Intrinsic Disorder in Protein Interactions: Insights From a Comprehensive Structural Analysis
Tóm tắt
Từ khóa
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
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
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