seems somewhat incomplete to compare Proteins to Carbohydrates without also comparing them to other bio-macromolecules such as lipids and nucleic acids.  Is anyone adamantly opposed to removal or replacement of this line?

Banks 22:01, 24 Sep 2004 (UTC)
 * I agree that this is a junky sentence. I would be happy to see it go. Josh Cherry 22:06, 25 Sep 2004 (UTC)

Protein data bank
The Protein data bank has its own entry, and the small amount of infomation given about in this entry doesn't really add anything, mabye the PDB should be added as a see also --nixie 06:00, 8 Oct 2004 (UTC)
 * I demoted the section to be under Structure, and added a main article link. I think it's worth a small subsection within the larger article, but as you point out, it doesn't really need to be a top-level section. --Lexor|Talk 06:48, Oct 8, 2004 (UTC)

English translation
I added an English translation of the etymological quote near the bottom of the page. It was off the top of my head though, so I may have not quite hit the mark. It's at least approximately correct, but if anybody knows of a better translation, or can translate it better, please replace it. Jonathan Grynspan 02:36, 22 Nov 2004 (UTC)

Factual errors and misleading half-truths on nutrition
The section on nutrition currently contains a number of errors. Most glaring of these is the myth about "complete proteins." References to this outdated concept should be removed, or heavily qualified.
 * When protein is listed on a nutrition label it only refers to the amount of complete proteins in the food, though the food may be very strong in a subset of the essential amino acids.

This claim can't be correct. Gelatin, for instance, is completely deficient in the essential amino acid tryptophan. That is, 0% of the protein in gelatin is "complete protein." Look at a nutrition label for gelatin, however, and you'll see that the majority of the mass is listed as "protein."
 * Animal-derived foods contain all of those amino acids, while plants are typically stronger in some acids than others.

False. Take the aforementioned gelatin, for instance. It's an incomplete protein that is entirely animal-derived. And the comment on plant proteins is virtually meaningless, since all proteins (both plant- and animal-derived) are "stronger in some acids than others."
 * Complete proteins can be made in an all vegan diet by eating a sufficient variety of foods and by getting enough calories (and similar references to "complete protein" in subsequent paragraphs).

Half-true, at best. All plant-derived proteins are complete. (Source: "A basic course in vegetarian and vegan nutrition," by George Eisman, R.D.) Check a breakdown of amino acids for common plant foods, and you'll find all the EAAs are there. The second part of the statement is correct, however. According to the ADA, "Plant protein can meet requirements when a variety of plant foods is consumed and energy needs are met."
 * vegetarians and especially vegans should be careful to eat appropriate combinations of foods (e.g. nuts and green vegetables) so as to get all the essential amino acids in sufficient quantities that the body may produce all the proteins that it needs.

Misleading. The fact is, protein deficiency is virtually unheard of among vegetarians and vegans, unless they're not meeting their caloric needs (e.g., anorexics) or they're getting almost all their calories from a non-protein source (e.g., alcoholics). A more realistic concern might be getting too much protein. This is far easier to do in the industrialized nations where protein intake typically exceeds the RDA, which can lead to long-term damage to the kidneys and liver, osteoporosis, and some types of cancer.

