Related ArticlesRefinement of the protein backbone angle psi in NMR structure calculations.
J Biomol NMR. 2000 Jan;16(1):47-58
Authors: Sprangers R, Bottomley MJ, Linge JP, Schultz J, Nilges M, Sattler M
Cross-correlated relaxation rates involving the Calpha-Halpha dipolar interaction and the carbonyl (C') chemical shift anisotropy (CSA) have been measured using two complementary 3D experiments. We show that the protein backbone angle psi can be directly refined against such cross-correlated relaxation rates (gammaHalphaCalpha,C') and the three-bond H/D isotope effect on the Calpha chemical shifts (3 deltaCalpha(ND)). By simultaneously using both experimental parameters as restraints during NMR structure calculations, a unique value for the backbone angle psi is defined. We have applied the new refinement method to the alpha-Spectrin SH3 domain (a beta-sheet protein) and to the Sgs1p HRDC domain (an alpha-helical protein) and show that the quality of the NMR structures is substantially improved, judging from the atomic coordinate precision and the Ramachandran map. In addition, the psi-refined NMR structures of the SH3 domain deviate less from the 1.8 A crystal structure, suggesting an improved accuracy. The proposed refinement method can be used to significantly improve the quality of NMR structures and will be applicable to larger proteins.
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data
Abstract X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside...
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09-26-2011 06:42 AM
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data.
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data.
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data.
J Biomol NMR. 2011 Sep 22;
Authors: Tang M, Sperling LJ, Berthold DA, Schwieters CD, Nesbitt AE, Nieuwkoop AJ, Gennis RB, Rienstra CM
Abstract
X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular...
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09-23-2011 05:30 PM
Density functional calculations of backbone 15N shielding tensors in beta-sheet and turn residues of protein G
Density functional calculations of backbone 15N shielding tensors in beta-sheet and turn residues of protein G
Abstract We performed density functional calculations of backbone 15N shielding tensors in the regions of beta-sheet and turns of protein G. The calculations were carried out for all twenty-four beta-sheet residues and eight beta-turn residues in the protein GB3 and the results were compared with the available experimental data from solid-state and solution NMR measurements. Together with the alpha-helix data, our calculations cover 39 out of the 55 residues (or 71%) in GB3....
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02-11-2011 08:36 PM
[NMR paper] A protein backbone psi and phi angle dependence of 2J(N(i),C alpha(i-1)): the new NMR
A protein backbone psi and phi angle dependence of 2J(N(i),C alpha(i-1)): the new NMR experiment and quantum chemical calculations.
Related Articles A protein backbone psi and phi angle dependence of 2J(N(i),C alpha(i-1)): the new NMR experiment and quantum chemical calculations.
J Biomol NMR. 2005 Feb;31(2):87-95
Authors: Ko?mi?ski W, Zhukov I, Pecul M, Sadlej J
A new pulse sequence exploiting double- and zero-quantum evolution of two-spin 15N-13C' coherence is proposed for the accurate measurements of 2J(N(i),C alpha(i-1)) coupling...
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11-24-2010 11:14 PM
[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
[NMR paper] Improved efficiency of protein structure calculations from NMR data using the program
Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints.
Related Articles Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints.
J Biomol NMR. 1991 Nov;1(4):447-56
Authors: Güntert P, Wüthrich K
A new strategy for NMR structure calculations of proteins with the variable target function method (Braun, W. and Go, N. (1985) J. Mol. Biol., 186, 611) is described, which makes use of...
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08-21-2010 11:12 PM
[NMR paper] Improved efficiency of protein structure calculations from NMR data using the program
Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints.
Related Articles Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints.
J Biomol NMR. 1991 Nov;1(4):447-56
Authors: Güntert P, Wüthrich K
A new strategy for NMR structure calculations of proteins with the variable target function method (Braun, W. and Go, N. (1985) J. Mol. Biol., 186, 611) is described, which makes use of...
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08-21-2010 11:12 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):313–327, 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)...