Компьютерное моделирование макромолекулярных систем, имитирующих самоорганизацию белковых макромолекул и их взаимодействие с поверхностью
Диссертация
Одним из наиболее актуальных направлений физики полимеров является компьютерное моделирование макромолекулярных систем, имитирующих биологические объекты. Важность такого рода исследований определяется возможностью выявления основополагающих механизмов самоорганизации живых систем на основе построения простейших моделей, всестороннего их анализа и определения минимального набора свойств… Читать ещё >
Список литературы
- Волькенштейн, М.В. Биофизика. Москва, Наука, 1988
- Финкелыитейн, А.В.- Птицын, О.Б. Физика белка. Москва: Книжный дом «Университет», 2002
- Nelson, D.L.- Сох, М.М. Lehninger Principles of Biochemistry. N.Y.: Worth Publishers, 2000
- Anfinsen, С. B. Principles that govern the folding of protein chains. Science. 1973. 181, p.223.
- Fersht, A. R., and E. I. Shakhnovich. Protein folding: think globally, (interact locally. Curr. Biol., 1998. 8, pp. 478−479.
- Levitt, M., M. Gerstein, E. Huang, S. Subbiah, and J. Tsai. Protein folding: the endgame. Annu. Rev. Biochem., 1997. 66, pp. 549−579.
- Onuchic, J. N., Z. Luthey-Schulten, and P. G. Wolynes. Theory of protein folding: the energy landscape perspective. Annu. Rev. Phys. Chem., 1997. 48, pp. 545−600.
- Pande, V. S., A. Y. Grosberg, and T. Tanaka. Heteropolymer freezing and design: towards physical models of protein folding. Reviews of Modern Physics2000. 72, pp. 259−314.
- Plaxco, K. W., D. S. Riddle, V. Grantcharova, and D. Baker. Simplified proteins: minimalist solutions to the 'protein folding problem'. 1998.
- Shakhnovich, E. I. Theoretical studies of protein-folding thermodynamics and kinetics. Curr. Opin. Struct. Biol, 1997. 7, pp. 29−40.
- Abkevich, V. I., A. M. Gutin, and E. I. Shakhnovich. Specific nucleus as the transition-state for protein-folding: evidence from thelattice model. Biochemistry. 1994. 33, pp. 10 026−10 036.
- Bryngelson, J. D., and P. G. Wolynes., Spin-glasses and the statistical-mechanics of protein folding. Proc. Natl. Acad. Sci. USA., 1987. 84, pp. 7524−7528.
- Bryngelson, J. D., and P. G. Wolynes. Intermediates and barrier crossing in a random energy-model (with applications to protein folding). J. Phys. Chem., 1989. 93, pp. 6902−6915.
- Dill, K. A. Dominant forces in protein folding. Biochemistry., 1990. 29, pp. 7133−7155.
- Go, N., and H. Abe. Non interacting local-structure model of folding and unfolding transition in globular proteins. I. Formulation. Biopolymers, 1981. 20, pp. 991−1011.
- Irback, A., and F. Potthast. Studies of an off-lattice model for proteinfolding: sequence dependence and improved sampling at finitetemperature. J. Chem. Phys., 1995. 103, pp. 10 298−10 305.
- Klimov, D. K., and D. Thirumalai. Cooperativity in protein folding: from lattice models with sidechains to real proteins. Fold. Des., 1998. 3, pp. 127 139.
- Micheletti, C., F. Seno, A. Maritan, and J. R. Banavar., Protein design in a lattice model of hydrophobic and polar amino acids. Phys. Rev. Lett., 1998. 80, pp. 2237−2240.
- Shakhnovich, E. I., Modeling protein folding: the beauty and power of simplicity. Fold. Des., 1996. 1, pp. 50−54.
- Zhou, Y. & Karplus, M., Interpreting the folding kinetics of helical proteins, Nature 1999, 401, pp. 400−402.
- C. L. Brooks, M. Gruebele, J. N. Onuchic and P. G. Wolynes, Chemical physics of protein folding, Proc. Natl. Acad. Sci. USA, 1998, 95, pp. 1 103 711 038.
- Snow, C. D., Nguyen, H., Pande, V. S. & Gruebele, M., Absolute, Comparison of simulated and experimental protein-folding dynamics, Nature 2002, 420, pp. 102−104.
