Molecular Dynamics Studies of Hepatitis C Virus (HCV) Helicase

Hepatitis C virus (HCV) is the leading cause of chronic liver disease and is associated with hepatic carcinoma. It is estimated to affect 300 million carriers worldwide. The enzyme HCV helicase is one of a number of proteins expressed by HCV that facilitate viral replication, its major function being to separate double stranded RNA into single stranded RNA. We have performed molecular dynamics simulations to model the mechanism of HCV helicase. These simulations model the dynamic movement of the enzyme and a single strand of RNA. The simulations reveal that the movement of the enzyme is driven by an electrostatic interaction with adenosine triphosphate (ATP). A better understanding of the behaviour of HCV helicase will assist the development of anti-HCV drugs.

Principal Investigator

David Chalmers
Medicinal Chemistry
Monash University

Project

e94

Co-Investigators

Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Monash University

RFCD Codes

250699

Significant Achievements, Anticipated Outcomes and Future Work

Our previous molecular dynamics studies of hepatitis C helicase have provided support for the proposed 'inchworm' mechanism where the RNA is held by a cleft in the enzyme and is moved through one base pair at a time as the protein moves with a 'scissor' action. We propose that the movement of the enzyme is driven by electrostatic interactions between a molecule of adenosine triphosphate (ATP), which has a negative charge and binds to one domain of the protein, and a critical arginine residue, which has a positive charge, in the second domain.

During 2003 we have continued with the development of our model by running multiple simulations which have investigated the 'in stroke' of the helicase mechanism. We have made a number of refinements to our model system:

(1) we have updated our model to use the more recent CHARMM27 parameters
(2) we have changed from constant volume simulations to constant pressure
(3) we have added a number of constraints to prevent fraying of the protein C terminus
(4) we have refined the addition of moving constraints to drive the movement of the two domains

These alterations have produced a more consistent and reproducible system. Our improved model system is able to reproduce some features of the inchworm mechanism. However, to date we are only able to model some expected features of the 'in stroke' and we have not been able to model the 'out stroke'. This may be due to the relatively short duration of the simulations (4 ns). Further work on the modelling of hepatitis C helicase will concentrate on the introduction of additional constraints to attempt to model additional features of the proposed inchworm mechanism. This may allow us to model the 'out stroke' stage of the helicase mechanism.

 

Computational Techniques Used

This project uses molecular dynamics calculations run using the parallel molecular dynamics program NAMD (http://www.ks.uiuc.edu/Research/namd/namd.html). Our simulations consist of an all-atom model of the hepatitis C protein (6500 atoms), ATP, an oligonucleotide (RNA, 176 atoms) and 13700 water molecules. We use the particle-mesh Ewald (PME) method to calculate long-range electrostatic interactions which are particularly important for this problem because we propose that the mechanism is electrostatically driven.

 

Publications, Awards and External Funding

External Funding and Awards

None

Publications

Chalmers, D. K.; Wielens, J.; Crosby, I. T.; Horne, H. J.; Scanlon, M. J. The Challenge of Predicting Biological Activity in Drug Design. APAC 2003: Gold Coast, 2003