Improvement of Protein Structure Modeling Upon Coarse Grained Force Field Augmentation with Multitorsional Potentials Demonstrates the Significance of Along-Chain Coupling of Local Conformational States in Protein Folding

Continuing our work (Petrusevich, E.
F.; Liwo, A. J. Phys. Chem. B 2025, 129, 7119–7133), in
which the multitorsional potentials accounting for α-helix formation
cooperativity, Umtorf, have been implemented
in the coarse-grained UNRES force field, we have enhanced UNRES with
those accounting for the cooperativity of extended strand formation, Umtore. The parameters have been
determined by the maximum-likelihood principle using 190,577 extended
turn-bordered protein segments from the Protein Data Bank. UNRES augmented
with Umtorf and Umtore showed improved performance in ab
initio protein structure modeling with a set of 76 benchmark
proteins of different secondary structure and topology and sizes from
20 to 126 amino-acid residues. A significant part of this improvement
was the increased correctness of the secondary structure of the models
upon introducing the multitorsional terms. This result demonstrates
the significance of along-chain coupling of local conformational states
in protein folding, including secondary and tertiary structure formation.