Electron density redistribution accounts for half the cooperativity of alpha helix formation

Article Abstract:

The short- and long-range contributions to helix cooperativity are separated by studying the dimerization energy of a short probe helix with another helix of variable length. Density functional theory (DFT) calculations have shown that approximately half of the cooperativity of helix formation is because of electrostatic interactions between residues, while the other half is due to nonadditive many-body effects brought about by redistribution of electron density with helix length.

Hydrogen bonding, Hydrogen bonds, Density functionals, Density functional theory, Electron configuration, Structure

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Comparison of quantum mechanics and molecular mechanics dimerization energy landscapes for pairs of ring-containing amino acids in proteins

Article Abstract:

A promising approach to developing improved potential functions for modeling macromolecular interactions consists of combining protein structural analysis, quantum mechanical calculations on small molecule models, and molecular mechanics potential decomposition. This approach to the interactions of pairs of ring-containing amino acids in proteins is applied.

Science & research, Research, Quantum theory, Quantum mechanics, Proteins, Macromolecules, Amino acids

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Evaluation of models of electrostatic interactions in proteins

Article Abstract:

Evaluation of alternative models of electrostatic interactions in proteins is explained. The total electrostatic free energy is computed using the Poisson-Boltzmann equation.

Protein synthesis, Protein biosynthesis, Photosynthesis, Poisson's equation

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