User:Rokasj1/sandbox

#unit 4
p53 and MDM2 interaction inhibition by small molecules is of great interest to cancer biologists. Dr. Lu says that even though the PMI is very specific towards MDM2, "How to design MDMX-specific and, in particular, dual specific antagonists, however, still remains a challenge." To that end pDIQ was derived in Chen's lab and after testing for inhibitory activity were found to have low IC50 values.

Unit 7 work
References used for Histone Octamers:

This article is a review of the epigenetics involved with the histone octamer. The article will provide useful infomation concerning how and when histones are modified. It provides specific examples of histone tail modification and its role on the expression of genes as well as the physical effect of such modifications. The article is useful in giving perspective of the role of histones in genetic expression.

This article also touches on gene modification but goes into more depth on how the histones are positioned throughout the chromosomes and how that lends itself to DNA packaging. This article goes over how histones are important in condensation of genetic material and ultimately play a role in higher order organization. It provides both basic and in depth information about histone interaction with DNA. This article appears to be free so we could potentially use its pictures.

This review article also covers nucleosome positioning and its role in gene regulation. First off, this article has a lot of great figures to explain its ideas. The article is also good because it goes over how DNA attached to histones is accessed by transcriptional machinery. It covers the process of histone remodeling and removal for DNA access. This article adds some depth to the discussion of histones and gene expression as well as provides some great pictures.

histone octamer is a cylindrical wedge derived from an assembly of the four histone dimers into a left-handed protein supercoil. Surface topography of the histone octamer. This work helped identify fundamental components of the histone fold. Also, this group dentified DNA protein binding motifs and non-sequence-specific patterns of interactions

histone tails can undergo the following postranslational modifications:

deacetylation, demethylation, and dephosphorylation. All these modifications increase access of transcription factors to promoter region. Histone deacetylation can diminishes acetylation of histones and in turn cause compaction of DNA/histone complex. Histone deacetylation is carried out by enzyme named histone deacetylase (HDAC).

Histone deacetylase inhibitors have a potential cancer treatment and vorinostat is already approved for treating refractory cutaneuous T-cell lymphoma.

Basic Definition

 * Have a basic definition of the histone octamer out front. This can be a couple of sentences like the article already has. For people that just want to know what it is.

History of Research

 * This subsection will deal with breakthroughs in histone research up to this point.
 * Good way of introducing the overarching topics before going into them.
 * Brings the reader to the modern definition of histone octamer.
 * Not much information has been found regarding this topic yet. Subject to change or removal.

The Octamer in Molecular Detail

 * This section will go into the physical structure of the octamer
 * How the octamer is organized (dimers, tetramers)
 * Protein structure

Nucleosome

 * Epigenetic significance
 * Physical and chemical interaction with DNA
 * Modifications to histone tails
 * Restructuring for transcription
 * DNA packaging and higher order organization of chromosomes

Clinical Relevance

 * Role in modern health
 * Diseases associated with histone defects