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Synthesis of Information-bearing Peptoids and their Sequence-directed Dynamic Covalent Self-assembly

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Published on: February 6, 2020

Side-chain and backbone ordering in homopolymers.

Yanjie Wei¹, Walter Nadler, Ulrich H E Hansmann

¹Department of Physics, Michigan Technological University, Houghton, Michigan 49931, USA.

The Journal of Physical Chemistry. B

|April 5, 2007

Summary

Protein side chains influence ordering. Long, hydrogen-bonding side chains like Glutamic acid (Glu) and Glutamine (Gln) show distinct ordering transitions, unlike shorter or non-hydrogen-bonding chains.

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Area of Science:

Protein structure and dynamics
Computational biophysics
Polymer science

Background:

Understanding the relationship between protein backbone and side-chain ordering is crucial for protein folding.
Homopolymers with varying side groups provide a model system to study these interactions.

Purpose of the Study:

To investigate how different side-chain properties affect ordering transitions in deka-peptide chains.
To explore the influence of side-chain hydrogen bonding and length on structural ordering.

Main Methods:

Multicanonical simulations were performed on deka-peptide chains.
Peptides included Glutamic acid (Glu10), Glutamine (Gln10), Aspartic acid (Asp10), Asparagine (Asn10), and Lysine (Lys10).
Simulations were conducted in both gas and solvent phases.

Main Results:

All homopolymers exhibited helix-coil transitions.
Peptides with long, hydrogen-bonding side chains (Glu10, Gln10) showed a secondary transition related to side-chain ordering.
Short side chains (Asp10, Asn10) and Lys10 displayed side-chain ordering over a broad temperature range without distinct transitions.
Competition between backbone and side-chain hydrogen bonds was observed.

Conclusions:

Side-chain length and hydrogen-bonding capability significantly impact ordering behavior and transition characteristics.
The observed phenomena are largely independent of the environment (gas vs. solvent).
Results offer insights into protein folding mechanisms and the role of side-chain interactions.