New advance in computational chemistry: Full quantum mechanical ab initio computation of streptavidin - Biotin interaction energy

Da W. Zhang, Yun Xiang, John Zhang

Research output: Contribution to journalArticle

Abstract

Benchmark full quantum mechanical Hartree-Fock calculation has been carried out to compute interaction energies for the streptavidin-biotin binding complex. In this report, the entire streptavidin-biotin interaction system with a total of 1775 atoms is treated by quantum mechanics. The full quantum energy calculation for this protein system is made possible by applying a recently developed MFCC approach in which the protein molecule is decomposed into amino-acid-based fragments that are properly capped. Ab initio calculations are performed at the Hartree-Fock level with a 3-21G basis set. The energies are computed for geometries of the binding complex near two configurations, corresponding to the crystal structure of the binding complex and a minimum energy geometry found from molecular force field, respectively. Comparisons are made of the computed ab initio energies with those from a force field. The present calculation shows that ab initio binding energies (at HF/3-21G level) are almost 30 kcal/mol larger than those given by a force field.

Original languageEnglish (US)
Pages (from-to)12039-12041
Number of pages3
JournalJournal of Physical Chemistry B
Volume107
Issue number44
StatePublished - Nov 6 2003

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Computational chemistry
computational chemistry
biotin
Streptavidin
Biotin
field theory (physics)
interactions
Proteins
Geometry
energy
Quantum theory
proteins
Binding energy
Amino acids
geometry
Crystal structure
amino acids
quantum mechanics
Amino Acids
Atoms

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

New advance in computational chemistry : Full quantum mechanical ab initio computation of streptavidin - Biotin interaction energy. / Zhang, Da W.; Xiang, Yun; Zhang, John.

In: Journal of Physical Chemistry B, Vol. 107, No. 44, 06.11.2003, p. 12039-12041.

Research output: Contribution to journalArticle

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