Intrinsic Disorder in Protein Interactions: Insights From a Comprehensive Structural Analysis

PLoS Computational Biology - Tập 5 Số 3 - Trang e1000316
Jessica H. Fong1, Benjamin A. Shoemaker1, Sergiy O. Garbuzynskiy2, Michail Yu. Lobanov2, Oxana V. Galzitskaya2, Anna R. Panchenko1
1National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, United States of America
2Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia

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Tài liệu tham khảo

PE Wright, 1999, Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm., J Mol Biol, 293, 321, 10.1006/jmbi.1999.3110

VN Uversky, 2000, Why are “natively unfolded” proteins unstructured under physiologic conditions?, Proteins, 41, 415, 10.1002/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7

S Vucetic, 2003, Flavors of protein disorder., Proteins, 52, 573, 10.1002/prot.10437

AL Fink, 2005, Natively unfolded proteins., Curr Opin Struct Biol, 15, 35, 10.1016/j.sbi.2005.01.002

T Le Gall, 2007, Intrinsic disorder in the Protein Data Bank., J Biomol Struct Dyn, 24, 325, 10.1080/07391102.2007.10507123

R Huber, 1983, Functional significance of flexibility in proteins., Biopolymers, 22, 261, 10.1002/bip.360220136

AK Dunker, 2000, Intrinsic protein disorder in complete genomes., Genome Inform Ser Workshop Genome Inform, 11, 161

J Liu, 2001, Comparing function and structure between entire proteomes., Protein Sci, 10, 1970, 10.1110/ps.10101

P Tompa, 2003, Intrinsically unstructured proteins evolve by repeat expansion., Bioessays, 25, 847, 10.1002/bies.10324

H Xie, 2007, Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions., J Proteome Res, 6, 1882, 10.1021/pr060392u

NS Bogatyreva, 2006, Trend of amino acid composition of proteins of different taxa., J Bioinform Comput Biol, 4, 597, 10.1142/S0219720006002016

JJ Ward, 2004, Prediction and functional analysis of native disorder in proteins from the three kingdoms of life., J Mol Biol, 337, 635, 10.1016/j.jmb.2004.02.002

AK Dunker, 2002, Intrinsic disorder and protein function., Biochemistry, 41, 6573, 10.1021/bi012159+

K Gunasekaran, 2003, Extended disordered proteins: targeting function with less scaffold., Trends Biochem Sci, 28, 81, 10.1016/S0968-0004(03)00003-3

DE Draper, 1999, RNA binding strategies of ribosomal proteins., Nucleic Acids Res, 27, 381, 10.1093/nar/27.2.381

P Tompa, 2002, Intrinsically unstructured proteins., Trends Biochem Sci, 27, 527, 10.1016/S0968-0004(02)02169-2

K Sugase, 2007, Mechanism of coupled folding and binding of an intrinsically disordered protein., Nature, 447, 1021, 10.1038/nature05858

T Bordelon, 2004, A disorder to order transition accompanies catalysis in retinaldehyde dehydrogenase type II., J Biol Chem, 279, 43085, 10.1074/jbc.M406139200

BA Shoemaker, 2000, Speeding molecular recognition by using the folding funnel: the fly-casting mechanism., Proc Natl Acad Sci U S A, 97, 8868, 10.1073/pnas.160259697

P Radivojac, 2007, Intrinsic disorder and functional proteomics., Biophys J, 92, 1439, 10.1529/biophysj.106.094045

K Gunasekaran, 2004, Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers., J Mol Biol, 341, 1327, 10.1016/j.jmb.2004.07.002

B Meszaros, 2007, Molecular principles of the interactions of disordered proteins., J Mol Biol, 372, 549, 10.1016/j.jmb.2007.07.004

P Romero, 2001, Sequence complexity of disordered protein., Proteins, 42, 38, 10.1002/1097-0134(20010101)42:1<38::AID-PROT50>3.0.CO;2-3

HJ Dyson, 2005, Intrinsically unstructured proteins and their functions., Nat Rev Mol Cell Biol, 6, 197, 10.1038/nrm1589

LM Iakoucheva, 2004, The importance of intrinsic disorder for protein phosphorylation., Nucleic Acids Res, 32, 1037, 10.1093/nar/gkh253

