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Compositional Characteristics of Disordered Regions in Proteins

By Russ Altman Christopher, Section On Medical Informatics and Altman Et Al

Abstract

Many high resolution protein structures derived from crystallographic studies contain regions in which the temperature factor (or B-factor, a measure related inversely to occupancy) is large. These regions can have low occupancy for two (not mutually exclusive) reasons; either there is motion within the individual molecules which smears out the density over time, or there are numerous specific conformations adopted by different molecules within the lattice, and therefore the conformations are averaged over the population. In either case, these regions of low occupancy are examples of protein substructures in which there is no single stable conformation, but either a dynamic, flexible set of conformations, or a relatively static set of alternative conformation. These regions may therefore contain valuable information about the ways in which protein structural stability can be achieved. In this paper, we have investigated the characteristics of high B-factor regions within otherwise well-resolved protein structures. Most noteworthy, we have shown that amino acids LYS, SER, GLN, ALA, GLU, PRO, ASN, ASP and ARG occur more frequently in disordered regions, that 40% of disordered residues are in coil conformation (with as much as 30% in a regular repeating secondary structure such as alpha-helix or beta-strand), and that disordered amino acids make on average 2.6 fewer intersidechain contacts than ordered residues. 1

Topics: protein crystallography, structural uncertainty, protein structure prediction, sequence analysis, temperature factor, B-factor
Year: 2007
OAI identifier: oai:CiteSeerX.psu:10.1.1.18.6394
Provided by: CiteSeerX
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