2017
Modeling of Receptor Tyrosine Kinase Signaling: Computational and Experimental Protocols
Fey D, Aksamitiene E, Kiyatkin A, Kholodenko BN. Modeling of Receptor Tyrosine Kinase Signaling: Computational and Experimental Protocols. Methods In Molecular Biology 2017, 1636: 417-453. PMID: 28730495, DOI: 10.1007/978-1-4939-7154-1_27.Peer-Reviewed Original ResearchConceptsReceptor tyrosine kinasesReceptor tyrosine kinase signalingMultiple cellular processesTyrosine kinase signalingCellular processesProtein phosphorylationKinase signalingNetwork biologySystems biologyTyrosine kinaseCell survivalIntegration of experimentsPowerful approachIntegrative approachBiologyComputational protocolQuantitative datasetsKinasePhosphorylationSignalingIdentification of salientApoptosisDifferentiationGlucose metabolismRegulation
2003
Tyr-317 Phosphorylation Increases Shc Structural Rigidity and Reduces Coupling of Domain Motions Remote from the Phosphorylation Site as Revealed by Molecular Dynamics Simulations*
Suenaga A, Kiyatkin AB, Hatakeyama M, Futatsugi N, Okimoto N, Hirano Y, Narumi T, Kawai A, Susukita R, Koishi T, Furusawa H, Yasuoka K, Takada N, Ohno Y, Taiji M, Ebisuzaki T, Hoek JB, Konagaya A, Kholodenko BN. Tyr-317 Phosphorylation Increases Shc Structural Rigidity and Reduces Coupling of Domain Motions Remote from the Phosphorylation Site as Revealed by Molecular Dynamics Simulations*. Journal Of Biological Chemistry 2003, 279: 4657-4662. PMID: 14613932, DOI: 10.1074/jbc.m310598200.Peer-Reviewed Original ResearchConceptsPhosphotyrosine bindingTyr-317Shc phosphorylationSH2 domainC-terminal Src homology 2 domainSrc homology 2 domainRas/Raf/MEK/ERK pathwayShc adaptor proteinRaf/MEK/ERK pathwayMEK/ERK pathwayReceptor tyrosine kinasesShc functionPhosphorylated ShcPhosphorylation sitesAdaptor proteinLinker regionShcTyrosine kinaseERK pathwayMembrane receptorsPhosphorylationDomain motionMolecular dynamics simulationsNumerous partnersDomain coupling
2001
Temperature Dependence of the Epidermal Growth Factor Receptor Signaling Network Can Be Accounted for by a Kinetic Model †
Moehren G, Markevich N, Demin O, Kiyatkin A, Goryanin I, Hoek JB, Kholodenko BN. Temperature Dependence of the Epidermal Growth Factor Receptor Signaling Network Can Be Accounted for by a Kinetic Model †. Biochemistry 2001, 41: 306-320. PMID: 11772030, DOI: 10.1021/bi011506c.Peer-Reviewed Original ResearchConceptsEpidermal growth factorEGF receptorEGFR kinaseDomain-mediated interactionsEGF receptor dimerizationProtein-protein interactionsRapid tyrosine phosphorylationMultiple signaling proteinsEGFR kinase activityReceptor phosphataseSignaling networksSignaling proteinsProtein interactionsPhosphorylation patternTyrosine phosphorylationReceptor dimerizationKinase activityTarget proteinsMembrane lipidsMolecular termsDephosphorylation reactionsEGFR pathwayPhosphataseKinasePhosphorylation
1995
Control of erythrocyte metabolism by redox-regulated tyrosine phosphatases and kinases
Low P, Kiyatkin A, Li Q, Harrison M. Control of erythrocyte metabolism by redox-regulated tyrosine phosphatases and kinases. Protoplasma 1995, 184: 196-202. DOI: 10.1007/bf01276920.Peer-Reviewed Original ResearchTyrosine phosphataseN-terminusBand 3Cytoplasmic tyrosine phosphataseGlyceraldehyde-3-phosphate dehydrogenase bindsEnzyme bindingCytoplasmic domainTyrosine phosphorylationTyr-8Tyrosine kinaseElectron transport pathwaysGlycolytic enzymesMetabolic regulationCoordinate mannerTyr-21KinaseNovel mechanismPhosphorylationRedox changesPhosphataseFull activityTransport pathwaysEnzymePathwayBinding