Pseudodihedrals: Simplified protein backbone representation with knowledge‐based energy

Abstract

Pairwise contact energies do not explicitly take protein secondary structure into account, and so provide an incomplete description of conformational energy. In order to construct a Hamiltonian that specifically relates to protein backbone conformations, a simplified backbone angle is used. The pseudodihedral angle (the torsion angle between planes defined by 4 consecutive a-carbon atoms) provides a simplified backbone representation and continues to manifest information about secondary-structure elements: the pseudo-Ramachandran plot contains helical and sheetlike regions. The distribution of pseudodihedral angles is highly sensitive to the identity of the central pair of amino acids. Therefore, a sequence-dependent, knowledge-based potential energy was found according to a quasichemical approximation. These functions form complementary additions to the contact potentials currently in use. This pseudodihedral potential greatly enhances the ability to design sequences that are specific to a given conformation and also improves the ability to discriminate a native conformation from many other conformations.

Insights into the induced fit mechanism in antithrombin–heparin interaction using molecular dynamics simulations

“…In this context the pseudo dihedral angle j (the torsion angle between planes defined by four consecutive a-carbon atoms) provides a simplified backbone representation and continues to give information about secondary-structure elements. It could be seen in the plot helical and sheet like regions [48]. The a-helices for instance are marked by a j = 458.…”

The relationship between peptide plane rotation (PPR) and similar conformations

“…psi i rphi i q 1 angles on the contour lines between C and B in Figure 1. Although this single projected angle representation for each residue is similar to the reduced number of variables used in conformational search methods for the virtual bond or pseudodihedral angle model, 12,13,15 this model retains a full atom description of residues in a protein sequence. As shown for the Rooman conformation database, only a limited number of torsion angles in the form of projected or frame-shifted psi values may be required in protein folding simulations.…”

Predicting helical hairpins from sequences by Monte Carlo simulations

“…Because various terms can be added to the present energy model and the missing factors may vary from one topology to another, it is necessary to examine their influence on representative models such as helical hairpins, three antiparallel β-strands, 24 and nonstandard α-topologies exhibited by the 43-residue protein extracted from pyruvate dehydrogenase. 25 These factors include position-dependent effects on amino acid structural propensities, torsional potentials, 26 i → i + 3 hydrogen bonds, and N-cap and C-cap effects (i.e., hydrogen bonds between the side chain and the main chain at the N-and C-termini of helices). Such a systematic study will have implications for structure prediction, but also for protein folding, and notably the stages of structural reorganization during the early steps of folding.…”