Unless someone has facts to dispute any of the above, I'd like to change the page to remove these common myths about protein requirements in human nutrition. --Hoss Firooznia
 * I don't see anything misleading or negative about the "vegans being careful to combine foods". Although plants have all EAA, some of them are in minuscule amounts. The article only says that people "should be careful", not that they should or must combine foods, or that protein deficiency is common in vegs. Some of the symptoms of protein deficiency are pretty vague and can be attributed to a lot of things, so I wonder how often it is diagnosed at all, or even considered a potential problem. Maybe it's virtually unheard of, but that's not necessarily because it doesn't happen. For example, if a limiting AA is mostly used in proteins of muscle, tthen is it possible that a vegan bodybuilder might have a protein deficiency? Point is, there's just so many variables here that it's unwise to remove anything based on "virtually unheard of". I basically agree with the rest of your points. --jag123 06:10, 15 Apr 2005 (UTC)
 * Although plants have all EAA, some of them are in minuscule amounts.
 * I don't know your definition of minuscule, but no relevant plant protein has a BV much below 50%. And that was usually determined before it was found out that growth experiments in rats are misleading (since rats have a 50% higher methionine requirement in proportion to total protein than humans), which especially lead to legumes getting undeservedly low scores. With this mistake corrected, soy and sweet lupine actually have a PDCAAS of 1.0, or simply speaking, they are complete.
 * Some of the symptoms of protein deficiency are pretty vague
 * For example? I rather think that some doctors like to attribute rather vague symptoms to "protein deficiency" in spite of a total lack of evidence.
 * For example, if a limiting AA is mostly used in proteins of muscle, tthen is it possible that a vegan bodybuilder might have a protein deficiency?
 * Much speculation, but no evidence. BTW, the idea that bodybuilders would need a higher ratio of protein to total calories is still unproven (although of course some companies make a lot of money off it, of course). If you exercise your muscles and make sure to meet caloric demands, you'll automatically consume more calories, and thus, if protein ratio is unchanged, get more protein.
 * Point is, there's just so many variables here that it's unwise to remove anything based on "virtually unheard of".
 * Scientists have known for at least two decades that human protein requirements are incredibly low, much lower than they used to believe. In terms of total calories, human mother's milk contains only 5-7% protein, which is less than half that of a typical herbivore (cow, >15%) and one third that of a typical omnivore used as a lab animal (rat, 20%). Studies have shown that edema attributed to protein deficiency in famined people (similar to "Kwashiorkor", only in adults) can be cured just by meeting caloric demands, even if protein makes up for only 2.5% of total calories. I mean, that's less than 1/3 the protein content of rice, which at 8% is by far the grain with the lowest protein content (wheat and rye, e.g. contain about twice that, and thus about as much protein as cow's milk).
 * IOW: Just about the only way to miss out on protein for a strict vegetarian is to
 * Eat too little (caloric demands not met)
 * Get most calories out of empty foods such as sugar, vegetable oils and fats, alcohol.
 * Eat no protein-rich foods (like pulses) at all. This includes soy, of course, which contains 40% complete protein.
 * I'm sure there are people who manage to do this, but this will inevitably lead to all kinds of deficiencies including severe mineral and vitamin deficiencies anyway. It has nothing to do with strict vegetarianism as such, though, because an unbalanced diet will make you sick in any case. (If you don't believe me, try watching Super Size Me.)
 * So the warning is a) redundant, b) misleading (it suggests an extraordinary risk that isn't there) and c) not backed by the evidence. What more does it take to warrant its removal? Aragorn2 22:50, 16 Apr 2005 (UTC)
 * Can you provide references for the claims you make? I still think making that statement isn't really a big deal. If I decide to eat to salad for most of my meals, it's unlikely for me to have a protein deficiency? --jag123 16:33, 17 Apr 2005 (UTC)
 * Sure. Let's start with the protein content of different species' milk:
 * I have trouble finding appropriate figures for rats, but Bell G. Textbook of Physiology and Biochemestry, 4th ed., Williams and Wilkins, Baltimore, 1959, p. 12. is quoted to state a protein ratio of 8 to 11% of _total mass_, mind you, not total calories, and this web page states that rat's milk contains "8.8% of protein" (search for this exact text), which is probably an average. So though rat's milk is probably thicker than cow's milk and human milk, it should be obvious that it's very high in protein.
 * Now for cow's (whole fat) milk. Here, figures are more easily available, e.g., though better matches the average composition of cow's milk actually sold in Western countries, which is: 3.8% fat, 4.8% lactose, and 3.3% protein. With about 400kcal per 100g of protein and carbohydrate, and 900kcal per 100g of fat, that leaves us with a protein to total calories ratio of 19.8%, slightly higher than the numbers I gave above, but note that these are subject to some fluctuation anyway.
 * Next stop human milk. Most sources report a pretty constant 7% lactose (i.e. carbohydrate) and 3-5% fat, while protein content varies widely from 0.8 to 1.6%, see, , , and . That leaves us with a protein to total calories ratio of 4.2% (for 0.8g protein and 5g fat) to 10.4% (for 1.6g and 3g fat), but in practice the range is of course narrower since you'll hardly ever find the minimum protein and maximum fat contents I used, or vice versa, in the same individual. Not the 5-7% I had in mind from other sources, but it's close. Please take note of the last link in particular. The colored triangle at the top provides the caloric ratio. The blue corner would denote foods that are 100% protein (wrt total calories). The line that connects the green and red corners represents foods that contain no protein at all. And while you're at it examining this page: 100g of human milk are stated to provide 2% of the protein DV, which means an adult would have to consume 5kg (about 11 US lbs, or more than 1.3 gallons) of human milk to meet his DV, that is the recommended minimum protein intake. This however corresponds to 3500kcal, or 1.75 times the caloric demands of an average woman rsp. about 1.4 times the average caloric demands of a man, which means that an adult person, who should be expected to have lower protein requirements than a newborn baby, would begin to suffer from severe protein deficiency if he/she got all his/her energy from human milk. That is, of course, if and only if the recommendations have any foundation in fact.
 * And finally: Soy milk. If it consists only of soybeans and water (the traditional Asian production process), it contains the same ratio as dried soybeans, that is about 35% in this case (note that approx. 1/3 of total carbohydrate is dietary fibre and thus has zero usable calories). If it's made into a replacement product for cow's milk, typically some sucrose is added for taste. In that case, the ratio will be somewhat lower.
 * Some PDCAAS ratings. Ok, I was wrong, wheat protein isolate ("seitan") is a plant protein that does have a very low PDCAAS, though whole wheat has got a much higher score. As User:Hoss Firooznia pointed out, there are examples of animal proteins with lower ratings though, namely, gelatine has a PDCAAS marginally above zero because of its lack of tryptophane.
 * And protein contents of other selected foods: Broccoli: 26%, spinach: 30%, lettuce: 22%, walnuts: 8%, peanuts: 14%, rice: white: 8%, brown: also 8%, rye flour: dark: 13%, light: 8%, wheat: whole-grain: 15%, white: 11%, durum wheat (used in noodle production): 14%, blackberries: 11%, oats: 15%. I'm sorry - the ratios for white wheat and rye flour aren't that much higher than in rice, though those for whole-grain flours are, and even those only have 1.5 to 1.9 times the protein content, not 2 times.
 * Methionine requirements in rats - sorry, this is all I found at the moment. (Methionine is mostly found in meat, milk and grains, which means foods other than those scored worse than they should wrt to human requirements.)
 * A link to a study on Kwashiorkor. I think I misquoted this as a study on adults. It's actually a study that involved children, and it found that 2.5% protein is enough to cure symptoms of famine, provided caloric demands are met, even in children. It's uncertain whether even these measly 2.5% were "complete", that is, had a PDCAAS of 1.0. Note that while famine-related edema can be cured at these very low protein intakes, I do not claim that children can experience maximum growth on these diets. This might be the case or it might not.
 * The WHO recommends at least 37g of protein a day for an adult, which corresponds to about 6-7.5% of total calories.
 * If I decide to eat to salad for most of my meals, it's unlikely for me to have a protein deficiency? - Lettuce contains 22% of its calories in the form of protein (see above), so I think it's rather less likely to suffer a protein deficiency than if you'd decide to eat nothing but gummy bears. Both constellations are about equally representative of strict vegetarians on the one hand and omnivores on the other.
 * I hope that was all that you asked for. Best regards, Aragorn2 21:36, 17 Apr 2005 (UTC)
 * I was more interested in references re: the minimum amount of proteins needed. The McDougall reference (hardly neutral, by the way) doesn't even reference the WHO, it just says they said so-and-so. In any event, I'll use the value you quote, 37g. According to reference [7],, someone would have to consume 12 cups of human milk to meet their protein requirement. That's just shy of 3kg. Sure, that sounds like a lot, but it's not a big feat considering it's mostly water. As for the lettuce, according to , a head of lettuce (360g) gives me 5g of proteins. Sure, 22% of the calories come from protein, which sounds really nice, but only 1.4% of the total weight is protein. I'd have to eat 7 heads of lettuce per day to get the daily minimum of protein, and that would only give me 400 calories! Personally, I'd rather drink 3kg of milk. But that's besides the point.
 * You're right that eating only gummy bears would leave me malnutrionned. However, the important difference is that no one really claims, nor is it generally associated to be a good idea, to eat nothing but gummy bears. There are a lot of warnings regarding eating a lot of meat as well, but there is nothing even remotely similar regarding vegeterianism. If I decide to eat nothing but salad all day, I *will* become malnourished (unless I can eat seven heads a day, and even then it's extremely hypocaloric), and everyone will tell me "Eating vegetables is good. Keep it up". You pretty much prove the point when your take on my salad-only diet was "It's better than eating just gummy bears". If I was someone who used a lot of energy, like a physically-demanding job, then frankly, I'd rather eat only gummy bears. At least my body wouldn't resort to breaking down muscle protein for energy. I do get more protein from salad than gummy bears, but the protein intake would definitely be smaller than the protein breakdown. Considering that I could never eat seven heads of salad per day, then I *would* be deficient in proteins. It's not even necessary to break down EAA intake at this point. Having said all that, how can you say that "careful to eat combiniations of food" is misleading or a half-truth? --jag123 07:32, 18 Apr 2005 (UTC)
 * You're right, Jag123, that my claim about kwashiorkor being "virtually unheard of" was too vague. My apologies.  Working backwards through your comments:
 * Considering that I could never eat seven heads of salad per day, then I *would* be deficient in proteins
 * Yes, but this would primarily be a problem of caloric intake, and not protein per se. And as Aragorn2 pointed out, just as "eating gummi bears all day" seems a caricature of omnivorous diets, so "eating salad all day" seems an unrealistic oversimplification of vegan diets.
 * I don't see anything misleading or negative about the "vegans being careful to combine foods".
 * The problem isn't that the statement is "negative," but rather, it seems to imply that vegan diets pose greater risks associated with protein intake than omnivorous diets. Yet this implication simply isn't true (at least, not in the USA).
 * As mentioned previously, omnivorous eaters tend to get too much protein on average, yet there doesn't seem to be any evidence (none that I've seen so far, at least) that vegetarians or vegans get too little protein on average. So, if we want to be consistent in the pursuit of NPOV, we'd probably need to change this warning to read something like: Vegans typically eat a sufficient variety of foods that this is not an issue, however, vegetarians and especially omnivores should be careful to limit protein intake so as not to exceed RDA.
 * But of course, when phrased this way, such a statement seems unnecessary, no? :-) --Hoss Firooznia 01:16, 19 Apr 2005 (UTC)
 * The heads of lettuce has nothing to do with calories, it has to do with proteins. Aragorn showed protein content of various greens. Sure, spinach may have 30% proteins, but you'd neet to eat almost 1kg of it to meet the daily needs quoted above. By contrast, one can (~110g) of tuna gives me 27g of protein. Unless you have studies (from a serious establishment [ie: not the McDougall newsletter]) regarding protein content of vegetarian diets, with a decent population size, then I don't know how you can say that it "simply isn't true". Back in high school, I knew a lot of girls who went vegetarian, and most of them did not eat nearly enough proteins, let alone calories, so I seriously question the veracity of your claims. I have no doubt it may be unheard of, but that doesn't mean it doesn't happen. Getting scurvy is unheard of, but it did happen to a college student in the United States about two years ago.
 * I don't see this as a pursuit of NPOV. You seem to want to add that eating too much proteins is bad to counterbalance the supposedly "non-neutral" claim that vegetarians should be careful to eat appropriate combinations of food. That's not how this works. Besides, it's already in there anyway. So far though, regarding your points, all I've seen is that "it's simply unheard of" for vegans to not have enough proteins, without anything to back it up. I know it's possible because I've met many vegetarians/vegans who weren't eating right at all, and wouldn't have to look very far to find more. Much as the case is here, it's nigh impossible to say anything bad about it, or even suggest improvements, because if it's green and it grows in dirt, then it's just got to be good.
 * By the way, I accepted the 37g of proteins because a higher value wasn't necessary, but personally, I find this extremely low. Aragorn's reference, the McDougall Newsletter, doesn't even reference the WHO document from where this figure comes, and I wasn't able to find it on the WHO site. For all I know, that figure could be the minimum protein intake to basically survive. I'd rather stick with the 10-15% of total calorie intake that is recommended. Although there was some talk about amino acids, there was nothing about lysine, which is the limiting AA in human diet, and especially a concern in vegetarian diets. Unfortunately, I don't have a lot of time to research all of this right now, but there isn't a shadow of doubt in my mind that many vegetarians out there don't eat right. Don't assume that every vegetarian out there knows the difference between an amino acid and battery acid. It seems you want to remove the statement because *some* vegans who actually know what they are doing eat right. That's like saying Westerners should continue to eat junk food because some of them do, and they are thin. --jag123 02:30, 19 Apr 2005 (UTC)
 * Ok, ok, this page is getting out of control. I put my answers for today on Talk:Protein/Aragorn2_2005_04_24. Aragorn2 21:07, 24 Apr 2005 (UTC)
 * The heads of lettuce has nothing to do with calories, it has to do with proteins. Aragorn showed protein content of various greens. Sure, spinach may have 30% proteins, but you'd neet to eat almost 1kg of it to meet the daily needs quoted above.  True, but I'm still not sure you've demonstrated anything relevant to a page on protein requirements for humans.  The same argument could be made for other nutrients, e.g., vitamin C.  To reach the USRDA, you'd need to eat similarly large volumes of Iceberg Lettuce.  Yet it would make little sense to add a warning to the vitamin C page saying that "vegetarians, and especially vegans, need to be careful..." etc.  Such a statement would only make sense if vegetarian and vegan diets typically consisted of nothing but iceberg lettuce.
 * Back in high school, I knew a lot of girls who went vegetarian... And you did a thorough analysis of their protein intake at that time, did you?    Personally, I know about 50 people who have been vegan for more than several years, and none of them exhibits any obvious signs of protein deficiency.  But again, this is simply anecdote.   Extraordinary claims require extraordinary evidence, and anecdote simply isn't good enough. Unless someone has epidemological evidence indicating that vegans are at significant risk of protein deficiency, this one-sided claim about "being careful" is unwarranted.
 * I don't see this as a pursuit of NPOV. You seem to want to add that eating too much proteins is bad to counterbalance the supposedly "non-neutral" claim that vegetarians should be careful to eat appropriate combinations of food. That's not how this works. Besides, it's already in there anyway. No, it isn't.  Please re-read the section carefully.  There is one statement describing problems associated with excess protein consumption, but it contains no mention of diet.  This is an NPOV issue because the current text is misleading: it highlights a relatively minor risk (protein deficiency from vegan diets) and utterly ignores a much more prevalent one (protein excess from omnivorous diets).
 * Much as the case is here, it's nigh impossible to say anything bad about it, or even suggest improvements, because if it's green and it grows in dirt, then it's just got to be good. This claim was never made here: not by me, and not (as far as I can tell) by anyone else.  While you may have encountered such an attitude in your personal experiences, it doesn't apply here. --Hoss Firooznia 14:03, 19 Apr 2005 (UTC)
 * Protein excess in omnivorous diet? I know about 100x the number of omnivorous consumers and not a single one of them has any complications from consuming "excess protein".
 * "excess protein" may be a problem for people with existing health problems such as poor kidney function. Download and read a Recent review article (PDF format). --JWSchmidt 15:03, 9 October 2005 (UTC)
 * This is the most recent free full text review I could find for bone: "Dietary protein, calcium metabolism, and skeletal homeostasis revisited"; Seems to suggest that high protein diet increases both calcium excretion and absorption. Says epidemiology is suggesting that low protein diets are a problem for bone mineral density. --JWSchmidt 15:25, 9 October 2005 (UTC)

