Structure Calculation and Reconstruction of Discrete State Dynamics from Residual Dipolar Couplings using REDCRAFT

TL;DR

This paper introduces a comprehensive method using REDCRAFT software to calculate and reconstruct protein structures and their discrete state dynamics from Residual Dipolar Couplings (RDCs), accurately identifying dynamic regions and conformational ensembles.

Contribution

The authors develop a novel strategy combining fragmented structure determination with dynamic-profile analysis to reconstruct protein dynamics from RDC data, including occupancy estimation.

Findings

Reproduced protein structures within less than 2Å accuracy.

Successfully identified and reconstructed dynamic regions with >20% occupancy.

Recognized internal arc motions with >30° rotation accurately.

Abstract

Residual Dipolar Couplings (RDCs) acquired by Nuclear Magnetic Resonance (NMR) spectroscopy can be an indispensable source of information in investigation of molecular structures and dynamics. Here we present a complete strategy for structure calculation and reconstruction of discrete state dynamics from RDC data. Our method utilizes the previously presented REDCRAFT software package and its dynamic-profile analysis to complete the task of fragmented structure determination and identification of the onset of dynamics from RDC data. Fragmented structure determination was used to demonstrate successful structure calculation of static and dynamic domains for several models of dynamics. We provide a mechanism of producing an ensemble of conformations for the dynamical regions that describe any observed order tensor discrepancies between the static and dynamic domains within a protein. In addition, the presented method is capable of approximating relative occupancy of each conformational state. The developed methodology has been evaluated on simulated RDC data with 1Hz of error from an 83 residue {\alpha} protein (PDBID 1A1Z), and a 213 residue {\alpha}/\b{eta} protein DGCR8 (PDBID 2YT4). Using 1A1Z, various models of arc and complex two and three discrete-state dynamics were simulated. MD simulation was used to generate a 2-state dynamics for DGCR8. In both instances our method reproduced structure of the protein including the conformational ensemble to within less than 2{\AA}. Based on our investigations, arc motions with more than 30{\deg} of rotation are recognized 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 magnitude of 15{\deg} or relative occupancy of less than 10% are consistently unrecognizable as dynamical regions.