Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein–molecule interaction energy
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- 15 August 2003
- journal article
- conference paper
- Published by AIP Publishing in The Journal of Chemical Physics
- Vol. 119 (7) , 3599-3605
- https://doi.org/10.1063/1.1591727
Abstract
A scheme to calculate fully quantum mechanical (ab initio) interaction energy involving a macromolecule like protein is presented. In this scheme, the protein is decomposed into individual amino acid-based fragments that are treated with proper molecular caps. The interaction energy between any molecule and the given protein is given by the summation of interactions between the molecule and individually capped protein fragments. This scheme, termed molecular fractionation with conjugate caps (MFCC), makes it possible and practical to carry out full quantum mechanical (ab initio) calculation of intermolecular interaction energies involving proteins or other similar biological molecules. Numerical tests performed on the interaction energies between a water molecule and three small peptides demonstrate that the MFCC method can give excellent ab initio interaction energies compared to the exact treatment in which the whole peptides are included in the calculation. The current scheme scales linearly with the atomic size of the protein and can be directly applied to calculating real protein–molecule interaction energies by using fully quantum (ab initio) methods that are otherwise impossible. The success of the current method is expected to have a powerful impact in our prediction of protein interaction energies including, e.g., protein–drug interactions.Keywords
This publication has 42 references indexed in Scilit:
- AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of moleculesComputer Physics Communications, 1995
- Calculation of solvation free energies using a density functional/molecular dynamics coupled potentialThe Journal of Physical Chemistry, 1993
- A Priori Evaluation of Aqueous Polarization Effects through Monte Carlo QM-MM SimulationsScience, 1992
- A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulationsJournal of Computational Chemistry, 1990
- A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl− exchange reaction and gas phase protonation of polyethersJournal of Computational Chemistry, 1986
- Molecular dynamics with coupling to an external bathThe Journal of Chemical Physics, 1984
- CHARMM: A program for macromolecular energy, minimization, and dynamics calculationsJournal of Computational Chemistry, 1983
- Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acidsThe Journal of Physical Chemistry, 1983
- Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozymeJournal of Molecular Biology, 1976
- Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystalsJournal of the American Chemical Society, 1974