If you tell me you eat a salad for lunch five times a week, and pasta, rice or can of baked beans for dinner, you're barely ingesting at most (with the beans) 40g of protein daily. You don't need a lab or sophisticated equipment to calculate the protein content, just a little mental math. So far, I've seen absolutely nothing that supports your claim. No references for the 37g, no studies thats proves otherwise. Maybe you haven't noticed, but 10-15% of calorie = protein is often stated (I won't say established) and I have found the warning in many places, including a federal health agency. This "claim" makes sense with what I've learned in biochemistry, what I know about the nutritional breakdown of various foods, the diets I've heard vegetarians explain to me, etc etc etc. I don't believe every vegetarian is lacking proteins, but I do believe some of them, especially those who've recently started, should keep it in mind and perhaps take another look at their menu. Like I said above, neither of you even mentionned limiting amino acids, especially lysine. It's not really the protein content that matters, but the content of the amino acids which are limited in plants and you don't seem to care (or even aware) about that. Instead I get stuff like lettuce has 22% protein and milk only has 9%, so lettuce is better, suggestions to add warnings about ascorbic acid, clarifications that it's a "caloric problem", (whatever that's supposed to mean) and reminders that plants make all AAs. (The latter is true, but an omnivore is benefiting from macro-concentration, unlike the vegetarian.) You know what, I'll spare you the trouble of coming up with more arguments. You want to remove it because there are no epidemiological studies, fine, but that's really weak and you're certainly not fooling me about it being a question of neutrality. --jag123 22:00, 19 Apr 2005 (UTC)
 * So far, I've seen absolutely nothing that supports your claim.
 * What claim are you referring to? I believe I've backed up the claims I've made so far. As acknowledged earlier, I was perhaps overly vague with the statement that kwashiorkor is virtually nonexistent in industrialized countries in people who get adequate calories from non-alcohol sources. This statement appears in at least one nutrition text, which I've already cited, but if it helps, here are some other references:
 * D. Joe Millward (1999) "The nutritional value of plant-based diets in relation to human amino acid and protein requirements". Proceedings of the Nutrition Society 58 (2) ("The adequacy of plant-based diets in developed and developing countries as sources of protein and amino acids for human subjects of all ages is examined. Protein quantity is shown not to be an issue.")
 * American Dietetic Association and Dieticians of Canada (2003) "Position of the American Dietetic Association and Dietitians of Canada: Vegetarian diets". Journal of the American Dietetic Association 103, 748-765. ("Although some vegan women have protein intakes that are marginal, typical protein intakes of lacto-ovo-vegetarians and of vegans appear to meet and exceed requirements.") Note: this reference was previously cited in the comment that started this discussion section.
 * If you tell me you eat a salad for lunch five times a week, and pasta, rice or can of baked beans for dinner, you're barely ingesting at most (with the beans) 40g of protein daily... Maybe you haven't noticed, but 10-15% of calorie = protein is often stated (I won't say established) and I have found the warning in many places, including a federal health agency.
 * All right, then. Let's examine this 'girl you knew in high school' example.  We'll assume, as you claim, that she was getting only 40g of protein from her diet.  (We'll ignore the fact that her diet may well have been hypocaloric which would make this primarily an issue of inadequate calories, and not inadequate protein.)  We'll also make the (not unreasonable) assumption that she weighed about 110 lbs (~50 kg), making her daily caloric need about 1620 kcal (basal metabolic energy use = 50kg x 0.9 kcal/kg/hr x 24 hrs = 1080 kcal) + (voluntary activity energy use = ~50% BME for a sedentary lifestyle = 540 kcal).  40 g of protein, at 4 kcal/g, makes 160 kcal, or just under 10%.  So, even in this hypothetical, worst-case example, the subject is still getting a near-optimal amount of protein.
 * Now, I don't have a reference for the WHO figure of 37g/day (and I wasn't the one who mentioned it), but this WHO/FAO paper from 1991 recommends a daily intake of 0.75g/kg body weight/day. For our 50kg subject, that yields an RDA of 37.5g/day. So according to the WHO, the subject would be exceeding her RDA for protein.
 * neither of you even mentionned limiting amino acids, especially lysine. It's not really the protein content that matters, but the content of the amino acids which are limited in plants and you don't seem to care (or even aware) about that.
 * I'm afraid you're mistaken. Please re-read the discussion to date. In particular, note the discussion of Protein Digestibility–Corrected Amino Acid Score (PDCAAS).  This is a standard measure of protein quality, based on the concentration of the limiting essential amino acid relative to human need.
 * You know what, I'll spare you the trouble of coming up with more arguments. You want to remove it because there are no epidemiological studies, fine, but that's really weak and you're certainly not fooling me about it being a question of neutrality.
 * I'm not trying to fool you into anything; I'm just trying to make the article more accurate. If you want to spare me something, you could leave out the unnecessary ad hominem attacks, please. I'd appreciate that. :-) --Hoss Firooznia 02:46, 20 Apr 2005 (UTC)
 * Ad hominem attacks? Please. Perhaps you don't like it, but it doesn't make it an attack.
 * When was PDCAAS discussed? I see a statement that soy and sweet lupine have a PDCAAS of 1 with "this" mistake corrected (of course, no reference for the mistake). So what if if soy and sweet lupine have a PDCAAS of 1? Does every vegan consume 37g of soy protein or lupin every day?
 * "Although some vegan women have protein intakes that are marginal, typical protein intakes of lacto-ovo-vegetarians and of vegans appear to meet and exceed requirements" The reference for that is a book. I'd like to see exactly how that was determined in the book, especially since "appear" is used. Besides, that statement does show that some vegans do have marginal protein intakes, which, to me, only supports leaving the notice in the article.
 * No one ever claimed that vegans suffer from kwashiorkor. There's a big difference between suffering from protein defiency and having a protein deficiency, unless your point is that it's no big deal until you're actually suffering from it. I'm not interested at all in kwashiorkor.
 * Calculating protein requirements for a high school girl who weights 110 pounds with a sedentary lifestyle is not a worst case example, it's a best-case example. This is a worst case example: 80kg male who needs 3500-4000 kcal/day. That's 60g of protein, according to the FAO/WHO and 88g if we use the 10% of calorie figure. To be part of the group of veg. in which protein deficiency is unheard of, I'd have to eat almost a pound of tofu every day. (I use tofu because soy protein has a PDCAAS of 1.) Is it seriously realistic of me to "naturally" eat that much tofu on a daily basis? This isn't even a vegetarian diet, it's a tofu diet. For me to get enough proteins from a veg. diet, I'd have to actually sit down and seriously research thngs to determine what meals to prepare to suit my needs. I don't get it. Are vegetarians born with an innate knowledge of the PDCAAS rating of various veg. foods, as well as their protein content, that I don't have? Of course not. So why is it so hard for you to accept that it's possible for a vegetarian to not eat enough protein? If I was clueless on the subject, I would easily be lacking protein (unless I went out of way to eat lots of tofu, which I would not do because I wouldn't have a reason to) and I came to this article to read on protein nutrition, then I'd be made aware that perhaps I should re-examine my diet. But you think this is misleading and should be removed. As a clueless person looking for information, I should be kept in the dark because typical vegans (who probably have more insight on their diet than I, or are less active) appear to meet or exceed requirements? How is that a better scenario for me?
 * Perhaps the article should include more information on when and why this might be a concern. This way, indifferent (for lack of a better word) readers won't be given a blanket impression that "veg. diet lacks protein" (which I don't think is the case), but someone truly interested in, or looking exactly for this will have some information on which they can decide if they should re-examine their diet, and if so, what aspects to consider.
 * I'm still not convinced a protein deficiency is unlikely, unless the person is of very low weight and leads a sedentary lifestyle. Instead, I see mentions in that Nutrition care professionals should be aware that protein needs might be higher than the RDA in vegetarians, that ... some vegan women have protein intakes that are marginal and the conclusion of that report (Appropriately planned vegetarian diets ) says that not just any vegetarian diet is good enough, but an appropriately planned vegetarian diet, so I really can't agree with you. Anyway, I don't have time to research this properly so I'm just going to sit this one out for the time being. --jag123 09:00, 20 Apr 2005 (UTC)
 * Ad hominem attacks? Please.
 * I don't want to let this degenerate into a pissing match, but when you impugn someone's motives (e.g., when you say things like, "you're certainly not fooling me"), that's ad_hominem. Enough said.
 *  So what if if soy and sweet lupine have a PDCAAS of 1? Does every vegan consume 37g of soy protein or lupin every day?
 * You're missing the point. Your initial complaint was, "it's not really the protein content that matters, but the content of the amino acids which are limited in plants and you don't seem to care (or even aware) about that."  I was pointing out that this discussion started with -- and has continued to revolve around -- the concept of protein quality.  And that's determined by the concentration of the limiting essential amino acid.
 * Since the point of all this seems to have been forgotten, the sentence in dispute is:
 * vegetarians and especially vegans should be careful to eat appropriate combinations of foods (e.g. nuts and green vegetables) so as to get all the essential amino acids in sufficient quantities that the body may produce all the proteins that it needs.
 * So this is really a question of protein quality, not quantity. The need to "combine foods" is a myth. Therefore, this sentence is misleading.
 * This is a worst case example: 80kg male who needs 3500-4000 kcal/day. That's 60g of protein, according to the FAO/WHO and 88g if we use the 10% of calorie figure. To be part of the group of veg. in which protein deficiency is unheard of, I'd have to eat almost a pound of tofu every day.
 * No, and this issue has already been addressed, several times. You wouldn't have to eat a pound of tofu, nor would you need any knowledge of the relative protein qualities of various foods. You'd simply need to meet your caloric needs, and avoid some clearly unrealistic pitfalls -- such as eating a diet of nothing but gummi bears.
 * --Hoss Firooznia 14:50, 20 Apr 2005 (UTC)

