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.
authors.affiliation: Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, MN 55905, USA. Electronic address: pang@mayo.edu.
authors.forename: Yuan-Ping
authors.initials: YP
authors.lastname: Pang
mesh_terms: D030562:Databases, Protein; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D055672:Static Electricity
chemical_list: D011506:Proteins
keywords: 1–4 Nonbonded interaction scaling factors; Force field; Protein backbone torsions; Secondary structure elements; α-Helix; β-Strand