- Ruhong Zhou, Trp-cage: Folding free energy landscape in explicit water, PNAS, 2003, 100, 23, pp. 13 280−13 285
- Chowdhury, S., M. C. Lee, G. M. Xiong, and Y. Duan. Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution. J. Mol. Biol., 2003. 327, pp. 711−717.
- Pitera, J. W., and W. Swope. Understanding folding and design: replica-exchange simulations of «Trp-cage» fly miniproteins. Proc. Natl. Acad. Sci. USA., 2003. 100, pp. 7587−7592.
- Zagrovic, В., and V. Pande. Solvent viscosity dependence of the folding rate of a small protein: distributed computing study. J. Comput. Chem2003. 24, pp. 1432−1436.
- Peter L. Freddolino, Feng Liu, Sanghyun Park, Martin Gruebele and Klaus Schulten, Microsecond Explicit Solvent Molecular Dynamics Simulations of Protein Folding, Biophys. J., 2009, 96, 3, p. 590.
- Vincent A. Voelz, Gregory R. Bowman, Kyle Beauchamp and Vijay S. Pande, Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder, J. Am. Chem. Soc., 2010, 132, 5, pp. 1526−1528
- Peter L. Freddolino, Feng Liu, Martin Gruebele, and Klaus Schulten. Ten-Microsecond Molecular Dynamics Simulation of a Fast-Folding WW Domain, Biophys. J., 2008, 94, pp. 75−77.
- Peter L. Freddolino and Klaus Schulten. Common Structural Transitions in Explicit-Solvent Simulations of Villin Headpiece Folding, Biophys. J., 2009, 97, pp. 2338−2347.
- Qiu, L., Pabit, S. A., Roitberg, A. E. & Hagen, S. J. Smaller and Faster: The 20-Residue Trp-Cage Protein Folds in 4 jj. s, J. Am. Chem. Soc., 2002, 124, pp. 12 952−1295
- R. C. Rizzo- W. L. Jorgensen. OPLS all-atom model for amines: resolution of the amine hydration problem", J. Am. Chem. Soc., 1999, 121, pp. 48 274 836
- G. A. Kaminski- R. A. Friesner- J. Tirado-Rives- W. L. Jorgensen- Evaluation and Reparametrization of the OPLS-AA Force Field for Proteinsvia Comparison with Accurate Quantum Chemical Calculations on Peptides, J. Phys. Chem. B, 2001, 105, pp. 6474−6487
- H.J.C.Berendsen, J.P.M.Postma, W.F.van Gunsteren and Jan Hermans, Interaction models for water in relation to protein hydration, in «Intermolecular Forces, ed. B. Pullman, Reidel, Dordrecht, 1981, pp. 331 342.
- Zhou, R., Harder, E., Xu, H. & Berne, B. J. Efficient multiple time step method for use with Ewald and Particle-Mesh Ewald for large biomolecular systems J. Chem. Phys., 2001, 115, pp. 2348−2358
- Hukushima, K. & Nemoto, K. Equi-energy sampler with applications in statistical inference and statistical mechanics J. Phys. Soc. Jpn., 1996, 65, pp. 1604−1608
- Papoian, G.A.- Ulander, J.- Eastwood, M.P.- Luthey-Schulten Z.- Wolynes P.G. Water in Protein Structure Prediction, PNAS, 2004, 10, 101, pp. 33 523 357
- Papoian, G. A.- Ulander, J.- Wolynes, P.G.- The Role of Water Mediated Interactions in Protein-Protein Recognition Landscapes, J. Amer.Chem. Soc., 2003, 125, pp. 9170−9178
- Papoian, G. A.- Wolynes, P.G. The Physics and Bioinformatics of Binding and Folding an Energy Landscape Perspective, Biopolymers, 2003, 68, pp. 333−349
- Dubin R., Eddy S., Krogh A., Mitchinson G., Biological sequence analysis. Probabilistic models of proteins and nucleic acids, Cambridge, Cambridge University Press. 2001.