How does boiling water affect proteins?
Many people believe that boiling vegetables makes them lose nutrients.Reference_desk So does it somehow destroy the nutrients, or just leach the nutrients into the water? Boiling water is not anywhere close to hot enough to destroy minerals (elements). But what about proteins? Which is right? Can humans actually use any protein directly? Or does the digestive system break all proteins down into individual amino acids, and then re-assemble those amino acids into human proteins? -DavidCary 07:21, 25 Jun 2005 (UTC)
 * Some people tell me that while boiling water "denatures" proteins, but they curl right back up again after they cool off.
 * Others claim that the heat destroys the nutritional value of some proteins.
 * Proteins are broken down to amino acids during digestion. (Iiuc, some protein does make it through partially intact, which is how it can cause food allergies.)  Many proteins are denatured by boiling; some return spontaneously to the native conformation when cooled and others are denatured irreversibly.  (If egg albumin weren't irreversibly denatured, you couldn't hard-boil an egg.)  Extreme heat that scorches food will destroy protein entirely, of course. --dsws 02:34, 15 July 2005 (UTC)
 * Either way, denaturing proteins doesn't really matter, since they're digested and broken down (as denatured as you can get). The only risk would be if proteins could make it out of the stomach without being digested. Our body may be adapted to normal proteins, but not denatured proteins. That's the theory my psychiatrist offered when we discussed it, but I honestly don't know if they can even get out, or how proteins react in the body as opposed to amino acids. I'd assume if they could get there it would be pretty weird. Tyciol 18:28, 1 March 2006 (UTC)

