Physical Folding Codes for Proteins

TL;DR

This paper uncovers physical folding codes in proteins through molecular dynamics simulations, revealing how electrostatic interactions and hydrogen bonds drive rapid and reproducible protein folding in aqueous environments.

Contribution

It introduces a novel method to decode amino acid sequences into physical folding codes that predict native protein structures, verified against experimental data.

Findings

Folding is driven by electrostatic attractions and hydrogen bonds.

Temperature-induced torsional waves initiate folding.

Decoding amino acid sequences predicts native structures accurately.

Abstract

Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded proteins fold reproducibly following explicit physical folding codes in aqueous environments due to electrostatic attractions. Superfast folding of protein is found to be powered by the contribution of the formation of hydrogen bonds. Temperature-induced torsional waves propagating along unfolded proteins break the parallel distributed state of specific amino acids, inferred as the beginning of folding. Electric charge and rotational resistance differences among neighboring side-chains are used to decipher the physical folding codes by means of which precise secondary structures develop. We present a powerful method of decoding amino acid sequences to predict native structures of proteins. The method is verified by comparing the results available from experiments in the literature.