This Article Full Text Full Text (PDF) Supplement All Versions of this Article: biophysj.106.088203v1 91/6/2097    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Yu, J. Articles by Schulten, K. Search for Related Content PubMed PubMed Citation Articles by Yu, J. Articles by Schulten, K.

Structure-Based Model of the Stepping Motor of PcrA Helicase

Jin Yu ^* , Taekjip Ha   and Klaus Schulten ^* 

^* Beckman Institute, Department of Physics, and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois

Correspondence: Address reprint requests to K. Schulten, Tel.: 217-244-1604; E-mail: kschulte{at}ks.uiuc.edu.

DNA helicases are ubiquitous molecular motors involved in cellular DNA metabolism. They move along single-stranded DNA (ssDNA) and separate duplex DNA into its component strands, utilizing the free energy from ATP hydrolysis. The PcrA helicase from Bacillus stearothermophilus translocates as a monomer progressively from the 3' end to the 5' end of ssDNA and is one of the smallest motor proteins structurally known in full atomic detail. Using high-resolution crystal structures of the PcrA-DNA complex, we performed nanosecond molecular dynamics simulations and derived potential energy profiles governing individual domain movement of the PcrA helicase along ssDNA. Based on these profiles, the millisecond translocation of the helicase along ssDNA was described through Langevin dynamics. The calculations support a domain stepping mechanism of PcrA helicase, in which, during one ATP hydrolysis cycle, the pulling together and pushing apart of domains 2A and 1A are synchronized with alternating mobilities of the individual domains in such a fashion that PcrA moves unidirectionally along ssDNA. By combining short timescale (nanoseconds) molecular dynamics and long timescale (milliseconds) stochastic-dynamics descriptions, our study suggests a structure-based mechanism of the ATP-powered unidirectional movement of PcrA helicase.

This article has been cited by other articles:

				J. Yu, T. Ha, and K. Schulten How Directional Translocation is Regulated in a DNA Helicase Motor Biophys. J., December 1, 2007; 93(11): 3783 - 3797. [Abstract] [Full Text] [PDF]