Abstract The amount of experimental restraints e.g., NOEs is often too small for calculating high quality three-dimensional structures by restrained molecular dynamics. Considering this as a typical missing value problem we propose here a model based data imputation technique that should lead to an improved estimation of the correct structure. The novel automated method implemented in AUREMOL makes a more efficient use of the experimental information to obtain NMR structures with higher accuracy. It creates a large set of substitute restraints that are used either alone or together with the experimental restraints. The new approach was successfully tested on three examples: firstly, the Ras-binding domain of Byr2 from Schizosaccharomyces pombe, the mutant HPr (H15A) from Staphylococcus aureus, and a X-ray structure of human ubiquitin. In all three examples, the quality of the resulting final bundles was improved considerably by the use of additional substitute restraints, as assessed quantitatively by the calculation of RMSD values to the â??trueâ?? structure and NMR R-factors directly calculated from the original NOESY spectra or the published diffraction data.
Content Type Journal Article
Pages 397-411
DOI 10.1007/s10858-009-9379-y
Authors
Carolina Cano, University of Regensburg Institut für Biophysik und physikalische Biochemie Universitätstr. 31 93053 Regensburg Germany
Konrad Brunner, University of Regensburg Institut für Biophysik und physikalische Biochemie Universitätstr. 31 93053 Regensburg Germany
Kumaran Baskaran, University of Regensburg Institut für Biophysik und physikalische Biochemie Universitätstr. 31 93053 Regensburg Germany
Ralph Elsner, University of Regensburg Institut für Biophysik und physikalische Biochemie Universitätstr. 31 93053 Regensburg Germany
Claudia E. Munte, University of Regensburg Institut für Biophysik und physikalische Biochemie Universitätstr. 31 93053 Regensburg Germany
Hans Robert Kalbitzer, University of Regensburg Institut für Biophysik und physikalische Biochemie Universitätstr. 31 93053 Regensburg Germany
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...
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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
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Structure Calculation from Unambiguous Long-Range Amide and Methyl (1)H-(1)H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy.
Structure Calculation from Unambiguous Long-Range Amide and Methyl (1)H-(1)H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy.
Structure Calculation from Unambiguous Long-Range Amide and Methyl (1)H-(1)H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy.
J Am Chem Soc. 2011 Mar 24;
Authors: Linser R, Bardiaux B, Higman V, Fink U, Reif B
Magic-angle spinning (MAS) solid-state NMR becomes an increasingly important tool for the determination of structures of membrane...
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Structure Calculation from Unambiguous Long-Range Amide and Methyl 1H-1H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy
Structure Calculation from Unambiguous Long-Range Amide and Methyl 1H-1H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy
Rasmus Linser, Benjamin Bardiaux, Victoria Higman, Uwe Fink and Bernd Reif
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja110222h/aop/images/medium/ja-2010-10222h_0004.gif
Journal of the American Chemical Society
DOI: 10.1021/ja110222h
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[NMR paper] Protein structure calculation from NMR data.
Protein structure calculation from NMR data.
Related Articles Protein structure calculation from NMR data.
Methods Mol Biol. 2002;173:267-83
Authors: Mal TK, Bagby S, Ikura M
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[NMR paper] Carbonyl CSA restraints from solution NMR for protein structure refinement.
Carbonyl CSA restraints from solution NMR for protein structure refinement.
Related Articles Carbonyl CSA restraints from solution NMR for protein structure refinement.
J Am Chem Soc. 2001 Nov 7;123(44):11065-6
Authors: Lipsitz RS, Tjandra N
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11-19-2010 08:44 PM
protein structure calculation
Hi! every one!
I wanted to get in contact with people solving the structure of protein by using NMR. I am learning the process and i have many basics problem related with the work.
cheers!
premprakash
NMR Questions and Answers
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03-29-2007 02:33 PM
Binding Kd calculation and simulation from NMR data
http://structbio.vanderbilt.edu/chazin/rpa_cell.jpg
If you go to this page on Prof. Chazin website, you will find explanation how to calculate Kd from NMR titration and a program to simulate Kd and estimate its error.
Protein structure calculation with data imputation: the use of substitute restraints
Linear Mode
