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Protein Structure Validation and Identification from Unassigned Residual Dipolar Coupling Data Using 2D-PDPA
Department of Computer Science & Engineering, University of South Carolina, Columbia, SC 29208, USA
Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
* Author to whom correspondence should be addressed.
Received: 23 May 2013; in revised form: 10 August 2013 / Accepted: 13 August 2013 / Published: 22 August 2013
Abstract: More than 90% of protein structures submitted to the PDB each year are homologous to some previously characterized protein structure. The extensive resources that are required for structural characterization of proteins can be justified for the 10% of the novel structures, but not for the remaining 90%. This report presents the 2D-PDPA method, which utilizes unassigned residual dipolar coupling in order to address the economics of structure determination of routine proteins by reducing the data acquisition and processing time. 2D-PDPA has been demonstrated to successfully identify the correct structure of an array of proteins that range from 46 to 445 residues in size from a library of 619 decoy structures by using unassigned simulated RDC data. When using experimental data, 2D-PDPA successfully identified the correct NMR structures from the same library of decoy structures. In addition, the most homologous X-ray structure was also identified as the second best structural candidate. Finally, success of 2D-PDPA in identifying and evaluating the most appropriate structure from a set of computationally predicted structures in the case of a previously uncharacterized protein Pf2048.1 has been demonstrated. This protein exhibits less than 20% sequence identity to any protein with known structure and therefore presents a compelling and practical application of our proposed work.
Keywords: PDPA; RDC; unassigned; dipolar; protein; structure; model
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Fahim, A.; Mukhopadhyay, R.; Yandle, R.; Prestegard, J.H.; Valafar, H. Protein Structure Validation and Identification from Unassigned Residual Dipolar Coupling Data Using 2D-PDPA. Molecules 2013, 18, 10162-10188.
Fahim A, Mukhopadhyay R, Yandle R, Prestegard JH, Valafar H. Protein Structure Validation and Identification from Unassigned Residual Dipolar Coupling Data Using 2D-PDPA. Molecules. 2013; 18(9):10162-10188.
Fahim, Arjang; Mukhopadhyay, Rishi; Yandle, Ryan; Prestegard, James H.; Valafar, Homayoun. 2013. "Protein Structure Validation and Identification from Unassigned Residual Dipolar Coupling Data Using 2D-PDPA." Molecules 18, no. 9: 10162-10188.