{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,7]],"date-time":"2025-10-07T05:18:47Z","timestamp":1759814327866},"reference-count":60,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2011,10,13]],"date-time":"2011-10-13T00:00:00Z","timestamp":1318464000000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1002192","type":"journal-article","created":{"date-parts":[[2011,10,13]],"date-time":"2011-10-13T21:01:23Z","timestamp":1318539683000},"page":"e1002192","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":18,"title":["Quantifying Intramolecular Binding in Multivalent Interactions: A Structure-Based Synergistic Study on Grb2-Sos1 Complex"],"prefix":"10.1371","volume":"7","author":[{"given":"Anurag","family":"Sethi","sequence":"first","affiliation":[]},{"given":"Byron","family":"Goldstein","sequence":"additional","affiliation":[]},{"given":"S.","family":"Gnanakaran","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2011,10,13]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1016\/0092-8674(92)90167-B","article-title":"The SH2 and SH3 domain-containing protein GRB2 links receptor tyrosine kinases to ras signaling.","volume":"70","author":"EJ Lowenstein","year":"1992","journal-title":"Cell"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1006\/jmbi.2000.4396","article-title":"Solution structure of Grb2 reveals extensive exibility necessary for target recognition.","volume":"306","author":"S Yuzawa","year":"2001","journal-title":"J Mol Biol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1126\/science.279.5350.560","article-title":"Coupling of ras and rac guanosine triphosphatases through the ras exchanger Sos.","volume":"279","author":"AS Nimnual","year":"1998","journal-title":"Science"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1299","DOI":"10.1126\/science.1062023","article-title":"The guanine nucleotide-binding switch in three dimensions.","volume":"294","author":"IR Vetter","year":"2001","journal-title":"Science"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1263","DOI":"10.1083\/jcb.200203043","article-title":"T cell receptor ligation induces the formation of dynamically regulated signaling assemblies.","volume":"158","author":"SC Bunnell","year":"2002","journal-title":"J Cell Biol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"798","DOI":"10.1038\/nsmb1133","article-title":"Oligomerization of signaling complexes by the multipoint binding of GRB2 to both LAT and SOS1.","volume":"13","author":"JCD Houtman","year":"2006","journal-title":"Nat Struct Mol Biol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1083\/jcb.200104049","article-title":"High resolution mapping of mast cell membranes reveals primary and secondary domains of Fc<italic>\u03b5<\/italic>RI and LAT.","volume":"154","author":"BS Wilson","year":"2001","journal-title":"J Cell Biol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"2604","DOI":"10.1016\/j.bpj.2009.01.019","article-title":"Aggregation of membrane proteins by cytosolic cross-linkers: theory and simulation of the LAT-Grb2-SOS1 system.","volume":"96","author":"A Nag","year":"2009","journal-title":"Biophys J"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1016\/S0167-5699(00)01716-3","article-title":"Lymphocytes with a complex: adapter proteins in antigen receptor signaling.","volume":"21","author":"MG Tomlinson","year":"2000","journal-title":"Immunol Today"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/1074-5521(95)90080-2","article-title":"Grb2 SH3 binding to peptides from Sos: evaluation of a general model for SH3-ligand interactions.","volume":"2","author":"JA Simon","year":"1995","journal-title":"Chem Biol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"1540","DOI":"10.1073\/pnas.93.4.1540","article-title":"Distinct ligand preferences of Src homology 3 domains from Src, Yes, Abl, Cortactin, p53bp2, PLC, Crk, and Grb2.","volume":"93","author":"AB Sparks","year":"1996","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/j.abb.2008.08.012","article-title":"Structural basis of the differential binding of the SH3 domains of Grb2 adaptor to the guanine nucleotide exchange factor Sos1.","volume":"479","author":"CB McDonald","year":"2008","journal-title":"Arch Biochem Biophys"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"4074","DOI":"10.1021\/bi802291y","article-title":"SH3 domains of Grb2 adaptor bind to PX<italic>\u03c8<\/italic>PXR motifs within the Sos1 nucleotide exchange factor in a discriminate manner.","volume":"48","author":"CB McDonald","year":"2009","journal-title":"Biochemistry"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1126\/science.7526465","article-title":"Two binding orientations for peptides to the Src SH3 domain: development of a general model for SH3-ligand interactions.","volume":"266","author":"S Feng","year":"1994","journal-title":"Science"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1016\/j.jmb.2003.10.060","article-title":"The tryptophan switch: changing ligand-binding specificity from type I to type II in SH3 domains.","volume":"335","author":"G Fernandez-Ballester","year":"2004","journal-title":"J Mol Biol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1006\/jmbi.1999.2899","article-title":"Molecular and cellular analysis of Grb2 SH3 domain mutants: interaction with Sos and dynamin.","volume":"290","author":"M Vidal","year":"1999","journal-title":"J Mol Biol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"18212","DOI":"10.1074\/jbc.270.31.18212","article-title":"Differential interactions of human Sos1 and Sos2 with Grb2.","volume":"270","author":"SS