Computing Reaction Pathways of Rare Biomolecular Transitions using Atomistic Force-Fields

P Faccioli; S a Beccara

doi:10.1016/j.bpc.2015.06.014

Computing Reaction Pathways of Rare Biomolecular Transitions using Atomistic Force-Fields

Biophys Chem. 2016 Jan:208:62-7. doi: 10.1016/j.bpc.2015.06.014. Epub 2015 Aug 14.

Authors

P Faccioli¹, S a Beccara²

Affiliations

¹ Dipartimento di Fisica, Università degli Studi di Trento, Via Sommarive 14 Povo, Trento, 38123 Italy; Trento Institute for Fundamental Physics and Applications (INFN-TIFPA), Via Sommarive 14 Povo, Trento, 38123 Italy. Electronic address: faccioli@science.unitn.it.
² European Centre for Theoretical Studies in Nuclear Physics and Related Areas (ECT*-FBK), via Sommarive 18, I-38123 Trento, Italy; Trento Institute for Fundamental Physics and Applications (INFN-TIFPA), Via Sommarive 14 Povo, Trento, 38123 Italy.

PMID: 26320390
DOI: 10.1016/j.bpc.2015.06.014

Abstract

The Dominant Reaction Pathway (DRP) method is an approximate variational scheme which can be used to compute reaction pathways in conformational transitions undergone by large biomolecules (up to ~10(3) amino-acids) using realistic all-atom force fields. We first review the status of development of this method. Next, we discuss its validation against the results of plain MD protein folding simulations performed by the DE-Shaw group using the Anton supercomputer. Finally, we review a few representative applications of the DRP approach to study reactions which are far too complex and rare to be investigated by plain MD, even on the Anton machine.

Keywords: Computational Biophysics; Folding; Molecular Simulations; Path Sampling; Protein; Rare events.

Publication types

Review

MeSH terms

Kinetics
Molecular Dynamics Simulation*
Protein Folding
Proteins / chemistry*

Substances

Proteins