Simulating Biomolecular Machines: ATP Powered DNA Translocation in Helicases

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DESCRIPTION (provided by applicant): Helicase proteins induce duplex melting of double stranded DNA (dsDNA). Strand cleavage is a pivotal step in numerous DNA related cellular processes including transcription, replication and repair. Most helicases translocate along single stranded DNA (ssDNA) and induce melting of DNA base pairs at the dsDNA/ssDNA junction. Processes such as transcription are done subsequent to the unwinding of the duplex by pairing RNA bases to the now separated DNA base. Both translocation along DNA and unwinding of DNA base pairs are powered by ATP hydrolysis. While significant attention has been given to the mechanism of helicase translocation along DNA, a full understanding of the coupling between ATP hydrolysis, base pair cleavage and translocation along DNA is missing. The reactive and multi-scale nature of helicase motion along DNA makes it a difficult problem to approach computationally. Significant strides in this direction can be made with the coupling and modification of two simulation methods. The ATP hydrolysis reaction can be treated explicitly with the use of a modified multi-state empirical valence bond (MS-EVB) method. MS-EVB is a reactive force field developed to treat proton transfer in aqueous environments. The underlying method, however, is general and can be adapted to treat numerous chemical reactions. The energy from ATP hydrolysis is converted into mechanical work for two purposes by the helicase protein. The first is to induce base pair melting and the second is to move along the DNA backbone. This multi-scale behavior combined with the long time scale of the processes present a challenge for standard atomistic or coarse-grained (CG) molecular dynamics (MD). Multi-scale coarse graining (MS-CG) techniques exist to systematically coarse-grain a system using the underlying atomistic forces. This allows for seamless integration of multiple length scales in a single MD simulation. Combining MS-EVB and MS-CG techniques will allow for the first direct simulation of hydrolysis driven motion of helicase proteins.