- Горбань A.H., Попова Т. Г., Садовский М. Г., Классификация нуклеотидиых последовательностей по частотным словарям обнаруживает связь между их структурой и таксономическим положением организмов, Журн. общ. биологии, 2003, 64, 1, с. 51−63
- Yu Z.-G., Anh V., Lau K.-S., Multifractal and correlation analysis of protein sequences from complete genome, Phys. Rev. E, 2003, 68, pp. 2 1913(1)-2 1913(10)
- V.V. Vasilevskaya, L.V. Gusev, A.R. Khokhlov. Protein sequences as literature text. Macromolecul. Theory Simul. 2006, 15, 5, pp.425−431
- А.Ш. Зиятдинов, Л. В. Гусев, B.B. Василевская, A.P. Хохлов. Анализ корреляций в размещении гидрофобных и гидрофильных звеньев в белковых последовательностях, Доклады Академии Наук, 2006, 411, 6, с. 829−832.
- Вейр Б. «Анализ генетических данных: Дискретные генетические признаки». 1995, (Пер. с англ.), Москва, Мир, 400 B.S. Weir. Genetic data analysis. Methods for discrete population genetic data. Massachusetts, Sinauer Associates. 1990.
- Dill, K. A. Theory for the folding and stability of globular-proteins. Biochemistry., 1985. 24, pp. 1501−1509.
- K.F. Lau, K.A. Dill, A Lattice Statistical-Mechanics Model of the Conformational and Sequence-Spaces of Proteins, Macromolecules, 1989, 22, p. 3986.
- B. Lindman, P. Alexandridis, AMPHIPHILIC BLOCK COPOLYMERS, Hardbound, 2000.
- Birte Reining, Helmut Keul and Hartwig Hocke, Amphiphilic block copolymers comprising poly (ethylene oxide) and poly (styrene) blocks: synthesis and surface morphology, Polymer, 2002, 43, 25, p. 7145
- D.F. Parsons, D.R.M. Williams, Single chains of block copolymers in poor solvents: Handshake, spiral, and lamellar globules formed by geometric frustration, Phys.Rev.Lett., 2007, 99, p. 228 302
- A. R. Khokhlov, P. G. Khalatur, Protein-like copolymers: Computer simulation, Physica A, 1998, 249, p.253.
- A. R. Khokhlov, P. G. Khalatur, Conformation-Dependent Sequence Design (Engineering) of AB Copolymers, Phys. Rev. Lett., 1999, 82, pp.3456−3460
- A.R. Khokhlov, P.G. Khalatur, V.A. Ivanov, A.V. Chertovich, A.A. Lazutin, Conformation-Dependent Sequence Design: a Review of the Method and Recent Theoretical and Computer Simulation Results, SIMU Newsletter, 2002, 4, p.79
- E.N. Govorun, V. A. Ivanov, A. R. Khokhlov, P. G. Khalatur, A. L. Borovinsky, and A. Y. Grosberg, Primary sequences of proteinlike copolymers: Levy-flight-type long-range correlations, Physical Review E, 2001,64, 4, p.40 903.
- L.V. Gusev, V.V. Vasilevskaya, V.Ju. Makeev, P.G. Khalatur, A.R. Khokhlov. Segmentation of heteropolymer sequences specifying subsequences with different composition and statistical properties, Macromolecul. Theory Simul., 2003, 12, 8, pp.604−613.
- Govorun E N, Khokhlov A R, Semenov A N, Stability of dense hydrophobic-polar copolymer globules: Regular, random and designed sequences, Eur Phys JE, 2003, 12, 2, p.255−264.
- Semenov A N, Core/Shell Structures of Proteinlike Copolymers: Are Finite Aggregates Thermodinamically Stable?, Macromolecules, 2004, 37, 1, pp.266−237
- Khokhlov A R, Semenov A N and Subbotin A V, Shape transformations of protein-like copolymer globules, Eur. Phys. J. E, 2005, 17, 3, pp. 283−306.
- Virtanen J., Baron C., Tenhu H., Grafting of Poly (e-isopropylacrylamide) with Poly (ethylene oxide) under Various Reaction Conditions, Macromolecules, 2000, 33, 2, p. 336.
- J. Virtanen, H. Tenhu, Thermal Properties of Poly (N-isopropylacrylamide)-g-poly (ethylene oxide) in Aqueous Solutions: Influence of the Number and Distribution of the Grafts, Macromolecules, 2000, 33, 16, p. 5970.