L Bordoli, 2007, Assessment of disorder predictions in CASP7., Proteins, 69, 129, 10.1002/prot.21671

R Linding, 2003, GlobPlot: Exploring protein sequences for globularity and disorder., Nucleic Acids Res, 31, 3701, 10.1093/nar/gkg519

R Linding, 2003, Protein disorder prediction: implications for structural proteomics., Structure, 11, 1453, 10.1016/j.str.2003.10.002

Z Dosztanyi, 2005, IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content., Bioinformatics, 21, 3433, 10.1093/bioinformatics/bti541

K Coeytaux, 2005, Prediction of unfolded segments in a protein sequence based on amino acid composition., Bioinformatics, 21, 1891, 10.1093/bioinformatics/bti266

OV Galzitskaya, 2006, FoldUnfold: web server for the prediction of disordered regions in protein chain., Bioinformatics, 22, 2948, 10.1093/bioinformatics/btl504

OV Galzitskaya, 2006, Prediction of amyloidogenic and disordered regions in protein chains., PLoS Comput Biol, 2, 10.1371/journal.pcbi.0020177

A Schlessinger, 2007, Natively unstructured regions in proteins identified from contact predictions., Bioinformatics, 23, 2376, 10.1093/bioinformatics/btm349

K Peng, 2006, Length-dependent prediction of protein intrinsic disorder., BMC Bioinformatics, 7, 208, 10.1186/1471-2105-7-208

Z Obradovic, 2005, Exploiting heterogeneous sequence properties improves prediction of protein disorder., Proteins, 61, 176, 10.1002/prot.20735

Z Obradovic, 2003, Predicting intrinsic disorder from amino acid sequence., Proteins, 53, 566, 10.1002/prot.10532

J Hecker, 2008, Protein disorder prediction at multiple levels of sensitivity and specificity., BMC Genomics, 9, S9, 10.1186/1471-2164-9-S1-S9

CT Su, 2006, Protein disorder prediction by condensed PSSM considering propensity for order or disorder., BMC Bioinformatics, 7, 319, 10.1186/1471-2105-7-319

ZR Yang, 2005, RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins., Bioinformatics, 21, 3369, 10.1093/bioinformatics/bti534

BA Shoemaker, 2007, Deciphering protein-protein interactions. Part I. Experimental techniques and databases., PLoS Comput Biol, 3, 10.1371/journal.pcbi.0030042

RS Spolar, 1994, Coupling of local folding to site-specific binding of proteins to DNA., Science, 263, 777, 10.1126/science.8303294

AP Demchenko, 2001, Recognition between flexible protein molecules: induced and assisted folding., J Mol Recognit, 14, 42, 10.1002/1099-1352(200101/02)14:1<42::AID-JMR518>3.0.CO;2-8

P Tompa, 2005, Structural disorder throws new light on moonlighting., Trends Biochem Sci, 30, 484, 10.1016/j.tibs.2005.07.008

Y Levy, 2004, Protein topology determines binding mechanism., Proc Natl Acad Sci U S A, 101, 511, 10.1073/pnas.2534828100

CJ Oldfield, 2005, Coupled folding and binding with alpha-helix-forming molecular recognition elements., Biochemistry, 44, 12454, 10.1021/bi050736e

A Mohan, 2006, Analysis of molecular recognition features (MoRFs)., J Mol Biol, 362, 1043, 10.1016/j.jmb.2006.07.087

Y Zhang, 2007, Between order and disorder in protein structures: analysis of “dual personality” fragments in proteins., Structure, 15, 1141, 10.1016/j.str.2007.07.012

BA Shoemaker, 2006, Finding biologically relevant protein domain interactions: conserved binding mode analysis., Protein Sci, 15, 352, 10.1110/ps.051760806

HM Berman, 2000, The Protein Data Bank and the challenge of structural genomics., Nat Struct Biol, 7, 957, 10.1038/80734

A Marchler-Bauer, 2002, CDD: a database of conserved domain alignments with links to domain three-dimensional structure., Nucleic Acids Res, 30, 281, 10.1093/nar/30.1.281

