Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts
Abstract We present a program, named Promega, to predict the Xaa-Pro peptide bond conformation on the basis of backbone chemical shifts and the amino acid sequence. Using a chemical shift database of proteins of known structure together with the PDB-extracted amino acid preference of cis Xaa-Pro peptide bonds, a cis/trans probability score is calculated from the backbone and 13Cβ chemical shifts of the proline and its neighboring residues. For an arbitrary number of input chemical shifts, which may include Pro-13Cγ, Promega calculates the statistical probability that a Xaa-Pro peptide bond is cis. Besides its potential as a validation tool, Promega is particularly useful for studies of larger proteins where Pro-13Cγ assignments can be challenging, and for on-going efforts to determine protein structures exclusively on the basis of backbone and 13Cβ chemical shifts.
Content Type Journal Article
DOI 10.1007/s10858-009-9395-y
Authors
Yang Shen, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health Laboratory of Chemical Physics Building 5, Room 126 Bethesda MD 20892-0520 USA
Ad Bax, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health Laboratory of Chemical Physics Building 5, Room 126 Bethesda MD 20892-0520 USA
CS23D - generating protein structure from NMR chemical shifts and sequence homology
CS23D website
CS23D is a web server for rapidly generating accurate 3D protein structures using only assigned NMR chemical shifts as input. CS23D uses a combination of maximal subfragment assembly, chemical shift threading, shift-based torsion angle prediction and chemical shift refinement to generate and refine the protein coordinates. CS23D accepts chemical shift files in either SHIFTY or BMRB formats and produces a set of PDB coordinates for the protein normally within 10-15 minutes (3 hours max). CS23D performance is dependent on the completeness of the chemical shift assignments and...
markber
NMR software
0
02-23-2012 09:40 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...
4D prediction of protein 1H chemical shifts
4D prediction of protein 1H chemical shifts
Abstract A 4D approach for protein 1H chemical shift prediction was explored. The 4th dimension is the molecular flexibility, mapped using molecular dynamics simulations. The chemical shifts were predicted with a principal component model based on atom coordinates from a database of 40 protein structures. When compared to the corresponding non-dynamic (3D) model, the 4th dimension improved prediction by 6â??7%. The prediction method achieved RMS errors of 0.29 and 0.50 ppm for Hα and HN shifts, respectively. However, for individual proteins...
nmrlearner
Journal club
0
01-09-2011 12:46 PM
[NMR paper] Sequence-dependent correction of random coil NMR chemical shifts.
Sequence-dependent correction of random coil NMR chemical shifts.
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Authors: Schwarzinger S, Kroon GJ, Foss TR, Chung J, Wright PE, Dyson HJ
Random coil chemical shifts are commonly used to detect secondary structure elements in proteins in chemical shift index calculations. While this technique is very reliable for folded proteins, application to unfolded proteins reveals significant deviations from measured random coil...
nmrlearner
Journal club
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J Biomol NMR. 2000 Oct;18(2):165-71
Authors: Sharma D, Rajarathnam K
The presence of disulfide bonds can be detected unambiguously only by X-ray crystallography, and otherwise must be inferred by chemical methods. In this study we demonstrate that 13C NMR chemical shifts are diagnostic of disulfide bond formation, and can discriminate between cysteine in the reduced (free) and oxidized (disulfide bonded)...
nmrlearner
Journal club
0
11-19-2010 08:29 PM
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Proc Natl Acad Sci U S A. 2000 Sep 12;97(19):10371-6
Authors: Ash EL, Sudmeier JL, Day RM, Vincent M, Torchilin EV, Haddad KC, Bradshaw EM, Sanford DG, Bachovchin WW
13C-selective NMR, combined with inhibitor perturbation...
Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts
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