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Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

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Published on: January 26, 2024

Selectivity in ROS-induced peptide backbone bond cleavage.

Hannah M Stringfellow¹, Michael R Jones, Mandy C Green

¹Department of Chemistry, Purdue University , West Lafayette, Indiana 47907-2084, United States.

The Journal of Physical Chemistry. A

|November 5, 2014

Summary

Reactive oxygen species (ROS) cause protein oxidation through various modifications. Quantum mechanical studies reveal specific fragmentation pathways in peptides, aiding understanding of oxidative stress.

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Area of Science:

Biochemistry
Computational Chemistry
Physical Chemistry

Background:

Protein oxidation is a key post-translational modification.
Reactive oxygen species (ROS) induce diverse chemical changes in proteins.
Understanding these modifications is crucial for biochemical processes.

Purpose of the Study:

To investigate the selectivity of radical-mediated fragmentation in proteins.
To characterize site, conformation, and pathway trends in peptide fragmentation.
To elucidate the energetic favorability of different fragmentation pathways.

Main Methods:

Employed quantum mechanical investigations.
Utilized ab initio and density functional theory methods.
Studied small trialanine peptides mimicking β-strand and β-turn conformations.

Main Results:

Identified site, conformation, and pathway selectivity in radical-mediated fragmentation.
Found the diamide pathway to be more energetically favorable than the α-amidation pathway.
Demonstrated that both pathways exhibit significant site and conformational selectivity.

Conclusions:

Fragmentation pathways are highly selective.
Findings contribute to understanding oxidative stress mechanisms.
Provides insights into post-translational protein modifications by ROS.