The structure in solution of crambin, a small protein of 46 residues, has been determined from 2D NMR data using an iterative relaxation matrix approach (IRMA) together with distance geometry, distance bound driven dynamics, molecular dynamics, and energy minimization. A new protocol based on an "ensemble" approach is proposed and compared to the more standard initial rate analysis approach and a "single structure" relaxation matrix approach. The effects of fast local motions are included and R-factor calculations are performed on NOE build-ups to describe the quality of agreement between theory and experiment. A new method for stereospecific assignment of prochiral groups, based on a comparison of theoretical and experimental NOE intensities, has been applied. The solution structure of crambin could be determined with a precision (rmsd from the average structure) of 0.7 A on backbone atoms and 1.1 A on all heavy atoms and is largely similar to the crystal structure with a small difference observed in the position of the side chain of Tyr-29 which is determined in solution by both J-coupling and NOE data. Regions of higher structural variability (suggesting higher mobility) are found in the solution structure, in particular for the loop between the two helices (Gly-20 to Pro-22).
[Question from NMRWiki Q&A forum] What is the easiest way to emulate the "array" command from VNMR in XWINNMR/TOPSPIN?
What is the easiest way to emulate the "array" command from VNMR in XWINNMR/TOPSPIN?
What is the easiest way to emulate the "array" command from VNMR in XWINNMR/TOPSPIN? I recently moved from a lab using a Varian (Unity plus 500) with VNMR 6.whatever to a lab with only Bruker (AVANCE 300/400/500) spectrometers available. I am used to using the "array" caommand in VNMR and viewing the spectra with "dssa" or "dssh." I don't know a convenient way to do the same thing in XWINNMR. I know there are some AU programs but I'm not sure what they all do or if what I want is available. I tried...
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09-24-2010 07:36 PM
[NMR paper] Complete relaxation matrix refinement of NMR structures of proteins using analyticall
Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities.
Related Articles Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities.
J Biomol NMR. 1991 Sep;1(3):257-69
Authors: Mertz JE, Güntert P, Wüthrich K, Braun W
A new method for refining three-dimensional (3D) NMR structures of proteins is described, which takes account of the complete relaxation pathways....
nmrlearner
Journal club
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08-21-2010 11:12 PM
[NMR paper] Complete relaxation matrix refinement of NMR structures of proteins using analyticall
Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities.
Related Articles Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities.
J Biomol NMR. 1991 Sep;1(3):257-69
Authors: Mertz JE, Güntert P, Wüthrich K, Braun W
A new method for refining three-dimensional (3D) NMR structures of proteins is described, which takes account of the complete relaxation pathways....
nmrlearner
Journal club
0
08-21-2010 11:12 PM
Postdoctoral Position "Solution Dynamics of Protein Kinases" in New York
Postdoctoral Position "Solution Dynamics of Protein Kinases" in New York
A postdoctoral position to study the solution dynamics and structure
of protein kinases is available on a NIH funded project (REF#:
HS-R-6453-10-08-S). Our group is interested in how static and dynamic
changes of protein structure affect the activity of protein kinases.
We combine X-ray crystallography, NMR and ligand binding kinetics with
collaborative molecular dynamic studies (See e.g. ref 1 and 2). Our
research group is located at Stony Brook University in a highly
interactive environment with the New York...
nmrlearner
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08-21-2010 05:17 AM
Postdoctoral Position "Solution Dynamics of Protein Kinases" in New York
Postdoctoral Position "Solution Dynamics of Protein Kinases" in New York
A postdoctoral position to study the solution dynamics and structure
of protein kinases is available on a NIH funded project (REF#:
HS-R-6453-10-08-S). Our group is interested in how static and dynamic
changes of protein structure affect the activity of protein kinases.
We combine X-ray crystallography, NMR and ligand binding kinetics with
collaborative molecular dynamic studies (See e.g. ref 1 and 2). Our
research group is located at Stony Brook University in a highly
interactive environment with the New York...
"Ensemble" iterative relaxation matrix approach: a new NMR refinement protocol applie
Linear Mode