- V.I. Lozinsky, Approaches to Chemical Synthesis of Protein-Like Copolymers, Adv. Polym. Sci., 2006, 196, p. 87.
- Лозинский В.И., Сименел И. А., Курская Е. А., Кулакова В. К., Гринберг В. Я., Дубовик А. С., Галаев И. Ю., Маттиассон В., Хохлов А. Р. Синтез и свойства «белковоподобного» сополимера., ДАН., 2000, 375. с. 637.
- A.V. Chertovich, V.A. Ivanov, A.A. Lazutin, A.R. Khokhlov, 2000 Sequence design of biomimetic copolymers: modeling of membrane proteins and globular proteins with active enzymatic center, Macromol. Symp. 160, p.41
- Okhapkin I.M., Makhaeva E.E., Khokhlov A.R. Two-dimensional classification of amphiphilic monomers based on interfacial and partitioning properties. 1. Monomers of synthetic water-soluble polymers., Colloid Polym Sci. 2005.284, p. 117.
- Okhapkin I.M., Askadskii A.A., Markov V.A., Makhaeva E.E., Khokhlov A.R. Two-dimensional classification of amphiphilic monomers based on interfacial and partitioning properties.2.Amino acids and amino acid residues. Colloid Polym Set 2006. 284. p. 575.
- A.A. Askadskii. Physical properties of polymers. Prediction and control. Gordon and Breach Publishers, Amsterdam, 1996.
- A.A. Askadskii. Computational materials science of polymers. Cambridge International Science of Polymers, Cambridge, 2003.
- Vasilevskaya V.V., Khalatur P.G., Khokhlov A.R. Conformational polymorphism of amphiphilic polymers in a poor solvent. Macromolecules, 2003. 36. p. 10 103.
- Vasilevskaya V.V., Klochkov A.A., Lazutin A.A., Khalatur P.G., Khokhlov A.R., HA (Hydrophobic/Amphiphilic) copolymer model: coil-globule transition versus aggregation. Macromolecules, 2004. 37. p. 5444.
- Старостина A.A., Клочков A.A., Василевская B.B., Хохлов А. Р. Амфифильные гребнеобразные макромолекулы с различной статистикой распределения точек пришивки боковых цепей: математическое моделирование. Высокомолек. Соед., 2008. 50А. с. 1691.
- S. Basu, D. R. Vutukuri, S. Shyamroy, В. S. Sandanaraj, and S. Thayumanavan, Invertible Amphiphilic Homopolymers, J. AM. CHEM. SOC., 2004,126, p. 9890
- E. N. Savariar, S. V. Aathimanikandan, and S. Thayumanava, Supramolecular Assemblies from Amphiphilic Homopolymers: Testing the Scope, J. AM. CHEM. SOC. 2006, 128, p. 16 224
- E. A. Maresov, and A. N. Semenov, Mesoglobule Morphologies of Amphiphilic Polymers, Macromolecules, 2008, 41, pp. 9439−9457
- Vasilevskaya V.V., Markov V.A., Khalatur P. G., Khokhlov A.R. Semiflexible amphiphilic polymers: cylindrical-shaped, collagen-like, and toroidal structures. J.Chem.Phys., 2006. 24. p. 44 914
- Markov V.A., Vasilevskaya V.V., Khalatur P.G., ten Brinke G., Khokhlov A.R. Diagram of state of stiff amphiphilic macromolecules., Macromol. Symposia, 2007, 252, pp. 24−35
- Марков B.A., Василевская B.B., Халатур П. Г., тен Бринке Г., Хохлов А. Р. Конформационные свойства жесткоцепных амфифильных макромолекул: фазовая диаграмма., Высокомолек. Соед. 2008. 50А. с. 965.
- Vasilevskaya V.V., Markov V.A., ten Brinke, G. Khokhlov A.R. Self-organization in solutions of stiff-chain amphiphilic macromolecules. Macromolecules, 2008, 41. p.7722.
- M. Bockstaller, W. Kohler, G. Wegner, D. Vlassopoulos, and G. Fytas, Levels of Structure Formation in Aqueous Solutions of Anisotropic Association Colloids Consisting of Rodlike Polyelectrolytes, Macromolecules, 2001, 34, pp. 6359−6366
- Глаголев M., Василевская B.B., Хохлов A.P., Высокомолек. Coed., 2010, 7, в печати
- Н.С. Andersen, Rattle: A «velocity» version of the shake algorithm for molecular dynamics calculations, J. Comput. Phys., 1983, 52, p.24.
