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IBM Journal of Research and Development
Applications of Massively Parallel Systems   Volume 52, Number 1/2, 2008
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Massively parallel molecular dynamics simulations of lysozyme unfolding - References

 by R. Zhou,
M. Eleftheriou,
C.-C. Hon,
R. S. Germain,
A. K. Royyuru,
and B. J. Berne
References

  1. B. L. Kagan, “Amyloidosis and Protein Folding,” Science 307, No. 5706, 42–43 (2005).
  2. J. Klein-Seetharaman, M. Oikawa, S. B. Grimshaw, J. Wirmer, E. Duchardt, T. Ueda, T. Imoto, L. J. Smith, C. M. Dobson, and H. Schwalbe, “Long-Range Interactions Within a Nonnative Protein,” Science 295, No. 5560, 1719–1722 (2002).
  3. M. Dumoulin, A. Last, A. Desmyter, K. Decanniere, D. Canet, A. Spencer, D. Archer, et al., “A Camelid Antibody Fragment Inhibits the Formation of Amyloid Fibrils by Human Lysozyme,” Nature 424, No. 6950, 783–788 (2003).
  4. F. Chiti, M. Stefani, N. Taddei, G. Ramponi, and C. M. Dobson, “Rationalization of the Effects of Mutations on Peptide and Protein Aggregation Rates,” Nature 424, No. 6950, 805–808 (2003).
  5. T. Ueda, H. Yamada, H. Aoki, and T. Imoto, “Effect of Chemical Modifications of Tryptophan Residues on the Folding of Reduced Hen Egg-White Lysozyme,” J. Biochem. (Tokyo) 108, No. 5, 886–892 (1990).
  6. T. Mishima, T. Ohkuri, A. Monji, T. Imoto, and T. Ueda, “A Particular Hydrophobic Cluster in the Residual Structure of Reduced Lysozyme Drastically Affects the Amyloid Fibrils Formation,” Biochem. Biophys. Res. Comm. 356, No. 3, 769–772 (2007).
  7. F. Allen, G. Almasi, W. Andreoni, D. Beece, B. J. Berne, A. Bright, J. Brunheroto, et al., “Blue Gene: A Vision for Protein Science Using a Petaflop Supercomputer,” IBM Syst. J. 40, No. 2, 310–327 (2001).
  8. A. R. Fersht and V. Daggett, “Protein Folding and Unfolding at Atomic Resolution,” Cell 108, No. 4, 573–582 (2002).
  9. C. M. Dobson, A. Sali, and M. Karplus, “Protein Folding: A Perspective from Theory and Experiment,” Angew Chem. Int. Edit. Engl. 37, 868–893 (1998).
  10. C. L. Brooks, M. Gruebele, J. N. Onuchic, and P. G. Wolynes, “Chemical Physics of Protein Folding,” Proc. Natl. Acad. Sci. USA 95, No. 19, 11037–11038 (1998).
  11. Y. Duan and P. A. Kollman, “Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution,” Science 282, No. 5389, 740–744 (1998).
  12. R. Zhou, X. Huang, C. J. Margulius, and B. J. Berne, “Hydrophobic Collapse in Multidomain Protein Folding,” Science 305, No. 5690, 1605–1609 (2004).
  13. P. Liu, X. Huang, R. Zhou, and B. J. Berne, “Observation of a Dewetting Transition in the Collapse of the Melittin Tetramer,” Nature 437, No. 7055, 159–162 (2005).
  14. C. D. Snow, H. Nguyen, V. S Pande, and M. Gruebele, “Absolute Comparison of Simulated and Experimental Protein-Folding Dynamics,” Nature 420, No. 6911, 102–106 (2002).
  15. V. Daggett, “Long Timescale Simulations,” Curr. Opin. Struct. Biol. 10, No. 2, 160–164 (2000).
  16. K. A. Dill, S. Bromberg, K. Yue, K. M. Fiebig, D. P. Yee, P. D. Thomas, and H. S. Chan, “Principles of Protein Folding—A Perspective from Simple Exact Models,” Protein Sci. 4, No. 4, 561–602 (1995).
  17. F. Ding, S. V. Buldyrev, and N. V. Dokholyan, “Folding Trp-Cage to NMR Resolution Native Structure Using a Coarse-Grained Protein Model,” Biophys. J. 88, No. 1, 147–155, (2005).
  18. W. L Jorgensen, D. Maxwell, and J. Tirado-Rives, “Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids,” J. Am. Chem. Soc. 118, No. 45, 11225–11236 (1996).
