title: Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues.
abstract: Coarse-grained force fields for protein simulations are usually designed and parameterized to treat proteins composed of natural L-amino-acid residues. However, D-amino-acid residues occur in bacterial, fungal (e.g., gramicidins), as well as human-designed proteins. For this reason, we have extended the UNRES coarse-grained force field developed in our laboratory to treat systems with D-amino-acid residues. We developed the respective virtual-bond-torsional and double-torsional potentials for rotation about the Cα· · · Cαvirtual-bond axis and two consecutive Cα· · · Cαvirtual-bond axes, respectively, as functions of virtual-bond-dihedral anglesγ. In turn, these were calculated as potentials of mean force (PMFs) from the diabatic energy surfaces of terminally-blocked model compounds for glycine, alanine, and proline. The potential-energy surfaces were calculated by using theab initiomethod of molecular quantum mechanics at the Møller-Plesset (MP2) level of theory and the 6-31G(d,p) basis set, with the rotation angles of the peptide groups about [Formula: see text] and [Formula: see text] used as variables, and the energy was minimized with respect to the remaining degrees of freedom. The PMFs were calculated by numerical integration for all pairs and triplets with all possible combinations of types (glycine, alanine, and proline) and chirality (D or L); however, symmetry relations reduce the number of non-equivalent torsional potentials to 13 and the number of double-torsional potentials to 63 for a given C-terminal blocking group. Subsequently, one- (for torsional) and two-dimensional (for double-torsional potentials) Fourier series were fitted to the PMFs to obtain analytical expressions. It was found that the torsional potentials of the x-Y and X-y types, where X and Y are Ala or Pro, respectively, and a lowercase letter denotes D-chirality, have global minima for small absolute values ofγ, accounting for the double-helical structure of gramicidin A, which is a dimer of two chains, each possessing an alternating D-Tyr-L-Tyr sequence, and similar peptides. The side-chain and correlation potentials for D-amino-acid residues were obtained by applying the reflection about the [Formula: see text] plane to the respective potentials for the L-amino-acid residues.
authors.affiliation: Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland ; Department of Chemistry and Biochemistry, Oklahoma University, Norman, OK, 73019, U.S.A.
authors.forename: Adam K
authors.initials: AK
authors.lastname: Sieradzan
authors.affiliation: Department of Chemistry and Biochemistry, Oklahoma University, Norman, OK, 73019, U.S.A.
authors.forename: Ulrich H E
authors.initials: UH
authors.lastname: Hansmann
authors.affiliation: Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, N.Y., 14853-1301, U.S.A.
authors.forename: Harold A
authors.initials: HA
authors.lastname: Scheraga
authors.affiliation: Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland.
authors.forename: Adam
authors.initials: A
authors.lastname: Liwo
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