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Author Pang, Yuan-Ping
Source United States Department of Energy Office of Scientific and Technical Information
Content type Text
Language English
Subject Keyword APPLIED LIFE SCIENCES ♦ CHEMICAL BONDS ♦ CONFORMATIONAL CHANGES ♦ EQUILIBRIUM ♦ EXPERIMENTAL DATA ♦ INTERACTIONS ♦ LENNARD-JONES POTENTIAL ♦ MOLECULAR DYNAMICS METHOD ♦ MOLECULES ♦ PROTEINS ♦ RESIDUES ♦ ROOTS ♦ SCALING ♦ SIMULATION ♦ TORSION ♦ VAN DER WAALS FORCES
Abstract Highlights: • 1–4 interaction scaling factors are used to adjust conformational energy. • This article reports the effects of these factors on protein conformations. • Reducing these factors changes a helix to a strand in molecular dynamics simulation. • Increasing these factors causes the reverse conformational change. • These factors control the conformational equilibrium between helix and 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){sub 3}-NH{sub 2} 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.
ISSN 0006291X
Educational Use Research
Learning Resource Type Article
Publisher Date 2015-02-06
Publisher Place United States
Journal Biochemical and Biophysical Research Communications
Volume Number 457
Issue Number 2


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