Separate page for protein nomenclatures?
It might be nice to have one page to bring together the whole mess: the CD listings, and the names like p52, and the names like hedgehog based on phenotypes of mutations with the capitalization and italicization conventions. Obviously, the casual (non-technical) reader doesn't want to be deluged with this stuff in the basic protein article.--dsws 02:45, 15 July 2005 (UTC)
 * That idea gets my vote :) How can we organise a community effort on protein naming nomenclature? EC is great for enzymes, but we need to extend it to non enzymatic proteins. Also TC works for transporter proteins.--Dan|(talk) 11:09, 5 August 2005 (UTC)
 * Please make efforts to organize wikipedia coverage of proteins a part of WikiProject Molecular and Cellular Biology. --JWSchmidt 20:02, 28 August 2005 (UTC)

Changes made by 202.63.115.2
On 24 July, 202.63.115.2 made a large number of changes, primarily removing information from the article. While I am specifically not arguing that this article is perfect, or even good, as it is now, I think changes of this magnitude should be discussed first. I've reverted the changes for now, pending discussion. Opinions? Banks 19:40, 24 July 2005 (UTC)

Help with L-Ornithine and L-Arginine
I am new here and while I find the articles fascinating, I don't really understand it all. I am exploring the world of Amino Acids and could use some feedback. I recently went to a GNC store and asked if they carried a weight management/loss product that does not contain caffeine or stimulants and the manager recommended L-Ornithine and L-Arginine. The facts about these two amino acids that he read aloud to me helped pursuade me to purchase them, but I still am not clear on how these two compounds can help me lose weight. Can anyone help explain?? Please use 'simple terms' when responding as I am not at all educated in all of this 'stuff'. Thanks!!
 * It always puzzles me when I go to the drugstore and read ingredients on some bottles that sell for high prices. I saw "L-Proline" listed before and now you mention "L-Arginine".. The L- means Levorotary (see Chirality) and most naturally produced amino acids are L- (at least on Earth). So basically the pills just contain one specific type of regular amino acids. Ornithine seems to be related to Arginine through the Urea cycle. I'm not sure how they allow you to loose weight, maybe they make you pee more often? Looie 04:45, 17 November 2005 (UTC)

List of Proteins
Sorry MrBip, I couldn't find your comments anywhere, so I put the list back in, as I think an encyclopedia is the best place to develop a set of systematic protein names, a protein naming ontology and synonym dictionary. I know the List of proteins is very much a stub at the moment, but I know of no other way to 'get the ball rolling' if you know what I mean. I think as a community (biology / bioinformatics) we need a protein naming ontology, and in the abscence of any major funded project to develope one, wikipedia is an exelent place to stage this effort. Please let me know your thoughts, --Dan|(talk) 11:06, 5 August 2005 (UTC)
 * Dan - Sorry for not explaining myself clearly. I was at work, and forgot to say something on the talk page. I left a few comments on the List of proteins talk page. Basically, I think a list of proteins is worthless - we need a "List of lists of proteins." Honestly, listing proteins would be like creating a "List of famous people" - something which could theoretically be useful, but is far too general to be practical if it were even 10% complete. There are searchable databases on the web, such as SwissProt and the PDB, which as essentially lists of every protein known. These databases are major collaborative efforts that require a community of bioinformaticists to maintain. I think we can let them do their job, and use Wikipedia as a place to describe the most important proteins, not develop a list of every known protein. Maybe this page needs to be archived? It's getting pretty long. Mr.Bip 15:54, 5 August 2005 (UTC)
 * Hello Mr.Bip, thanks for the comments. I like the idea outlined under talk, but I feel I must take you up on one point you made above. You said "These databases are major collaborative efforts", which is true, but not a single one of them defines an accepted protein nameing ontology. SwissProt is the best, but when you said "which as essentially lists of every protein known" you were correct, but missed a fundamental point, the protein lists in these databases are highly redundant, with the same protein occuring in 1000's of organisms. What is missing is a convenient list of known properties and english description of 'the protein in general', which isn't maintained anywhere. The GO ontology is very good for 'function tagging' and automatic procesesing of protein sets, but having in plain text protein W does x, y and z in eukaryotes for reason p, q and s, while in bacteria a, b and c. Like a canned 'bio' for each of the (well) known proteins. You are right that we should group into higher level lists, but we do need a protein naming ontology, and it should be a community project, but perhaps for elswhere. --Dan|(talk) 11:37, 6 August 2005 (UTC)
 * Dan - I agree with you - the SwissProt database is rather unwieldy for someone who just wants to know what "dystropin" is, or a protein like that. I'd be happy to try to tackle this ontology project with you. I think grouping proteins by their role in cellular processes would be a good place to start. We could also group proteins by function, so we could have a list of kinases, a list of motor proteins, etc. I'm sure this would take a loooong time, but you have to start somewhere, right? :) If you're interestedin talking about it sometime, leave a message on my talk page. Mr.Bip 22:37, 6 August 2005 (UTC)
 * We can organize wikipedia coverage of proteins a part of WikiProject Molecular and Cellular Biology. --JWSchmidt 20:05, 28 August 2005 (UTC)

Bringing balance to nutrition section
The current content of the nutrition section appears to be a thinly veiled treatise about "Why vegan diets aren't deficient in protein", probably the product of past contention. I am neither pro nor anti-vegan, and I do believe the information presented is accurate. But I question whether vegan polemics should occupy the entire body of nutritional information on protein. It's re-enacting a debate rather than characterizing it, and we don't do that on Wikipedia. I think some revision is in order, and I will get to work on it. The Hokkaido Crow 16:40, 21 September 2005 (UTC)
 * I've performed the refactor. Some of the information ended up in Veganism and some of it ended up in PDCAAS.The Hokkaido Crow 01:21, 22 September 2005 (UTC)

References drive
I suggest that this article have a section called "references" with numbered citations and references using this method. We can start by trying to find references to support this:
 * "Excess protein can cause problems as well, such as causing the immune system to overreact, liver dysfunction from increased toxic residues, bone loss due to increased acidity" --JWSchmidt 15:58, 9 October 2005 (UTC)

Protein research
I suggest this site as I research protein function and thought this site to be a very good reference especially for bioinformatics, (the biggest).
 * Protein Research Home Protein research protocols, protein bioinformatics database, protein news, and protein research discussion.
 * If someone take his time to investigate, he will see that you spammed more that 20 articles with a links to molecularstation.com . The most rediculos spamming was a link to abovementioned web site plesed on disambiguation page. The articles that got spammed include but not limited by: Transcription (genetics), Enhancer, Promoter, Mammalian embryogenesis, Stem cell line, Stem cell, Vergina Sun, Bioinformatics, Arabidopsis, Drosophila melanogaster, Caenorhabditis elegans, RNA interference, Small interfering RNA, Peptide mass fingerprinting, DNA, RNA, Protein, Proteomics, RT-PCR, Complementary DNA, Gene Ontology, DNA microarray, Splicing (genetics)
 * And most of thouse links lead to simple links directories pages. Have fun.  TestPilot  07:47, 10 January 2006 (UTC)

Edits
I have severly trimmed the protein in nutrition section of the article which was basically being used as a platform to justify vegetarianism. I think an article on Protein in human nutrition might be a useful place for such discussion, but not in a general article on protein. --nixie 12:31, 17 January 2006 (UTC)

Proteoses
Does anyone use the term "proteoses" anymore? --JWSchmidt 15:32, 6 February 2006 (UTC)

Spelling/grammatical errors
Bhulsepga, you have been editing this page a lot recently. Please check your edits for spelling and grammatical errors before submitting. Isopropyl 22:21, 18 February 2006 (UTC)

Negative health effects of certain proteins, amino acids, or excess protein?
I've divided up the nutrition into two parts to reflect the division of presentation, which I think is fine. Even so, I'm questionable about certain aspects attributed to proteins. It's a much-debated field, especially in health and athletic circles. Can we discuss how to better present these views in the article? Tyciol 18:28, 1 March 2006 (UTC)

