Structure Calculation and Reconstruction of Discrete-State Dynamics from Residual Dipolar Couplings.

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Article

Abstract

Residual dipolar couplings (RDCs) acquired by nuclear magnetic resonance (NMR) spectroscopy are an indispensable source of information in investigation of molecular structures and dynamics. Here, we present a comprehensive strategy for structure calculation and reconstruction of discrete-state dynamics from RDC data that is based on the singular value decomposition (SVD) method of order tensor estimation. In addition to structure determination, we provide a mechanism of producing an ensemble of conformations for the dynamical regions of a protein from RDC data. The developed methodology has been tested on simulated RDC data with ±1 Hz of error from an 83 residue α protein (PDB ID 1A1Z) and a 213 residue α/β protein DGCR8 (PDB ID 2YT4). In nearly all instances, our method reproduced the structure of the protein including the conformational ensemble to within less than 2 Å. On the basis of our investigations, arc motions with more than 30° of rotation are identified as internal dynamics and are reconstructed with sufficient accuracy. Furthermore, states with relative occupancies above 20% are consistently recognized and reconstructed successfully. Arc motions with a magnitude of 15° or relative occupancy of less than 10% are consistently unrecognizable as dynamical regions within the context of ±1 Hz of error.

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© Journal of Chemical Theory and Computation 2016, ACS Publications

Cole, C., Mukhopadhyay, R., Omar, H., Hennig, M., & Valafar, H. (2016). Structure Calculation and Reconstruction of Discrete-State Dynamics from Residual Dipolar Couplings. Journal Of Chemical Theory And Computation, 12(4), 1408-1422. doi: 10.1021/acs.jctc.5b01091

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