Publication date: Available online 7 March 2015 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
Author(s): Arun.V. Kumar , Rehana F.M. Ali , Yu Cao , V.V. Krishnan
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 necessary to develop new computational methods and tools for protein structural information that is directly related to function. Nuclear magnetic resonance (NMR) provides powerful means to determine three-dimensional structures of proteins in the solution state. However, translation of the NMR spectral parameters to even low-resolution structural information such as protein class requires multiple time consuming steps. In this paper, we present an unorthodox method to predict the protein structural class directly by using the residue’s averaged chemical shifts (ACS) based on machine learning algorithms. Experimental chemical shift information from 1491 proteins obtained from Biological Magnetic Resonance Bank (BMRB) and their respective protein structural classes derived from structural classification of proteins (SCOP) were used to construct a data set with 119 attributes and 5 different classes. Twenty four different classification schemes were evaluated using several performance measures. Overall the residue based ACS values can predict the protein structural classes with 80 % accuracy measured by Matthew Correlation coefficient. Specifically protein classes defined by mixed ?? or small proteins are classified with > 90% correlation. Our results indicate that this NMR-based method can be utilized as a low-resolution tool for protein structural class identification without any prior chemical shift assignments. Graphical abstract
[NMR paper] Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.
Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.
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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...
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[NMR paper] A suite of amino acid residue type classification pulse sequences for (13)C-detected NMR of proteins.
A suite of amino acid residue type classification pulse sequences for (13)C-detected NMR of proteins.
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J Magn Reson. 2013 Jul 11;234C:190-196
Authors: Pantoja-Uceda D, Santoro J
Abstract
A suite of (13)C-detected NMR pulse sequences to edit the correlation peaks of the CACO and CON spectra according to the amino acid residue type is presented. The pulse sequences exploit the topology of the C(?) carbon and led to the...
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[NMR paper] A suite of amino acid residue type classification pulse sequences for 13C-detected NMR of proteins
A suite of amino acid residue type classification pulse sequences for 13C-detected NMR of proteins
Publication date: Available online 10 July 2013
Source:Journal of Magnetic Resonance</br>
Author(s): David Pantoja-Uceda , Jorge Santoro</br>
A suite of 13C-detected NMR pulse sequences to edit the correlation peaks of the CACO and CON spectra according to the amino acid residue type is presented. The pulse sequences exploit the topology of the C? carbon and led to the sorting of the CACO or CON signals into several classes depending on the nature of the generating...
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07-11-2013 12:07 PM
[NMR paper] Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins.
Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins.
J Phys Chem B. 2013 Feb 1;
Authors: Camilloni C, Cavalli A, Vendruscolo M
Abstract
It has been recently...
[NMR paper] Protein structural class identification directly from NMR spectra using averaged chem
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Authors: Mielke SP, Krishnan VV
Knowledge of the three-dimensional structure of proteins is integral to understanding their functions, and a necessity in the era of proteomics. A wide range of computational methods is employed to estimate the secondary, tertiary, and quaternary structures of...
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11-24-2010 09:16 PM
[NMR paper] Application of 1H NMR chemical shifts to measure the quality of protein structures.
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http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Application of 1H NMR chemical shifts to measure the quality of protein structures.
J Mol Biol. 1995 Apr 7;247(4):541-6
Authors: Williamson MP, Kikuchi J, Asakura T
We have developed a program that can calculate proton NMR chemical shifts for proteins, using a set of co-ordinates provided for example from an X-ray or NMR structure. When...
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Mapping of protein structural ensembles by chemical shifts
Abstract Applying the chemical shift prediction programs SHIFTX and SHIFTS to a data base of protein structures with known chemical shifts we show that the averaged chemical shifts predicted from the structural ensembles explain better the experimental data than the lowest energy structures. This is in agreement with the fact that proteins in solution occur in multiple conformational states in fast exchange on the chemical shift time scale. However, in contrast to the real conditions in solution at ambient temperatures, the standard NMR structural calculation methods as well chemical shift...
Application of Data Mining Tools for Classification of Protein Structural Class from Residue Based Averaged NMR Chemical Shifts
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