scholarly journals A graphical method for analyzing distance restraints using residual dipolar couplings for structure determination of symmetric protein homo-oligomers

2011 ◽  
Vol 20 (6) ◽  
pp. 970-985 ◽  
Author(s):  
Jeffrey W. Martin ◽  
Anthony K. Yan ◽  
Chris Bailey-Kellogg ◽  
Pei Zhou ◽  
Bruce R. Donald
Keyword(s):  
Structure Determination ◽  
Residual Dipolar Couplings ◽  
Graphical Method ◽  
Dipolar Couplings ◽  
Distance Restraints

Residual Dipolar Couplings in Structure Determination of Biomolecules

ChemInform ◽  
2004 ◽  
Vol 35 (45) ◽  
Author(s):  
J. H. Prestegard ◽  
C. M. Bougault ◽  
A. I. Kishore
Keyword(s):  
Structure Determination ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings

Paramagnetically Induced Residual Dipolar Couplings for Solution Structure Determination of Lanthanide Binding Proteins

2002 ◽  
Vol 124 (19) ◽  
pp. 5581-5587 ◽  
Author(s):  
Renato Barbieri ◽  
Ivano Bertini ◽  
Gabriele Cavallaro ◽  
Yong-Min Lee ◽  
Claudio Luchinat ◽  
...  
Keyword(s):  
Structure Determination ◽  
Solution Structure ◽  
Binding Proteins ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Solution Structure Determination

Incorporating residual dipolar couplings into the NMR solution structure determination of nucleic acids

Biopolymers ◽  
1999 ◽  
Vol 52 (4) ◽  
pp. 168-180 ◽  
Author(s):  
Hongjun Zhou ◽  
Annaleen Vermeulen ◽  
Fiona M. Jucker ◽  
Arthur Pardi
Keyword(s):  
Nucleic Acids ◽  
Structure Determination ◽  
Solution Structure ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Nmr Solution Structure ◽  
Solution Structure Determination

scholarly journals Residual Dipolar Couplings in Structure Determination of Natural Products

2018 ◽  
Vol 8 (4) ◽  
pp. 279-295 ◽  
Author(s):  
Gao-Wei Li ◽  
Han Liu ◽  
Feng Qiu ◽  
Xiao-Juan Wang ◽  
Xin-Xiang Lei
Keyword(s):  
Natural Products ◽  
Structure Determination ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings

Residual Dipolar Couplings in Structure Determination of Biomolecules

2004 ◽  
Vol 104 (8) ◽  
pp. 3519-3540 ◽  
Author(s):  
J. H. Prestegard ◽  
C. M. Bougault ◽  
A. I. Kishore
Keyword(s):  
Structure Determination ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings

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

2020 ◽  
Author(s):  
Casey A. Cole ◽  
Nourhan S. Daigham ◽  
Gaohua Liu ◽  
Gaetano T. Montelione ◽  
Homayoun Valafar
Keyword(s):  
Nmr Spectroscopy ◽  
Structure Determination ◽  
Software Package ◽  
Residual Dipolar Couplings ◽  
Protein Structures ◽  
Dipolar Couplings ◽  
Large Proteins ◽  
Perdeuterated Proteins ◽  
Small Proteins

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.

A Novel Method for the Determination of Stereochemistry in Six-Membered Chairlike Rings Using Residual Dipolar Couplings

2003 ◽  
Vol 68 (5) ◽  
pp. 1786-1795 ◽  
Author(s):  
Jiangli Yan ◽  
Allen D. Kline ◽  
Huaping Mo ◽  
Michael J. Shapiro ◽  
Edward R. Zartler
Keyword(s):  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Novel Method

Determination of the Relative Configuration of β-Amino Acid Esters Based on Residual Dipolar Couplings

2015 ◽  
Vol 2015 (31) ◽  
pp. 6801-6805 ◽  
Author(s):  
Thomas Niklas ◽  
Christian Steinmetzger ◽  
Weiping Liu ◽  
Daniel Zell ◽  
Dietmar Stalke ◽  
...  
Keyword(s):  
Amino Acid ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Amino Acid Esters ◽  
Relative Configuration ◽  
Acid Esters

scholarly journals Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings

2011 ◽  
Vol 133 (16) ◽  
pp. 6288-6298 ◽  
Author(s):  
Nikolaos G. Sgourakis ◽  
Oliver F. Lange ◽  
Frank DiMaio ◽  
Ingemar André ◽  
Nicholas C. Fitzkee ◽  
...  
Keyword(s):  
Residual Dipolar Couplings ◽  
Chemical Shifts ◽  
Dipolar Couplings ◽  
Nmr Chemical Shifts
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