Effect of the hydrogen bond network in carbonic anhydrase II zinc binding site: a theoretical study

Article Abstract:

The effect of the hydrogen bond network on the zinc binding site of carbonic anhydrase II (CAII) has been investigated from a theoretical perspective through use of the semiempirical AM1 method. The quantum mechanical models, reduced, of wild CAII and several CAII variants were prepared. The direct metal ligand gives up a hydrogen bond to an indirect metal ligand and the first-shell residues improve electrostatic interaction with the zinc cation. The hydrogen bond network can affect the zinc binding affinity, making it more moderate, and can do the same to the zinc-water pKa.

Observations, Enzymes, Metalloenzymes, Hydrogen bonding, Hydrogen bonds, Ligands, Ligands (Chemistry), Enzyme structure-activity relationships, Zinc compounds

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The hydrolysis of RNA: from theoretical calculations to the hammerhead ribozyme-mediated cleavage of RNA

Article Abstract:

A study was conducted to examine reports of theoretical research on RNA hydrolysis and to compare conclusions from theoretical computations with experimental data. RNA hydrolysis is mediated by a nucleophilic attack by the 2'-oxygen wherein the 2'-OH is activated by a base and a proton transfer induces the phosphodiester. The general conclusions drawn from ab initio computations on phosphates and phosphoranes revolve around the lifetime of phosphorane intermediates and dianionic phosphorane intermediates.

RNA, Phosphatases, Hydrolysis

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Coriolis coupling constants and inertial defect of B(sub2)F(sub4) ab initio calculations and the iterative method

Article Abstract:

Two sets of structural parameters, harmonic frequencies and force constants were generated for diboron tetrafluoride using an iterative method and ab initio Hartree-Fock calculations. Both methods produce similar vibrational wave numbers, Coriolis coupling constants and inertial defects.

Measurement, Boron, Boron (Chemical element), Coriolis force

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