Related ArticlesSolid-State NMR Structure Determination from Diagonal-Compensated Proton-Proton Restraints.
J Am Chem Soc. 2014 Jul 2;
Authors: Linser R, Bardiaux B, Andreas LB, Hyberts SG, Morris VK, Pintacuda G, Sunde M, Kwan AH, Wagner G
Abstract
We report acquisition of diagonal-compensated protein structural restraints from 4-dimensional solid-state NMR spectra on extensively deuterated and 1H back-exchanged proteins. To achieve this, we use homonuclear 1H-1H correlations with diagonal suppression and non-uniform sampling (NUS). Suppression of the diagonal allows the accurate identification of cross-peaks which are otherwise obscured by the strong autocorrelation or whose intensity is biased due to partial overlap with the diagonal. The approach results in unambiguous spectral interpretation and relatively few but reliable restraints for structure calculation. In addition, the diagonal suppression produces a spectrum with low dynamic range for which ultra-sparse-NUS data sets can be readily reconstructed, allowing straightforward application of NUS with only 2% sampling density with the advantage of more heavily sampling time-domain regions of high signal intensity. The method is demonstrated here for two proteins, ?-spectrin SH3 microcrystals and hydrophobin functional amyloids. For the case of SH3, suppression of the diagonal results in facilitated identification of unambiguous restraints and improvement of the quality of the calculated structural ensemble compared to non-diagonal-suppressed 4D spectra. For the only partly assigned hydrophobin rodlets, the structure is yet unknown. Applied to this protein of biological significance with large inhomogeneous broadening, the method is shown to allow identification of unambiguous crosspeaks that are otherwise obscured by the diagonal.
PMID: 24988008 [PubMed - as supplied by publisher]
[Question from NMRWiki Q&A forum] Generate inter-proton distance restraints from an X-ray structure
Generate inter-proton distance restraints from an X-ray structure
Hello,
Does anyone know of any program that can generate inter-proton distance restraints from an X-ray structure?I was able to use Molmol to generate dihedral angles. MolMol can also generate inter-atom distances, however, I could not figure out how to just generate 1H-1H distances. I have a total of 50,000 inter-atom distance (H-H, C-O, C-N...all types).
Any help is highly appreciated.
Winston
nmrlearner
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04-25-2011 03:43 AM
Proton-Detected Solid-State NMR Spectroscopy of Fibrillar and Membrane Proteins.
Proton-Detected Solid-State NMR Spectroscopy of Fibrillar and Membrane Proteins.
Proton-Detected Solid-State NMR Spectroscopy of Fibrillar and Membrane Proteins.
Angew Chem Int Ed Engl. 2011 Apr 20;
Authors: Linser R, Dasari M, Hiller M, Higman V, Fink U, Lopez Del Amo JM, Markovic S, Handel L, Kessler B, Schmieder P, Oesterhelt D, Oschkinat H, Reif B
nmrlearner
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04-22-2011 02:00 PM
Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints.
Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints.
Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints.
J Am Chem Soc. 2011 Apr 4;
Authors: Ryabov Y, Schwieters CD, Clore GM
(15)N R(2)/R(1) relaxation data contain information on molecular shape and size as well as on bond vector orientations relative to...
nmrlearner
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04-06-2011 10:54 AM
Impact of 15N R2/R1 Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints
Impact of 15N R2/R1 Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints
Yaroslav Ryabov, Charles D. Schwieters and G. Marius Clore
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja201020c/aop/images/medium/ja-2011-01020c_0002.gif
Journal of the American Chemical Society
DOI: 10.1021/ja201020c
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/3J1IyCLkQMQ
nmrlearner
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04-05-2011 10:37 AM
A Proton-Detected 4D Solid-State NMR Experiment for Protein Structure Determination.
A Proton-Detected 4D Solid-State NMR Experiment for Protein Structure Determination.
A Proton-Detected 4D Solid-State NMR Experiment for Protein Structure Determination.
Chemphyschem. 2011 Apr 4;12(5):915-8
Authors: Huber M, Hiller S, Schanda P, Ernst M, Böckmann A, Verel R, Meier BH
nmrlearner
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03-29-2011 07:04 PM
[NMR paper] NMR structure determination and investigation using a reduced proton (REDPRO) labelin
NMR structure determination and investigation using a reduced proton (REDPRO) labeling strategy for proteins.
Related Articles NMR structure determination and investigation using a reduced proton (REDPRO) labeling strategy for proteins.
FEBS Lett. 2002 Jul 31;524(1-3):177-82
Authors: Shekhtman A, Ghose R, Goger M, Cowburn D
We present here a stable isotope labeling technique for proteins, which seeks the appropriate compromise between the advantages of (a) random isotope labeling, with its large number of protons available for structure...
nmrlearner
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11-24-2010 08:58 PM
[NMR paper] Direct refinement against proton-proton dipolar couplings in NMR structure determinat
Direct refinement against proton-proton dipolar couplings in NMR structure determination of macromolecules.
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J Magn Reson. 2000 Feb;142(2):393-6
Authors: Tjandra N, Marquardt J, Clore GM
The computational tools necessary for making use of (1)H-(1)H dipolar couplings in macromolecular structure refinement are presented. Potentials are described for direct refinement against (1)H-(1)H dipolar couplings of known sign as well...
nmrlearner
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11-18-2010 09:15 PM
Mechanisms of proton conduction and gating in influenza m2 proton channels from solid
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Related Articles Mechanisms of proton conduction and gating in influenza m2 proton channels from solid-state NMR.
Science. 2010 Oct 22;330(6003):505-8
Authors: Hu F, Luo W, Hong M
The M2 protein of influenza viruses forms an acid-activated tetrameric proton channel. We used solid-state nuclear magnetic resonance spectroscopy to determine the structure and functional dynamics of the pH-sensing and proton-selective histidine-37 in M2 bound to a...
Solid-State NMR Structure Determination from Diagonal-Compensated Proton-Proton Restraints.
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