A Marchler-Bauer, 2004, CD-Search: protein domain annotations on the fly., Nucleic Acids Res, 32, W327, 10.1093/nar/gkh454

E Krissinel, 2007, Inference of macromolecular assemblies from crystalline state., J Mol Biol, 372, 774, 10.1016/j.jmb.2007.05.022

E Camon, 2004, The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology., Nucleic Acids Res, 32, D262, 10.1093/nar/gkh021

S Hirose, 2007, POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions., Bioinformatics, 23, 2046, 10.1093/bioinformatics/btm302

PM Quigley, 2004, A new native EcHsp31 structure suggests a key role of structural flexibility for chaperone function., Protein Sci, 13, 269, 10.1110/ps.03399604

DS Goodsell, 2000, Structural symmetry and protein function., Annu Rev Biophys Biomol Struct, 29, 105, 10.1146/annurev.biophys.29.1.105

J Monod, 1965, On the Nature of Allosteric Transitions: a Plausible Model., J Mol Biol, 12, 88, 10.1016/S0022-2836(65)80285-6

SC Johnston, 1997, Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 A resolution., Embo J, 16, 3787, 10.1093/emboj/16.13.3787

S Misaghi, 2005, Structure of the ubiquitin hydrolase UCH-L3 complexed with a suicide substrate., J Biol Chem, 280, 1512, 10.1074/jbc.M410770200

P Tompa, 2008, Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions., Trends Biochem Sci, 33, 2, 10.1016/j.tibs.2007.10.003

JT Stivers, 1996, 15N NMR relaxation studies of free and inhibitor-bound 4-oxalocrotonate tautomerase: backbone dynamics and entropy changes of an enzyme upon inhibitor binding., Biochemistry, 35, 16036, 10.1021/bi961834q

ET Olejniczak, 1997, Changes in the NMR-derived motional parameters of the insulin receptor substrate 1 phosphotyrosine binding domain upon binding to an interleukin 4 receptor phosphopeptide., Biochemistry, 36, 4118, 10.1021/bi963050i

L Zidek, 1999, Increased protein backbone conformational entropy upon hydrophobic ligand binding., Nat Struct Biol, 6, 1118, 10.1038/70057

AP Loh, 2001, An increase in side chain entropy facilitates effector binding: NMR characterization of the side chain methyl group dynamics in Cdc42Hs., Biochemistry, 40, 4590, 10.1021/bi002418f

AB Sigalov, 2007, Binding of intrinsically disordered proteins is not necessarily accompanied by a structural transition to a folded form., Biochimie, 89, 419, 10.1016/j.biochi.2006.11.003

SM Simon, 2008, Regulation of Escherichia coli SOS mutagenesis by dimeric intrinsically disordered umuD gene products., Proc Natl Acad Sci U S A, 105, 1152, 10.1073/pnas.0706067105

B Ma, 1999, Folding funnels and binding mechanisms., Protein Eng, 12, 713, 10.1093/protein/12.9.713

HJ Dyson, 2002, Coupling of folding and binding for unstructured proteins., Curr Opin Struct Biol, 12, 54, 10.1016/S0959-440X(02)00289-0

J Wang, 2007, Optimal specificity and function for flexible biomolecular recognition., Biophys J, 92, L109, 10.1529/biophysj.107.105551

OF Lange, 2008, Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution., Science, 320, 1471, 10.1126/science.1157092

CJ Tsai, 2001, Structured disorder and conformational selection., Proteins, 44, 418, 10.1002/prot.1107

DD Boehr, 2008, Biochemistry. How do proteins interact?, Science, 320, 1429, 10.1126/science.1158818

TL Blundell, 1996, Symmetry, stability, and dynamics of multidomain and multicomponent protein systems., Proc Natl Acad Sci U S A, 93, 14243, 10.1073/pnas.93.25.14243

DB Lukatsky, 2006, Statistically enhanced self-attraction of random patterns., Phys Rev Lett, 97, 178101, 10.1103/PhysRevLett.97.178101

A Andreeva, 2006, Evolution of protein fold in the presence of functional constraints., Curr Opin Struct Biol, 16, 399, 10.1016/j.sbi.2006.04.003