Available online 18 March 2013
Publication year: 2013 Source:Journal of Molecular Structure
NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from experimental structural data gathered from entries in the Protein Data Bank (PDB) as well as isotropic chemical shift values from the RefDB database. Rigorous statistical analysis of the maps led to the conclusion that specific correlations between triplets of backbone chemical shifts are best able to differentiate between different secondary structures such as ?-helices, ?-strands and turns. The method is compared with similar techniques that use NMR chemical shift information as aids in biomolecular structure determination and performs well in tests done on experimental data determined for different types of proteins, including large multi-domain proteins and membrane proteins.
Solid state NMR of proteins at high MAS frequencies: symmetry-based mixing and simultaneous acquisition of chemical shift correlation spectra
Solid state NMR of proteins at high MAS frequencies: symmetry-based mixing and simultaneous acquisition of chemical shift correlation spectra
Abstract We have carried out chemical shift correlation experiments with symmetry-based mixing sequences at high MAS frequencies and examined different strategies to simultaneously acquire 3D correlation spectra that are commonly required in the structural studies of proteins. The potential of numerically optimised symmetry-based mixing sequences and the simultaneous recording of chemical shift correlation spectra such as: 3D NCAC and 3D NHH...
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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
Chemical shift correlation at high MAS frequencies employing low-power symmetry-based mixing schemes
Chemical shift correlation at high MAS frequencies employing low-power symmetry-based mixing schemes
Abstract An approach for conveniently implementing low-power CN n ν and RN n ν symmetry-based band-selective mixing sequences for generating homo- and heteronuclear chemical shift correlation NMR spectra of low γ nuclei in biological solids is demonstrated. Efficient magnetisation transfer characteristics are achieved by selecting appropriate symmetries requiring the application of basic RF elements of relatively long duration and numerically tailoring the RF field modulation profile...
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06-20-2011 03:31 PM
31P NMR correlation maps of 18O/16O chemical shift isotopic effects for phosphometabolite labeling studies
31P NMR correlation maps of 18O/16O chemical shift isotopic effects for phosphometabolite labeling studies
Abstract Intramolecular correlations among the 18O-labels of metabolic oligophosphates, mapped by J-decoupled 31P NMR 2D chemical shift correlation spectroscopy, impart stringent constraints to the 18O-isotope distributions over the whole oligophosphate moiety. The multiple deduced correlations of isotopic labels enable determination of site-specific fractional isotope enrichments and unravel the isotopologue statistics. This approach ensures accurate determination of 18O-labeling...
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06-06-2011 12:53 AM
Protein secondary structure prediction using NMR chemical shift data.
Protein secondary structure prediction using NMR chemical shift data.
Related Articles Protein secondary structure prediction using NMR chemical shift data.
J Bioinform Comput Biol. 2010 Oct;8(5):867-84
Authors: Zhao Y, Alipanahi B, Li SC, Li M
Accurate determination of protein secondary structure from the chemical shift information is a key step for NMR tertiary structure determination. Relatively few work has been done on this subject. There needs to be a systematic investigation of algorithms that are (a) robust for large datasets; (b)...
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10-29-2010 07:05 PM
[NMR paper] 1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary struct
1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary structure of glutamine-binding protein of Escherichia coli.
Related Articles 1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary structure of glutamine-binding protein of Escherichia coli.
J Biomol NMR. 1997 Feb;9(2):167-80
Authors: Yu J, Simplaceanu V, Tjandra NL, Cottam PF, Lukin JA, Ho C
1H, 13C, and 15N NMR assignments of the backbone atoms and beta-carbons have been made for liganded glutamine-binding protein (GlnBP) of Escherichia...
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08-22-2010 03:31 PM
[NMR paper] 1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary struct
1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary structure of glutamine-binding protein of Escherichia coli.
Related Articles 1H, 13C, and 15N NMR backbone assignments and chemical-shift-derived secondary structure of glutamine-binding protein of Escherichia coli.
J Biomol NMR. 1997 Feb;9(2):167-80
Authors: Yu J, Simplaceanu V, Tjandra NL, Cottam PF, Lukin JA, Ho C
1H, 13C, and 15N NMR assignments of the backbone atoms and beta-carbons have been made for liganded glutamine-binding protein (GlnBP) of Escherichia...
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08-22-2010 03:03 PM
Four-dimensional heteronuclear correlation experiments for chemical shift assignment of solid proteins
Four-dimensional heteronuclear correlation experiments for chemical shift assignment of solid proteins
W. Trent Franks, Kathryn D. Kloepper, Benjamin J. Wylie and Chad M. Rienstra
Journal of Biomolecular NMR; 2007; 39(2); pp 107 - 131
Abstract:
Chemical shift assignment is the first step in all established protocols for structure determination of uniformly labeled proteins by NMR. The explosive growth in recent years of magic-angle spinning (MAS) solid-state NMR (SSNMR) applications is largely attributable to improved methods for backbone and side-chain chemical shift correlation...
Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps
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