Journal Article

FZJ-2015-03616

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png RNA/Peptide Binding Driven by Electrostatics—Insight from Bidirectional Pulling Simulations

Do, T. N. ; Carloni, P.FZJ* ; Varani, G. ; Bussi, G. (Corresponding Author)

2013
American Chemical Society (ACS) Washington, DC

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Please use a persistent id in citations: doi:10.1021/ct3009914

Abstract: RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking methods are insufficient. We here present a computational method which allows studying the binding of RNA molecules and charged peptides with atomistic, explicit-solvent molecular dynamics. In our method, a suitable estimate of the electrostatic interaction is used as an order parameter (collective variable) which is then accelerated using bidirectional pulling simulations. Since the electrostatic interaction is only used to enhance the sampling, the approximations used to compute it do not affect the final accuracy. The method is employed to characterize the binding of TAR RNA from HIV-1 and a small cyclic peptide. Our simulation protocol allows blindly predicting the binding pocket and pose as well as the binding affinity. The method is general and could be applied to study other electrostatics-driven binding events.

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Contributing Institute(s):

1. GRS (GRS)
2. Computational Biomedicine (IAS-5)

Research Program(s):

1. 899 - ohne Topic (POF2-899) (POF2-899)

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Database coverage:
; Current Contents - Physical, Chemical and Earth Sciences ; IF >= 5 ; JCR ; SCOPUS ; Science Citation Index ; Science Citation Index Expanded ; Thomson Reuters Master Journal List ; Web of Science Core Collection

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