Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions

被引:186
作者
Vucetic, Slobodan
Xie, Hongbo
Iakoucheva, Lilia M.
Oldfield, Christopher J.
Dunker, A. Keith
Obradovic, Zoran
Uversky, Vladimir N.
机构
[1] Indiana Univ, Sch Med, Dept Biochem & Mol Biol, Ctr Computat Biol & Bioinformat, Indianapolis, IN 46202 USA
[2] Temple Univ, Ctr Informat Sci & Technol, Philadelphia, PA 19122 USA
[3] Rockefeller Univ, Lab Stat Genet, New York, NY 10021 USA
[4] Russian Acad Sci, Inst Biol Instrumentat, Pushchino 142290, Moscow Region, Russia
关键词
intrinsic disorder; protein structure; protein function; intrinsically disordered proteins; bioinformatics; disorder prediction;
D O I
10.1021/pr060393m
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Biologically active proteins without stable ordered structure (i.e., intrinsically disordered proteins) are attracting increased attention. Functional repertoires of ordered and disordered proteins are very different, and the ability to differentiate whether a given function is associated with intrinsic disorder or with a well-folded protein is crucial for modern protein science. However, there is a large gap between the number of proteins experimentally confirmed to be disordered and their actual number in nature. As a result, studies of functional properties of confirmed disordered proteins, while helpful in revealing the functional diversity of protein disorder, provide only a limited view. To overcome this problem, a bioinformatics approach for comprehensive study of functional roles of protein disorder was proposed in the first paper of this series (Xie, H.; Vucetic, S.; Iakoucheva, L. M.; Oldfield, C. J.; Dunker, A. K.; Obradovic, Z.; Uversky, V. N. Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J. Proteome Res. 2007, 5, 1882-1898). Applying this novel approach to Swiss-Prot sequences and functional keywords, we found over 238 and 302 keywords to be strongly positively or negatively correlated, respectively, with long intrinsically disordered regions. This paper describes similar to 90 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes, and coding sequence diversities possessing strong positive and negative correlation with long disordered regions. Keywords: intrinsic disorder center dot protein structure center dot protein function center dot intrinsically disordered proteins center dot bioinformatics center dot disorder prediction
引用
收藏
页码:1899 / 1916
页数:18
相关论文
共 257 条
[1]   STRUCTURE AT 2.8-ANGSTROM RESOLUTION OF F1-ATPASE FROM BOVINE HEART-MITOCHONDRIA [J].
ABRAHAMS, JP ;
LESLIE, AGW ;
LUTTER, R ;
WALKER, JE .
NATURE, 1994, 370 (6491) :621-628
[2]   Comparison of the stabilities and unfolding pathways of human apolipoprotein E isoforms by differential scanning calorimetry and circular dichroism [J].
Acharya, P ;
Segall, ML ;
Zaiou, M ;
Morrow, J ;
Weisgraber, KH ;
Phillips, MC ;
Lund-Katz, S ;
Snow, J .
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS, 2002, 1584 (01) :9-19
[3]   The kelch repeat superfamily of proteins: propellers of cell function [J].
Adams, J ;
Kelso, R ;
Cooley, L .
TRENDS IN CELL BIOLOGY, 2000, 10 (01) :17-24
[4]   The other trinucleotide repeat: polyalanine expansion disorders [J].
Albrecht, A ;
Mundlos, S .
CURRENT OPINION IN GENETICS & DEVELOPMENT, 2005, 15 (03) :285-293
[5]   Interspecies diversity of the occludin sequence: cDNA cloning of human, mouse, dog, and rat-kangaroo homologues [J].
AndoAkatsuka, Y ;
Saitou, M ;
Hirase, T ;
Kishi, M ;
Sakakibara, A ;
Itoh, M ;
Yonemura, S ;
Furuse, M ;
Tsukita, S .
JOURNAL OF CELL BIOLOGY, 1996, 133 (01) :43-47
[6]  
Apel E D, 1992, Perspect Dev Neurobiol, V1, P3
[7]   How did alternative splicing evolve? [J].
Ast, G .
NATURE REVIEWS GENETICS, 2004, 5 (10) :773-782
[8]   THE REFINED CRYSTAL-STRUCTURE OF HEXON, THE MAJOR COAT PROTEIN OF ADENOVIRUS TYPE-2, AT 2-CENTER-DOT-9 ANGSTROM RESOLUTION [J].
ATHAPPILLY, FK ;
MURALI, R ;
RUX, JJ ;
CAI, ZP ;
BURNETT, RM .
JOURNAL OF MOLECULAR BIOLOGY, 1994, 242 (04) :430-455
[9]   The LIM domain: regulation by association [J].
Bach, I .
MECHANISMS OF DEVELOPMENT, 2000, 91 (1-2) :5-17
[10]   Retroelements and the human genome: New perspectives on an old relation [J].
Bannert, N ;
Kurth, R .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 :14572-14579