  19. A. D. MacKerell, Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, M. J. Field, S. Fischer, et al., “All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins,” J. Phys. Chem. B 102, No. 18, 3586–3616 (1998).
  20. M. Eleftheriou, R. S. Germain, A. K. Royyuru, and R. Zhou, “Thermal Denaturing of Mutant Lysozyme with Both the OPLSAA and the CHARMM Force Fields,” J. Am. Chem. Soc. 128, No. 41, 13388–13395 (2006).
  21. G. Moraitakis and J. M. Goodfellow, “Simulations of Human Lysozyme: Probing the Conformations Triggering Amyloidosis,” Biophys. J. 84, No. 4, 2149–2158 (2003).
  22. C. Venclovas, A. Zenla, K. Fidelis, and J. Moult, “Some Measures of Comparative Performance in the Three CASPs,” Proteins S3, 231–237 (1999).
  23. P. I. de Bakker, P. H. Hunenberger, and J. A. McCammon, “Molecular Dynamics Simulations of the Hyperthermophilic Protein Sac7d from Sulfolobus acidocaldarius: Contribution of Salt Bridges to Thermostability,” J. Mol. Biol. 285, 1811–1830 (1999).
  24. D. Frishman and P. Argos, “Knowledge-Based Protein Secondary Structure Assignment,” Proteins 23, No. 4, 566–579 (1995).
  25. H. Hu, M. Elstner, and J. Hermans, “Comparison of a QM/MM Force Field and Molecular Mechanics Force Fields in Simulations of Alanine and Glycine Dipeptides (Ace-Ala-Nme and Ace-Gly-Nme) in Water in Relation to the Problem of Modeling the Unfolded Peptide Backbone in Solution,” Proteins 50, No. 3, 451–463 (2003).
  26. A. R. Dinner, T. Lazaridis, and M. Karplus, “Understanding Beta-Hairpin Formation,” Proc. Natl. Acad. Sci. USA 96, No. 16, 9068–9073 (1999).
  27. R. Zhou, B. J. Berne, and R. S. Germain, “The Free Energy Landscape for Beta-Hairpin Folding in Explicit Water,” Proc. Natl. Acad. Sci. USA 98, No. 26, 14931–14936 (2001).
  28. R. Zhou, M. Eleftheriou, A. Royyuru, and B. J. Berne, “Destruction of Long-Range Interactions by a Single Mutation in Lysozyme,” Proc. Natl. Acad. Sci. USA 104, No. 14, 5824–5829 (2007).
  29. J. P. Gallivan and D. A. Dougherty, “Cation–Pi Interactions in Structural Biology,” Proc. Natl. Acad. Sci. USA 96, No. 17, 9459–9464 (1999).
  30. A. Magalhaes, B. Maigret, J. Hoflack, J. N. Gomes, and H. A. Scheraga, “Contribution of Unusual Arginine–Arginine Short-Range Interactions to Stabilization and Recognition in Proteins,” J. Protein Chem. 13, No. 2, 195–215 (1994).
  31. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Herman, “Interaction Models for Water in Relation to Protein Hydration,” Intermolecular Forces, B. Pullman, Ed., Reidel, Dordrecht, 1981, pp. 331–342.
  32. E. Neria, S. Fischer, and M. Karplus, “Simulation of Activation Free Energies in Molecular Systems,” J. Chem. Phys. 105, No. 5, 1902–1921 (1996).
  33. W. L. Jorgensen, J. Chandrasekhar, J. Madura, R. W. Impey, and M. L. Klein, “Comparison of Simple Potential Functions for Simulating Liquid Water,” J. Chem. Phys. 79, No. 2, 926–935 (1983).
  34. U. Essman, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, “A Smooth Particle Mesh Ewald Method,” J. Chem. Phys. 103, No. 19, 8577–8593 (1995).
  35. B. G. Fitch, R. S. Germain, M. Mendell, J. Pitera, M. Pitman, A. Rayshubskiy, Y. Sham, et al., “Blue Matter, an Application Framework for Molecular Simulation on Blue Gene,” J. Parallel Distrib. Comput. 63, No. 7–8, 759–773 (2003).
  36. A. Caflisch and M. Karplus, “Structural Details of Urea Binding to Barnase: A Molecular Dynamics Analysis,” Structure 7, No. 5, 477–488 (1999).
  37. J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, and K. Schulten, “Scalable Molecular Dynamics with NAMD,” J. Comput. Chem. 26, No. 16, 1781–1802 (2005).


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