Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors

Flexible peptides that fold upon binding to another protein molecule mediate a large number of regulatory interactions in the living cell and may provide highly specific recognition modules. We present Rosetta FlexPepDock ab-initio, a protocol for simultaneous docking and de-novo folding of peptides, starting from an approximate specification of the peptide binding site. Using the Rosetta fragments library and a coarse-grained structural representation of the peptide and the receptor, FlexPepDock ab-initio samples efficiently and simultaneously the space of possible peptide backbone conformations and rigid-body orientations over the receptor surface of a given binding site. The subsequent all-atom refinement of the coarse-grained models includes full side-chain modeling of both the receptor and the peptide, resulting in high-resolution models in which key side-chain interactions are recapitulated. The protocol was applied to a benchmark in which peptides were modeled over receptors in either their bound backbone conformations or in their free, unbound form. Near-native peptide conformations were identified in 18/26 of the bound cases and 7/14 of the unbound cases. The protocol performs well on peptides from various classes of secondary structures, including coiled peptides with unusual turns and kinks. The results presented here significantly extend the scope of state-of-the-art methods for high-resolution peptide modeling, which can now be applied to a wide variety of peptide-protein interactions where no prior information about the peptide backbone conformation is available, enabling detailed structure-based studies and manipulation of those interactions

Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock

<p>Abstract</p> <p>Background</p> <p>Molecular docking methods are commonly used for predicting binding modes and energies of ligands to proteins. For accurate complex geometry and binding energy estimation, an appropriate method for calculating partial charges is essential. AutoDockTools software, the interface for preparing input files for one of the most widely used docking programs AutoDock 4, utilizes the Gasteiger partial charge calculation method for both protein and ligand charge calculation. However, it has already been shown that more accurate partial charge calculation - and as a consequence, more accurate docking- can be achieved by using quantum chemical methods. For docking calculations quantum chemical partial charge calculation as a routine was only used for ligands so far. The newly developed Mozyme function of MOPAC2009 allows fast partial charge calculation of proteins by quantum mechanical semi-empirical methods. Thus, in the current study, the effect of semi-empirical quantum-mechanical partial charge calculation on docking accuracy could be investigated.</p> <p>Results</p> <p>The docking accuracy of AutoDock 4 using the original AutoDock scoring function was investigated on a set of 53 protein ligand complexes using Gasteiger and PM6 partial charge calculation methods. This has enabled us to compare the effect of the partial charge calculation method on docking accuracy utilizing AutoDock 4 software. Our results showed that the docking accuracy in regard to complex geometry (docking result defined as accurate when the RMSD of the first rank docking result complex is within 2 Å of the experimentally determined X-ray structure) significantly increased when partial charges of the ligands and proteins were calculated with the semi-empirical PM6 method.</p> <p>Out of the 53 complexes analyzed in the course of our study, the geometry of 42 complexes were accurately calculated using PM6 partial charges, while the use of Gasteiger charges resulted in only 28 accurate geometries. The binding affinity estimation was not influenced by the partial charge calculation method - for more accurate binding affinity prediction development of a new scoring function for AutoDock is needed.</p> <p>Conclusion</p> <p>Our results demonstrate that the accuracy of determination of complex geometry using AutoDock 4 for docking calculation greatly increases with the use of quantum chemical partial charge calculation on both the ligands and proteins.</p

Theoretical evidence for a reentrant phase diagram in ortho-para mixtures of solid H-2 at high pressure

We develop a multiorder parameter mean-field formalism for systems of coupled quantum rotors. The scheme is developed to account for systems where ortho-para distinction is valid. We apply our formalism to solid H-2 and D-2. We find an anomalous reentrant orientational phase transition for both systems at thermal equilibrium. The correlation functions of the order parameter indicate short-range order at low temperatures. As the temperature is increased the correlation increases along the phase boundary. We also find that even extremely small odd-J concentrations (1%) can trigger short-range orientational ordering

Reconstruction of frozen-core all-electron orbitals from pseudo-orbitals

We investigate the numerical feasibility of reconstructing frozen-core all-electron molecular orbitals from corresponding pseudo-orbitals. We perform density-functional calculations on simple atomic and molecular model systems using ultrasoft pseudopotentials to represent the atomic cores. We apply a transformation due to Blochl [Phys. Rev. B 50, 17953 (1994)] to each calculated pseudo-orbital to obtain a corresponding frozen-core all-electron molecular orbital. Our model systems include the reconstruction of the 5d orbital of a gold atom, and the occupied valence states of the TiO2 molecule. Comparison of the resulting all-electron orbitals to corresponding ones that were obtained from calculations in which the core electrons were explicitly included indicates that all-electron molecular orbital reconstruction is a feasible and useful operation in reproducing the correct behavior of molecular orbitals in the nuclear core regions. (C) 2001 American Institute of Physics

Phase diagram of a frustrated quantum antiferromagnet on the honeycomb lattice: Magnetic order versus valence-bond crystal formation

We present a comprehensive computational study of the phase diagram of the frustrated S = 1/2 Heisenberg antiferromagnet on the honeycomb lattice, with second-nearest (J(2)) and third-neighbor (J(3)) couplings. Using a combination of exact diagonalizations (EDs) of the original spin model, of the Hamiltonian projected into the nearest-neighbor short-range valence-bond basis, and of an effective quantum dimer model, as well as a self-consistent cluster mean-field theory, we determine the boundaries of several magnetically ordered phases in the region J(2), J(3) is an element of [0,1], and find a sizable magnetically disordered region in between. We characterize part of this magnetically disordered phase as a plaquette valence-bond crystal phase. At larger J(2), we locate a sizable region in which staggered valence-bond crystal correlations are found to be important, either due to genuine valence-bond crystal (VBC) ordering or as a consequence of magnetically ordered phases, which break lattice rotational symmetry. Furthermore, we find that a particular parameter-free Gutzwiller projected tight-binding wave function has remarkably accurate energies compared to finite-size extrapolated ED energies along the transition line from conventional Neel to plaquette VBC phases, a fact that points to possibly interesting critical behavior-such as a deconfined critical point-across this transition. We also comment on the relevance of this spin model to model the spin liquid region found in the half filled Hubbard model on the honeycomb lattice