Related ArticlesPrediction of (19)F NMR Chemical Shifts in Labeled Proteins: Computational Protocol and Case Study.
Mol Pharm. 2016 May 24;
Authors: Isley Iii WC, Urick AK, Pomerantz WC, Cramer CJ
Abstract
The structural analysis of ligand complexation in biomolecular systems is important in the design of new medicinal therapeutic agents; however, monitoring subtle structural changes in a protein's microenvironment is a challenging and complex problem. In this regard, the use of protein-based (19)F NMR for screening low molecular weight molecules (i.e., fragments) can be an especially powerful tool to aid in drug design. NMR resonance assignment of the protein's (19)F NMR spectrum is necessary for structural analysis. Here, a quantum chemical method has been developed as an initial approach to facilitate the assignment of a fluorinated protein's (19)F NMR spectrum. The epigenetic "reader" domain of protein Brd4 was taken as a case study to assess the strengths and limitations of the method. The overall modeling protocol predicts chemical shifts for residues in rigid proteins with good accuracy; proper accounting for explicit solvation of fluorinated residues by water is critical.
PMID: 27218275 [PubMed - as supplied by publisher]
Equilibrium simulations with NMR chemical shifts [Biophysics and Computational Biology]
Equilibrium simulations with NMR chemical shifts
Boomsma, W., Tian, P., Frellsen, J., Ferkinghoff-Borg, J., Hamelryck, T., Lindorff-Larsen, K., Vendruscolo, M....
Date: 2014-09-23
Methods of protein structure determination based on NMR chemical shifts are becoming increasingly common. The most widely used approaches adopt the molecular fragment replacement strategy, in which structural fragments are repeatedly reassembled into different complete conformations in molecular simulations. Although these approaches are effective in generating individual structures consistent with... Read...
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09-24-2014 06:03 AM
Type I and II β-turns prediction using NMR chemical shifts
Type I and II β-turns prediction using NMR chemical shifts
Abstract
A method for predicting type I and II β-turns using nuclear magnetic resonance (NMR) chemical shifts is proposed. Isolated β-turn chemical-shift data were collected from 1,798 protein chains. One-dimensional statistical analyses on chemical-shift data of three classes β-turn (type I, II, and VIII) showed different distributions at four positions, (i) to (iÂ*+Â*3). Considering the central two residues of type I β-turns, the mean values of Cο, Cα, HN, and NH chemical shifts...
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06-19-2014 10:21 PM
[NMR paper] Type I and II ?-turns prediction using NMR chemical shifts.
Type I and II ?-turns prediction using NMR chemical shifts.
Related Articles Type I and II ?-turns prediction using NMR chemical shifts.
J Biomol NMR. 2014 May 17;
Authors: Wang CC, Lai WC, Chuang WJ
Abstract
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05-20-2014 11:10 PM
[NMR paper] NMRDSP: An Accurate Prediction of Protein Shape Strings from NMR Chemical Shifts and Sequence Data.
NMRDSP: An Accurate Prediction of Protein Shape Strings from NMR Chemical Shifts and Sequence Data.
Related Articles NMRDSP: An Accurate Prediction of Protein Shape Strings from NMR Chemical Shifts and Sequence Data.
PLoS One. 2013;8(12):e83532
Authors: Mao W, Cong P, Wang Z, Lu L, Zhu Z, Li T
Abstract
Shape string is structural sequence and is an extremely important structure representation of protein backbone conformations. Nuclear magnetic resonance chemical shifts give a strong correlation with the local protein structure, and are...
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01-01-2014 03:05 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...
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07-15-2011 09:10 PM
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...
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01-09-2011 12:46 PM
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...
Prediction of (19)F NMR Chemical Shifts in Labeled Proteins: Computational Protocol and Case Study.
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