Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations - September 10-14, 2014, Istanbul, Turkey

Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery Poster Session II

75-POS Board 28 Hamiltonian Replica-Exchange Simulations of NS3 HCV Helicase Translocation along ssRNA Andrea Pérez-Villa , Giovanni Bussi. Scuola Internazionale Superiore di Studi Avanzati, SISSA, Trieste, Italy. RNA helicases are enzymes crucial for RNA metabolism. One member of this group of proteins is the NS3 helicase from the Hepatitis C virus (NS3h HCV) which translocates along RNA hydrolyzing ATP. Single molecule experiments and crystallographic structures suggest an “inchworm” mechanism, with a processivity of one base pair unwinding per cycle. In spite of the available data in literature, a direct and clear evidence of the mechanism is still missing. The aim of this study is to model the NS3h-ssRNA complex at atomistic detail and to compute the free-energy landscape associated to translocation. We employ well-tempered metadynamics in combination with Hamiltonian replica-exchange molecular dynamics in explicit solvent. Using these techniques we are able to observe the transition between the available experimental snapshots.

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