Use of 1-4 interaction scaling factors to control the conformational equilibrium between α-helix and β-strand

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

1-4 interaction scaling factors are used in AMBER forcefields to reduce the exaggeration of short-range repulsion caused by the 6-12 Lennard-Jones potential and a nonpolarizable charge model and to obtain better agreements of small-molecule conformational energies with experimental data. However, the effects of these scaling factors on protein secondary structure conformations have not been investigated until now. This article reports the finding that the 1-4 interactions among the protein backbone atoms separated by three consecutive covalent bonds are more repulsive in the α-helix conformation than in two β-strand conformations. Therefore, the 1-4 interaction scaling factors of protein backbone torsions φ and ψ control the conformational equilibrium between α-helix and β-strand. Molecular dynamics simulations confirm that reducing the φ and ψ scaling factors readily converts the α-helix conformation of AcO-(AAQAA)3-NH2 to a β-strand conformation, and the reverse occurs when these scaling factors are increased. These results suggest that the φ and ψ scaling factors can be used to generate the α-helix or β-strand conformation in situ and to control the propensities of a forcefield for adopting secondary structure elements.

Original languageEnglish (US)
Pages (from-to)183-186
Number of pages4
JournalBiochemical and Biophysical Research Communications
Volume457
Issue number2
DOIs
StatePublished - Feb 6 2015

Fingerprint

Conformations
Secondary Protein Structure
Molecular Dynamics Simulation
Proteins
Lennard-Jones potential
Covalent bonds
Torsional stress
Molecular dynamics
Atoms
Molecules
Computer simulation

Keywords

  • 1-4 nonbonded interaction scaling factors
  • Force field
  • Protein backbone torsions
  • Secondary structure elements
  • α-Helix
  • β-Strand

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Cell Biology
  • Molecular Biology
  • Medicine(all)

Cite this

@article{215efb2a07e6477db3cdf2acfb99a50c,
title = "Use of 1-4 interaction scaling factors to control the conformational equilibrium between α-helix and β-strand",
abstract = "1-4 interaction scaling factors are used in AMBER forcefields to reduce the exaggeration of short-range repulsion caused by the 6-12 Lennard-Jones potential and a nonpolarizable charge model and to obtain better agreements of small-molecule conformational energies with experimental data. However, the effects of these scaling factors on protein secondary structure conformations have not been investigated until now. This article reports the finding that the 1-4 interactions among the protein backbone atoms separated by three consecutive covalent bonds are more repulsive in the α-helix conformation than in two β-strand conformations. Therefore, the 1-4 interaction scaling factors of protein backbone torsions φ and ψ control the conformational equilibrium between α-helix and β-strand. Molecular dynamics simulations confirm that reducing the φ and ψ scaling factors readily converts the α-helix conformation of AcO-(AAQAA)3-NH2 to a β-strand conformation, and the reverse occurs when these scaling factors are increased. These results suggest that the φ and ψ scaling factors can be used to generate the α-helix or β-strand conformation in situ and to control the propensities of a forcefield for adopting secondary structure elements.",
keywords = "1-4 nonbonded interaction scaling factors, Force field, Protein backbone torsions, Secondary structure elements, α-Helix, β-Strand",
author = "Yuan-Ping Pang",
year = "2015",
month = "2",
day = "6",
doi = "10.1016/j.bbrc.2014.12.084",
language = "English (US)",
volume = "457",
pages = "183--186",
journal = "Biochemical and Biophysical Research Communications",
issn = "0006-291X",
publisher = "Academic Press Inc.",
number = "2",

}

TY - JOUR

T1 - Use of 1-4 interaction scaling factors to control the conformational equilibrium between α-helix and β-strand

AU - Pang, Yuan-Ping

PY - 2015/2/6

Y1 - 2015/2/6

N2 - 1-4 interaction scaling factors are used in AMBER forcefields to reduce the exaggeration of short-range repulsion caused by the 6-12 Lennard-Jones potential and a nonpolarizable charge model and to obtain better agreements of small-molecule conformational energies with experimental data. However, the effects of these scaling factors on protein secondary structure conformations have not been investigated until now. This article reports the finding that the 1-4 interactions among the protein backbone atoms separated by three consecutive covalent bonds are more repulsive in the α-helix conformation than in two β-strand conformations. Therefore, the 1-4 interaction scaling factors of protein backbone torsions φ and ψ control the conformational equilibrium between α-helix and β-strand. Molecular dynamics simulations confirm that reducing the φ and ψ scaling factors readily converts the α-helix conformation of AcO-(AAQAA)3-NH2 to a β-strand conformation, and the reverse occurs when these scaling factors are increased. These results suggest that the φ and ψ scaling factors can be used to generate the α-helix or β-strand conformation in situ and to control the propensities of a forcefield for adopting secondary structure elements.

AB - 1-4 interaction scaling factors are used in AMBER forcefields to reduce the exaggeration of short-range repulsion caused by the 6-12 Lennard-Jones potential and a nonpolarizable charge model and to obtain better agreements of small-molecule conformational energies with experimental data. However, the effects of these scaling factors on protein secondary structure conformations have not been investigated until now. This article reports the finding that the 1-4 interactions among the protein backbone atoms separated by three consecutive covalent bonds are more repulsive in the α-helix conformation than in two β-strand conformations. Therefore, the 1-4 interaction scaling factors of protein backbone torsions φ and ψ control the conformational equilibrium between α-helix and β-strand. Molecular dynamics simulations confirm that reducing the φ and ψ scaling factors readily converts the α-helix conformation of AcO-(AAQAA)3-NH2 to a β-strand conformation, and the reverse occurs when these scaling factors are increased. These results suggest that the φ and ψ scaling factors can be used to generate the α-helix or β-strand conformation in situ and to control the propensities of a forcefield for adopting secondary structure elements.

KW - 1-4 nonbonded interaction scaling factors

KW - Force field

KW - Protein backbone torsions

KW - Secondary structure elements

KW - α-Helix

KW - β-Strand

UR - http://www.scopus.com/inward/record.url?scp=84921818173&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84921818173&partnerID=8YFLogxK

U2 - 10.1016/j.bbrc.2014.12.084

DO - 10.1016/j.bbrc.2014.12.084

M3 - Article

VL - 457

SP - 183

EP - 186

JO - Biochemical and Biophysical Research Communications

JF - Biochemical and Biophysical Research Communications

SN - 0006-291X

IS - 2

ER -