2011
Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions
Bhardwaj N, Abyzov A, Clarke D, Shou C, Gerstein MB. Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions. Protein Science 2011, 20: 1745-1754. PMID: 21826754, PMCID: PMC3218368, DOI: 10.1002/pro.710.Peer-Reviewed Original ResearchConceptsMulti-interface hubsMolecular networksConformational changesInteraction networksTransient interactionsStructural interaction networksProtein interaction networksClassification of proteinsDynamic conformational changesProtein structural featuresSmall conformational changesTransient associationGene expressionMore plasticityProtein motionsStructural databankProteinAlternate conformationDifferent mechanismsDrastic structural changesDomainInteraction
2009
RigidFinder: A fast and sensitive method to detect rigid blocks in large macromolecular complexes
Abyzov A, Bjornson R, Felipe M, Gerstein M. RigidFinder: A fast and sensitive method to detect rigid blocks in large macromolecular complexes. Proteins Structure Function And Bioinformatics 2009, 78: 309-324. PMID: 19705487, DOI: 10.1002/prot.22544.Peer-Reviewed Original ResearchConceptsLarge macromolecular complexesMacromolecular complexesLarge-scale conformational changesRNA polymerase IIT7 RNA polymeraseMultiple polypeptide chainsPolymerase IIRNA polymeraseDistance conservationPhosphate dikinaseDifferent conformationsInter-residue distancesLarge complexesConformational changesPolypeptide chainDomain motionPartial refoldingFurther distinguishing featureConformationStructure determinationComplexesDikinaseSensitive identificationGroELIdentification