Related ArticlesQuantum calculation of protein NMR chemical shifts based on the automated fragmentation method.
Adv Exp Med Biol. 2015;827:49-70
Authors: Zhu T, Zhang JZ, He X
Abstract
The performance of quantum mechanical methods on the calculation of protein NMR chemical shifts is reviewed based on the recently developed automatic fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. By using the Poisson-Boltzmann (PB) model and first solvation water molecules, the influence of solvent effect is also discussed. Benefiting from the fragmentation algorithm, the AF-QM/MM approach is computationally efficient, linear-scaling with a low pre-factor, and thus can be applied to routinely calculate the ab initio NMR chemical shifts for proteins of any size. The results calculated using Density Functional Theory (DFT) show that when the solvent effect is included, this method can accurately reproduce the experimental (1)H NMR chemical shifts, while the (13)C NMR chemical shifts are less affected by the solvent. However, although the inclusion of solvent effect shows significant improvement for (15)N chemical shifts, the calculated values still have large deviations from the experimental observations. Our study further demonstrates that AF-QM/MM calculated results accurately reflect the dependence of (13)C? NMR chemical shifts on the secondary structure of proteins, and the calculated (1)H chemical shift can be utilized to discriminate the native structure of proteins from decoys.*
A Simple Method to Measure Protein Side-Chain MobilityUsing NMR Chemical Shifts
A Simple Method to Measure Protein Side-Chain MobilityUsing NMR Chemical Shifts
Mark V. Berjanskii and David S. Wishart
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja407509z/aop/images/medium/ja-2013-07509z_0003.gif
Journal of the American Chemical Society
DOI: 10.1021/ja407509z
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/qRQjRZhXxAM
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09-23-2013 09:41 PM
[NMR paper] A simple method to measure protein side-chain mobility using NMR chemical shifts.
A simple method to measure protein side-chain mobility using NMR chemical shifts.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles A simple method to measure protein side-chain mobility using NMR chemical shifts.
J Am Chem Soc. 2013 Sep 13;
Authors: Berjanskii MV, Wishart DS
Abstract
Protein side-chain motions are involved in many important biological processes including enzymatic catalysis, allosteric regulation, and the mediation of protein-protein,...
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09-17-2013 11:36 PM
[NMR paper] Ab initio NMR chemical-shift calculations based on the combined fragmentation method.
Ab initio NMR chemical-shift calculations based on the combined fragmentation method.
Related Articles Ab initio NMR chemical-shift calculations based on the combined fragmentation method.
Phys Chem Chem Phys. 2013 Apr 12;
Authors: Tan HJ, Bettens RP
Abstract
NMR chemical shift is a molecular property that can be computed from first principles. In this work we show that by utilizing our combined fragmentation method (CFM), one is able to accurately compute this property for small proteins. Without nonbonded interactions, the root mean...
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04-16-2013 07:46 PM
Structure-based prediction of methyl chemical shifts in proteins
Structure-based prediction of methyl chemical shifts in proteins
Abstract Protein methyl groups have recently been the subject of much attention in NMR spectroscopy because of the opportunities that they provide to obtain information about the structure and dynamics of proteins and protein complexes. With the advent of selective labeling schemes, methyl groups are particularly interesting in the context of chemical shift based protein structure determination, an approach that to date has exploited primarily the mapping between protein structures and backbone chemical shifts. In order to...
A new method for the determination of free L: -carnitine in serum samples based on high field single quantum coherence filtering (1)H-NMR spectroscopy.
A new method for the determination of free L: -carnitine in serum samples based on high field single quantum coherence filtering (1)H-NMR spectroscopy.
A new method for the determination of free L: -carnitine in serum samples based on high field single quantum coherence filtering (1)H-NMR spectroscopy.
Anal Bioanal Chem. 2011 Jan 11;
Authors: Tsiafoulis CG, Exarchou V, Tziova PP, Bairaktari E, Gerothanassis IP, Troganis AN
The rapid and accurate determination of specific metabolites present in biofluids is a very demanding task which is essential...
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01-12-2011 11:11 AM
[NMR paper] Automated NMR structure calculation with CYANA.
Automated NMR structure calculation with CYANA.
Related Articles Automated NMR structure calculation with CYANA.
Methods Mol Biol. 2004;278:353-78
Authors: Güntert P
This chapter gives an introduction to automated nuclear magnetic resonance (NMR) structure calculation with the program CYANA. Given a sufficiently complete list of assigned chemical shifts and one or several lists of cross-peak positions and columns from two-, three-, or four-dimensional nuclear Overhauser effect spectroscopy (NOESY) spectra, the assignment of the NOESY...
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11-24-2010 09:25 PM
[NMR paper] Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE).
Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE).
Related Articles Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE).
J Biomol NMR. 2002 Aug;23(4):271-87
Authors: Gronwald W, Moussa S, Elsner R, Jung A, Ganslmeier B, Trenner J, Kremer W, Neidig KP, Kalbitzer HR
Automated assignment of NOESY spectra is a prerequisite for automated structure determination of biological macromolecules. With the program KNOWNOE we present a novel, knowledge based approach to this problem. KNOWNOE...