Computation of the structure-dependent pKa shifts in a polypentapeptide of the poly[fv(IPGVG),fe(IPGEG)] family
Article Abstract:
A theoretical study was undertaken to explain the pKa shifts of charged glutamic acid groups related to the changes of composition in polypentapeptides (PPP) of the family poly[fv(IPGVG),fE(IPGEGE)] using a multigrid boundary element method in combination with conformational sampling techniques. It has been suggested that this family of PPPs uses a folded beta-spiral conformation with approximately three parameters per turn. Results revealed that the hydrophobicity of the Glu and Ile residues influenced the large pKa shift related to the conformation.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 1998
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Constant-pH molecular dynamics with ionic strength effects: Protonation-conformation coupling in decalysine
Article Abstract:
A new implementation of the stochastic method for constant-pH molecular dynamics which introduces ionic strength effects in the simulations is presented. The new method is applied to a decalysine peptide and the results show a shift of the protonation and helix-coil transition curves toward lower pH which reveal significant dependence on ionic strength.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2006
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Effects of solute-solvent proton exchange on polypeptide chain dynamics: A constant-pH molecular dynamics study
Article Abstract:
Implicit-solvent molecular dynamics simulations at constant pH are applied to a pentapeptide acetyl-Ala-Asp-Ala-Lys-Ala-amide at pH 4. Results show that the relaxation time for the transitions, derived from the constant-pH simulations, is very close to the relaxation time characterizing a permanently protonated molecule.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2005
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