Abstract.
Molecular dynamics (MD) simulation is important theme in the parallel computing. MD simulations are widely used for simulating the motion of molecules in order to gain a deeper understanding of the chemical reactions, fluid flow, phase transitions, and other physical phenomena due to molecular interactions. In this study, we performed molecular dynamics simulations on monomeric and dimeric HuPrP at 300K and 500K for 10 ns to investigate the differences in the properties of the monomer and the dimer from the perspective of dynamic and structural behaviors. Simulations were also undertaken with Asp178Asn and acidic pH known as a disease-associated factor.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Case, D.A., Pearlman, D.A., Caldwell, J.W., Cheatham III, T.E., Wang, J., Ross, W.S., Simmerling, C.L., Darden, T.A., Merz, K.M., Stanton, R.V., Cheng, A.L., Vincent, J.J., Crowley, M., Tsui, V., Gohlke, H., Radmer, R.J., Duan, Y., Pitera, J., Massova, I., Seibel, G.L., Singh, U.C., Weiner, P.K., Kollman, P.A.: AMBER 7. University of California, San Francisco (2002)
Day, R., Bennion, B., Ham, S., Daggett, V.: Increasing temperature accelerates protein unfolding without changing the pathway of unfolding. J. Mol. Biol. 322, 189–203 (2002)
Glockshuber, R., Hornemann, S., Riek, R., Wider, G., Billeter, M., Wuthrich, K.: Three-dimensional NMR structure of a self-folding domain of the prion protein PrP(121-231). Trends in Biochemical Sciences 22, 241–242 (1997)
Hori, A., Tezuka, H., Ishikawa, Y., Soda, N., Konaka, H., Maeda, M.: Implementation of gang-scheduling on workstation cluster. In: Feitelson, D.G., Rudolph, L. (eds.) IPPS-WS 1996 and JSSPP 1996. LNCS, vol. 1162, pp. 76–83. Springer, Heidelberg (1996)
Kabsch, W., Sander, C.: Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577–2637 (1983)
Kaneko, K., Zulianello, L., Scott, M., Cooper, C.M., Wallace, A.C., James, T.L., Cohen, F.E., Prusiner, S.B.: Evidence for protein X binding to a discontinuous epitope on the cellular prion protein during scrapie prion propagation. Proc. Natl. Acad. Sci. USA 94, 10069–10074 (1997)
Knaus, K.J., Morillas, M., Swietnicki, W., Malone, M., Surewicz, W.K., Yee, V.C.: Crystal structure of the human prion protein reveals a mechanism for oligomerization. Nat. Struct. Biol. 8, 770–774 (2001)
Koradi, R., Billeter, M., Wuthrich, K.: MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graphics 14, 51–55 (1996)
Korth, C., Stierli, B., Streit, P., Moser, M., Schaller, O., Fischer, R., Schulz- Schaeffer, W., Kretzschmar, H., Raeber, A., Braun, U., Ehrensperger, F., Hornemann, S., Glockshuber, R., Riek, R., Billeter, M., Wuthrich, K., Oesch, B.: Prion(PrPSc) -specific epitope defined by a monoclonal antibody. Nature 390, 74–77 (1997)
Meyer, R.K., Lustig, A., Oesch, B., Fatzer, R., Zurbriggen, A., Vandevelde, M.: A monomer-dimer equilibrium of a cellular prion protein (PrPC) not observed with recombinant PrP. J. Biol. Chem. 275, 38081–38087 (2000)
Monod, J., Wyman, J., Changeux, J.-P.: On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12, 88–118 (1965)
Muramoto, T., Scott, M., Cohen, F.E., Prusiner, S.B.: Recombinant scrapie-like prion protein of 106 amino acids is soluble. Proc. Natl. Acad. Sci. USA 93, 15457–15462 (1996)
Parchment, O., Essex, J.: Molecular dynamics of mouse and Syrian hamster PrP: implication for activity. Proteins 38, 327–340 (2000)
Prusiner, S.B.: Novel proteinaceous infectious particles cause scrapie. Science 216, 136–144 (1982)
Prusiner, S.B.: Trends Biochem Sci. Molecular biology and pathogenesis of prion diseases 21, 482–487 (1996)
Riek, R., Hornemann, S., Wider, G., Billeter, M., Glockshuber, R., Wuthrich, K.: NMR structure of the mouse prion protein domain PrP(121-321). Nature 382, 180–182 (1996)
Sekijima, M., Motono, C., Yamasaki, S., Kaneko, K., Akiyama, Y.: Molecular Dynamics Simulation of Dimeric and Monomeric Forms of Human Prion Protein: Insight into Dynamics and Properties. Biophysical J. 85, 1–10 (2003)
Tompa, P., Tusnady, G.E., Friedrich, P., Simon, I.: The role of dimerization in prion replication. Biophysical J. 82, 1711–1718 (2002)
Welker, E., Wedemeyer, W.J., Scheraga, H.A.: A role for intermolecular disulfide bonds in prion diseases? Proc. Natl. Acad. Sci. USA 98, 4334–4336 (2001)
Zuegg, J., Greedy, J.E.: Molecular dynamics simulations of human prion protein: importance of correct treatment of electrostatic interactions. Biochemistry 38, 13862–13876 (1999)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2003 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Sekijima, M., Motono, C., Yamasaki, S., Kaneko, K., Akiyama, Y. (2003). Molecular Dynamics Simulation of Prion Protein by Large Scale Cluster Computing. In: Veidenbaum, A., Joe, K., Amano, H., Aiso, H. (eds) High Performance Computing. ISHPC 2003. Lecture Notes in Computer Science, vol 2858. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-39707-6_43
Download citation
DOI: https://doi.org/10.1007/978-3-540-39707-6_43
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-20359-9
Online ISBN: 978-3-540-39707-6
eBook Packages: Springer Book Archive