Journal
SCIENTIFIC REPORTS
Volume 5, Issue -, Pages -Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/srep13652
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Funding
- NSF [PHY-1427654, MCB-1214457]
- Cancer Prevention and Research Institute of Texas (CPRIT)
- Welch Foundation [C-1792]
- State of Sao Paulo Research Foundation (FAPESP) [2013/11950-0]
- Direct For Biological Sciences
- Div Of Molecular and Cellular Bioscience [1214457] Funding Source: National Science Foundation
- Direct For Mathematical & Physical Scien
- Division Of Physics [1427654] Funding Source: National Science Foundation
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We develop a procedure to characterize the association of protein structures into homodimers using coevolutionary couplings extracted from Direct Coupling Analysis (DCA) in combination with Structure Based Models (SBM). Identification of dimerization contacts using DCA is more challenging than intradomain contacts since direct couplings are mixed with monomeric contacts. Therefore a systematic way to extract dimerization signals has been elusive. We provide evidence that the prediction of homodimeric complexes is possible with high accuracy for all the cases we studied which have rich sequence information. For the most accurate conformations of the structurally diverse dimeric complexes studied the mean and interfacial RMSDs are 1.95 angstrom and 1.44 angstrom, respectively. This methodology is also able to identify distinct dimerization conformations as for the case of the family of response regulators, which dimerize upon activation. The identification of dimeric complexes can provide interesting molecular insights in the construction of large oligomeric complexes and be useful in the study of aggregation related diseases like Alzheimer's or Parkinson's.
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