Related ArticlesCombining NMR and EPR to Determine Structures of Large RNAs and Protein-RNA Complexes in Solution.
Methods Enzymol. 2015;558:279-331
Authors: Duss O, Yulikov M, Allain FH, Jeschke G
Abstract
Although functional significance of large noncoding RNAs and their complexes with proteins is well recognized, structural information for this class of systems is very scarce. Their inherent flexibility causes problems in crystallographic approaches, while their typical size is beyond the limits of state-of-the-art purely NMR-based approaches. Here, we review an approach that combines high-resolution NMR restraints with lower resolution long-range constraints based on site-directed spin labeling and measurements of distance distribution restraints in the range between 15 and 80Å by the four-pulse double electron-electron resonance (DEER) EPR technique. We discuss sample preparation, the basic assumptions behind data analysis in the EPR-based distance measurements, treatment of the label-based constraints in generation of the structure, and the back-calculation of distance distributions for structure validation. Step-by-step protocols are provided for DEER distance distribution measurements including data analysis and for CYANA based structure calculation using combined NMR and EPR data.
PMID: 26068745 [PubMed - as supplied by publisher]
Scientists Determine 1000 Protein Structures Of Deadly Diseases - Medical News Today
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Scientists Determine 1000 Protein Structures Of Deadly Diseases
Medical News Today
Working together, two scientific organizations have achieved a key milestone earlier than planned: using X-ray crystallography and nuclear magnetic resonance to probe at the atomic level, they have determined the structure of 1000 proteins from more ...
Scientists Determine 1000 Protein Structures Of Deadly Diseases - Medical News Today
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06-12-2012 10:36 AM
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
Abstract While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein 1H chemical shifts in which molecular motions, the...
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02-11-2012 10:31 AM
[NMR paper] Rapid analysis of large protein-protein complexes using NMR-derived orientational con
Rapid analysis of large protein-protein complexes using NMR-derived orientational constraints: the 95 kDa complex of LpxA with acyl carrier protein.
Related Articles Rapid analysis of large protein-protein complexes using NMR-derived orientational constraints: the 95 kDa complex of LpxA with acyl carrier protein.
J Mol Biol. 2004 Nov 5;343(5):1379-89
Authors: Jain NU, Wyckoff TJ, Raetz CR, Prestegard JH
Characterization of protein-protein interactions that are critical to the specific function of many biological systems has become a primary...
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11-24-2010 10:03 PM
[NMR paper] TROSY and CRINEPT: NMR with large molecular and supramolecular structures in solution
TROSY and CRINEPT: NMR with large molecular and supramolecular structures in solution.
Related Articles TROSY and CRINEPT: NMR with large molecular and supramolecular structures in solution.
Trends Biochem Sci. 2000 Oct;25(10):462-8
Authors: Riek R, Pervushin K, Wüthrich K
TROSY and CRINEPT are new techniques for solution NMR studies of molecular and supramolecular structures. They allow the collection of high-resolution spectra of structures with molecular weights >100 kDa, significantly extending the range of macromolecular systems that can...
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11-19-2010 08:29 PM
[NMR paper] Determining the structures of large proteins and protein complexes by NMR.
Determining the structures of large proteins and protein complexes by NMR.
Related Articles Determining the structures of large proteins and protein complexes by NMR.
Trends Biotechnol. 1998 Jan;16(1):22-34
Authors: Clore GM, Gronenborn AM
Recent advances in multidimensional NMR methodology to obtain 1H, 15N and 13C resonance assignments, interproton-distance and torsion-angle restraints, and restraints that characterize long-range order have, coupled with new methods of structure refinement, permitted solution structure of proteins in excess...
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11-17-2010 11:06 PM
Solid-State (17)O NMR Spectroscopy of Large Protein-Ligand Complexes.
Solid-State (17)O NMR Spectroscopy of Large Protein-Ligand Complexes.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_120x27.gif Related Articles Solid-State (17)O NMR Spectroscopy of Large Protein-Ligand Complexes.
Angew Chem Int Ed Engl. 2010 Jul 28;
Authors: Zhu J, Ye E, Terskikh V, Wu G
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08-17-2010 03:36 AM
Using relaxation dispersion NMR spectroscopy to determine structures of excited, invisible protein states
Using relaxation dispersion NMR spectroscopy to determine structures of excited, invisible protein states
D. Flemming Hansen, Pramodh Vallurupalli and Lewis E. Kay
Journal of Biomolecular NMR; 2008; 41(3); pp 113 - 120
Abstract:
Currently the main focus of structural biology is the determination of static three-dimensional representations of biomolecules that for the most part correspond to low energy (ground state) conformations. However, it is becoming increasingly well recognized that higher energy structures often play important roles in function as well. Because these conformers...
Combining NMR and EPR to Determine Structures of Large RNAs and Protein-RNA Complexes in Solution.
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