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

Cole, Casey A.; Mukhopadhyay, Rishi; Omar, Hanin; Hennig, Mirko; Valafar, Homayoun

doi:10.1021/acs.jctc.5b01091

Cited by 6 publications

(7 citation statements)

References 112 publications

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“…Recent developments (Tian et al, 2001b;Dosset et al, 2001;Prestegard et al, 2005;Valafar et al, 2005;Simin et al, 2014) have demonstrated the success of structure determination of macromolecules by using primarily or exclusively RDC data. The use of RDCs can lead to a significant reduction in data collection and analysis (Raman et al, 2010;Shealy et al, 2010;Lange et al, 2012;Valafar et al, 2012;Tang et al, 2015) while providing simultaneous resonance assignment, structure determination, and identification of dynamical regions (Tian et al, 2001b;Bernadó and Blackledge, 2004;Prestegard et al, 2005;Valafar et al, 2005;Shealy et al, 2011;Cole et al, 2016).…”

Section: Theoretical Background Residual Dipolar Couplings Datamentioning

confidence: 99%

“…This is the primary principle that we employ in the development of our analysis. A systematic departure in OTMs reported from different portions of the protein are due to internal dynamics and can be used to identify dynamical regions, internally orchestrated motions, and be used in some instances to reconstruct the trajectory of motion (Cole et al, 2016).…”

Section: The Effect Of Motion On Saupe Order Tensormentioning

confidence: 99%

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Concurrent Identification and Characterization of Protein Structure and Continuous Internal Dynamics with REDCRAFT

Omar

Hein

Cole

et al. 2022

Front. Mol. Biosci.

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Internal dynamics of proteins can play a critical role in the biological function of some proteins. Several well documented instances have been reported such as MBP, DHFR, hTS, DGCR8, and NSP1 of the SARS-CoV family of viruses. Despite the importance of internal dynamics of proteins, there currently are very few approaches that allow for meaningful separation of internal dynamics from structural aspects using experimental data. Here we present a computational approach named REDCRAFT that allows for concurrent characterization of protein structure and dynamics. Here, we have subjected DHFR (PDB-ID 1RX2), a 159-residue protein, to a fictitious, mixed mode model of internal dynamics. In this simulation, DHFR was segmented into 7 regions where 4 of the fragments were fixed with respect to each other, two regions underwent rigid-body dynamics, and one region experienced uncorrelated and melting event. The two dynamical and rigid-body segments experienced an average orientational modification of 7° and 12° respectively. Observable RDC data for backbone C′-N, N-HN, and C′-HN were generated from 102 uniformly sampled frames that described the molecular trajectory. The structure calculation of DHFR with REDCRAFT by using traditional Ramachandran restraint produced a structure with 29 Å of structural difference measured over the backbone atoms (bb-rmsd) over the entire length of the protein and an average bb-rmsd of more than 4.7 Å over each of the dynamical fragments. The same exercise repeated with context-specific dihedral restraints generated by PDBMine produced a structure with bb-rmsd of 21 Å over the entire length of the protein but with bb-rmsd of less than 3 Å over each of the fragments. Finally, utilization of the Dynamic Profile generated by REDCRAFT allowed for the identification of different dynamical regions of the protein and the recovery of individual fragments with bb-rmsd of less than 1 Å. Following the recovery of the fragments, our assembly procedure of domains (larger segments consisting of multiple fragments with a common dynamical profile) correctly assembled the four fragments that are rigid with respect to each other, categorized the two domains that underwent rigid-body dynamics, and identified one dynamical region for which no conserved structure could be defined. In conclusion, our approach was successful in identifying the dynamical domains, recovery of structure where it is meaningful, and relative assembly of the domains when possible.

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Section: Theoretical Background Residual Dipolar Couplings Datamentioning

confidence: 99%

Section: The Effect Of Motion On Saupe Order Tensormentioning

confidence: 99%

Concurrent Identification and Characterization of Protein Structure and Continuous Internal Dynamics with REDCRAFT

Omar

Hein

Cole

et al. 2022

Front. Mol. Biosci.

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“…The recent reintroduction of RDCs due to the development of alignment media has presented this source of data as a possible substitute to the conventional approach to structure determination by NMR spectroscopy. RDCs have been shown to be valuable for structural characterization of aqueous proteins (10,12,43,44) and challenging proteins (40,(45)(46)(47)(48)(49), while enabling simultaneous study of structure and dynamics of proteins (9,27,40,45,(50)(51)(52)(53). Because RDCs can be used to characterize the structure of proteins with far less data than the traditional approaches, it presents a viable and cost-effective method of protein structure elucidation.…”

Section: Residual Dipolar Couplingsmentioning

confidence: 99%

REDCRAFT: A Computational Platform Using Residual Dipolar Coupling NMR Data for Determining Structures of Perdeuterated Proteins Without NOEs

