Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers

Cathal T. Leahy, Ronan D. Murphy, Gerhard Hummer, Edina Rosta, Nicolae-viorel Buchete

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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 a quantitative discrimination 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.
Original languageEnglish
Pages (from-to)2676-2682
Number of pages7
JournalJournal of physical chemistry letters
Volume7
Issue number14
Early online date20 Jun 2016
DOIs
Publication statusPublished - 21 Jul 2016

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