2037-Pos Board B23 Mechanism of Flexibility Control for ATP Access of Hepatitis C Virus NS3 Helicase Computational Investigation of the Effect of Ions on the Secondary Struc- ture of Small Peptides

Journal Article (Academic article)

Hepatitis C virus NS3 helicase couples ATP binding and hydrolysis to polynu-cleotide unwinding. Understanding its regulation mechanism of ATP binding will facilitate targeting of ATP binding site for potential hepatitis C treatment. T324, a residue connecting domain I and domain II of NS3 helicase, has been suggested as part of a flexible hinge responsible for opening of ATP binding cleft, although the detailed mechanism remains largely unclear. We used com-putational simulation to examine the mutational effect of T324 on the dynamics of ATP binding site. A mutant model of T324A of NS3 helicase apo structure was created and energy minimized. Molecular dynamics simulation was con-ducted for both wild-type apo structure and T324A mutant to compare their dif-ferences. For the mutant structure, histogram analysis of pairwise distances between residues in domains I and II (E291-Q460, K210-R464 and R467-T212) showed that separation between the two domains was reduced by 10% and the standard deviation was reduced by 33%. Principal component analysis (PCA) revealed a drastic change in the motion of first principal mode, where the mutant structure moves differently from a scissor-like opening of do-mains I-II of wild-type structure. RMS fluctuation (RMSF) analysis showed residues in close proximity of residue 324 (S211 and E291 in domain I as well as A458 and Q459 in domain II) have at least 30% RMSF value reductions in the mutant structure. RMSF analysis of solvent showed more water mole-cules are trapped near K210, S211, D290, and H293 in domain I as well as T483 and D454 in domain II to form an extensive interaction network con-straining cleft opening. Our mechanistic studies revealed that an atomic inter-action cascade from T324 to residues in domains I and II controls the flexibility of ATP binding cleft. 2038-Pos Board B24 Multidomain Dynamics of a Fatty Acid b-Oxidation Multienzyme Com-plex Studied by Molecular Dynamics Simulation Tadaomi Furuta, Tohru Terada, Akinori Kidera. A fatty acid b-oxidation multienzyme complex (FOM) has been the subject of intense investigation for the elucidation of the important role in the catabolic processes for fatty acid utilization, serving as a ”hub” in the metabolic net-work. The crystal structures of FOM revealed that FOM forms a heterotetra-meric structure of two a and two b subunits, which covers three steps of the enzymatic reactions in the fatty acid b-oxidation. It has been proposed that the process of the multi-step reactions needs significant structure changes as ob-served in the large structural difference in the two crystal structures (Form I and Form II; RMSD = 4.6 Å). To examine the flexibility of FOM, we performed 100-ns molecular dynamics simulations for the two forms without ligands (the systems contain almost 4x10 5 atoms). As the results of the simulations, we observed extremely large conformational fluctuations (RMSD R 5 Å) in both forms. The center of mass of the a subunits (domains a M , and a C) moved more than 10 Å against the b subunits. During the fluctuations, the domains in the a subunits behave as rigid-bodies. We will discuss the structural basis of the large flexibility. The conformational change upon ligand binding is also dis-cussed using the linear response theory. A. Merchant. Experimental results show that ions affect the conformations of proteins in so-lution. The mechanism by which ions create shifts in the conformational equi-librium of proteins is not fully understood. Our hypothesis is that ions modulate the hydration of the peptide, which causes the shift in pep-tide configurations. To test this hypothesis, we have used MD simulations to investigate peptide conformations in different salt solu-tions at different concentrations. The primary structure for the peptides studied is AX-AAAXA, where X represents glutamate or ly-sine. Salts used were chloride salts of sodium and potassium for glutamate, while sodium perchlorate and sodium sulfate were used for lysine. Four different salt concentrations have been examined, 0.01M, 0.1M, 1.0M, and 2.0M. Analysis of the simulation data will be presented (see Figure 1). Free en-ergy calculations have been performed for transitions between different confor-mations (i.e. PPII to alpha helix).

Full Text

Duke Authors

Cited Authors

  • Palla, M; Chen, C-P; Zhang, Y; Li, J; Liao, J-C; Gaborek, TJ; Madura, JD

Published Date

  • 2011

Published In

  • Biophysj

Volume / Issue

  • 100 /

Start / End Page

  • 378a - 378a

Digital Object Identifier (DOI)

  • 10.1016/j.bpj.2010.12.2252