These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


Pubmed for Handhelds

PUBMED FOR HANDHELDS

Search MEDLINE/PubMed

  • Title: The determinants of carboxyl pKa values in turkey ovomucoid third domain.
    Author: Li H, Robertson AD, Jensen JH.
    Journal: Proteins; 2004 May 15; 55(3):689-704. PubMed ID: 15103631.
    Abstract:
    A computational methodology for protein pK(a) predictions, based on ab initio quantum mechanical treatment of part of the protein and linear Poisson-Boltzmann equation treatment of the bulk solvent, is presented. The method is used to predict and interpret the pK(a) values of the five carboxyl residues (Asp7, Glu10, Glu19, Asp27, and Glu43) in the serine protease inhibitor turkey ovomucoid third domain. All the predicted pK(a) values are within 0.5 pH units of experiment, with a root-mean-square deviation of 0.31 pH units. We show that the decreased pK(a) values observed for some of the residues are primarily due to hydrogen bonds to the carboxyl oxygens. Hydrogen bonds involving amide protons are shown to be particularly important, and the effect of hydrogen bonding is shown to be nonadditive. Hydrophobic effects are also shown to be important in raising the pK(a). Interactions with charged residues are shown to have relatively little effect on the carboxyl pK(a) values in this protein, in general agreement with experiment.
    [Abstract] [Full Text] [Related] [New Search]