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• W2466292742 endingPage "2682" @default.
• W2466292742 startingPage "2676" @default.
• W2466292742 abstract "We characterize the kinetics of dimer formation of the short amyloid microcrystal-forming tetrapeptides NNQQ by constructing coarse master equations for the conformational dynamics of the system, using temperature replica-exchange molecular dynamics (REMD) simulations. We minimize the effects of Kramers-type recrossings by assigning conformational states based on their sequential time evolution. Transition rates are further estimated from short-time state propagators by maximizing the likelihood that the extracted rates agree with the observed atomistic trajectories without any a priori assumptions about their temperature dependence. Here, we evaluate the rates for both continuous replica trajectories that visit different temperatures and for discontinuous data corresponding to each REMD temperature. While the binding–unbinding kinetic process is clearly Markovian, the conformational dynamics of the bound NNQQ dimer has a complex character. Our kinetic analysis allows us to discriminate between short-lived encounter pairs and strongly bound conformational states. The conformational dynamics of NNQQ dimers supports a kinetically driven aggregation mechanism, in agreement with the polymorphic character reported for amyloid aggregates such as microcrystals and fibrils." @default.
• W2466292742 created "2016-07-22" @default.
• W2466292742 creator A5048889853 @default.
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• W2466292742 date "2016-06-30" @default.
• W2466292742 modified "2023-09-25" @default.
• W2466292742 title "Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers" @default.
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• W2466292742 doi "https://doi.org/10.1021/acs.jpclett.6b00518" @default.
• W2466292742 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/27323250" @default.
• W2466292742 hasPublicationYear "2016" @default.
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