Abstract
We investigate the phase transition properties of isolated and aggregated protein by exhaustive numerical study in the confined conformation space with maximally compact lattice model. The study within the confined conformation space shows some general folding properties. Various sequences show different folding properties: two-state folding, three-state folding and prion-like folding behavior. We find that the aggregated protein holds a more evident transition than isolated one and the transition temperature is generally lower than that in isolated case.
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Glenner, G.: Amyloid deposits and amyloidosis: the B-fibrilloses. N. Engl. J. Med. 302, 1283 (1980)
Blake, C., Serpell, L.: Synchrotron X-ray studies suggest that the core of the transthyretin amyloid fibril is a continuous Â-sheet helix. Structure 4(8), 989 (1996)
McKintosh, E., Tabrizi, S.J., Collinge, J.: Prion diseases. J. Neurovirol. 9, 183 (2003)
Ross, C.A., Poirier, M.A.: Protein aggregation and neurodegenerative disease. Nat. Med. 10, S10 (2004)
Buyong, M., Ruth, N.: Molecular dynamics simulations of alanine rich-sheet oligomers: Insight into amyloid formation. Protein Sci. 11, 2335 (2002)
Zhou, H.J., Zhou, J., Ou-Yang, Z.C., Kumar, S.: Collapse transition of two-dimensional flexible and semiflexible polymers. Phys. Rev. Lett. 97, 158302 (2006)
Sherman, E., Haran, G.: Coil-globule transition in the denatured state of a small protein. Proc. Natl. Acad. Sci. USA 103, 11539 (2006)
Baldwin, R.L.: The nature of protein folding pathways: The classical versus the new view. J. Biomol. NMR 5, 103 (1995)
Wolynes, P.G., Onuchic, J.N., Thirumalai, D.: Navigating the folding routes. Science 267, 1619 (1995)
Bryngelson, J.D., Wolynes, P.G.: Intermediates and barrier crossing in a random energy model (with applications to protein folding). J. Phys. Chem. 93, 6902 (1989)
Garcia-Mira, M.M., Sadqi, M., Fischer, M., Sanchez, J.M.: Experimental identification of downhill protein folding. Science 298, 2191 (2002)
Dyer, R.B.: Ultrafast and downhill protein folding. Curr. Opin. Struct. Biol. 17(1), 38 (2007)
Dinner, A., Slai, A., Karplus, M., Shakhnovich, E.: Phase diagram of a model protein derived by exhaustive enumeration of the conformations. J. Chem. Phys. 101, 1444 (1994)
Giugliarellia, G., Micheletti, C., Banavar, J.R., Maritan, A.: Compactness, aggregation, and prionlike behavior of protein: A lattice model study. J. Chem. Phys. 113, 5072 (2000)
Broglia, R.A., Tiana, G., Pasquali, S., Roman, H.E., Vigezzi, E.: Folding and aggregation of designed proteins. Proc. Natl. Acad. Sci. USA 95, 12930 (1998)
Harrison, P.M., Chan, H.S., Prusiner, S.B., Cohen, F.E.: Conformational propagation with prion-like characteristics in a simple model of protein folding. Protein Sci. 10, 819 (2001)
Dima, R.I., Thirumalai, D.: Exploring protein aggregation and self-propagation using lattice models: Phase diagram and kinetics. Protein Sci. 11, 1036 (2002)
Gupta, P., Hall, C.K., Voegler, A.C.: Effect of denaturant and protein concentrations upon protein refolding and aggregation: A simple lattice model. Protein Sci. 7, 2642 (1998)
Li, M.S., Klimov, D.K., Straub, J.E., Thirumalai, D.: Probing the mechanisms of fibril formation using lattice models. J. Chem. Phys. 129, 175101 (2008)
Banavar, J.R., Cieplak, M., Maritan, A.: Lattice tube model of proteins. Phys. Rev. Lett. 93, 238101 (2004)
Banavar, J.R., Maritan, A.: Physics of proteins. Annu. Rev. Biophys. Biomol. Struct. 36, 261 (2007)
Maritan, A., Micheletti, C., Trovato, A., Banavar, J.R.: Optimal shapes of compact strings. Nature 406, 287 (2000)
Luheshi, L.M., Crowther, D.C., Dobson, C.M.: Protein misfolding and disease: from the test tube to the organism. Curr. Opin. Chem. Biol. 12, 25 (2008)
Thirumalai, D., Klimov, D.K., Dima, R.I.: Emerging ideas on the molecular basis of protein and peptide aggregation. Curr. Opin. Struct. Biol. 13, 1 (2003)
Dill, K.A.: Theory for the folding and stability of globular proteins. Biochemistry 24(6), 1501 (1985)
Salvi, G., Rios, P.D.L.: Effective interactions cannot replace solvent effects in a lattice model of proteins. Phys. Rev. Lett. 91, 258102 (2003)
Orly, N.B., Ron, U., Amnon, H.: Analysing the origin of long-range interactions in proteins using lattice models. BMC Struct. Biol. 9, 4 (2009)
Zhao, X.C.: Advances on protein folding simulations based on the lattice HP models with natural computing. Appl. Soft Comput. 8, 1029 (2008)
Liu, Y.X., Prem, P.C., Jose, L.P., Bernard, S.G.: Lattice model simulation of interchain protein interactions and the folding dynamics and dimerization of the GCN4 Leucine zipper. J. Chem. Phys. 128, 045106 (2008)
Li, H., Helling, R., Tang, C., Wingreen, N.S.: Emergence of preferred structures in a simple model of protein folding. Science 273, 666 (1996)
Li, Y.Q., Ji, Y.Y., Mao, J.W., Tang, X.W.: Medium effects on the selection of sequences folding into stable proteins in a simple model. Phys. Rev. E 72, 021904 (2005)
Ji, Y.Y., Li, Y.Q., Mao, J.W., Tang, X.W.: Model study of prionlike folding behavior in aggregated proteins. Phys. Rev. E 72, 041912 (2005)
Ji, Y.Y., Li, Y.Q.: The role of secondary structure in protein structure selection. Eur. Phys. J. E 32, 103 (2010)
Kauzmann, W.: Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14, 1 (1959)
Wind, A.F., Kemp, J.P., Ermoshkin, A.V., Chen, J.Z.Y.: Structural and folding properties of a lattice prion model. Phys. Rev. E 66, 031909 (2002)
Lemak, A.S., Lepock, J.R., Chen, J.Z.Y.: Unfolding proteins in an external field: Can we always observe the intermediate states? Phys. Rev. E 67, 031910 (2003)
Li, A., Daggett, V.: Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2. Proc. Natl. Acad. Sci. USA 91, 10430 (1994)
Lazaridis, T., Karplus, M.: “New View” of protein folding reconciled with the old through multiple unfolding simulations. Science 278, 1997 (1928)
Daggett, V., Fersht, A.: The present view of the mechanism of protein folding. Nat. Rev. Mol. Cell Biol. 4, 497 (2003)
Wong, K.B., Clarke, J. Bond C.J., et al.: Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding. J. Mol. Biol. 296, 1257 (2000)
Li, A., Daggett, V.: Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate. J. Mol. Biol. 275, 677 (1998)
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Ji, YY., Yi, WQ. & Zhang, LX. Simple Model Study of Phase Transition Properties of Isolated and Aggregated Protein. J Stat Phys 142, 975–983 (2011). https://doi.org/10.1007/s10955-011-0148-4
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DOI: https://doi.org/10.1007/s10955-011-0148-4