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M603826200v1
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Papers In Press, published online ahead of print June 8, 2006
J. Biol. Chem, 10.1074/jbc.M603826200
Submitted on April 20, 2006
Revised on June 6, 2006
Accepted on June 8, 2006

Comprehensive and quantitative mapping of energy landscapes for protein-protein interactions by rapid combinatorial scanning

Gabor Pal, Jean-Louis K. Kouadio, Dean R. Artis, Anthony A. Kossiakoff, and Sachdev S. Sidhu

Protein Engineering, Genentech, Inc., South San Francisco, CA 94080

Corresponding Author: sidhu{at}gene.com

A novel, quantitative saturation (QS) scanning strategy was developed to obtain a comprehensive database of the structural and functional effects of all possible mutations across a large protein-protein interface. The QS scan approach was applied to the high affinity site of human growth hormone (hGH) for binding to its receptor (hGHR). Although the published structure-function database describing this system is probably the most extensive for any large protein-protein interface, it is nonetheless too sparse to accurately describe the nature of the energetics governing the interaction. Our comprehensive database affords a complete view of the binding site and provides important new insights into the general principles underlying protein-protein interactions. The hGH binding interface is highly adaptable to mutations, but the nature of the tolerated mutations challenges generally accepted views about the evolutionary and biophysical pressures governing protein-protein interactions. Many substitutions that would be considered chemically conservative are not tolerated, while conversely, many non-conservative substitutions can be accommodated. Furthermore, conservation across species is a poor predictor of the chemical character of tolerated substitutions across the interface. Numerous deviations from generally accepted expectations indicate that mutational tolerance is highly context dependent, and furthermore, cannot be predicted by our current knowledge base. The type of data produced by the comprehensive QS scan can fill the gaps in the structure-function matrix. The compilation of analogous databases from studies of other protein-protein interactions should greatly aid the development of computational methods for explaining and designing molecular recognition.


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