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- W1973164090 abstract "Conformational changes in proteins are often crucial to their function. However understanding the mechanisms underlying these movements remains a significant challenge. Because of the long time-scales on which conformational change occurs, coarse graining methods are needed to provide a realistic approximation to detailed atomistic interactions while reducing the computational cost. Elastic network models (ENMs),which approximate protein structure as a network of alpha carbons connected by harmonic potentials, predict the direction of large-scale motion in many systems. However, since ENMs stabilize only one conformation, effective modeling of the transition pathways between two local minima is precluded. Rather than using uniform spring constants as in conventional ENM, we systematically obtain spring constants for each of two stable conformations using the heteroENM approach recently reported by our group. The potentials describing pairwise interactions from these two states are then individually mixed using a combination of harmonic, double well, and Morse potentials to allow for transitions between minima. Langevin dynamics simulations using the new methodology display multiple energy minima and intermediates between states, suggesting that this approach can realistically model a frustrated energy landscape. We evaluate equilibrium dynamics trajectories and minimum energy paths for the transition between the two local minima obtained using this approach for several model proteins." @default.
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- W1973164090 date "2009-02-01" @default.
- W1973164090 modified "2023-09-28" @default.
- W1973164090 title "Exploring Protein Conformational Change Using The Double Well Network Model" @default.
- W1973164090 doi "https://doi.org/10.1016/j.bpj.2008.12.1634" @default.
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