Link Spam by Western Blotting.org
Removed link spam by Western Blotting .org. No information relevant to protein science on the page. Bioinformin

20 Amino Acids
Under the components and synthesis of protiens it is stated in the first paragraph that proteins are biopolymers built from 20 different L-alpha-amino acids. That gives the impression that all proteins made from the same 20 different amino acids. I thought it was only 20 for humans, who produced 12 and needs to take 8, while other organisms needed and have their proteins made with different amounts. Pseudoanonymous 02:44, 1 April 2006 (UTC)
 * See amino acid. There are twenty naturally occurring amino acids which are dictated by combinations of three DNA base pairs. Isopropyl 20:11, 29 April 2006 (UTC)
 * I would like to comment that the 20 amino acid number is somewhat outdated. I think selenocysteine and pyrollysine at least deserve a mention. The way it stands now, the number 20 seems like some sort of universal law, which it isn't. Peter Znamenskiy 18:42, 21 May 2006 (UTC)
 * The main point is that DNA only encodes for 20 aminoacids (at least in most organisms). Amino acids like hydroxyproline, or hydroxylysine are components of the collagen, the most abundant human protein, but these arise from psttranslational modifications, should we be discussing these like they are normal DNA encoded-aminoacids? Adenosine | Talk 01:03, 23 May 2006 (UTC)

Can someone add a few lines about the diet components, which are rich in proteins. I guess that should be an integral part in any write up about proteins.

Cooking proteins
What happens when proteins are cooked? (Like eggs for example.) Obviously they get hard, is that entirely because they "unravel" and intertwine? Or are there changes in the molecular makeup?

Also humans can't digest some foods (like potato) until they are cooked, is that also true for proteins? Or is it the revese, cooking damages the protein (in term of neutrition), but makes it more palatable? 71.199.123.24
 * The nutritional quality of a protein comes from its amino acids. When you cook proteins you subject them to incredibly high amounts of energy; all the weaker bonds, such as hydrogen bonding and van der waal forces, are ripped apart and proteins lose most of their structure, 2°, 3°, and 4°. The primary structure would be fairly resistant to cooking. The amino acids should remain fairly stable, but too much heat, oxygen, etc. You may be able to destroy them. Hope that's what helps... Adenosine | Talk 01:09, 23 May 2006 (UTC)

Nutrition
Is there a good reason to have nutritional aspects discussed in two different parts of the article? ike9898 20:57, 16 August 2006 (UTC)
 * I don't think so. I have cut excessive nutrition info from this article before, and it is expanding again. I have also previously recommended that to create room for more biologically relvant material, to remove questionable nutrition sceince and to prevent dull vegetarian edit wars tthat the nutrition stuff should be split off into a daughter article and mentioned here in summary style. --Peta 04:36, 18 August 2006 (UTC)
 * The role of protein in human nutrition is out of place in an article about the larger role of protein in all living things. A disambiguation link would make much more sense. // Internet Esquire 04:40, 23 August 2006 (UTC)
 * Added: After rewording the intro section on nutrition to include all animals rather than just humans, I finally figured out why the role of protein in human nutrition is so out of place in an article on biochemistry.  To wit, I looked up protein in a dictionary, and there were two definitions that were strikingly different:  One defined protein as a molecule that is important to biochemistry, and the other one defined protein as a sort of biological tissue that was rich in protein molecules.  As it stands right now, the protein article conflates these two definitions. // Internet Esquire 19:29, 25 August 2006 (UTC)

I'm not arguing with the decision to limit the nutritional aspect of this article, but I think that idea that the word 'protein' is used to mean 'high protein tissues' is strange to me. The only context I've every heard this in is from pseudo-nutritionists, along the lines of 'you should have a starch and a protein at every meal'. In "real" nutrition, protein means exactly the same thing that it does in biochemistry; nutritionists are just interested in protein for different reasons. ike9898 20:07, 25 August 2006 (UTC)
 * If you query Google for "protein tissue," you will find quite a few references. By way of comparison, consider the use of the term "earth" to refer to the planet Earth as well as to the soil on the surface of the planet.  While tangentially related, these are two very different things, and nutritionists are doing the same thing when they conflate dietary sources of protein with protein molecules. // Internet Esquire 20:40, 25 August 2006 (UTC)
 * There isn't exactly a "conflation"; one is made of the other. A summary of the role of protein in nutrition is appropriate here; however, it should be kept in general terms and especially should not include controversial or uncommon usage, since nutrition is an often-debated subject. Specifically I don't see much benefit in the usage of "protein tissue" here - Google seems to have a rather low number of hits for the phrase in the context of nutrition, while many hits for the phrase seem to be some variant of "...protein, tissue,..." . If you have references for the term in common usage, it would probably be best discussed in the nutrition article to keep this one general. Opabinia regalis 00:38, 26 August 2006 (UTC)

Miscellaneous to-dos
Ongoing reorg in progress, comments appreciated. Opabinia regalis 04:35, 18 August 2006 (UTC)
 * Diversity section still needs cleanup. mostly better
 * Separate section needed to summarize protein folding. Section exists, may need cleanup
 * "Role of protein" section is lengthy and very redundant.
 * Nutrition information needs cleanup and references. Nice, Peta
 * History is way too stubby. getting better
 * External linkfarm needs a trim.


 * Nature's robots : a history of proteins by Charles Tanford & Jacqueline Reynolds, would be a good place to start for hisotry info if you can get a hold of a copy.--Peta 04:50, 18 August 2006 (UTC)
 * Sounds like a cool book, but one of the disadvantages of not working at a university is not having a good library to raid. Unless it's really good, Wikipedia articles are probably not quite enough inspiration to buy a copy :) Opabinia regalis 02:34, 19 August 2006 (UTC)

"Role of protein" section
Trimmed this text from the article as redundant, or at least misplaced. Duplicating here for easy reference. Opabinia regalis 06:07, 19 August 2006 (UTC)

''Proteins are involved in practically every function performed by a cell, including regulation of cellular functions such as signal transduction and metabolism. Proteins control almost all the molecular processes of the body and are the actors that do everything that happens within us. Several particularly important functional classes may be recognized:
 * 1) enzymes, which catalyze all of the reactions of metabolism;
 * 2) structural proteins, such as tubulin, or collagen;
 * 3) regulatory proteins, such as transcription factors or cyclins that regulate the cell cycle;
 * 4) signalling molecules or their receptors such as some hormones and their receptors;
 * 5) defensive proteins, which can include everything from antibodies of the immune system, to toxins (e.g., dendrotoxins of snakes), to proteins that include unusual amino acids like canavanine.
 * 6) proteins to protect proteins, which include heat-shock proteins and LEA (Late Embryogenesis Abundant) proteins.''

-- This content has found its way back into the main article under Function and regulation/Cellular functions. // Internet Esquire 04:35, 23 August 2006 (UTC)

Sectioning
I think the article might be more clear if it was in the following arrangement: --Peta 04:48, 21 August 2006 (UTC)
 * Biochemisty (to replace Components and nomenclature)
 * Synthesis (mabye a combination of biochemistry and synthesis would work too)
 * Structure
 * Folding
 * Structure determination
 * Function (merege regulation and diverstiy sections, also needs info on protein-protein interactions and a bit more on enzymes, divided into subsections as necessary. I'm not keen on the diversity section, the mass info could be moved to where proteins are first defined, it offers a structural classification (globular, filamentous and membrane) of proteins which would be more relevant in the structure section)
 * Nutrition
 * History
 * Study
 * Good idea. I agree that the diversity section isn't so great - just hadn't thought of a good place to put what's there. Classification should definitely go under structure. I'm not sure I'd put synthesis before structure, as the "what it is" aspect of the article seems like it should precede the "how it's made". I think study/methodology should go after function - keeping the molecular stuff separate from the more "macro" discussion of nutrition - but that may be the bias of someone who's not terribly interested in things that are bigger than cells. Opabinia regalis 05:46, 21 August 2006 (UTC)

