TCB Publications - Abstract
Jin Yu, Taekjip Ha, and Klaus Schulten. Structure-based model of the stepping motor of PcrA helicase. Biophysical Journal, 91:2097-2114, 2006. (PMC: 1557568)
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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 a fashion that PcrA moves unidirectionally along ssDNA. By combining short time-scale (nanoseconds) molecular dynamics and long time-scale (milliseconds) stochastic dynamics descriptions, our study suggests a structure-based mechanism of the ATP-powered unidirectional movement of PcrA helicase.
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