Publication year: 2011 Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 17 August 2011
Sungsool, Wi , Justin, Spano
A solid-state rotational-echo double resonance (REDOR) NMR method was introduced to identify the ?- and ?-torsion angle from a 1H–15N or 1H–13C? spin system of alanine-like residues in a selectively, uniformly, or extensively 15N-/13C-labeled peptide. When a C?(i) or a 15N peak is site-specifically obtainable in the NMR spectrum of a uniformly 15N/13C-labeled sample system, the ?- or ?-torsion angle specified by the conformational structure of peptide geometry involving 15N(i)–1H?(i)–15N(i+1) or 13C?(i-1)–1HN(i)–13C?(i) spin system can be identified based on 13C?- or 15N-detected 1H?–15N or 1HN–13C REDOR experiment. This method will conveniently be utilized to identify major secondary motifs, such as... Graphical abstract
*Graphical abstract:**Highlights:*? Determination of ?- and ?-torsion angles of a uniformly 13C-/15N-labeled peptide. ? Rotational-echo double resonance (REDOR) NMR. ? Tri-spin systems, 15N(i)-1H?(i)-15N(i+1) and 13C?(i-1)-1HN(i)-13C?(i).
Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space
Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space
Abstract A method is introduced to represent an ensemble of conformers of a protein by a single structure in torsion angle space that lies closest to the averaged Cartesian coordinates while maintaining perfect covalent geometry and on average equal steric quality and an equally good fit to the experimental (e.g. NMR) data as the individual conformers of the ensemble. The single representative â??regmean structureâ?? is obtained by simulated annealing in torsion angle space with the...
nmrlearner
Journal club
0
02-25-2012 12:16 AM
Asymmetry of 13C labeled 3-pyruvate affords improved site specific labeling of RNA for NMR spectroscopy
Asymmetry of 13C labeled 3-pyruvate affords improved site specific labeling of RNA for NMR spectroscopy
Abstract Selective isotopic labeling provides an unparalleled window within which to study the structure and dynamics of RNAs by high resolution NMR spectroscopy. Unlike commonly used carbon sources, the asymmetry of 13C-labeled pyruvate provides selective labeling in both the ribose and base moieties of nucleotides using Escherichia coli variants, that until now were not feasible. Here we show that an E. coli mutant strain that lacks succinate and malate dehydrogenases (DL323) and...
nmrlearner
Journal club
0
11-19-2011 07:51 AM
Asymmetry of 13C labeled 3-pyruvate affords improved site specific labeling of RNA for NMR spectroscopy
Asymmetry of 13C labeled 3-pyruvate affords improved site specific labeling of RNA for NMR spectroscopy
Abstract Selective isotopic labeling provides an unparalleled window within which to study the structure and dynamics of RNAs by high resolution NMR spectroscopy. Unlike commonly used carbon sources, the asymmetry of 13C-labeled pyruvate provides selective labeling in both the ribose and base moieties of nucleotides using E. coli variants, that until now were not feasible. Here we show that an E. coli mutant strain that lacks succinate and malate dehydrogenases (DL323) and grown on...
nmrlearner
Journal club
0
11-14-2011 08:45 AM
[NMR paper] Site-specific 13C chemical shift anisotropy measurements in a uniformly 15N,13C-labeled microcrystalline protein by 3D magic-angle spinning NMR spectroscopy.
Site-specific 13C chemical shift anisotropy measurements in a uniformly 15N,13C-labeled microcrystalline protein by 3D magic-angle spinning NMR spectroscopy.
Related Articles Site-specific 13C chemical shift anisotropy measurements in a uniformly 15N,13C-labeled microcrystalline protein by 3D magic-angle spinning NMR spectroscopy.
J Am Chem Soc. 2005 Aug 31;127(34):11946-7
Authors: Wylie BJ, Franks WT, Graesser DT, Rienstra CM
In this Communication, we introduce a 3D magic-angle spinning recoupling experiment that correlates chemical shift...
nmrlearner
Journal club
0
12-01-2010 06:56 PM
[NMR paper] Torsion angle dynamics for NMR structure calculation with the new program DYANA.
Torsion angle dynamics for NMR structure calculation with the new program DYANA.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Torsion angle dynamics for NMR structure calculation with the new program DYANA.
J Mol Biol. 1997 Oct 17;273(1):283-98
Authors: Güntert P, Mumenthaler C, Wüthrich K
The new program DYANA (DYnamics Algorithm for Nmr Applications) for efficient calculation of three-dimensional protein and nucleic acid structures from distance constraints and...
nmrlearner
Journal club
0
08-22-2010 05:08 PM
[NMR paper] Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculatio
Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation.
J Magn Reson. 1997 Jan;124(1):154-64
Authors: Stein EG, Rice LM, Brünger AT
Molecular dynamics in torsion-angle space was applied to nuclear magnetic resonance structure calculation using nuclear Overhauser effect-derived distances and...
nmrlearner
Journal club
0
08-22-2010 03:31 PM
[NMR paper] Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculatio
Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation.
J Magn Reson. 1997 Jan;124(1):154-64
Authors: Stein EG, Rice LM, Brünger AT
Molecular dynamics in torsion-angle space was applied to nuclear magnetic resonance structure calculation using nuclear Overhauser effect-derived distances and...
nmrlearner
Journal club
0
08-22-2010 03:03 PM
[NMR paper] Phosphorylation-induced torsion-angle strain in the active center of HPr, detected by
Phosphorylation-induced torsion-angle strain in the active center of HPr, detected by NMR and restrained molecular dynamics refinement.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Phosphorylation-induced torsion-angle strain in the active center of HPr, detected by NMR and restrained molecular dynamics refinement.
Protein Sci. 1996...