Recent Publications

Gareth Tribello

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  1. Title: Probing the Unfolded Configurations of a β-Hairpin Using Sketch-Map

    Author(s): Ardevol A, Tribello G., Ceriotti M., Parrinello M.

    Journal of Chemical Theory and Computation, 11, No. 3, pp. 1086-1093 (10 February 2015)

    doi: 10.1021/ct500950z
    Abstract


    This work examines the conformational ensemble involved in β-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent molecules is used, and this complex energy landscape is sampled by means of parallel tempering metadynamics simulations. The ensemble of configurations explored is analyzed using the recently proposed sketch-map algorithm. Further simulations allow us to probe how mutations affect the structures adopted by this protein. We find that many of the configurations adopted by a mutant are the same as those adopted by the wild-type protein. Furthermore, certain mutations destabilize secondary-structure-containing configurations by preventing the formation of hydrogen bonds or by promoting the formation of new intramolecular contacts. Our analysis demonstrates that machine-learning techniques can be used to study the energy landscapes of complex molecules and that the visualizations that are generated in this way provide a natural basis for examining how the stabilities of particular configurations of the molecule are affected by factors such as temperature or structural mutations.

  2. Title: Understanding the Interaction between Low-Energy Electrons and DNA Nucleotides in Aqueous Solution

    Author(s): McAllister M., Smyth, M., Gu B., Tribello G.A., Kohanoff J.,

    Journal of Physical Chemistry Letters, 6, No. 15, pp. 3091-3097 (6 August 2015)

    doi: 10.1021/acs.jpclett.5b01011
    Abstract

    Full Text

    Reactions that can damage DNA have been simulated using a combination of molecular dynamics and density functional theory. In particular, the damage caused by the attachment of a low energy electron to the nucleobase. Simulations of anionic single nucleotides of DNA in an aqueous environment that was modeled explicitly have been performed. This has allowed us to examine the role played by the water molecules that surround the DNA in radiation damage mechanisms. Our simulations show that hydrogen bonding and protonation of the nucleotide by the water can have a significant effect on the barriers to strand breaking reactions. Furthermore, these effects are not the same for all four of the bases.

  3. Title: Demonstrating the Transferability and the Descriptive Power of Sketch-Map

    Author(s): Ceriotti M., Tribello G., Parrinello M.,

    J. Chem. Theory Comput. , 9, pp. 1521- (2013)

    Abstract

  4. Title: Locating binding poses in protein-ligand systems using reconnaissance metadynamics

    Author(s): Soderhjelm P., Tribello G., Parrinello M.

    Proc. Natl. Acad. Sci. U.S.A. , 109, pp. 5170-5175 (2012)

    Abstract

  5. Title: Using sketch-map coordinates to analyze and bias molecular dynamics simulations

    Author(s): Tribello G., Ceriotti M., Parrinello M.

    Proc. Natl. Acad. Sci. U.S.A., 109, pp. 5196-5201 (2012)

    Abstract

  6. Title: Exploring the free energy surfaces of clusters using reconnaissance metadynamics

    Author(s): Tribello G., Cuny J., Eshet H., Parrinello M.

    J. Chem. Phys., 135, pp. 114109 - (2011)

    Abstract

  7. Title: Simplifying the representation of complex free-energy landscapes using sketch-map

    Author(s): Ceriotti M., Tribello G. Parrinello M.

    Proc. Natl. Acad Sci. U.S.A , 108, pp. 13023-13028 (2011)

    Abstract

  8. Title: Isomorhpism between ice and silica

    Author(s): Tribello G., Slater B., Zwijnenburg M., Bello R.

    Phys. Chem. Chem. Phys. , 12, pp. 8597-8606 (2011)

    Abstract

  9. Title: Surface energy and surface proton order of the ice Ih basal and prism surfaces

    Author(s): Pang D., Liu L., . Tribello G., Slater B., Michaelides A., Wang E.

    J Phys. Condens. Matter, 22, pp. 074209- (2011)

    Abstract

  10. Title: A self-learning algorithm for biased molecular dynamics

    Author(s): Tribello G., Ceriotti M., Parrinello M.

    Proc. Natl. Acad Sci U.S.A. , 107, pp. 17509-17514 (2010)

    Abstract

  11. Title: Asprich peptides are occluded in calcite and permanently disorder biomineral crystals

    Author(s): Metzler R., Tribello G., Parrinello M., Gilbert P.

    J. Am. Chem. Soc. , 132, pp. 11585-11591 (2010)

    Abstract

  12. Title: A molecular dynamics study of the early states of calcium carbonate growth

    Author(s): Tribello G., Bruneval F., Liew C.C., Parrinello M.

    J. Phys. Chem. B,, 113, pp. 11680-11687 (2009)

    Abstract

  13. Title: The phase diagram of water at negative pressures: virtual ices

    Author(s): Conde M., Vega C., Tribello G., Slater B.

    J. Chem. Phys., 131, pp. 034510- (2009)

    Abstract

  14. Title: A theoretical examination of known and hypothetical clathrate hydrate stability

    Author(s): Tribello G., Slater B.

    J. Chem. Phys. , 131, pp. 024703- (2009)

    Abstract

  15. Title: Binding of calcium and carbonate to polyacrylates

    Author(s): Tribello G., Liew C., Parrinello M.

    J. Phys. Chem. B. , 113, pp. 7081-7085 (2009)

    Abstract

  16. Title: On thin ice: surface order and disorder during pre-melting

    Author(s): Bishop C.L., Pan G., Liu L.M., Tribello G., . Michaelides A., Wang E., Slater B.

    Faraday Discussions, 141, pp. 277-292 (2008)

    Abstract

  17. Title: Surface Energy and surface proton order of ice Ih

    Author(s): Pan D., Liu L.-M., Tribello G., Slater B., Michaelides A., E. Wang E.

    Phys. Rev. Lett., 101, pp. 155703- (2008)

    Abstract

  18. Title: A blind structure prediction of ice XIV

    Author(s): Tribello G., Slater B., Saltzmann C.G.

    J. Am. Chem. Soc., 128, pp. 12594-12595 (2006)

    Abstract

  19. Title: Proton ordering energetics in ice phases

    Author(s): Tribello G., Slater B.

    Chem. Phys. Lett. , 425, pp. 246-250 (2006)

    Abstract