scholarly journals Detection of methylation, acetylation and glycosylation of protein residues by monitoring 13C chemical-shift changes

2016 ◽  
Author(s):  
Pablo G. Garay ◽  
Osvaldo A. Martin ◽  
Harold A. Scheraga ◽  
Jorge A. Vila
Keyword(s):  
Chemical Shift ◽  
Chemical Shifts ◽  
Biological Processes ◽  
Proof Of Concept ◽  
Post Translational Modifications ◽  
13C Chemical Shifts ◽  
Protein Residues ◽  
Lysine Residues ◽  
13C Chemical Shift ◽  
Good Agreement

Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. Their detection by experimental methods is not free of limitations such as the amount of sample needed or the use of destructive procedures to obtain the sample. Certainly, new approaches are needed and, therefore, we explore here, as a proof-of-concept, the feasibility of using 13C chemical shifts of different nuclei to detect methylation, acetylation and glycosylation of protein residues by monitoring the deviation of the 13C chemical shifts from the expected (mean) experimental value of the non-modified residue. As a validation test of this approach, we compare our theoretical computations of the 13Ce chemical-shift values against experimental data, obtained from NMR spectroscopy, for methylated and acetylated lysine residues with good agreement within ~1 ppm. Then, further use of this approach to select the most suitable 13C-nucleus, with which to determine other modifications commonly seen, such as methylation of arginine and glycosylation of serine, asparagine and threonine, shows encouraging results.

scholarly journals Detection of methylation, acetylation and glycosylation of protein residues by monitoring 13C chemical-shift changes

2016 ◽  
Author(s):  
Pablo G. Garay ◽  
Osvaldo A. Martin ◽  
Harold A. Scheraga ◽  
Jorge A. Vila
Keyword(s):  
Chemical Shift ◽  
Chemical Shifts ◽  
Biological Processes ◽  
Proof Of Concept ◽  
Post Translational Modifications ◽  
13C Chemical Shifts ◽  
Protein Residues ◽  
Lysine Residues ◽  
13C Chemical Shift ◽  
Good Agreement

Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. Their detection by experimental methods is not free of limitations such as the amount of sample needed or the use of destructive procedures to obtain the sample. Certainly, new approaches are needed and, therefore, we explore here, as a proof-of-concept, the feasibility of using 13C chemical shifts of different nuclei to detect methylation, acetylation and glycosylation of protein residues by monitoring the deviation of the 13C chemical shifts from the expected (mean) experimental value of the non-modified residue. As a validation test of this approach, we compare our theoretical computations of the 13Ce chemical-shift values against experimental data, obtained from NMR spectroscopy, for methylated and acetylated lysine residues with good agreement within ~1 ppm. Then, further use of this approach to select the most suitable 13C-nucleus, with which to determine other modifications commonly seen, such as methylation of arginine and glycosylation of serine, asparagine and threonine, shows encouraging results.

scholarly journals Detection of methylation, acetylation and glycosylation of protein residues by monitoring13C chemical-shift changes: A quantum-chemical study

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2253 ◽  
Author(s):  
Pablo G. Garay ◽  
Osvaldo A. Martin ◽  
Harold A. Scheraga ◽  
Jorge A. Vila
Keyword(s):  
Chemical Shift ◽  
Chemical Shifts ◽  
Quantum Chemical Study ◽  
Chemical Study ◽  
Biological Processes ◽  
Proof Of Concept ◽  
Post Translational Modifications ◽  
Protein Residues ◽  
Lysine Residues ◽  
Good Agreement

Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. Their detection by experimental methods is not free of limitations such as the amount of sample needed or the use of destructive procedures to obtain the sample. Certainly, new approaches are needed and, therefore, we explore here the feasibility of using13C chemical shifts of different nuclei to detect methylation, acetylation and glycosylation of protein residues by monitoring the deviation of the13C chemical shifts from the expected (mean) experimental value of the non-modified residue. As a proof-of-concept, we used13C chemical shifts, computed at the DFT-level of theory, to test this hypothesis. Moreover, as a validation test of this approach, we compare our theoretical computations of the13Cεchemical-shift values against existing experimental data, obtained from NMR spectroscopy, for methylated and acetylated lysine residues with good agreement within ∼1 ppm. Then, further use of this approach to select the most suitable13C-nucleus, with which to determine other modifications commonly seen, such as methylation of arginine and glycosylation of serine, asparagine and threonine, shows encouraging results.