- Binder. K., Monte Carlo and Molecular Dynamics Simulations in Polymer Science, University Press: Oxford, 1995.
- Kim, J. U.- O’Shaughnessy, B. Nanoinclusions in dry polymer brushes. Macromolecules, Macromol. 2006, 39, p. 413.
- Milchev, A.- Dimitrov, D. I.- Binder, K., Excess free energy of nanoparticles in a polymer brush, Polymer, 2008, 49, p. 3611
- Jeon, S. I.- Lee, I.- Andrade, J. H.- de Gennes, P. G. J. Colloid Interface Sci. 1991, 142, p.149.
- I. Szleifer, Protein Adsorption on Surfaces with Grafted Polymers: A Theoretical Approach, Biophys. J1997, 72, pp. 595−612
- Halperin, A., Polymer Brushes that Resist Adsorption of Model Proteins: Design Parameters, Langmuir, 1999, 15, p. 2525.
- Currie, E. P. K.- Van der Gucht, J.- Borisov, О. V.- Cohen Stuart, M. A. Stuffed brushes: theory and experiment, Pure Appl. Chem. 1999, 71, p. 1227.
- Steels, В. M.- Koska, J.- Haynes, C. A., Analysis of brush-particle interactions using self-consistent-field theory, J. Chromatogr В. 2000, 41, p. 743.
- Halperin, A.- Fragneto, G.- Schollier, A.- Sferrazza, M., Primary versus Ternary Adsorption of Proteins onto PEG Brushes, Langmuir, 2007, 23, p. 10 603.
- Andrade, J. D., and V. Hlady. Protein adsorption and materials biocompatibility: a tutorial review and suggested hypotheses. Adv. Polym. Sci. 1986. 79, pp. 1−63.
- Horbett, T. A. Principles underlying the role of adsorbed plasma proteins in blood interactions with foreign materials. Cardiovasc. Pathol. 1993. 2, pp. 137S-148S.
- Luscher, E. F., and S. Weber. The formation of the haemostatic plug-a special case of platelet aggregation: an experiment and a survery of the literature. Thromb. Haemostasis., 1993. 70, pp. 234−237.
- Elbert, D. L.- Hubbell, J. A. Surface Treatments of Polymers for Biocompatibility, Annu. Rev. Mater. Sci. 1996, 26, p. 365.
- Harris, J. M., Poly (Ethylene Glycol) Chemistry: Biotechnical and Biomedical Applications- Ed.- Plenum Press: 1992. New York.
- Lee, J. H.- Lee, H. В.- Andrade, J. D. Blood compatibility of polyeth- ylene oxide surfaces. Prog. Polym. Sci. 1995, 20, p. 1043.
- Goddard, J. M.- Hotchkiss, J. H. Polymer surface modification for the attachment of bioactive compounds, Prog. Polym. Sci., 2007, 32, p. 698.
- Harris, J. M. Poly (Ethylene Glycol) Chemistry: Biotechnical and Biomedical Applications. Plenum Press, 1992. New York.
- Lee, J. H., J. Kopecek, and J. D. Andrade. Protein-resistant surfaces prepared by PEO-containing block copolymer surfactants. J. Biomed. Mater. Res. 1989. 23, pp. 351−368
- Lee, J., P. A. Martic, and J. S. Tan. Protein adsorption on pluronic copolymer-coated polystyrene particles. J. Colloid Interface Sci. 1989. 131, pp. 252−266.
- Tan, J. S., and P. A. Martic. Protein adsorption and conformational change on small polymer particles. J. Colloid Interface Sci. 1990. 136, pp. 415−431.
- Ishihara, K., N. P. Ziats, B. P. Tiemey, N. Nakabayashi, and J. M. Anderson. Protein adsorption from human plasma is reduced on phospholipid polymers. J. Biomed. Mater. Res. 1991. 25, pp. 1397−1407.
- Desai, N. P., and J. A. Hubbell. Biological responses to polyethylene oxide modified polyethylene terephthalate surfaces. J. Biomed. Mater. Res. 1991. 25, pp. 829−843.
