Brownian Ratchet Seen in Action: How Directional Translocation is Regulated by a DNA Helicase Motor

Klaus Schulten(, Director of the Theoretical Biophysics Group, UIUC

Biological motors utilize energy released in a chemical reaction, the hydrolysis of ATP, for directed mechanical motion even against considerable loads. However, the mechanical energy of ATP hydrolysis cannot be stored and transformed beyond nanoseconds, while biological motors cycle at 1/ ms frequency. Funneling chemical energy directly into translocation is then impossible and it was suggested that biological motors rather operate near thermal equilibrium as Brownian motors according to the ratchet mechanism used in engineering. Richard Feynman discussed in his famous lectures, though, that a Brownian ratchet with a single heat bath cannot induce directed motion as this would violate the second law of thermodynamics. But directed motion based on a Brownian ratchet mechanism can be realized when the ratchet potential is modulated in time (Astumian, 1997).

In this lecture we present evidence for the ratchet mechanism at work for PcrA helicase, one of the smallest motor proteins structurally known and, hence, amenable to rigorous analysis. We demonstrate a mechanism in which, during one ATP hydrolysis cycle, the pulling together and pushing apart of two PcrA domains is synchronized with alternating mobilities of the individual domains such that PcrA moves unidirectionally along single stranded DNA. Multiscale modeling involving quantum mechanical, classical mechanical, and stochastic calculations shows in particular how ATP binding and subsequent hydrolysis influence in a highly delocalized fashion the ability of the individual PcrA domains to move along DNA. The mechanism seen is supported by a variety of computational analysis methods, that offer thereby an atomic level view of PcrA's ratchet type motion along DNA. Our investigation revealed also a close similarity between structures and reaction pathways in PcrA helicase and in F1-ATPase, the latter being a motor found in every biological cell. This suggests that the mechanochemical mechanism identified in PcrA helicase is actually shared by many other biological motors.

[1] R.D. Astumian: Thermodynamics and Kinetics of a Brownian Motor, Science 276, p. 917-922 (1997).
[2] Markus Dittrich and Klaus Schulten. PcrA helicase, a prototype ATP-driven molecular motor. Structure, 14:1345-1353, 2006.
[3] Jin Yu, Taekjip Ha, and Klaus Schulten. Structure-based model of the stepping motor of PcrA helicase. Biophysical Journal, 91:2097-2114, 2006
[4] Markus Dittrich, Jin Yu, and Klaus Schulten. PcrA helicase, a molecular motor studied from the electronic to the functional level. Topics in Current Chemistry, 268:319-347, 2006.
[5] Jin Yu, Taekjip H, and Klaus Schulten. How Directional Translocation is Regulated in a DNA helicase motor. Biophysical Journal, 93:3783-3797, 2007.