I think synthesis logically follows from primary structure. This is how my old undergrad biochem textbook does it --Peta 09:30, 21 August 2006 (UTC)
 * 1st chapter, "Primary structure", amino acids, peptide bonds, protein sequence, from gene to protein (protein biosynthesis)
 * 2nd chapter, "Three dimensional structure", secondary structure - fibrous and globular proteins; tertiary structure - factors (folding and disulphide bonds); structure prediction; Quaternary structure (multisubunit and heterotypic protein-protein interactions)
 * 3rd chapter, protein function and evolution, it uses heme proteins as an example
 * Hm, I dug up my old biochem book for comparison, and it's all kinds of messed up. Roughly primary structure > purification methods > gene expression and molecular cloning > secondary and tertiary structure, at which point I gave up on using it as inspiration. I have no objections to biochem (amino acids and such) > synthesis > structure > function, but I think the next section should be methodology, rather than shunting that to the end. With dietary uses of "protein" now split into its own article, I'd also like to see the nutrition section cover other organisms besides humans. Opabinia regalis 02:37, 22 August 2006 (UTC)

I like the idea of describing methods with their relevant section, rather than a long section on methods since it makes it harder to skip over the details, eg. sequence of a protein, how to sequence a protein - but I'm not sure how well it would work. I might mess around with the order and add some stuff later since we seem to be in agreement. I'm not sure what you have in mind for nutrition - but I agree it should cover proteins in nutrition in general mabye somethin glike plants+bacteria (make all their own aa), obligate parasites+animals (need external aa sources); what protein is used for?--Peta 02:47, 22 August 2006 (UTC)
 * I had some time so I did some reordering and reorganization tonight. I left protein folding as a top-level section, since it's such a big research issue these days. Opabinia regalis 03:11, 23 August 2006 (UTC)
 * As I alluded to above, I think it's a mistake to give the role of protein in human nutrition equal time in an article that is essentially a technical exposition about biochemistry in all living creatures. A disambiguation link at the beginning of the article, as was suggested years ago, would make much more sense. // Internet Esquire 04:31, 23 August 2006 (UTC)
 * It doesnt get equal time, a small section is included in summary style since it is logical to expect that someone might come to this page loooking for info on protein and nutrition.--Peta 04:50, 23 August 2006 (UTC)
 * The role of protein in human nutrition actually gets a great deal more than equal time in the protein article if you consider the fact that this article is not about human biochemistry but rather about the biochemistry of all living things. // Internet Esquire 05:00, 23 August 2006 (UTC)
 * Which is why OR and I were discussing rewritng the section to be about protein in nutrition in general.--Peta 05:03, 23 August 2006 (UTC)
 * Yes, I don't see why the section should be limited to human nutrition. Let's make it more general and leave the specifics of protein in human nutrion to the article of that name. ike9898 20:19, 23 August 2006 (UTC)

tell the obvious
The article doesn't contain the words "meat" nor "bean" nor "milk" nor any other protein-rich food I can think of. Shouldn't that piece of fact be included in the article too? TERdON 17:05, 26 August 2006 (UTC)
 * You want Protein in human nutrition, down the hall and to the left. Opabinia regalis 18:50, 26 August 2006 (UTC)
 * Hmm. That's info that should be on this page IMHO. The chapter about nutrition (which links above mentioned article), is totally incomprehensible for most people who don't have university education. In fact, most of this article is at that level...
 * There's no need for both articles to be dumbed down. People with higher education can learn about biochemical/cell physiology aspects in protein, those wondering how many servings of beans they should eat daily should go to protein in human nutrition.   But perhaps some disambiguation is in order, considering how many people think that protein is most notable in the dietary sense.  The Crow 22:37, 26 August 2006 (UTC)
 * Of course it shouldn't be dummed down. But all the people looking for protein in human nutrition are more likely to go here first. Basically, the article is biochemistry-POV! ;-) TERdON 07:25, 14 September 2006 (UTC)
 * Proteins are one of the main subjects of biochemistry. They are the building blocks of living matter and that's their main role on this world -them being a part of our nutrition is just an (important for us) sidenote. Saying that's the article is biochemistry-POV is like saying the article about Sun is astronomy-POV. --Cyclopia 09:17, 14 September 2006 (UTC)

Nutrition redux
I am satisfied that the role of protein in nutrition has been successfully exported to the separate article by that name with a wikisummary included in the main protein article. However, it now seems that the content found in the nutrition section should properly follow the section on biosynthesis. // Internet Esquire 21:54, 27 August 2006 (UTC)
 * Glad that you're satisfied with the separation of content. However, of all the places the nutrition section in this article could go, where you put it is extremely awkward - between biosynthesis and chemical synthesis, which are logically related, seriously disrupts the continuity of that section. There's also no reason anyone would expect to find nutrition information under a header labeled "synthesis". There may be a better place that its current position near the end, but interrupting the synthesis section isn't it. Peta, what do you think? Opabinia regalis 06:12, 28 August 2006 (UTC)
 * The Nutrition section should be first. It is context that the majority of people are thinking when they hear protein.  It is however quite inadquate, but I won't repeat all my comments from the peer review here.  My additional thought however are that the nutrition section is a summary of a daughter article which really focused on human nutrition which is somewhat problamatic.  I think the main point of the nutrition section on this page should be establishing that protein is notable topic in nutrition and explaining why.-- Birgitte§β  ʈ  Talk  22:38, 9 September 2006 (UTC)
 * There's been some discussion of the over-emphasis on humans in the nutrition article, which you might be able to improve with your knowledge of agriculture. We can see what other people think, but I strongly disagree that nutrition should come first - this is and should be an article on proteins as molecules, which is undoubtedly the primary meaning of the term. In fact, I like its current position, as the article progresses from protein components to structure to usage. However, you're right that the nutrition section is a bit scraggly at the moment - I've moved the specifics of digestion to the daughter article and rearranged the text. I had at one point added the nutrition article to the disambig statement at the top - perhaps restoring that would help direct people looking for nutritional information to the right place? Opabinia regalis 00:18, 10 September 2006 (UTC)
 * I don't particularly like the idea of having both a section and a note at top in general. Maybe this article should lose the nutrition section altogether and the current daugthter article be re-named Protein (nutrition) ?  Then have the hatnote.  Although proteins in nutrition are still the same molecules it is in a way a different concept, or at level being treated at a different level.  The only problem I can see in overlap is if this article ever talk of the concept of synthesizing proteins specifically for animal consumptions.  I wish I could help more with the broading the nutrition article, but I never kept up with my original education and do not have the sources is on hand.  It is really a widespread problem here, and I hope to get on it in the future.-- Birgitte§β  ʈ  Talk  02:21, 10 September 2006 (UTC)

I don't really have an opinion on whether the nutrition article should reside at Protein (nutrition) or Protein in nutrition (presumably the one that isn't chosen would stay a redirect anyway). I do think there ought to be some mention of nutrition here, both to serve as a catch for anyone who wanted the other article and to tie in amino acids in the diet with protein biosynthesis. I'm not sure what you mean by "synthesizing proteins specifically for animal consumptions" - designing animal feed? (It sounds unlikely that proteins would be chemically synthesized for consumption.) Good luck with the agricultural contributions if you get to it. Opabinia regalis 07:37, 10 September 2006 (UTC)

Rate enhancement versus catalytic proficiency
I find this quite confusing. However, as I understand it, rate enhancement is kcat/kuncat and is a ratio between two first-order rate constants with no units. This ratio simply gives how much faster the catalytic reaction is than the uncatalysed reaction at Vmax. Catalytic proficiency on the other hand, is (kcat/Km)/kuncat and is a ratio between a second order and first order constant. The physical meaning of this ratio is less clear and seems to have something to do with the enzyme's affinity for the transition state. TimVickers 23:00, 5 September 2006 (UTC)
 * Sorry, I should have read the reference more thoroughly before I copied the data. The best of my knowledge is that kuncat/(kcat/km) is the "apparent dissociation constant" reflecting the collapse of the enzyme-transition state complex, so you must be right about its reciprocal as a measure of transition state affinity. I'm just never sure with experimental kinetics what physical process it is that's actually being measured. Opabinia regalis 02:53, 6 September 2006 (UTC)

History section a separate article?
The history section has really been fleshed out (nice job, Peta, Willow, and Tim) and deserves its own article. It's also a bit large compared to some of the other subsections (my occasional wordiness notwithstanding). Any thoughts? Opabinia regalis 05:16, 12 September 2006 (UTC)


 * I think its a pretty neat and comprehensive section, a bit wordy in places perhaps - but at this point I can't see any real reason to shift it into a daughter article.--Peta 05:20, 12 September 2006 (UTC)


 * I've been uneasy over its uncomfortable length, too &mdash; especially since I want to expand it a lot more! ;) But a smaller section would suffer by being less lively and colorful, less personal :(  What do you all think?  I guess I'm in favor of reducing the history section to its essence; I'm even willing to undertake the distillation, if we're agreed.