Yang","year":"1995","journal-title":"J Biol Chem"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"2509","DOI":"10.1002\/j.1460-2075.1995.tb07248.x","article-title":"Biochemical and genetic analysis of the Drk SH2\/SH3 adaptor protein of Drosophila.","volume":"14","author":"T Raabe","year":"1995","journal-title":"EMBO J"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"2785","DOI":"10.1002\/jcc.21256","article-title":"AutoDock4 and AutoDockTools4: Automated docking with selective receptor exibility.","volume":"30","author":"GM Morris","year":"2009","journal-title":"J Comput Chem"},{"key":"ref20","article-title":"Autodock version 4.2 userguide.","author":"GM Morris","year":"2009"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1016\/S0969-2126(94)00106-5","article-title":"Solution structure and ligand-binding site of the carboxy-terminal SH3 domain of GRB2.","volume":"2","author":"D Kohda","year":"1994","journal-title":"Structure"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1007\/s10822-007-9159-2","article-title":"An improved relaxed complex scheme for receptor exibility in computer-aided drug design.","volume":"22","author":"RE Amaro","year":"2008","journal-title":"J Comput Aided Mol Des"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"1316","DOI":"10.1002\/jcc.20893","article-title":"Assessment of programs for ligand binding affinity prediction.","volume":"29","author":"R Kim","year":"2008","journal-title":"J Comput Chem"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1038\/nsb0894-546","article-title":"High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides.","volume":"1","author":"A Musacchio","year":"1994","journal-title":"Nat Struct Biol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1016\/S0969-2126(01)00151-4","article-title":"Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk.","volume":"3","author":"X Wu","year":"1995","journal-title":"Structure"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"3170","DOI":"10.1529\/biophysj.106.090258","article-title":"Quantitative relation between intermolecular and intramolecular binding of pro-rich peptides to SH3 domains.","volume":"91","author":"HX Zhou","year":"2006","journal-title":"Biophys J"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1275","DOI":"10.1016\/j.bpj.2008.10.052","article-title":"Biochemistry on a leash: the roles of tether length and geometry in signal integration proteins.","volume":"96","author":"D Van Valen","year":"2009","journal-title":"Biophys J"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1002\/recl.19490681203","article-title":"R\u00f6ntgenuntersuchung gel\u00f6ster fadenmolek\u00fcle.","volume":"68","author":"O Kratky","year":"1949","journal-title":"Rec Trav Chim Pays-Bas"},{"key":"ref29","doi-asserted-by":"crossref","DOI":"10.1002\/bip.1969.360080514","article-title":"Statistical Mechanics of Chain Molecules","author":"P Flory","year":"1969"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"6763","DOI":"10.1021\/jp011355n","article-title":"Loops in proteins can be modeled as worm-like chains.","volume":"105","author":"H Zhou","year":"2001","journal-title":"Journal of Physical Chemistry B"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1429","DOI":"10.1110\/ps.072845607","article-title":"An experimental study of GFPbased FRET, with application to intrinsically unstructured proteins.","volume":"16","author":"T Ohashi","year":"2007","journal-title":"Protein Sci"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"165104","DOI":"10.1063\/1.3251769","article-title":"Size, shape, and exibility of proteins and DNA.","volume":"131","author":"N Rawat","year":"2009","journal-title":"J Chem Phys"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"1416","DOI":"10.1016\/j.jmb.2007.11.063","article-title":"Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding.","volume":"375","author":"YC Kim","year":"2008","journal-title":"J Mol Biol"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"30472","DOI":"10.1074\/jbc.271.48.30472","article-title":"The Grb2-mSos1 complex binds phosphopeptides with higher affinity than Grb2.","volume":"271","author":"YM Chook","year":"1996","journal-title":"J Biol Chem"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"12408","DOI":"10.1073\/pnas.92.26.12408","article-title":"Specific interactions outside the proline-rich core of two classes of src homology 3 ligands.","volume":"92","author":"S Feng","year":"1995","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1016\/S0065-3233(02)61006-X","article-title":"How SH3 domains recognize proline.","volume":"61","author":"A Musacchio","year":"2002","journal-title":"Adv Protein Chem"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1110\/ps.062558507","article-title":"Studying multisite binary and ternary protein interactions by global analysis of isothermal titration calorimetry data in SEDPHAT: application to adaptor protein complexes in cell signaling.","volume":"16","author":"JCD Houtman","year":"2007","journal-title":"Protein Sci"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"2449","DOI":"10.4049\/jimmunol.175.4.2449","article-title":"Early phosphorylation kinetics of proteins involved in proximal TCR-mediated signaling pathways.","volume":"175","author":"JCD Houtman","year":"2005","journal-title":"J Immunol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"4170","DOI":"10.1021\/bi0357311","article-title":"Binding specificity of multiprotein signaling complexes is determined by both cooperative interactions and affinity preferences.","volume":"43","author":"JCD