4/15/2023 0 Comments Monte carlo sampling![]() The stability of the protein as a whole, as well as the stability of its particular conformational sub-ensembles is essential to understand and regulate protein function. We demonstrate that a state-of-the-art intramolecular force field can be combined with an implicit solvent model to obtain a high quality of the folded structures and also discuss limitations that still remain.Ĭonformational change is one of the most prominent mechanisms of protein function and regulation 1, 2, 3, 4. We fully characterize the free energy landscape, transition states, energy barriers between different states, and the per-residue stability of individual amino acids over a wide temperature range. ![]() We demonstrate extensive thermodynamic characterization of the folding process of the α-helical Trp-cage, the Villin headpiece and the β-sheet WW-domain. Here, we report the development of an all-atom Monte Carlo approach that permits the modelling of the large-scale conformational change of proteins using standard off-the-shelf computational hardware and standard all-atom force fields. ![]() For this reason, many biologically interesting questions cannot be addressed using accessible state-of-the-art computational resources. Computer simulation provides an increasingly realistic picture of large-scale conformational change of proteins, but investigations remain fundamentally constrained by the femtosecond timestep of molecular dynamics simulations.
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