Data integration in structural biology has become a paradigm for the characterization of biomolecular systems, and it is now accepted that combining different techniques can fill the gaps in each otherâ??s blind spots. In this frame, one of the combinations, which we have implemented in REFMAC-NMR, is residual dipolar couplings from NMR together with experimental data from X-ray diffraction. The first are exquisitely sensitive to the local details but does not give any information about overall shape, whereas the latter encodes more the information about the overall shape but at the same time tends to miss the local details even at the highest resolutions. Once crystals are obtained, it is often rather easy to obtain a complete X-ray dataset, however it is time-consuming to obtain an exhaustive NMR dataset. Here, we discuss the effect of including a-priori knowledge on the properties of the system to reduce the number of experimental data needed to obtain a more complete picture. We thus introduce a set of new features of REFMAC-NMR that allow for improved handling of RDC data for multidomain proteins and multisubunit biomolecular complexes, and encompasses the use of pseudo-contact shifts as an additional source of NMR-based information. The new feature may either help in improving the refinement, or assist in spotting differences between the crystal and the solution data. We show three different examples where NMR and X-ray data can be reconciled to a unique structural model without invoking mobility.
ImprovedAccuracy from Joint X-ray and NMRRefinement of a Protein–RNA Complex Structure
ImprovedAccuracy from Joint X-ray and NMRRefinement of a Protein–RNA Complex Structure
Azzurra Carlon, Enrico Ravera, Janosch Hennig, Giacomo Parigi, Michael Sattler and Claudio Luchinat
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/jacs.5b11598/20160129/images/medium/ja-2015-11598y_0009.gif
Journal of the American Chemical Society
DOI: 10.1021/jacs.5b11598
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/4w5mwIM6SB8
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01-30-2016 07:56 AM
[NMR paper] Improved accuracy from joint X-ray and NMR refinement of a protein-RNA complex structure.
Improved accuracy from joint X-ray and NMR refinement of a protein-RNA complex structure.
Improved accuracy from joint X-ray and NMR refinement of a protein-RNA complex structure.
J Am Chem Soc. 2016 Jan 13;
Authors: Carlon A, Ravera E, Hennig J, Parigi G, Sattler M, Luchinat C
Abstract
Integrated experimental approaches play an increasingly important role in structural biology, taking advantage of the complementary information provided by different techniques. In particular, the combination of NMR data with X-ray diffraction...
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01-14-2016 11:53 PM
[NMR paper] NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores.
NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores.
Related Articles NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores.
Bioinformatics. 2015 Oct 26;
Authors: Ryu H, Lim G, Sung BH, Lee J
Abstract
Protein structure refinement is a necessary step for the study of protein function. In particular, some nuclear magnetic resonance (NMR) structures are of lower quality than X-ray crystallographic structures. Here, we present NMRe, a...
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10-28-2015 05:05 PM
[NMR paper] Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences.
Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences.
Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences.
Acta Crystallogr D Biol Crystallogr. 2014 Apr 1;70(Pt 4):958-67
Authors: Rinaldelli M, Ravera E, Calderone V, Parigi G, Murshudov GN, Luchinat C
Abstract
The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact...
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04-06-2014 02:01 AM
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data
Abstract X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside...
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09-26-2011 06:42 AM
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data.
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data.
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data.
J Biomol NMR. 2011 Sep 22;
Authors: Tang M, Sperling LJ, Berthold DA, Schwieters CD, Nesbitt AE, Nieuwkoop AJ, Gennis RB, Rienstra CM
Abstract
X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular...
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09-23-2011 05:30 PM
[NMR paper] Joint X-ray and NMR refinement of the yeast L30e-mRNA complex.
Joint X-ray and NMR refinement of the yeast L30e-mRNA complex.
Related Articles Joint X-ray and NMR refinement of the yeast L30e-mRNA complex.
Structure. 2004 Jul;12(7):1165-76
Authors: Chao JA, Williamson JR
L30e, a Saccharomyces cervisiae ribosomal protein, regulates its own expression by binding to a purine-rich asymmetric internal loop located in both its pre-mRNA and mature mRNA. A crystal structure of an MBP-L30e fusion protein in complex with an RNA containing the pre-mRNA regulatory site was solved at 3.24 A. Interestingly, the...
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11-24-2010 09:51 PM
[NMR paper] Joint refinement as a tool for thorough comparison between NMR and X-ray data and str
Joint refinement as a tool for thorough comparison between NMR and X-ray data and structures of HU protein.
Related Articles Joint refinement as a tool for thorough comparison between NMR and X-ray data and structures of HU protein.
J Biomol NMR. 2001 Nov;21(3):235-48
Authors: Raves ML, Doreleijer JF, Vis H, Vorgias CE, Wilson KS, Kaptei R
Joint refinement, i.e., the simultaneous refinement of a structure against both nuclear magnetic resonance (NMR) spectroscopic and X-ray crystallographic data, was performed on the HU protein from Bacillus...
Joint X-ray/NMR structure refinement of multidomain/multisubunit systems
Linear Mode
