Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers
Files in This Item:
|buchete.2016.JPCLett.REMD_dimers.pdf||414.3 kB||Adobe PDF||Download|
|Title:||Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers||Authors:||Leahy, Cathal
Murphy, Ronan D.
|Permanent link:||http://hdl.handle.net/10197/9196||Date:||Jul-2016||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.||Funding Details:||Irish Research Council||Type of material:||Journal Article||Publisher:||ACS||Journal:||Journal of Physical Chemistry Letters||Volume:||7||Issue:||14||Start page:||2676||End page:||2682||Copyright (published version):||2017 American Chemical Society||Keywords:||Replica-exchange molecular dynamics; Dimer formation||DOI:||10.1021/acs.jpclett.6b00518||Language:||en||Status of Item:||Peer reviewed|
|Appears in Collections:||Physics Research Collection|
CASL Research Collection
Show full item record
This item is available under the Attribution-NonCommercial-NoDerivs 3.0 Ireland. No item may be reproduced for commercial purposes. For other possible restrictions on use please refer to the publisher's URL where this is made available, or to notes contained in the item itself. Other terms may apply.