Manipulations of PPIs (protein–protein interactions) are important for many biological applications such as synthetic biology and drug design. Combinatorial methods have been traditionally used for such manipulations, failing, however, to explain the effects achieved. We developed a computational method for prediction of changes in free energy of binding due to mutation that bring about deeper understanding of the molecular forces underlying binding interactions. Our method could be used for computational scanning of binding interfaces and subsequent analysis of the interfacial sequence optimality. The computational method was validated in two biological systems. Computational saturated mutagenesis of a high-affinity complex between an enzyme AChE (acetylcholinesterase) and a snake toxin Fas (fasciculin) revealed the optimal nature of this interface with only a few predicted affinity-enhancing mutations. Binding measurements confirmed high optimality of this interface and identified a few mutations that could further improve interaction fitness. Computational interface scanning of a medium-affinity complex between TIMP-2 (tissue inhibitor of metalloproteinases-2) and MMP (matrix metalloproteinase) 14 revealed a non-optimal nature of the binding interface with multiple mutations predicted to stabilize the complex. Experimental results corroborated our computational predictions, identifying a large number of mutations that improve the binding affinity for this interaction and some mutations that enhance binding specificity. Overall, our computational protocol greatly facilitates the discovery of affinity- and specificity-enhancing mutations and thus could be applied for design of potent and highly specific inhibitors of any PPI.
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October 2013
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Conference Article|
September 23 2013
Predicting affinity- and specificity-enhancing mutations at protein–protein interfaces
Oz Sharabi;
Oz Sharabi
*Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Jason Shirian;
Jason Shirian
*Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Julia M. Shifman
Julia M. Shifman
1
*Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
1To whom any correspondence should be addressed (email jshifman@mail.huji.ac.il).
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Biochem Soc Trans (2013) 41 (5): 1166–1169.
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Received:
June 26 2013
Citation
Oz Sharabi, Jason Shirian, Julia M. Shifman; Predicting affinity- and specificity-enhancing mutations at protein–protein interfaces. Biochem Soc Trans 1 October 2013; 41 (5): 1166–1169. doi: https://doi.org/10.1042/BST20130121
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