Recent advances in the field of protein structure determination using liquid-state NMR enable the elucidation of multi-state protein conformations that can provide insight into correlated and non-correlated protein dynamics at atomic resolution. So far, NMR-derived multi-state structures were typically evaluated by means of visual inspection of structure superpositions, target function values that quantify the violation of experimented restraints and root-mean-square deviations that quantify similarity between conformers. As an alternative or complementary approach, we present here the use of a recently introduced structural correlation measure, PDBcor, that quantifies the clustering of protein states as an additional measure for multi-state protein structure analysis. It can be used for various assays including the validation of experimental distance restraints, optimization of the number of protein states, estimation of protein state populations, identification of key distance restraints, NOE network analysis and semiquantitative analysis of the protein correlation network. We present applications for the final quality analysis stages of typical multi-state protein structure calculations.
Validation of protein backbone structures calculated from NMR angular restraints using Rosetta
Validation of protein backbone structures calculated from NMR angular restraints using Rosetta
Abstract
Multidimensional solid-state NMR spectra of oriented membrane proteins can be used to infer the backbone torsion angles and hence the overall protein fold by measuring dipolar couplings and chemical shift anisotropies, which depend on the orientation of each peptide plane with respect to the external magnetic field. However, multiple peptide plane orientations can be consistent with a given set of angular restraints. This ambiguity is further...
nmrlearner
Journal club
0
05-11-2019 07:56 PM
[NMR paper] Membrane Protein Structural Validation by Oriented Sample Solid-State NMR: Diacylglycerol Kinase.
Membrane Protein Structural Validation by Oriented Sample Solid-State NMR: Diacylglycerol Kinase.
Related Articles Membrane Protein Structural Validation by Oriented Sample Solid-State NMR: Diacylglycerol Kinase.
Biophys J. 2014 Apr 15;106(8):1559-69
Authors: Murray DT, Li C, Gao FP, Qin H, Cross TA
Abstract
The validation of protein structures through functional assays has been the norm for many years. Functional assays perform this validation for water-soluble proteins very well, but they need to be performed in the same...
nmrlearner
Journal club
0
04-18-2014 01:35 PM
Membrane Protein Structural Validation by Oriented Sample Solid-State NMR: Diacylglycerol Kinase
Membrane Protein Structural Validation by Oriented Sample Solid-State NMR: Diacylglycerol Kinase
Publication date: 15 April 2014
Source:Biophysical Journal, Volume 106, Issue 8</br>
Author(s): Dylan*T. Murray , Conggang Li , F.*Philip Gao , Huajun Qin , Timothy*A. Cross</br>
The validation of protein structures through functional assays has been the norm for many years. Functional assays perform this validation for water-soluble proteins very well, but they need to be performed in the same environment as that used for the structural analysis. This is difficult...
nmrlearner
Journal club
0
04-15-2014 11:00 PM
[NMR paper] An overview of tools for the validation of protein NMR structures.
An overview of tools for the validation of protein NMR structures.
An overview of tools for the validation of protein NMR structures.
J Biomol NMR. 2013 Jul 23;
Authors: Vuister GW, Fogh RH, Hendrickx PM, Doreleijers JF, Gutmanas A
Abstract
Biomolecular structures at atomic resolution present a valuable resource for the understanding of biology. NMR spectroscopy accounts for 11*% of all structures in the PDB repository. In response to serious problems with the accuracy of some of the NMR-derived structures and in order to facilitate...
nmrlearner
Journal club
0
07-24-2013 04:52 PM
Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures.
Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures.
Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures.
Proteins. 2011 Jan 6;
Authors: Bernard A, Vranken WF, Bardiaux B, Nilges M, Malliavin TE
The classical procedure for nuclear magnetic resonance structure calculation allocates empirical distance ranges and uses historical values for weighting factors. However, Bayesian analysis suggests that there are more optimal...
nmrlearner
Journal club
0
03-03-2011 12:34 PM
[NMR paper] Rapid assessment of protein structural stability and fold validation via NMR.
Rapid assessment of protein structural stability and fold validation via NMR.
Related Articles Rapid assessment of protein structural stability and fold validation via NMR.
Methods Enzymol. 2005;394:142-75
Authors: Hoffmann B, Eichmüller C, Steinhauser O, Konrat R
In structural proteomics, it is necessary to efficiently screen in a high-throughput manner for the presence of stable structures in proteins that can be subjected to subsequent structure determination by X-ray or NMR spectroscopy. Here we illustrate that the (1)H chemical...
nmrlearner
Journal club
0
11-24-2010 11:14 PM
[NMR paper] Structures of larger proteins, protein-ligand and protein-DNA complexes by multi-dime
Structures of larger proteins, protein-ligand and protein-DNA complexes by multi-dimensional heteronuclear NMR.
Related Articles Structures of larger proteins, protein-ligand and protein-DNA complexes by multi-dimensional heteronuclear NMR.
Prog Biophys Mol Biol. 1994;62(2):153-84
Authors: Clore GM, Gronenborn AM
nmrlearner
Journal club
0
08-22-2010 03:33 AM
Validation of NMR-derived protein structures, Chris Spronk
Here's a good PowerPoint presentation by Chris Spronk (University of Nijmegen, The Netherlands) on the subject of validating NMR protein structure results (adapted by Jurgen F. Doreleijers - University of Wisconsin, Madison, USA)
http://tang.bmrb.wisc.edu/~jurgen/presents/Madison/Biochem%20801/NMR_validation_biochem801_2005.ppt
The presentation is very well-annotated, so be sure to adjust your view in PowerPoint so that you can see the notes.
Optimization and validation of multi-state NMR protein structures using structural correlations
Linear Mode
