Side-chain and backbone ordering in Homopolymers

TL;DR

This study uses multicanonical simulations to explore how side chain and backbone ordering in homopolymers relate, revealing different transition behaviors based on side chain length and hydrogen bonding capacity, with implications for protein folding.

Contribution

It provides new insights into the temperature-dependent ordering of side chains and backbones in homopolymers, highlighting the effects of side chain length and hydrogen bonding on phase transitions.

Findings

Long side chains with hydrogen bonding show a second transition at lower temperatures.

Short side chains exhibit no phase transition, with side chain ordering over a wide temperature range.

Non-backbone hydrogen bonds compete with backbone bonds, affecting folding behavior.

Abstract

In order to study the relation between backbone and side chain ordering in proteins, we have performed multicanonical simulations of deka-peptide chains with various side groups. Glu10, Gln10, Asp10, Asn10, and Lys10 were selected to cover a wide variety of possible interactions between the side chains of the monomers. All homopolymers undergo helix-coil transitions. We found that peptides with long side chains that are capable of hydrogen bonding, i.e. Glu10, and Gln10, exhibit a second transition at lower temperatures connected with side chain ordering. This occurs in gas phase as well as in solvent, although the character of the side chain structure is different in each case. However, in polymers with short side chains capable of hydrogen bonding, i.e. Asp10 and Asn10, side chain ordering takes place over a wide temperature range and exhibits no phase transition like character. Moreover, non-backbone hydrogen bonds show enhanced formation and fluctuations already at the helix-coil transition temperature, indicating competition between side chain and backbone hydrogen bond formation. Again, these results are qualitatively independent of the environment. Side chain ordering in Lys10, whose side groups are long and polar, also takes place over a wide temperature range and exhibits no phase transition like character in both environments. Reasons for the observed chain length threshold and consequences from these results for protein folding are discussed.