- Gombotz, W. R., W. Guanghui, T. A. Horbett, and A. S. Hoffman. Protein adsorption to poly (ethylene oxide) surfaces. J. Biomed. Mater. Res. 1991. 25, pp. 1547−1562.
- Han, D. K., S. Y. Jeong, Y. H. Kim, B. G. Min, and H. I. Cho. Negative cilia concept for thromboresistance: synergistic effect of PEO and sulfonate groups grafted onto polyurethanes. J. Biomed. Mater. Res. 1991. 25, pp. 561−575.
- Amiji, M., and K. Park. 1992. Prevention of protein adsorption and platelet adhesion on surfaces by PEO/PPO/PEO triblock copolymers. Biomaterials. 13, pp. 682−692.
- Park, K. D., and S. W. Kim. PEO-modified surfaces: in vitro, ex vivo, and in-vivo blood compatibility. In Poly (Ethylene Glycol) Chemistry: Biotechnical and Biomedical Applications. J. Miltion Harris, editor. Plenum Press, 1992. New York.
- Bergstrom, К., K. Holmberg, A. Safranj, A. S. Hoffman, M. J. Edgell, A. Kozlowski, B. A. Hovanes, J. M. Harris. Reduction of fibrinogen adsorption on PEG-coated polystyrene surfaces. J. Biomed. Materials Res. 1992. 26, pp. 779−790.
- Fujimoto, К., H. Inoue, and Y. Ikada. Protein adsorption and platelet adhesion onto polyurethane grafted with methoxy-poly (ethylene glycol) methacrylate by plasma technique. J. Biomed. Mater. Res. 1993. 27, pp. 1559−1567.
- Llanos, G. R., and M. V. Sefton. Immobilization of poly (ethylene glycol) onto a poly (vinyl alcohol) hydrogen. 2. Evaluation of thrombogenicity. J. Biomed. Mater. Res., 1993. 27, pp. 1383−1391.
- Lin, Y. S., V. Hlady, and C.-G. Golander. The surface density gradient of grafted poly (ethylene glycol): preparation, characterization and protein adsorption. Colloids Surfaces В Biointerfaces., 1994. 3, pp. 49−62.
- Allen, Т. M., C. Hansen, F. Martin, C. Redemann, and A. Yau-Young. Liposomes containing synthetic lipid derivatives of poly (ethylene glycol) show prolonged circulation half-lives in vivo. Biochim. Biophys. Acta. 1991. 1066, pp. 29−36.
- McPherson, Т. В., S. J. Lee, and K. Park. Proteins at interfaces. II. Fundamental applications. ACS Symp. Ser. 1995, 602, pp. 395−404.
- Yang, J.- Yamato, M.- Okano, Т., Cell-sheet engineering using intelligent surfaces, MRS Bull. 2005, 30, p. 189.
- Kanazawa H., Matsushima Y., and Okano Temperature-responsive chromatography. Trends in analytical chemistry.. 1998, 17, pp. 435−440
- Harris, J. M.- Chess, R. Drug Discovery, Nature Rev, 2003, 2, p. 214.
- Janoff, A. S., Liposomes Rational Design- Ed., Marcel Dekker, New York. 1998.
- Malin Jonsson, Hans-Olof Johansson, Effect of surface grafted polymers on the adsorption of different model proteins, Colloids and Surfaces B: Biointerfaces, 2004, 37, pp. 71−81
- Lai, P.-Y.- Binder, K. Structure and dynamics of grafted polymer layers: A Monte Carlo simulation, J. Chem. Phys., 1991, 95, p. 9288.
- Lai, P. Y.- Zhulina, E. В., J. Monte Carlo test of the self-consistent theory of a polymer brush, Phys. IIFr. 1992, 2, p. 547.
- Widom, B. J., Some Topics in the Theory of Fluids, J. Chem. Phys. 1963, 39, p. 2808
- Frenkel, D.- Smit, B. Understanding Molecular Simulation. From Algorithms to Applications, 2nd ed.- Academic Press: London, 2002.
- Leach, A. R. Molecular Modeling Principles and Applications, Longman Essex, 1996. p. 860
- Ferrenberg, A. M.- Swendsen, R. H., Optimized Monte Carlo data analysis, Phys. Rev. Lett., 1989, 63, p. 1195.