Energy landscapes for proteins described by the UNRES coarse-grained potential

Biophys Chem. 2023 Sep 12;303:107107. doi: 10.1016/j.bpc.2023.107107. Online ahead of print.ABSTRACTThe self-assembly of proteins is encoded in the underlying potential energy surface (PES), from which we can predict structure, dynamics, and thermodynamic properties. However, the corresponding analysis becomes increasingly challenging with larger protein sizes, due to the computational time required, which grows significantly with the number of atoms. Coarse-grained models offer an attractive approach to reduce the computational cost. In this Feature Article, we describe our implementation of the UNited RESidue (UNRES) coarse-grained potential in the Cambridge energy landscapes software. We have applied this framework to explore the energy landscapes of four proteins that exhibit native states involving different secondary structures. Here we have tested the ability of the UNRES potential to represent the global energy landscape of proteins containing up to 100 amino acid residues. The resulting potential energy landscapes exhibit good agreement with experiment, with low-lying minima close to the PDB geometries and to results obtained using the all-atom AMBER force field. The new program interfaces will allow us to investigate larger biomolecules in future work, using the UNRES potential in combination with all the methodology available in the computational energy landscapes framework.PMID:37862761 | DOI:10.1016/j.bpc.2023.107107

Source: Biophysical Chemistry - October 20, 2023 Category: Chemistry Authors: Patryk A Weso łowski Adam K Sieradzan Micha ł J Winnicki John W R Morgan David J Wales Source Type: research