A Poisson-Boltzmann study of charge insertion in an enzyme active site: the effect of dielectric relaxation

Article Abstract:

The charge insertion in the active site of the enzyme aspartyl-tRNA synthetase (AspRS) was analyzed using finite-difference Poisson-Boltzmann calculations to study the effect of dielectric relaxation. Results revealed a moderate protein polarizability in the AspRS that corresponds to a protein dielectric constant of about 4-8. This polarizability lowers the activation of free energies for charge-transfer processes in the active site.

Enzymes, Transfer RNA, Charge transfer, Ligases, Dielectric relaxation

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A residue-pairwise generalized born scheme suitable for protein design calculations

Article Abstract:

An efficient generalized born (GB) approximation for proteins in which the interaction energy between two amino acids depend on the whole protein structure, but can be calculated from residue pairwise information, is described. As the residue GB is pairwise, it is highly suitable for protein design calculations that search for amino acid sequences stabilizing a particular backbone fold or a particular protein-ligand complex.

Proteins, Ligands (Biochemistry), Protein structure, Protein research

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Electrostatic free energy calculations for macromolecules: a hybrid molecular dynamics/continuum electrostatics approach

Article Abstract:

A hybrid molecular dynamics/continuum electrostatics method is proposed for free energy calculations that involve the creation or deletion of net charges in a solvated macromolecule. The method is used to calculate the free energy to mutate a negatively charged aspartate ligand into a neutral asparagine in the active site of aspartyl-tRNA.

Methods, Molecular computing, Nanotechnology, Electrostatics

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