 * Can I ask for help on two other issues?


 * First, I'm kind of stuck on how to wikify Cyclol; I'm going to add a section on ergotamine derivatives, etc. but I'm not really sure what they're asking for with the wikify tag. Is it sectioning maybe?


 * Second, I've been working recently to bring Photon to FA status. We've had a good scientific peer review, but before the non-scientific peer review, I'd like to get a SNiFFipediaTM review (Smart, Nice, Friendly Folk at Wikipedia).  Could you all look it over as non-physicist scientists and make suggestions as to what could make the article more intelligible to lay-folk and more likely to reach FA status?  Thanks so much! :) Willow 21:19, 12 September 2006 (UTC)


 * That section really is very nice and comprehensive, and it seems like something people would plausibly search for on its own, independently of the chemistry aspect. Since Willow's written most of the current form, you're probably the best one to decide when and whether to distill :)


 * On the cyclol stuff, the article has a few blank sections (in progress, I assume) and the references list is longer than the text, but I don't see what the wikify tag is doing (and I'm not sure I trust the assessment of the original tagger). I'll have a look at photon when I get a chance. Opabinia regalis 01:49, 13 September 2006 (UTC)


 * The information is very interesting and well researched, but out of proportion to the rest of the article. I'd support a summary in this article, and splitting out the rest into a daughter article. --Arcadian 16:47, 18 December 2006 (UTC)


 * I agree, I'm going to be doing something similar with DNA, so this would fit nicely in the overall scheme. What about History of protein biochemistry TimVickers 00:42, 19 December 2006 (UTC)
 * Ah, good, I had forgotten about this. Yes, it'd be nice to have the two articles parallel - what will the DNA history article be titled? Opabinia regalis 03:20, 19 December 2006 (UTC)


 * It's been added to History of molecular biology, perhaps some of the protein stuff could go here also? TimVickers 04:17, 19 December 2006 (UTC)


 * Trimmed and moved to a new section in history of molecular biology. I'll let Willow know, she had some comments in there about planned expansions. Opabinia regalis 05:44, 20 December 2006 (UTC)

Protein breakdown
Can someone do an article on protein breakdown? As in how they're broken down to form amino acid pools to form other proteins? Tyciol 22:26, 14 October 2006 (UTC)

Beta-sheet is a secondary structure?
It is written here about secondary structures: The most common examples are the alpha helix and beta sheet.[5] Because secondary structures are local.... I always thought that secondary structure is beta-strand, not beta-sheet. Beta-sheet is not local, and it is not regular. A beta-sheet from 5 beta-strands can have a lot of different topologies. Thus, this is not even a definite structure. One can not define the geometry of beta sheet by a combination of repeating phi and psi angles, as for alpha-helix, 3-10 helix, poly-Pro helix, a beta-strand or any other really regular structure of a polymer. I think this is one of many obvious errors that can be found in textbooks.Biophys 06:22, 8 November 2006 (UTC)


 * You're technically right, of course; it should be 'beta-strand', but see the usage note in beta sheet. The terms are used interchangeably so often, especially in introductory material, that trying to classify it as an error is somewhat tilting at windmills. Opabinia regalis 07:33, 8 November 2006 (UTC)


 * Ummm, as I understand it, the current accepted definition for secondary structure is the DSSP program. Although secondary structure assignment was done "by eye" in the early days of crystallography, I believe that DSSP is how most modern entries to the PDB assign their HELIX and SHEET records.  The DSSP program assigns secondary structure only on the basis of patterns of hydrogen bonds (defined electrostatically), not on the regularity of, say, backbone dihedral angles.   Therefore, a single beta strand in isolation (which happens sometimes) has no secondary structure; only a beta sheet does, by virtue of its hydrogen bonds.  The heterogeneity of beta-sheet topology is more the province of tertiary structure; it doesn't influence secondary structure.  Willow 09:41, 8 November 2006 (UTC)


 * P.S. I think we need to define beta strand somewhere in the header of beta sheet; it probably doesn't deserve its own article, right?


 * Yes, one needs H-bonds to define beta-sheet; and a beta-strand without beta-sheet is simply an extended conformation (just as polyPro helix, another regular structure, although it might be not "secondary"). I also agree that beta-sheet topology belongs to tertiary structure and "it doesn't influence secondary structure", i.e. it does not influence which residues are included in the beta-strands, it only influences the structure of the beta-sheet.  However, the beta-sheet and beta-strand are certainly two different things; it is too bad if they are interchangeable in textbooks or Wikipedia.  I do not want tilting at windmills as you say. That was simply a comment.  Biophys 01:00, 9 November 2006 (UTC)
 * No, I think beta-strand does not deserve a separate article. Biophys 01:05, 9 November 2006 (UTC)
 * Well, you're right, it's just that IMO we should reflect common usage at this level of presentation - I suspect the distinction would be a very minor point for the typical audience for an encyclopedia article on protein. So not quite windmill-tilting :) (As a side note, STRIDE, an alternative secondary-structure assignment program, does use dihedrals as well as hydrogen-bonding criteria. It variously reports itself to outperform DSSP, though it's less commonly used.) Opabinia regalis 02:36, 10 November 2006 (UTC)

Synthesis Picture
So that picture is completely wrong. One gene can encode a single protein, a small RNA (i.e. microRNA) or multiple isoforms of a proteins. The picture should be removed.
 * It shows a common occurance, this is not incorrect, it is just not the complete picture. However, since this article deals with proteins, adding microRNAs, rRNAs or snoRNAs would be a distraction. TimVickers 18:06, 30 November 2006 (UTC)

I missed this previously, but I agree that I don't like that picture, US government-issued or not. It's too cartoony and simplistic. Of course, the synthesis section really ought to mention alternative splicing. Opabinia regalis 03:24, 19 December 2006 (UTC)

Jargon
Are normal people meant to understand this?? Comment added by User:Plokt 21:30, 3 January 2007 (UTC)

The narrator of the 'Protein Denaturation' animation can't pronounce 'denaturation'
Just thought you ought to know. —Preceding unsigned comment added by 81.77.98.12 (talk • contribs)

You can either pronounce it deNATurAtion or DEnatURation. TimVickers 20:44, 4 January 2007 (UTC)

My main issue is not with which syllables he stresses, but with him using a short 'a' sound rather than a long one. It should be 'Dee-ney-cher-ey-shun', not 'Dee-nah-cher-ey-shun'. —Preceding unsigned comment added by 81.77.98.12 (talk • contribs)


 * I hadn't watched that video before, but wow, pronunciations are the least of its problems. I'm surprised it was made by a textbook company. Apparently amino acids polymerize spontaneously into proteins and the only type of secondary structure is a helix. Any objections to removing the link? Opabinia regalis 01:38, 5 January 2007 (UTC)

None. TimVickers 03:58, 5 January 2007 (UTC)