Journal
PROTEIN SCIENCE
Volume 20, Issue 3, Pages 482-491Publisher
WILEY
DOI: 10.1002/pro.580
Keywords
protein-protein interaction; molecular recognition; binding free energy; conformation changes; allostery
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Funding
- Indo-French Centre for the Promotion of Advanced Research [4003-2]
- NIH [R01 GM084884]
- The Netherlands Organization for Scientific Research [700.56.442]
- Cancer Research UK
- Cancer Research UK [10748] Funding Source: researchfish
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We have assembled a nonredundant set of 144 protein-protein complexes that have high-resolution structures available for both the complexes and their unbound components, and for which dissociation constants have been measured by biophysical methods. The set is diverse in terms of the biological functions it represents, with complexes that involve G-proteins and receptor extracellular domains, as well as antigen/antibody, enzyme/inhibitor, and enzyme/substrate complexes. It is also diverse in terms of the partners' affinity for each other, with K-d ranging between 10(-5) and 10(-14) M. Nine pairs of entries represent closely related complexes that have a similar structure, but a very different affinity, each pair comprising a cognate and a noncognate assembly. The unbound structures of the component proteins being available, conformation changes can be assessed. They are significant in most of the complexes, and large movements or disorder-to-order transitions are frequently observed. The set may be used to benchmark biophysical models aiming to relate affinity to structure in protein-protein interactions, taking into account the reactants and the conformation changes that accompany the association reaction, instead of just the final product.
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