Assessing energetic contributions to binding from a disordered region in a protein-protein interaction .

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TitleAssessing energetic contributions to binding from a disordered region in a protein-protein interaction .
Publication TypeJournal Article
Year of Publication2010
AuthorsCho, S, Swaminathan, CP, Bonsor, DA, Kerzic, MC, Guan, R, Yang, J, Kieke, MC, Andersen, PS, Kranz, DM, Mariuzza, RA, Sundberg, EJ
JournalBiochemistry
Volume49
Issue43
Pagination9256-68
Date Published2010 Nov 2
ISSN1520-4995
KeywordsAnimals, Calorimetry, Directed Molecular Evolution, Mice, Protein Binding, Protein Conformation, Proteins, Thermodynamics
Abstract

Many functional proteins are at least partially disordered prior to binding. Although the structural transitions upon binding of disordered protein regions can influence the affinity and specificity of protein complexes, their precise energetic contributions to binding are unknown. Here, we use a model protein-protein interaction system in which a locally disordered region has been modified by directed evolution to quantitatively assess the thermodynamic and structural contributions to binding of disorder-to-order transitions. Through X-ray structure determination of the protein binding partners before and after complex formation and isothermal titration calorimetry of the interactions, we observe a correlation between protein ordering and binding affinity for complexes along this affinity maturation pathway. Additionally, we show that discrepancies between observed and calculated heat capacities based on buried surface area changes in the protein complexes can be explained largely by heat capacity changes that would result solely from folding the locally disordered region. Previously developed algorithms for predicting binding energies of protein-protein interactions, however, are unable to correctly model the energetic contributions of the structural transitions in our model system. While this highlights the shortcomings of current computational methods in modeling conformational flexibility, it suggests that the experimental methods used here could provide training sets of molecular interactions for improving these algorithms and further rationalizing molecular recognition in protein-protein interactions.

DOI10.1021/bi1008968
Alternate JournalBiochemistry
PubMed ID20836565
PubMed Central IDPMC2964404
Grant ListAI036900 / AI / NIAID NIH HHS / United States
AI06461 / AI / NIAID NIH HHS / United States
AI55882 / AI / NIAID NIH HHS / United States
AI65690 / AI / NIAID NIH HHS / United States
R01 AI064611-01 / AI / NIAID NIH HHS / United States
R01 AI065690-02 / AI / NIAID NIH HHS / United States
R21 AI055882-03 / AI / NIAID NIH HHS / United States
R37 AI036900-06 / AI / NIAID NIH HHS / United States