Conformational preferences and pKa value of selenocysteine residue

@article{Byun2011ConformationalPA,
  title={Conformational preferences and pKa value of selenocysteine residue},
  author={Byung Jin Byun and Young Kee Kang},
  journal={Biopolymers},
  year={2011},
  volume={95}
}
The conformational preferences of the L‐selenocysteine (Sec) dipeptides with selenol and selenolate groups (Ac‐Sec‐NHMe and Ac‐Sec−‐NHMe, respectively) and the apparent (i.e., macroscopic) pKa value of the Sec residue have been studied using the dispersion‐corrected density functionals M06‐2X and B2PLYP‐D with the implicit solvation method in the gas phase and in water. In the gas phase, the backbone‐to‐backbone and/or side chain‐to‐backbone hydrogen bonds are found to contribute in stabilizing… Expand
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References

SHOWING 1-10 OF 36 REFERENCES
Conformational preferences and pKa value of cysteine residue.
TLDR
The interactions between the thiolate group and the backbone amide groups appear to play a role in stabilizing the alpha- or 3 10-helical conformations for the Cys (-) dipeptide in the gas phase and in water. Expand
Conformational preferences of non-prolyl and prolyl residues.
  • Y. Kang
  • Chemistry, Medicine
  • The journal of physical chemistry. B
  • 2006
TLDR
The cis-trans isomerization for the non-prolyl and prolyl peptide bonds is proven to be entirely enthalpy driven in the gas phase and in the solutions. Expand
Selenocysteine derivatives I. Sidechain conformational potential energy surface of N-acetyl-l-selenocysteine-N-methylamide (MeCO-l-Sec-NH-Me) in its βl backbone conformation
Abstract Selenocysteine is expected to have 92=81 conformations [in the backbone: ψ(g+,a,g−)×φ(g+,a,g−); 32=9 and in the sidechain: χ1(g+,a,g−)×χ2(g+,a,g−); 32=9]. All torsional modes of theExpand
Co2+ binding cysteine and selenocysteine: a DFT study.
TLDR
From the present calculations, a metal-induced thiol deprotonation as observed in gas-phase experiments is explained, and a very small difference in cobalt binding affinity is found, thus justifying the use of this substitution in X-ray absorption experiments done on biomolecules containing cysteine metal binding pockets. Expand
Selenocysteine versus cysteine reactivity: a theoretical study of their oxidation by hydrogen peroxide.
TLDR
It is concluded that the high experimental reaction rate constant reported for the oxidation of the selenocysteine residue in the glutathione peroxidase (GPx) active center is due to an important interaction between selenocytesteine and its molecular environment. Expand
Isosteric replacement of sulfur with other chalcogens in peptides and proteins
  • L. Moroder
  • Chemistry, Medicine
  • Journal of peptide science : an official publication of the European Peptide Society
  • 2005
The review addresses the functional and structural properties of the two series of chalcogen analogues of amino acids in peptides and proteins, the methionine and the serine/cysteine series, andExpand
Understanding selenocysteine through conformational analysis, proton affinities, acidities and bond dissociation energies
Density functional methods have been employed to characterize the gas phase conformations of selenocysteine. The 33 stable conformers of selenocysteine have been located on the potential energyExpand
Gas-phase acidities of cysteine-polyglycine peptides: The effect of the cysteine position
TLDR
Both neutral and deprotonated peptides adopt many possible conformations of similar energies, and the stronger acidities of the former may come from the greater stability of the thiolate anion resulting from the interaction with the helix-macrodipole, in addition to the hydrogen bonding interactions. Expand
Assessment of density functionals with long‐range and/or empirical dispersion corrections for conformational energy calculations of peptides
TLDR
The B2PLYP‐D/6-311++G(d,p)//SMD M06‐2X/6‐31+G( d) level of theory provides the populations of backbone and/or prolyl peptide bond for the alanine and proline dipeptides in water that are consistent with the observed values. Expand
Theoretical Study on the Redox Cycle of Bovine Glutathione Peroxidase GPx1: pKa Calculations, Docking, and Molecular Dynamics Simulations.
TLDR
Three approaches of computational chemistry were used to investigate the redox cycle of bovine erythrocyte glutathione peroxidase from class 1 and new atomistic details for a generally accepted mechanism of GPx1 are proposed. Expand
...
1
2
3
4
...