User:Immcarle70/sandbox

https://www.ncbi.nlm.nih.gov/books/NBK27144/ A great resource that explains the different parts of the antibody and clearly defines the different regions of the antibody. The pictures it shows remain unclear though because they do not include all different aspects, allowing the reader to understand a full picture of what is going on. https://www.wiley.com/legacy/products/subject/life/elgert/CH04.pdf Contains much better pictures for the idea of how each portion of the antibody goes along with one another. It includes the V,D,J explanations and also the C regions on the antibody while simultaneously showing which portions are framework. It also has a great 3D picture which gives us a better idea of the 3 "Finger- like" projections on the antibody (resulting from the three main coding regions) making it more clear of how the antibody ends up folding and makes it clear which specific portions of the antibody end up binding to the antigen. Zhu K et al. Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction. Pro- teins 2014; 8: 1646–1655. This research experiment in 2004 used BioLuminate and Prime to predict second antibody modeling assessment to better understand the structures and locations of the CDR loops and H3 loops. This is a blinded approach for them to predict the CDR loops and where they are in the antibody itself. Brian D. Weitzner, Roland L. Dunbrack, Jeffrey J. Gray, The Origin of CDR H3 Structural Diversity, Structure, Volume 23, Issue 2, 2015, Pages 302-311, ISSN 0969-2126, https://doi.org/10.1016/j.str.2014.11.010. Attempts to explain how many CDR regions can be classifiable and why the H3 region does not have this same grouping, specifically focusing on the kink in the H3 region. They conclude that the H3 function is defined by the C terminal kink and that is why it is so important to the antibody. Explains the framework region has expected canonical conformations.

https://elifesciences.org/articles/33038 Important for talking about mutations in FR region for nab antibodies

My main goal for this wikipedia page is to clarify what exactly the framework region of an antibody is. While it is described on the page, it is described in a very convoluted way that does not make it clear to the reader what the framework region is. I want to make it clear that the framework region is part of the variable region on both the light and heavy chains, and how it relates to the VDJ regions of the antibody as well. I want to construct a clear images that can help explain what the framework region of the antibody is.

In molecular biology, a framework region is a subdivision of the variable region (Fab) of the antibody. The variable region is composed of seven amino acid regions, four of which are framework regions and three of which are hypervariable regions.[1] The framework region makes up about 85% of the variable region.[2] To increase its stability, the framework region has less variability in its amino acid sequences compared to the CDR.[2] The hypervariable regions(HV) are involved in direct contact with the antigen and are often called complementarity domain regions (CDR). Located on the tips of the Y-shaped molecule, the framework regions are responsible for acting as a scaffold for the hypervariable region (CDR) of the Fab, supporting the binding of the CDR to the antigen,[3] and maintaining the overall structure of the four variable domains on the antibody.[4]

Function
The antibody has a three-dimensional structure with beta pleated sheet and alpha helices. The antibody folds so the variable regions form three loops with the framework regions folded into one another and the CDR regions on the tips of each of these loops in direct contact with the antigen. Residues of the framework region responsible for supporting the binding of the antigen to the antibody can be divided into two categories; residues that are in contact with the antigen and are not in contact with the antigen. Framework residues that come in contact with the antigen are a part of the antibody's binding site, and are located either close in sequence to the CDRs or in close proximity to the CDR when in the folded three dimensional structure.[4] Framework residues are short amino acid sequences part of the framework region. Framework residues that do not come in contact with the antigen affect the binding indirectly by aiding in structural support for the CDR. This enables the CDR to take on the correct orientation and position so it is exposed on the surface of the chain ready to bind to an antigen.[2]

The framework regions are highly conserved regions of the variable portion of the antibody. The evolutionary reason for the conservation of these regions is to support proper folding of the antibody allowing the CDR regions to be stabilized. Folding in FR leads to antibody structure flexibility or rigidity of the binding region of the antibody.

Mutations
Mutations in the framework regions of antibodies occur in cells by somatic hypermutation and during affinity maturation of the antibody. In vitro, mutations of FR may occur by saturation mutagenesis. Recent studies of framework mutations imply that the framework region flexibility or rigidity could alter the specificity of the antibody to its intended epitope. While the framework region doesn't directly interact with antigen, its structure determines whether the CDRs can interact with antigen. If the CDR regions have high affinity for the epitope of antigen, it has been found to be more effective to have a more rigid framework region. When CDR does not have high affinity for antigen, mutations in the FR that create a more flexible structure may allow for higher affinity maturation.

In another experiment, the complementary domain region was conserved, and natural somatic hypermutation was utilized to change amino acids in the framework region to determine what change in structure this would have of the antibody. Since the CDR is the region of antigen affinity and was conserved, they hypothesized that affinity of the antibodies would not be altered. To further assess the function of FR in antibody structure, the surface FR near the CDR was conserved while the deeper FR that was further from the antigen binding site was mutated since it is the region hypothesized to take part in antibody folding and stability. Their results concluded that certain FR mutations led to increased expression and thermostability.

Antibody humanization is an example of beneficial mutations in medicine today. Humanized antibody refers to the usage of clinical animal antibodies, then the modification of these non-human antibodies to increase the similarity of the antibody to naturally produced human antibodies. This allows the formation of antibodies and testing of antibodies in rats and the use of these experiments clinically. It has been discovered that while these antibodies remain relatively intact upon transition, these modifications can also lead to decreased binding affinity in the humanized framework regions and result in improper folding in humans. Other studies noticed similar effects of humanization. To combat this, after humanization, mutations in certain framework residue regions that were not in contact with antigen were found to increase affinity and proper folding of antibody. This implies that the problem of framework mutations in humanization can be altered by further mutating the framework residues.