The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the 1H NMR and 13C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and 1H and 13C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA 1H and 13C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides.
[NMR paper] Application of Data Mining Tools for Classification of Protein Structural Class from Residue Based Averaged NMR Chemical Shifts.
Application of Data Mining Tools for Classification of Protein Structural Class from Residue Based Averaged NMR Chemical Shifts.
Application of Data Mining Tools for Classification of Protein Structural Class from Residue Based Averaged NMR Chemical Shifts.
Biochim Biophys Acta. 2015 Mar 7;
Authors: Kumar AV, Ali RF, Cao Y, Krishnan VV
Abstract
The number of protein sequences deriving from genome sequencing projects is outpacing our knowledge about the function of these proteins. With the gap between experimentally characterized...
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03-12-2015 10:33 AM
Application of Data Mining Tools for Classification of Protein Structural Class from Residue Based Averaged NMR Chemical Shifts
Application of Data Mining Tools for Classification of Protein Structural Class from Residue Based Averaged NMR Chemical Shifts
Publication date: Available online 7 March 2015
Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics</br>
Author(s): Arun.V. Kumar , Rehana F.M. Ali , Yu Cao , V.V. Krishnan</br>
The number of protein sequences deriving from genome sequencing projects is outpacing our knowledge about the function of these proteins. With the gap between experimentally characterized and uncharacterized proteins continuing to widen, it is...
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03-08-2015 01:23 PM
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
Database proton NMR chemical shifts for RNA signal assignment and validation
Database proton NMR chemical shifts for RNA signal assignment and validation
Abstract The Biological Magnetic Resonance Data Bank contains NMR chemical shift depositions for 132 RNAs and RNA-containing complexes. We have analyzed the 1H NMR chemical shifts reported for non-exchangeable protons of residues that reside within A-form helical regions of these RNAs. The analysis focused on the central base pair within a stretch of three adjacent base pairs (BP triplets), and included both Watsonâ??Crick (WC; G:C, A:U) and G:U wobble pairs. Chemical shift values were included for all 43...
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11-29-2012 03:14 AM
Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids
Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids
Abstract Unravelling the complex correlation between chemical shifts of 13 C α, 13 C β, 13 C�, 1 H α, 15 N, 1 H N atoms in amino acids of proteins from NMR experiment and local structural environments of amino acids facilitates the assignment of secondary structures of proteins. This is an important impetus for both determining the three-dimensional structure and understanding the biological function of proteins. The previous...
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11-14-2011 08:45 AM
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
[NMR paper] Unusual 1H NMR chemical shifts support (His) C(epsilon) 1...O==C H-bond: proposal for
Unusual 1H NMR chemical shifts support (His) C(epsilon) 1...O==C H-bond: proposal for reaction-driven ring flip mechanism in serine protease catalysis.
Related Articles Unusual 1H NMR chemical shifts support (His) C(epsilon) 1...O==C H-bond: proposal for reaction-driven ring flip mechanism in serine protease catalysis.
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...
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11-19-2010 08:29 PM
Chemical shifts in carbon atoms 13C?
This is a bit confusing for me, so i would like help with understanding this:Explain the order of the chemical shifts of the carbon atoms in the 13C spectra of cyclohexanone and adipic acid.if ur not sure about cyclohexanone and adipic acid, at least explain to me what the "order of chemical shifts in the carbon atoms in 13C" meansThanx!
Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression
Linear Mode