Carbon magnetic resonance studies of some phenyl, furyl and thienyl organometallics. Some comments on carbon-metal scalar coupling

1974 ◽  
Vol 27 (2) ◽  
pp. 417 ◽  
Author(s):  
D Doddrell ◽  
KG Lewis ◽  
CE Mulquiney ◽  
W Adcock ◽  
W Kitching ◽  
...  
Keyword(s):  
Chemical Shift ◽  
Chemical Shifts ◽  
Substituent Effects ◽  
Coupling Constants ◽  
Scalar Coupling ◽  
Coupling Constant ◽  
Aryl Substituent ◽  
Magnetic Resonance Studies ◽  
Thienyl Group ◽  
13C Chemical Shift

13C chemical shift variations within a series of phenyl, furyl and thienyl Group IVB organometallics appear to be best understood in terms of the usual alkyl and aryl substituent effects on 13C chemical shifts and not variations in dπ ?pπ metal-aryl interactions. Large changes in 13C-metal scalar coupling constants have been observed suggesting that other factors besides the s-character of the carbon-metal bond is responsible in determining the coupling constant.

scholarly journals Powder Crystallography by Combining NMR and Crystal Structure Predictions

2014 ◽  
Vol 70 (a1) ◽  
pp. C136-C136 ◽  
Author(s):  
Cory Widdifield ◽  
Maria Baias ◽  
Jean-Nicolas Dumez ◽  
Per H. Svensson ◽  
Hugh Thompson ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Chemical Shift ◽  
Structure Determination ◽  
Structure Prediction ◽  
Density Functional ◽  
De Novo ◽  
Chemical Shifts ◽  
2D Nmr ◽  
Other Information ◽  
13C Chemical Shift

State-of-the-art work in the field of NMR crystallography for molecular systems at natural abundance has recently focused on the accurate measurement of 1H chemical shift values. We will show how when coupled with crystal structure prediction (CSP) methods, this protocol is well-suited for solving the crystal structures of small to medium sized organic molecules, including cocaine and the de-novo structure determination of AZD8329.[1,2] As complementary 1D and 2D NMR experiments are needed for the 1H assignment process, other information, such as isotropic 13C chemical shift values (δiso) are measured. Unfortunately, 13C chemical shifts are not generally useful for structure determination. Additional NMR parameters that are sensitive to structure would ensure that the structure determination procedure is robust, and would provide more accurate refinements when studying larger or more challenging systems. Here, we measure 13C chemical shift tensors for a variety of prototypical organic pharmaceuticals and use density functional theory computations under the gauge-including projector augmented-wave (GIPAW) formalism to probe whether these parameters may be discriminatory for unit cell determinations and structure determination (notably when added to the CSP + 1H chemical shifts protocol).

CORE LEVEL CHEMICAL SHIFTS AND LINE SHAPES FOR SYSTEMS WITH DIFFERENT VALENCIES AND Cu-O NETWORKS

2000 ◽  
Vol 14 (32) ◽  
pp. 3791-3830 ◽  
Author(s):  
K. KARLSSON ◽  
O. GUNNARSSON ◽  
O. JEPSEN
Keyword(s):  
Chemical Shift ◽  
Chemical Shifts ◽  
Core Level ◽  
Photoemission Spectrum ◽  
Main Peak ◽  
Model Compounds ◽  
Line Shapes ◽  
Impurity Model ◽  
Anderson Impurity Model ◽  
Good Agreement

We have studied the Cu -2p core level photoemission spectrum of a variety of cuprates, mainly focusing on the chemical shift and the shape of the leading peak. The spectra are calculated using the Anderson impurity model and we obtain a very good agreement with the experimental data. We find that the shape of the leading peak depends crucially on the structure of the Cu - O network. The main peak turns out to be quite narrow if the network consists of Cu - O - Cu bond angels of the order of 90°. On the other hand, if the Cu - O atoms are arranged with bond angles of approximately 180°, the main peak becomes substantially broader and contains a rather complicated structure. However, in some cases it is not sufficient only to consider the Cu - O network because interactions with other atoms are also important. In the model compounds Cu 2 O , CuO and NaCuO 2, where Cu is formally monovalent, divalent and trivalent, respectively, we find that the number of 3d electrons is rather similar. Nevertheless, the binding energy increases with the valence as expected from chemical intuition. The spectra exhibit a large variation in the strength of the d9-like satellite and in the width of the main line. We, furthermore, study the chemical shift of three inequivalent Cu atoms in YBa 2 Cu 3 O 6.5, and compare the results with the model compounds, which suggests that the different Cu atoms in YBa 2 Cu 3 O 6.5 have formal valences of approximately one, two and three. These findings are analyzed and related to the formal valence.

