The Kernel Energy Method: application to a tRNA

Proc Natl Acad Sci U S A. 2006 Jan 31;103(5):1233-7. doi: 10.1073/pnas.0510342103. Epub 2006 Jan 23.

Abstract

The Kernel Energy Method (KEM) may be used to calculate quantum mechanical molecular energy by the use of several model chemistries. Simplification is obtained by mathematically breaking a large molecule into smaller parts, called kernels. The full molecule is reassembled from calculations carried out on the kernels. KEM is as yet untested for RNA, and such a test is the purpose here. The basic kernel for RNA is a nucleotide that in general may differ from those of DNA. RNA is a single strand rather than the double helix of DNA. KEM energy has been calculated for a tRNA, whose crystal structure is known, and which contains 2,565 atoms. The energy is calculated to be E = -108,995.1668 (a.u.), in the Hartree-Fock approximation, using a limited basis. Interaction energies are found to be consistent with the hydrogen-bonding scheme previously found. In this paper, the range of biochemical molecules, susceptible of quantum studies by means of the KEM, have been broadened to include RNA.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Sequence
  • Crystallography, X-Ray
  • Hydrogen Bonding
  • Models, Chemical
  • Models, Molecular
  • Models, Statistical
  • Models, Theoretical
  • Molecular Conformation
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Polymers / chemistry
  • RNA / chemistry
  • RNA, Transfer / chemistry*
  • Saccharomyces cerevisiae / metabolism
  • Software

Substances

  • Polymers
  • RNA
  • RNA, Transfer