A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding

Physical Chemistry Chemical Physics : PCCP
Jie HuZhuqing Zhang

Abstract

Structure-based coarse-grained Gō-like models have been used extensively in deciphering protein folding mechanisms because of their simplicity and tractability. Meanwhile, explicit-solvent molecular dynamics (MD) simulations with physics-based all-atom force fields have been applied successfully to simulate folding/unfolding transitions for several small, fast-folding proteins. To explore the degree to which coarse-grained Gō-like models and their extensions to incorporate nonnative interactions are capable of producing folding processes similar to those in all-atom MD simulations, here we systematically compare the computed unfolded states, transition states, and transition paths obtained using coarse-grained models and all-atom explicit-solvent MD simulations. The conformations in the unfolded state in common Gō models are more extended, and are thus more in line with experiment, than those from all-atom MD simulations. Nevertheless, the structural features of transition states obtained by the two types of models are largely similar. In contrast, the folding transition paths are significantly more sensitive to modeling details. In particular, when common Gō-like models are augmented with nonnative interactions, the predicted ...Continue Reading

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Citations

Mar 15, 2018·Physical Chemistry Chemical Physics : PCCP·Yanhua OuyangZhuqing Zhang
Aug 15, 2017·Physical Chemistry Chemical Physics : PCCP·Jing WuTao Chen
May 17, 2018·The Journal of Chemical Physics·Jing WuTao Chen
Jul 10, 2020·Physical Review. X·Andrei G GasicMargaret S Cheung
Mar 23, 2018·The Journal of Physical Chemistry Letters·Soundhararajan GopiAthi N Naganathan
Aug 25, 2018·The Journal of Physical Chemistry. B·Yong WangKresten Lindorff-Larsen
Jul 18, 2018·The Journal of Physical Chemistry. B·Chenqian ChengTao Chen

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