We have recently shown that an energy penalty for the incorporation of residual tensorial constraints into molecular structure calculations can be formulated without the explicit knowledge of the Saupe orientation tensor (Moltke and Grzesiek. J. Biomol. NMR, 1999, 15, 77-82). Here we report the implementation of such an algorithm into the program X-PLOR. The new algorithm is easy to use and has good convergence properties. The algorithm is used for the structure refinement of the HIV-1 Nef protein using 252 dipolar coupling restraints. The approach is compared to the conventional penalty function with explicit knowledge of the orientation tensor's amplitude and rhombicity. No significant differences are found with respect to speed, Ramachandran core quality or coordinate precision.
Structure, Dynamics, and Kinetics of Weak Protein-Protein Complexes from NMR Spin Relaxation Measurements of Titrated Solutions.
Structure, Dynamics, and Kinetics of Weak Protein-Protein Complexes from NMR Spin Relaxation Measurements of Titrated Solutions.
Structure, Dynamics, and Kinetics of Weak Protein-Protein Complexes from NMR Spin Relaxation Measurements of Titrated Solutions.
Angew Chem Int Ed Engl. 2011 Mar 18;
Authors: Salmon L, Ortega Roldan JL, Lescop E, Licinio A, van Nuland N, Jensen MR, Blackledge M
nmrlearner
Journal club
0
03-23-2011 05:41 PM
[NMR analysis blog] Alignment of NMR spectra – Part IV: Advanced Alignment
Alignment of NMR spectra – Part IV: Advanced Alignment
Previous posts on this series:
Alignment of NMR spectra – Part I: The problem
Alignment of NMR spectra – Part II: Binning / Bucketing
Alignment of NMR spectra – Part III: Global Alignment
As I mentioned in my previous post, simple alignment based on shifting or referencing the whole spectrum is not enough in cases where there are different local chemical shift fluctuations.
Resorting back to the synthetic data set used in the previous posts, let me introduce a semi-automatic method designed specifically to align spectra having...
nmrlearner
News from NMR blogs
0
02-07-2011 07:53 PM
[NMR analysis blog] Alignment of NMR spectra – Part III: Global Alignment
Alignment of NMR spectra – Part III: Global Alignment
Previous posts on this series:
Alignment of NMR spectra – Part I: The problem
Alignment of NMR spectra – Part II: Binning / Bucketing
We have seen that binning helps in minimizing, for example, the effect of pH-induced fluctuations in chemical shift so that, in the field of NMR-based metabonomics studies, ensuring that signals for a given metabolite appear at the same location in all spectra. One evident disadvantage of binning is that it greatly reduces the spectral resolution (e.g. in a 500 MHz instrument, a typical 64 Kb...
nmrlearner
News from NMR blogs
0
02-03-2011 06:51 PM
[NMR paper] Refinement of the protein backbone angle psi in NMR structure calculations.
Refinement of the protein backbone angle psi in NMR structure calculations.
Related Articles Refinement 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...
[NMR paper] Limits of NMR structure determination using variable target function calculations: ri
Limits of NMR structure determination using variable target function calculations: ribonuclease T1, a case study.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Limits of NMR structure determination using variable target function calculations: ribonuclease T1, a case study.
J Mol Biol. 1997 Feb 21;266(2):400-23
Authors: Pfeiffer S, Karimi-Nejad Y, Rüterjans H
Limits of NMR structure determination using multidimensional NMR spectroscopy, variable target function...
nmrlearner
Journal club
0
08-22-2010 03:03 PM
[NMR paper] Relaxation data in NMR structure determination: model calculations for the lysozyme-G
Relaxation data in NMR structure determination: model calculations for the lysozyme-Gd3+ complex.
Related Articles Relaxation data in NMR structure determination: model calculations for the lysozyme-Gd3+ complex.
Proteins. 1991;10(2):117-29
Authors: Sutcliffe MJ, Dobson CM
The effect of including paramagnetic relaxation data as additional restraints in the determination of protein tertiary structures from NMR data has been explored by a systematic series of model calculations. The system used for testing the method was the 2.0 A resolution...
nmrlearner
Journal club
0
08-21-2010 11:16 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...
An easy way to include weak alignment constraints into NMR structure calculations.
Linear Mode
