A Single Amino Acid Substitution Alters ClpS Binding Specificity

Published

March 27, 2020

Author(s)

Christina Bergonzo, Jennifer A. Tullman, Kunal Dharmadhikari, Emily Samuels, Makenzie Christensen

Abstract

ClpS is a small protein currently under development as a probe for detecting specific N-terminal amino acids of peptides. In order for ClpS to be used in this manner, it is important to understand the structural reasons for how and why ClpS recognizes specific residues. To understand the specificity of the recognition mechanism of ClpS, all atom molecular dynamics (MD) simulations were conducted on wild type (WT) ClpS, and ClpS mutants predicted to increase solubility by the Protein Repair One Stop Shop (PROSS) algorithm. Per-residue binding free energies were used to predict that Leu to Asn substitution at position 9 will confer specificity for an N-terminal tyrosine over the preferred phenylalanine. Experimental validation of the L9N mutant using yeast-display assay validated the predicted outcome, showing an increase in tyrosine binding over phenylalanine. Predicting other mutations that can stabilize binding for different N-terminal amino acid combinations will enable engineering artificial protein- interaction networks, and the methods used to conduct this study are transferable and useful in drug delivery problems.

Citation

Journal of Molecular Biology

Volume

88

Issue

9

Pub Type

Journals

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DOI Link

Keywords

molecular dynamics, binding energies, N-terminal

Citation

Bergonzo, C. , Tullman, J. , Dharmadhikari, K. , Samuels, E. and Christensen, M. (2020), A Single Amino Acid Substitution Alters ClpS Binding Specificity, Journal of Molecular Biology, [online], https://doi.org/10.1002/prot.25890 (Accessed December 9, 2024)