All-Atom Structure Prediction and Folding Simulations of a Stable Protein

Abstract

We present results from all-atom, fully unrestrained ab initio folding simulations for a stable protein with nontrivial secondary structure elements and a hydrophobic core. The construct, "trpcage", is a 20-residue sequence optimized by the Andersen group at University of Washington and is currently the smallest protein that displays two-state folding properties. Compared over the well-defined regions of the experimental structure, our prediction has a remarkably low 0.97 A Calpha root-mean-square-deviation (rmsd) and 1.4 A for all heavy atoms. The simulated structure family displays additional features that are suggested by experimental data, yet are not evident in the family of NMR-derived structures.

Comparison of multiple Amber force fields and development of improved protein backbone parameters

“…Any other amino acid will use both glycine set of parameters and a second set of dihedral parameters which are usually parametrized using alanine. Prior modifications of ff94, such as ff96, ff99, ff94gs, ff99ϕ, and our previous modification of ff99 18 only changed the first set of dihedrals, effectively overwriting glycine dihedral parameters with the ones intended for alanine, unaware that there existed a set of alanine dihedral parameters that do not use the traditional definition of φ and ψ. This resulted in incorrect parametrization of glycine.…”

“…This may artificially increase the glycine conformational transition rates. The plots for ff96, ff99ϕ as well as the plots obtained from simulations that used our previous modification of dihedral parameters 12,18 are shown in Figure S6 (supplementary material) and, similarly to ff99 and ff94gs, exhibit incorrect sampling for glycine dihedrals due to the lack of explicit treatment of both sets of backbone parameters. Alanine free energy maps for the different force fields (Figure 3) show more similarity to each other, with major regions represented by right handed α-helix, PP II and extended β conformations.…”

“…Because the backbone dihedral parameters are shared by all amino acids, regardless of the type of sidechain, their cumulative effect is most likely responsible for the bias towards the specific secondary structure. This recently motivated us 12,18 and others 13,19 to revisit backbone dihedral parametrization for ff94/ff99. Garcia and Sanbonmatsu 13 simply zeroed the torsion potential for φ and ψ (although as we explain below, only some of the φ/ψ terms were removed) and noted improved agreement with experimental helix-coil parameters.…”

“…This improved the agreement with experimental kinetic and thermodynamic measurements for folding of two 21-residue α-helical peptides. Our own modification of ff99 published previously 18 specifically addressed strong helical bias and, in this respect, succeeded to achieve better balance of major secondary structures.…”

“…This definition of dihedrals was originally implemented in ff94, with φ and ψ fit independently to glycine data and φ′ and ψ′ used to adjust the behavior for alanine. Later modifications of ff94, such as ff96, ff99, Garcia's 13 , Pande's 19 and ours 12,18 only changed the first set of φ/ψ terms, using them to adjust backbone preferences for alanine. Thus the new ϕ and ψ parameters were fit in the presence of the ff94 alanine-based φ′ and ψ′, and will only give their intended behavior when they accompany these φ′ and ψ′ dihedrals.…”