Programme

P.78 -- Posters, VCTP-50

Date: Thursday, 7 August 2025

Time: 08:30 - 10:00

A geometrical model for protein folding with directional interactions

Trinh Xuan Hoang (1), Le Hoang Phong (1), Bui Phuong Thuy (2)

(1) Institute of Physics, Vietnam Academy of Science and Technology, Hanoi 11108, Vietnam; (2) Institute of Theoretical and Applied Research, Duy Tan University, Hanoi 100000, Vietnam

Alpha-helices and beta-sheets are repetitive protein secondary structures stabilized by hydrogen bonding, the steric constraints of the polypeptide chain and also hydrophobic interactions specified by the amino acid sequence. Studies have shown that these structures can arise from simple geometrical considerations of a tube-like homopolymer represented by a chain of cylindrical discs or coins. Here, we develop a polymer model based on a chain of spherical beads, incorporating the geometrical constraints on local conformations of residues that form hydrogen bonds and directional poking contact interactions. Our model demonstrates that protein-like structures can emerge on the basis of these considerations. The model also yields a free-energy landscape with relatively few broad minima even for a homopolymer, consistent with the fact that proteins can be designed to enable rapid folding to their native states.

Presenter: Trinh Xuan Hoang