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Very fast prediction and rationalization of pKa values for protein–ligand complexes
- Delphine Bas, D. Rogers, Jan H. Jensen
- Biology, ChemistryProteins: Structure, Function, and Bioinformatics
- 15 November 2008
The results suggest that PROPKA 2.0 provides a good description of the protein–ligand interactions that have an important effect on the pKa values of titratable groups, thereby permitting fast and accurate determination of the protonation states of key residues and ligand functional groups within the binding or active site of a protein.
The glutaminase activity of L-asparaginase is not required for anticancer activity against ASNS-negative cells.
It is shown that L-Asparaginase's glutaminase activity is not always required for the enzyme's anticancer effect, suggesting the hypothesis that glutaminases-negative variants of L-ASP would provide larger therapeutic indices than wild-type L-asP for ASNS-negative cancers.
Quantifying signal changes in nano-wire based biosensors.
The method has the potential for even more quantitative predictions when key experimental parameters (such as the charge carrier density of the nano-wire or receptor density on the device surface) can be determined (and reported) more accurately.
First-principles calculations of protein circular dichroism in the near ultraviolet.
Protein CD calculations from first principles coupled with atomic-level modeling enhance the utility and interpretability of CD measurements in the near UV.
Quasichemical and structural analysis of polarizable anion hydration.
Quasichemical theory is utilized to analyze the relative roles of solute polarization and size in determining the structure and thermodynamics of bulk anion hydration for the Hofmeister series Cl(-), Br(-), and I(-; and a structural analysis is performed to examine the solvation anisotropy around the anions.
Probing the thermodynamics of competitive ion binding using minimum energy structures.
The resulting picture unifies field-strength, topological control, and phase activation viewpoints into a single theory that explicitly indicates the important role of solute coordination state on overall reaction energetics.
How focussing on hydrogen bonding interactions in amino acids can miss the bigger picture: a high-pressure neutron powder diffraction study of ε-glycine
The crystal structures of amino acids, which are composed of molecules in their zwitterionic tautomers, are usually interpreted in terms of strong NH⋯O hydrogen bond formation between the ammonium…
Modeling molecular and ionic absolute solvation free energies with quasichemical theory bounds.
A Bayesian estimation approach is developed to compute the inner-shell chemical and outer-shell packing contributions and should prove useful in computing solvation free energies in inhomogeneous, restricted environments.
Spatiotemporal pH dynamics in concentration polarization near ion-selective membranes.
A detailed analysis of the transient pH dynamics for a weak, buffered electrolyte subject to voltage-driven transport through an ion-selective membrane and shows that the present model can capture the experimentally observed pH fronts.