Cole

Daigham

Liu

et al. 2020

Preprint

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AbstractNuclear Magnetic Resonance (NMR) spectroscopy is one of the two primary experimental means of characterizing macromolecular structures, including protein structures. Structure determination by NMR spectroscopy has traditionally relied heavily on distance restraints derived from nuclear Overhauser effect (NOE) measurements. While structure determination of proteins from NOE-based restraints is well understood and broadly used, structure determination by NOEs imposes increasing quantity of data for analysis, increased cost of structure determination and is less available in the study of perdeuterated proteins. In the recent decade, Residual Dipolar Couplings (RDCs) have been investigated as an alternative source of data for structural elucidation of proteins by NMR. Several methods have been reported that utilize RDCs in addition to NOEs, and a few utilize RDC data alone. While these methods have individually demonstrated some successes, none of these methods have exposed the full potential of protein structure determination from RDCs. To date, structure determination of proteins from RDCs is limited to small proteins (less than 8.5 kDa) using RDC data from many alignment media (>3) that cannot be collected from larger proteins. Here we present the latest version of the REDCRAFT software package designed for structure determination of proteins from RDC data alone. We have demonstrated the success of REDCRAFT in structure determination of proteins ranging in size from 50 to 145 residues using experimentally collected data and large proteins (145 to 573 residues) using simulated RDC data that can be collected from perdeuterated proteins. Finally, we demonstrate the accuracy of structure determination of REDCRAFT from RDCs alone in application to the structurally novel PF.2048 protein. The RDC-based structure of PF.2048 exhibited 1.0 Å of BB-RMSD with respect to the NOE-based structure by only using a small amount of backbone RDCs (∼3 restraints per residue) compared to what is required by other approaches.Author SummaryResidual Dipolar Couplings have the potential to reduce the cost and the time needed to characterize protein structures. In addition, RDC data have been demonstrated to concurrently elucidate structure of proteins, perform assignment of resonances, and be used in characterization of the internal dynamics of proteins. Given all the advantages associated with the study of proteins from RDC data, based on the statistics provided by the Protein Databank (PDB), surprisingly the only 124 proteins (out of nearly 150,000 proteins) have utilized RDCs as part of their structure determination. Even a smaller subset of these proteins (approximately 7) have utilized RDCs as the primary source of data for structure determination. The impeding factor in the use of RDCs is the challenging computational and analytical aspects of this source of data. In this report, we demonstrate the success of the REDCRAFT software package in structure determination of proteins using RDC data that can be collected from small and large proteins in a routine fashion. REDCRAFT accomplishes the challenging task of structure determination from RDCs by introducing a unique search and optimization technique that is both robust and computationally tractable. Structure determination from routinely collectable RDC data using REDCRAFT can lead to faster and cheaper study of larger and more complex proteins by NMR spectroscopy in solution state.

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“…In recent years, the use of Residual Dipolar Coupling (RDC) data acquired from Nuclear Magnetic Resonance (NMR) spectroscopy has become a potential avenue for a significant reduction in the cost of structure determination of proteins [7]. In addition, RDC data have been demonstrated to overcome some long-standing challenges in NMR spectroscopy such as structure determination of membrane proteins [10][11][12][13][14], recognition of fold families [15] and the concurrent study of structure and dynamics of proteins [16][17][18][19][20][21][22][23][24]. Recent work [25][26][27][28][29][30] has demonstrated the challenges in structure calculation of proteins from RDC data alone, and some potential solutions have been introduced [26,27,[30][31][32][33].…”

Section: Introductionmentioning

confidence: 99%

“…Recent work [25][26][27][28][29][30] has demonstrated the challenges in structure calculation of proteins from RDC data alone, and some potential solutions have been introduced [26,27,[30][31][32][33]. One such approach named REDCRAFT [11,21,25] has been demonstrated to be successful in structure calculation of proteins from a reduced set of RDC data (and therefore reduced cost). While REDCRAFT has been very successful compared to other approaches, it exhibits some limitations that result in reduced usability and flexibility.…”

Section: Introductionmentioning

confidence: 99%

Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins with REDCRAFT software package

et al. 2020

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Background Traditional approaches to elucidation of protein structures by Nuclear Magnetic Resonance spectroscopy (NMR) rely on distance restraints also known as Nuclear Overhauser effects (NOEs). The use of NOEs as the primary source of structure determination by NMR spectroscopy is time consuming and expensive. Residual Dipolar Couplings (RDCs) have become an alternate approach for structure calculation by NMR spectroscopy. In previous works, the software package REDCRAFT has been presented as a means of harnessing the information containing in RDCs for structure calculation of proteins. However, to meet its full potential, several improvements to REDCRAFT must be made. Results In this work, we present improvements to REDCRAFT that include increased usability, better interoperability, and a more robust core algorithm. We have demonstrated the impact of the improved core algorithm in the successful folding of the protein 1A1Z with as high as ±4 Hz of added error. The REDCRAFT computed structure from the highly corrupted data exhibited less than 1.0 Å with respect to the X-ray structure. We have also demonstrated the interoperability of REDCRAFT in a few instances including with PDBMine to reduce the amount of required data in successful folding of proteins to unprecedented levels. Here we have demonstrated the successful folding of the protein 1D3Z (to within 2.4 Å of the X-ray structure) using only N-H RDCs from one alignment medium. Conclusions The additional GUI features of REDCRAFT combined with the NEF compliance have significantly increased the flexibility and usability of this software package. The improvements of the core algorithm have substantially improved the robustness of REDCRAFT in utilizing less experimental data both in quality and quantity.

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

Cited by 6 publications

References 112 publications

Concurrent Identification and Characterization of Protein Structure and Continuous Internal Dynamics with REDCRAFT

Concurrent Identification and Characterization of Protein Structure and Continuous Internal Dynamics with REDCRAFT

REDCRAFT: A Computational Platform Using Residual Dipolar Coupling NMR Data for Determining Structures of Perdeuterated Proteins Without NOEs

Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins with REDCRAFT software package

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