Protein model refinement a the crucial step in improving the quality of a predicted protein model. This study presents an NMR refinement protocol called TrioSA (torsion-angle and implicit-solvation-optimized simulated annealing) that improves the accuracy of backbone/side-chain conformations and the overall structural quality of proteins. TrioSA was applied to a subset of 3752 solution NMR protein structures accompanied by experimental NMR data: distance and dihedral angle restraints. We...
[NMR paper] Single-Molecule Force Spectroscopy Trajectories of a Single Protein and Its Polyproteins Are Equivalent: A Direct Experimental Validation Based on A Small Protein NuG2
Single-Molecule Force Spectroscopy Trajectories of a Single Protein and Its Polyproteins Are Equivalent: A Direct Experimental Validation Based on A Small Protein NuG2
Single-molecule force spectroscopy (SMFS) has become a powerful tool in investigating the mechanical unfolding/folding of proteins at the single-molecule level. Polyproteins made of tandem identical repeats have been widely used in atomic force microscopy (AFM)-based SMFS studies, where polyproteins not only serve as fingerprints to identify single-molecule stretching events, but may also improve statistics of data...
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12-27-2016 11:04 PM
A protocol for the refinement of NMR structures using simultaneously pseudocontact shift restraints from multiple lanthanide ions
A protocol for the refinement of NMR structures using simultaneously pseudocontact shift restraints from multiple lanthanide ions
Abstract
The binding of paramagnetic metal ions to proteins produces a number of different effects on the NMR spectra of the system. In particular, when the magnetic susceptibility of the metal ion is anisotropic, pseudocontact shifts (PCSs) arise and can be easily measured. They constitute very useful restraints for the solution structure determination of metal-binding proteins. In this context, there has been great...
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11-19-2016 08:35 PM
[NMR paper] NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores.
NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores.
Related Articles NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores.
Bioinformatics. 2015 Oct 26;
Authors: Ryu H, Lim G, Sung BH, Lee J
Abstract
Protein structure refinement is a necessary step for the study of protein function. In particular, some nuclear magnetic resonance (NMR) structures are of lower quality than X-ray crystallographic structures. Here, we present NMRe, a...
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10-28-2015 05:05 PM
Simple tests for the validation of multiple field spin relaxation data
Simple tests for the validation of multiple field spin relaxation data
Abstract 15N spin relaxation data is widely used to extract detailed dynamic information regarding bond vectors such as the amide Nā??H bond of the protein backbone. Analysis is typically carried using the Lipariā??Szabo model-free approach. Even though the original model-free equation can be determined from single field R 1, R 2 and NOE, over-determination of more complex motional models is dependent on the recording of multiple field datasets. This is especially important for the characterization of conformational...
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01-09-2011 12:46 PM
[NMR paper] NMR data collection and analysis protocol for high-throughput protein structure determination.
NMR data collection and analysis protocol for high-throughput protein structure determination.
Related Articles NMR data collection and analysis protocol for high-throughput protein structure determination.
Proc Natl Acad Sci U S A. 2005 Jul 26;102(30):10487-92
Authors: Liu G, Shen Y, Atreya HS, Parish D, Shao Y, Sukumaran DK, Xiao R, Yee A, Lemak A, Bhattacharya A, Acton TA, Arrowsmith CH, Montelione GT, Szyperski T
A standardized protocol enabling rapid NMR data collection for high-quality protein structure determination is presented that...
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12-01-2010 06:56 PM
[NMR paper] Joint refinement as a tool for thorough comparison between NMR and X-ray data and str
Joint refinement as a tool for thorough comparison between NMR and X-ray data and structures of HU protein.
Related Articles Joint refinement as a tool for thorough comparison between NMR and X-ray data and structures of HU protein.
J Biomol NMR. 2001 Nov;21(3):235-48
Authors: Raves ML, Doreleijer JF, Vis H, Vorgias CE, Wilson KS, Kaptei R
Joint refinement, i.e., the simultaneous refinement of a structure against both nuclear magnetic resonance (NMR) spectroscopic and X-ray crystallographic data, was performed on the HU protein from Bacillus...
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11-19-2010 08:44 PM
[NMR paper] "Ensemble" iterative relaxation matrix approach: a new NMR refinement protocol applie
"Ensemble" iterative relaxation matrix approach: a new NMR refinement protocol applied to the solution structure of crambin.
Related Articles "Ensemble" iterative relaxation matrix approach: a new NMR refinement protocol applied to the solution structure of crambin.
Proteins. 1993 Apr;15(4):385-400
Authors: Bonvin AM, Rullmann JA, Lamerichs RM, Boelens R, Kaptein R
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...
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08-21-2010 11:53 PM
A structure refinement protocol combining NMR residual dipolar couplings and small angle scattering restraints
A structure refinement protocol combining NMR residual dipolar couplings and small angle scattering restraints
F. Gabel, B. Simon, M. Nilges, M. Petoukhov, D. Svergun and M. Sattler
Journal of Biomolecular NMR; 2008; 41(4); pp 199-208
Abstract:
We present the implementation of a target function based on Small Angle Scattering data (Gabel et al. Eur Biophys J 35(4):313327, 2006) into the Crystallography and NMR Systems (CNS) and demonstrate its utility in NMR structure calculations by simultaneous application of small angle scattering (SAS) and residual dipolar coupling (RDC)...
Improving Geometric Validation Metrics and Ensuring Consistency with Experimental Data through TrioSA: An NMR Refinement Protocol
Linear Mode
