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.

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.

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.

SUMO: getting it on

2007 ◽  
Vol 35 (6) ◽  
pp. 1409-1413 ◽  
Author(s):  
J. Anckar ◽  
L. Sistonen
Keyword(s):  
Biological Processes ◽  
Amino Acid Residues ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Sumo Conjugation ◽  
Lysine Residues ◽  
Ubiquitin Conjugating Enzyme ◽  
Specificity Determinants ◽  
Conjugating Enzyme

Post-translational modification of cellular proteins by the SUMO (small ubiquitin-related modifier) is involved in numerous modes of regulation in widely different biological processes. In contrast with ubiquitination, SUMO conjugation is highly specific in terms of target lysine residues, but many aspects of substrate and lysine selection by the SUMO conjugating machinery are still poorly understood. SUMOylation events usually occur on the ΨKXE SUMO consensus motifs, which mediate binding to Ubc9 (ubiquitin-conjugating enzyme 9), the SUMO E2 conjugating enzyme. Although most, if not all, SUMO conjugations are catalysed by Ubc9, far from all ΨKXE tetrapeptides are modified, demonstrating a need for additional specificity determinants in SUMOylation. Recent results intimately link regulation of SUMOylation to other post-translational modifications, including phosphorylation and acetylation and reveal that certain lysine residues are marked for SUMOylation by negatively charged amino acid residues or phosphorylation events immediately downstream of the consensus site. In the present review, we explore the intriguing role of extended motifs in the regulation of SUMO conjugation.

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