Folding of Globular Proteins by Energy Minimization and Monte Carlo Simulations with Hydrophobic Surface Area Potentials

Christian Mumenthaler, Werner Braun

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

We describe an efficient method to calculate analytically the solvent accessible surface areas and their gradients in proteins for empirical force field calculations on serial and parallel computers. In an application to the small three helix bundle protein E r-10, energy minimizations and Monte Carlo simulations were performed with the empirical ECEPP/2 force field, which was extended by a protein solvent interaction term. We show that the NMR structure is stable when refined with the force field including the protein solvent interaction term, but large structural deviations are observed in energy minimization in vacuo. When we started from random structures with preformed helices and maintained the helical segments by dihedral angle constraints, the final structures with the lowest energies resembled the native form. The root-mean-square deviations for the backbone atoms of the three helices compared to the experimentally determined structure was 3 Å to 4 Å.

Original languageEnglish (US)
Pages (from-to)1-10
Number of pages10
JournalJournal of Molecular Modeling
Volume1
Issue number1
DOIs
StatePublished - 1995
Externally publishedYes

Fingerprint

folding
helices
field theory (physics)
proteins
Proteins
optimization
simulation
deviation
parallel computers
energy
Dihedral angle
bundles
dihedral angle
Nuclear magnetic resonance
interactions
Atoms
gradients
nuclear magnetic resonance
Monte Carlo simulation
atoms

Keywords

  • Keywords Protein folding, accesible surface areas, Monte Carlo simulations, FANTOM, parallel computers, three-helix bundle

ASJC Scopus subject areas

  • Catalysis
  • Inorganic Chemistry
  • Organic Chemistry
  • Physical and Theoretical Chemistry
  • Computational Theory and Mathematics
  • Computer Science Applications

Cite this

Folding of Globular Proteins by Energy Minimization and Monte Carlo Simulations with Hydrophobic Surface Area Potentials. / Mumenthaler, Christian; Braun, Werner.

In: Journal of Molecular Modeling, Vol. 1, No. 1, 1995, p. 1-10.

Research output: Contribution to journalArticle

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