SUBSTITUTIONAL AND CONFIGURATIONAL EFFECTS ON CHEMICAL SHIFT IN PYRANOID CARBOHYDRATE DERIVATIVES

1965 ◽  
Vol 43 (7) ◽  
pp. 2059-2070 ◽  
Author(s):  
R. U. Lemieux ◽  
J. D. Stevens
Keyword(s):  
Chemical Shift ◽  
Long Range ◽  
Chemical Shifts ◽  
Coupling Constants ◽  
Equatorial Orientation ◽  
Free Energies ◽  
Bonding Interaction ◽  
Conformational Properties ◽  
Good Agreement ◽  
Shielding Effects

The effects of long-range and virtual long-range coupling on the observed spectra of acetylated hexopyranoses and pentopyranoses are examined. Use is made of both spin decoupling and specific deuteration for the assignment of signals. It is seen that specific solvent effects on chemical shift can be superior to increasing the applied magnetic field for the resolution of the signals of closely related protons. The alteration of virtual long-range coupling effects in these ways can be useful in the diagnosis of spectra. Empirical rules are derived for estimating the long-range shielding effects which occur on changing configurations. It is seen that the inversion of a center can lead to deshielding of axial protons and to shielding of equatorial protons at other centers relative to the chemical shifts observed in reference compounds wherein all the acetoxy groups are in equatorial orientation. The effects in several cases result in equatorial protons giving their signal to higher field than chemically similar but axial protons. The conformational properties of pentopyranose tetraacetates as estimated from chemical shifts and coupling constants are seen to be in good agreement with expectations based on non-bonding interaction free energies. As expected, 2-deoxy-β-D-ribopyranose triacetate has the 1C-conformation when dissolved in chloroform.

13C Nuclear Magnetic Resonance of Oximes. I. Solvent and Isotope Effects on the 13C Chemical Shifts of Acetoxime

1972 ◽  
Vol 50 (12) ◽  
pp. 1956-1958 ◽  
Author(s):  
N. Gurudata
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Chemical Shift ◽  
Solvent Effects ◽  
Chemical Shifts ◽  
Isotope Effects ◽  
Solvent Interactions ◽  
13C Chemical Shifts ◽  
13C Nuclear Magnetic Resonance ◽  
Nuclear Magnetic

The 13C n.m.r. spectrum of acetoxime has been obtained in five representative solvents and the chemical shifts of the three carbon atoms measured. The solvent effects on the chemical shifts are found to reflect specific solute–solvent interactions. The effect of deuteration of the α-protons on the chemical shift of the oximino carbon is also discussed.

Origin and Nature of Transmission Modes of Anomalous Effects of meta-Substituents on the 13C Chemical Shift of the Carboxyl Carbon (δCO) of Benzoic Acid

2010 ◽  
Vol 63 (2) ◽  
pp. 321 ◽  
Author(s):  
Susanta K. Sen Gupta ◽  
Rajendra Prasad
Keyword(s):  
Chemical Shift ◽  
Benzoic Acid ◽  
Chemical Shifts ◽  
Substituent Effects ◽  
Basis Set ◽  
Benzoic Acids ◽  
Anomalous Effect ◽  
Atomic Orbitals ◽  
13C Chemical Shift ◽  
Carboxyl Carbon

Studies of substituent effects on NMR chemical shifts are of great benefit in determining fine details of electron distribution in molecules. Interestingly, NMR substituent effects are often different and even opposite to those associated with chemical reactivity. Among molecules exhibiting anomalous (reverse) substituent effects is benzoic acid, the standard model for studying substituent effects. The substituent effect on the 13C chemical shift of its carboxyl carbon (δ CO) is just the opposite of that on its acid strength or reactivity. To develop insights into the origin of the anomalous effect of a substituent on δ CO, occupancies of natural atomic orbitals at the carboxyl and ring carbons of a set of 10 meta-substituted benzoic acids have been calculated at the density functional theory level using the B3LYP function with split valance 6–311G++** basis set. Statistical correlations obtained for the 13C chemical shifts, δ CO and δ C-ring of these benzoic acids with the natural atomic orbital occupancies calculated for respective carbon atoms on one hand and with Taft’s inductive and resonance parameters (σ I and σ R BA ) of the substituents on the other hand have been critically analyzed. The findings have established firmly that a meta-substituent’s anomalous effect on δ CO is caused by the substituent-induced changes in the total occupancy of only the p z natural atomic orbitals at the carboxyl carbon. The study has demonstrated further that the transmission of the anomalous effect can be successfully interpreted by a 5.5:–2.5:1 combination of the localized, extended, and resonance-induced π-polarization effects.

Sign in / Sign up

Export Citation Format

Share Document