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J Mol Biol. 2018 Nov 22. pii: S0022-2836(18)31116-1. doi: 10.1016/j.jmb.2018.11.018. [Epub ahead of print]

Allosteric Modulation of Binding Specificity by Alternative Packing of Protein Cores.

Author information

1
The Donnelly Centre for Cellular and Biomolecular Research. University of Toronto, Toronto, ON M5S 3E1, Canada; Banting and Best Department of Medical Research. University of Toronto, Toronto, ON M5S 3E1, Canada.
2
The Donnelly Centre for Cellular and Biomolecular Research. University of Toronto, Toronto, ON M5S 3E1, Canada; Banting and Best Department of Medical Research. University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Computer Science. University of Toronto, Toronto, ON M5S 3E1, Canada.
3
Lunenfeld Tanenbaum Research Institute. Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics. University of Toronto, Toronto, ON M5S 3E1, Canada; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), CB10 1SD, Hinxton, UK.
4
Structural Genomics Consortium, University of Toronto, Toronto, ON M5S 3E1, Canada.
5
Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
6
Department of Molecular Genetics. University of Toronto, Toronto, ON M5S 3E1, Canada.
7
The Donnelly Centre for Cellular and Biomolecular Research. University of Toronto, Toronto, ON M5S 3E1, Canada; Banting and Best Department of Medical Research. University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Computer Science. University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics. University of Toronto, Toronto, ON M5S 3E1, Canada.
8
The Donnelly Centre for Cellular and Biomolecular Research. University of Toronto, Toronto, ON M5S 3E1, Canada; Banting and Best Department of Medical Research. University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics. University of Toronto, Toronto, ON M5S 3E1, Canada. Electronic address: sachdev.sidhu@utoronto.ca.

Abstract

Hydrophobic cores are often viewed as tightly packed and rigid, but they do show some plasticity and could thus be attractive targets for protein design. Here we explored the role of different functional pressures on the core packing and ligand recognition of the SH3 domain from human Fyn tyrosine kinase. We randomized the hydrophobic core and used phage display to select variants that bound to each of three distinct ligands. The three evolved groups showed remarkable differences in core composition, illustrating the effect of different selective pressures on the core. Changes in the core did not significantly alter protein stability, but were linked closely to changes in binding affinity and specificity. Structural analysis and molecular dynamics simulations revealed the structural basis for altered specificity. The evolved domains had significantly reduced core volumes, which in turn induced increased backbone flexibility. These motions were propagated from the core to the binding surface and induced significant conformational changes. These results show that alternative core packing and consequent allosteric modulation of binding interfaces could be used to engineer proteins with novel functions.

KEYWORDS:

SH3 domain; binding specificity; conformational flexibility; hydrophobic core; phage display

PMID:
30471255
DOI:
10.1016/j.jmb.2018.11.018

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