Houtman","year":"2004","journal-title":"Biochemistry"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"2754","DOI":"10.1002\/(SICI)1521-3773(19981102)37:20<2754::AID-ANIE2754>3.0.CO;2-3","article-title":"Polyvalent interactions in biological systems: Implications for design and use of multivalent ligands and inhibitors.","volume":"37","year":"1998","journal-title":"Angewandte Chemie"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"8245","DOI":"10.1021\/jo000943e","article-title":"Multivalency effects in protein\u2013 carbohydrate interaction: the binding of the shiga-like toxin 1 binding subunit to multivalent c-linked glycopeptides.","volume":"65","author":"JJ Lundquist","year":"2000","journal-title":"J Org Chem"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"15069","DOI":"10.1021\/bi015795g","article-title":"The affinity-enhancing roles of exible linkers in two-domain DNAbinding proteins.","volume":"40","author":"HX Zhou","year":"2001","journal-title":"Biochemistry"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0022-2836(03)00372-3","article-title":"Quantitative account of the enhanced affinity of two linked scFvs specific for different epitopes on the same antigen.","volume":"329","author":"HX Zhou","year":"2003","journal-title":"J Mol Biol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"7338","DOI":"10.1074\/jbc.M708359200","article-title":"Computational models of tandem src homology 2 domain interactions and application to phosphoinositide 3-kinase.","volume":"283","author":"D Barua","year":"2008","journal-title":"J Biol Chem"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool.","volume":"215","author":"SF Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.","volume":"22","author":"JD Thompson","year":"1994","journal-title":"Nucleic Acids Res"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"4045","DOI":"10.1073\/pnas.0409715102","article-title":"Evolutionary profiles from the QR factorization of multiple sequence alignments.","volume":"102","author":"A Sethi","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1186\/1471-2105-7-382","article-title":"Multiseq: unifying sequence and structure data for evolutionary analysis.","volume":"7","author":"E Roberts","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"Vmd: Visual molecular dynamics.","volume":"14","author":"AD William Humphrey","year":"1996","journal-title":"J Mol Graph"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1002\/prot.22488","article-title":"Improved prediction of protein sidechain conformations with scwrl4.","volume":"77","author":"GG Krivov","year":"2009","journal-title":"Proteins"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1126\/science.7716522","article-title":"Crystal structure of the mammalian Grb2 adaptor.","volume":"268","author":"S Maignan","year":"1995","journal-title":"Science"},{"key":"ref52","first-page":"Unit 2.9","article-title":"Comparative protein structure modeling using modeller.","volume":"2","author":"N Eswar","year":"2007","journal-title":"Curr Protoc Protein Sci Chapter"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1002\/jcc.20289","article-title":"Scalable molecular dynamics with namd.","volume":"26","author":"JC Phillips","year":"2005","journal-title":"J Comput Chem"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"3586","DOI":"10.1021\/jp973084f","article-title":"All-atom empirical potential for molecular modeling and dynamics studies of proteins.","volume":"102","author":"JA MacKerell","year":"1998","journal-title":"J Phys Chem B"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"9954","DOI":"10.1021\/jp003020w","article-title":"Structure and dynamics of the TIP3P, SPC, and SPC\/E water models at 298 k.","volume":"105","author":"P Mark","year":"2001","journal-title":"J Phys Chem A"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1002\/prot.22102","article-title":"Very fast prediction and rationalization of pKa values for protein-ligand complexes.","volume":"73","author":"DC Bas","year":"2008","journal-title":"Proteins"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"1382","DOI":"10.1016\/j.jmb.2008.01.073","article-title":"Dynamics of recognition between tRNA and elongation factor Tu.","volume":"377","author":"J Eargle","year":"2008","journal-title":"J Mol Biol"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle mesh Ewald: An nlog(n) method for Ewald sums in large systems.","volume":"98","author":"T Darden","year":"1993","journal-title":"J Chem Phys"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/0021-9991(83)90014-1","article-title":"Rattle: A \u201cvelocity\u201d version of the shake algorithm for molecular dynamics calculations.","volume":"52","author":"H Anderson","year":"1983","journal-title":"J Comput Phys"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"952","DOI":"10.1002\/jcc.540130805","article-title":"Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models.","volume":"13","author":"S Miyamoto","year":"1992","journal-title":"J Comput Chem"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002192","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,6,17]],"date-time":"2019-06-17T13:20:08Z","timestamp":1560777608000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002192"}},"subtitle":[],"editor":[{"given":"Gerhard","family":"Hummer","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2011,10,13]]},"references-count":60,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2011,10,13]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1002192","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,10,13]]}}}