Engineering gain-of-function mutants of a WW domain by dynamics and structural analysis.

Autor: Lu J; Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, USA., Rahman MI; School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA., Kazan IC; Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, USA., Halloran NR; School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA., Bobkov AA; Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, California, USA., Ozkan SB; Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona, USA., Ghirlanda G; School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.
Jazyk: angličtina
Zdroj: Protein science : a publication of the Protein Society [Protein Sci] 2023 Sep; Vol. 32 (9), pp. e4759.
DOI: 10.1002/pro.4759
Abstrakt: Proteins gain optimal fitness such as foldability and function through evolutionary selection. However, classical studies have found that evolutionarily designed protein sequences alone cannot guarantee foldability, or at least not without considering local contacts associated with the initial folding steps. We previously showed that foldability and function can be restored by removing frustration in the folding energy landscape of a model WW domain protein, CC16, which was designed based on Statistical Coupling Analysis (SCA). Substitutions ensuring the formation of five local contacts identified as "on-path" were selected using the closest homolog native folded sequence, N21. Surprisingly, the resulting sequence, CC16-N21, bound to Group I peptides, while N21 did not. Here, we identified single-point mutations that enable N21 to bind a Group I peptide ligand through structure and dynamic-based computational design. Comparison of the docked position of the CC16-N21/ligand complex with the N21 structure showed that residues at positions 9 and 19 are important for peptide binding, whereas the dynamic profiles identified position 10 as allosterically coupled to the binding site and exhibiting different dynamics between N21 and CC16-N21. We found that swapping these positions in N21 with matched residues from CC16-N21 recovers nature-like binding affinity to N21. This study validates the use of dynamic profiles as guiding principles for affecting the binding affinity of small proteins.
(© 2023 The Protein Society.)
Databáze: MEDLINE
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