Related ArticlesImproving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases.
Protein Sci. 1996 Jun;5(6):1067-80
Authors: Kuszewski J, Gronenborn AM, Clore GM
A new conformational database potential involving dihedral angle relationships in databases of high-resolution highly refined protein crystal structures is presented as a method for improving the quality of structures generated from NMR data. The rationale for this procedure is based on the observation that uncertainties in the description of the nonbonded contacts present a key limiting factor in the attainable accuracy of protein NMR structures and that the nonbonded interaction terms presently used have poor discriminatory power between high- and low-probability local conformations. The idea behind the conformational database potential is to restrict sampling during simulated annealing refinement to conformations that are likely to be energetically possible by effectively limiting the choices of dihedral angles to those that are known to be physically realizable. In this manner, the variability in the structures produced by this method is primarily a function of the experimental restraints, rather than an artifact of a poor nonbonded interaction model. We tested this approach with the experimental NMR data (comprising an average of about 30 restraints per residue and consisting of interproton distances, torsion angles, 3JHN alpha coupling constants, and 13C chemical shifts) used previously to calculate the solution structure of reduced human thioredoxin (Qin J, Clore GM, Gronenborn AM, 1994, Structure 2:503-522). Incorporation of the conformational database potential into the target function used for refinement (which also includes terms for the experimental restraints, covalent geometry, and nonbonded interactions in the form of either a repulsive, repulsive-attractive, or 6-12 Lennard-Jones potential) results in a significant improvement in various quantitative measures of quality (Ramachandran plot, side-chain torsion angles, overall packing). This is achieved without compromising the agreement with the experimental restraints and the deviations from idealized covalent geometry that remain within experimental error, and the agreement between calculated and observed 1H chemical shifts that provides an independent NMR parameter of accuracy. The method is equally applicable to crystallographic refinement, and should be particular useful during the early stages of either an NMR or crystallographic structure determination and in cases where relatively few experimental restraints can be derived from the measured data (due, for example, to broad lines in the NMR spectra or to poorly diffracting crystals).
[NMR paper] High-quality homology models derived from NMR and X-ray structures of E. coli protein
High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases.
Related Articles High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases.
Protein Sci. 2005 Jun;14(6):1597-608
Authors: Liu G, Li Z, Chiang Y, Acton T, Montelione GT, Murray D, Szyperski T
The structural...
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[NMR paper] Improving the accuracy of NMR structures of large proteins using pseudocontact shifts
Improving the accuracy of NMR structures of large proteins using pseudocontact shifts as long-range restraints.
Related Articles Improving the accuracy of NMR structures of large proteins using pseudocontact shifts as long-range restraints.
J Biomol NMR. 2004 Mar;28(3):205-12
Authors: Gaponenko V, Sarma SP, Altieri AS, Horita DA, Li J, Byrd RA
We demonstrate improved accuracy in protein structure determination for large (>/=30 kDa), deuterated proteins (e.g. STAT4(NT)) via the combination of pseudocontact shifts for amide and methyl protons...
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[NMR paper] The importance of being ordered: improving NMR structures using residual dipolar coup
The importance of being ordered: improving NMR structures using residual dipolar couplings.
Related Articles The importance of being ordered: improving NMR structures using residual dipolar couplings.
C R Biol. 2002 Sep;325(9):957-66
Authors: Gronenborn AM
Residual dipolar couplings arise from small degrees of alignment of molecules in a magnetic field. Most biomolecules lack sufficient intrinsic magnetic susceptibility anisotropies for practical purposes; however, alignment can be achieved using dilute aqueous phospholipid mixtures, colloidal...
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[NMR paper] Improving the quality of protein structures derived by NMR spectroscopy.
Improving the quality of protein structures derived by NMR spectroscopy.
Related Articles Improving the quality of protein structures derived by NMR spectroscopy.
J Biomol NMR. 2002 Mar;22(3):281-9
Authors: Spronk CA, Linge JP, Hilbers CW, Vuister GW
Biomolecular structures provide the basis for many studies in several research areas such as homology modelling, structure-based drug design and functional genomics. It is an important prerequisite that the structure is reliable in terms of accurate description of the experimental data, and in...
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[NMR paper] Improving the accuracy of NMR structures of DNA by means of a database potential of m
Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base-base positional interactions.
Related Articles Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base-base positional interactions.
J Am Chem Soc. 2001 May 2;123(17):3903-18
Authors: Kuszewski J, Schwieters C, Clore GM
NMR structure determination of nucleic acids presents an intrinsically difficult problem since the density of short interproton distance contacts is relatively low...
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[NMR paper] AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved
AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.
Related Articles AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.
J Biomol NMR. 1996 Dec;8(4):477-86
Authors: Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM
The AQUA and PROCHECK-NMR programs provide a means of validating the geometry and restraint violations of an ensemble of protein structures solved by solution NMR. The outputs include a detailed breakdown of the restraint violations, a...
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[NMR paper] Application of 1H NMR chemical shifts to measure the quality of protein structures.
Application of 1H NMR chemical shifts to measure the quality of protein structures.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Application of 1H NMR chemical shifts to measure the quality of protein structures.
J Mol Biol. 1995 Apr 7;247(4):541-6
Authors: Williamson MP, Kikuchi J, Asakura T
We have developed a program that can calculate proton NMR chemical shifts for proteins, using a set of co-ordinates provided for example from an X-ray or NMR structure. When...