Studies of structure function correlation of biological molecules requires one to explore large structural changes and to simulating long time processes as well as the need to sample multidimensional landscapes. Here we review advances in such challenging studies, focusing starting with our electrostatic augmented coarse grained (CG) model (1 ) and the renormalization approaches aimed at studying the very long time coupling between process (1) . We start with a short introduction outlining the use of the renormalization method and then move to consideration of the performance of the CG approach in simulating various challenging complex systems . It is shown that our CG model produces, for the first time, realistic landscapes for vectrorial process such as the actions of F1-ATPase (2) and F0-ATPase (3). It is also shown that such machines are working by exploiting free energy gradients and cannot just use Brownian motions as the vectroial driving force. Significantly, at present, to the best of our knowledge, theses studies are the only studies that reproduced consistently (rather than assumed) a structure based vectoraial action of molecular motors. We also describe a breakthrough in CG modeling of voltage activated ion channels (4) . Next , we outline a recent simulation of the tag of war between staled elongated peptide in the ribosome and the translocon as an illustration of the power of our CG approach (5). Finally we describe a CG study (6) that elucidated the previously unknown origin of the unidirectional motion of myosin V . References (1) S. C. L. Kamerlin, S. Vicatos, A. Dryga and A. Warshel, , Ann. Rev. Phys. Chem. 62,41 (2011). (2) , S. Mukherjee and A. Warshel, PNAS ,108, 20550 (2011). (3) S. Mukherjee and A. Warshel, PNAS ,109, 14876 (2012). (4) A. Dryga, S. Chakrabarty, S. Vicatos, and A. Warshel , PNAS , 109, 3335 ( 2012). (5) , A. Rychkova, S. Mukherjee, R. P. Bora, and A. Warshel, Proc. Natl. Acad. Sci. USA 110, 10195 (2013). (6) , S. Mukherjee and A. Warshel, Proc. Natl. Acad. Sci. USA 110, 17326 (2013).

Modeling the function of molecular motors and other challenging biological systems

249th National Meeting (2015)

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