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Kernel energy method applied to vesicular stomatitis virus nucleoprotein.

Lulu Huang1, Lou Massa, Jerome Karle

  • 1Naval Research Laboratory, 4555 Overlook Avenue, S.W., Washington, DC 20375, USA.

Proceedings of the National Academy of Sciences of the United States of America
|February 4, 2009
PubMed
Summary

The kernel energy method (KEM) was used to calculate the energy of vesicular stomatitis virus (VSV) nucleoprotein. This computational approach simplifies complex molecular energy calculations, revealing significant interchain hydrogen bond contributions.

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Vesicular stomatitis virus (VSV) nucleoprotein is a key viral component.
  • Accurate calculation of large biomolecular energies is computationally intensive.
  • The Kernel Energy Method (KEM) offers a potential solution for simplifying these calculations.

Purpose of the Study:

  • To apply the Kernel Energy Method (KEM) for calculating the ab initio energy of the VSV nucleoprotein.
  • To analyze the contribution of interchain hydrogen bonds to the total molecular energy.
  • To evaluate the impact of correlation energy on hydrogen bond interactions.

Main Methods:

  • Utilized atomic coordinates from the 2.8-Å crystal structure of VSV nucleoprotein (PDB ID: 2QVJ).
  • Modeled hydrogen atom positions using the HYPERCHEM software.

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  • Performed KEM calculations using Hartree-Fock (HF) and Møller-Plesset perturbation theory to second order (MP2) with 6-31G** basis orbitals.

    • Main Results:

    • Successfully calculated the KEM ab initio limited basis Hartree-Fock energy for the 33,175-atom VSV nucleoprotein molecule.
    • Determined the energy of each of the five similar chains within the VSV nucleoprotein.
    • Quantified interchain hydrogen bond energies, showing that correlation energy (MP2) is a significant factor.

    Conclusions:

    • The Kernel Energy Method (KEM) effectively simplifies energy calculations for large biomolecules like VSV nucleoprotein.
    • Interchain hydrogen bonds play a crucial role in the overall stability and energy of the VSV nucleoprotein structure.
    • MP2 calculations highlight the importance of electron correlation in accurately describing these interchain interactions.