Mô phỏng động lực học phân tử nhiệt độ thấp của cytochrome c tim ngựa và so sánh với dữ liệu tán xạ neutron không đàn hồi

Abel S, Waks M, Marchi M (2010) Molecular dynamics simulations of cytochrome c unfolding in AOT reverse micelles: the first steps. Eur Phys E Soft Matter 32:399–409 Autenrieth F, Tajkhorshid E, Baudry J, Luthey-Schulten Z (2004) Classical force field parameters for the heme prosthetic group of cytochrome c. J Comput Chem 25:1613–1622 Banci L, Gori-Savellini G, Turano P (1997) A molecular dynamics study in explicit water of the reduced and oxidized forms of yeast iso-1-cytochrome c. Eur J Biochem 249:716–723 Battistuzzi G, Borsari M, Sola M (2001) Redox properties of cytochrome c. Antioxid. Redox Signal 3:279–291 Beissenhirtz MK, Scheller FW, Lisdat F (2004) A superoxide sensor based on a multilayer cytochrome c electrode. Anal Chem 76:4665–4671 Bellissent-Funel MC (2004) Internal motions in proteins: a combined neutron scattering and molecular modelling approach. Pramana 63:91–97 Bertini I, Rosato A, Turano P (2004) Cytochrome c folding/unfolding: a unifying picture. J Porphyrins Phthalocyanines 8:238–245 Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187–217 Brown KG, Erfurth SC, Small EW, Peticolas WL (1972) Conformationally dependent low-frequency motions of proteins by laser Raman spectroscopy. Proc Natl Acad Sci USA 69:1467–1469 Bu L, Straub JE (2003a) Vibrational frequency shifts and relaxation rates for a selected vibrational mode in cytochrome c. Biophys J 85:1429–1439 Bu L, Straub JE (2003b) Simulating vibrational energy flow in proteins: relaxation rate and mechanism for heme cooling in cytochrome c. J Phys Chem B 107:12339–12345 Bushnell GW, Louie GV, Brayer GD (1990) High-resolution three-dimensional structure of horse heart cytochrome c. J Mol Biol 214:585–595 Connatser RW Jr, Belch H, Jirik L, Leach DJ, Trouw FR, Zanotti JM, Ren Y, Crawford RK, Carpenter JM, Price DL, Loong CK, Hodges JP, Herwig KW (2003) The QuasiElastic Neutron Spectrometer (QENS): recent upgrade and performance. In: Mank G, Conrad H (eds) Proceedings of the 16th meeting of the international collaboration on advanced neutron sources, Forschungszentrum Julich GmbH: Julich, pp 279–288 Cukier RI (2004) Quantum molecular dynamics simulation of proton transfer in cytochrome c oxidase. Biochim Biophys Acta 1656:189–202 Cukier RI (2005) A molecular dynamics study of water chain formation in the proton-conducting K channel of cytochrome c oxidase. Biochim Biophys Acta 1706:134–146 Cusack S, Smith J, Finney J, Karplus M, Trewhella J (1986) Low frequency dynamics of proteins studied by neutron time-of-flight spectroscopy. Physica B+C 136:256–259 Cusack S, Smith J, Finney J, Tidor B, Karplus M (1988) Inelastic neutron scattering analysis of picosecond internal protein dynamics: comparison of harmonic theory with experiment. J Mol Biol 202:903–908 Daidone I, Amadei A, Roccatano D, No AD (2003) Molecular dynamics simulation of protein folding by essential dynamics sampling: folding landscape of horse heart cytochrome c. Biophys J 85:2865–2871 de Biase PM, Paggi DA, Doctorovich F, Hildebrandt P, Estrin DA, Murgida DH, Marti MA (2009) Molecular basis for the electric field modulation of cytochrome c structure and function. J Am Chem Soc 131:16248–16256 Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577–8593 Gabel F, Bicout D, Lehnert U, Tehei M, Weik M, Zaccai G (2002) Protein dynamics studied by neutron scattering. Q Rev Biophys 35:327–367 Garcia AE, Hummer G (1999) Conformational dynamics of cytochrome c: correlation to hydrogen exchange. Proteins Struct Funct Genet 36:175–191 Genzel L, Keilmann F, Martin TP, Winterling G, Yacoby Y, Frohlich H, Makinen MW (1976) Low frequency Raman spectra of lysozyme. Biopolymers 15:219–225 Goupil-Lamy AV, Smith JC, Yunoki J, Parker SF, Kataoka M (1997) High-resolution vibrational inelastic neutron scattering: a new spectroscopic tool for globular proteins. J Am Chem Soc 119:9268–9273 Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein MLJ (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935 Joti Y, Kitao A, Go N (2004) Molecular simulation study to examine the possibility of detecting collective motion in protein by inelastic neutron scattering. Phys B 350:e627–e630 Karino K, Matubayasi N (2011) Communication: free-energy analysis of hydration effect on protein with explicit solvent: equilibrium fluctuation of cytochrome c. J Chem Phys 134:041105 Karplus M, Gao YQ, Ma JP, van der Vaart A, Yang W (2005) Protein structural transitions and their functional role. Philos Trans R Soc Lond Ser A 363:331–355 Kataoka M, Kamikubo H, Nakagawa H, Parker SF, Smith J (2003) Neutron inelastic scattering as a high-resolution vibrational spectroscopy: new tool for the study of protein dynamics. Spectroscopy 17:529–535 Kiel JL (1995) Type-b cytochromes: sensors and switches. CRC Press, Boca Raton Kumar A, Mishra PC, Verma CS, Renugopalakrishnan V (2005) Density functional study of the heme moiety of cytochrome c. Int J Quantum Chem 102:1002–1009 Loong CK, Ikeda S, Carpenter J (1987) The resolution function of a pulsed-source neutron chopper spectrometer. Nucl Instrum Methods Phys Res Sect A 260:381–402 MacKerell AD Jr, Banavali N, Foloppe N (2000) Development and current status of the CHARMM force field for nucleic acids. Biopolymers 56:257–265 Mao Y, Ratner MA, Jarrold MF (2001) Molecular dynamics simulations of the rehydration of folded and unfolded cytochrome C ions in the vapor phase. J Am Chem Soc 123:6503–6507 McCammon JA, Gelin BR, Karplus M, Wolynes PG (1976) The hinge-bending mode in lysozyme. Nature 262:325–326 McCammon JA, Gelin BR, Karplus M (1977) Dynamics of folded proteins. Nature 267:585–590 Miyamoto S, Kollman PA (1992) SETTLE: an analytical version of the SHAKE and RATTLE algorithms for rigid water models. J Comput Chem 13:952–962 Norberg J, Nilsson L (2003) Advances in biomolecular simulations: methodology and recent applications. Q Rev Biophys 36:257–306 Nordgren CE, Tobias DJ, Klein ML, Blasie JK (2002) Molecular dynamics simulations of a hydrated protein vectorially oriented on polar and nonpolar soft surfaces. Biophys J 83:2906–2917 Olkhova E, Hutter MC, Lill MA, Helms V, Michel H (2004) Dynamic water networks in cytochrome c oxidase from Paracoccus denitrificans investigated by molecular dynamics simulations. Biophys J 86:1873–1889 Parrish JC, Guillemette JG, Wallace CJ (2001) A tale of two charges: distinct roles for an acidic and a basic amino acid in the structure and function of cytochrome c. Biochem Cell Biol 79:83–91 Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781–1802 Prabhakaran M, Gursahani SH, Verma CS, Garduno-Juarez R, Renugopalakrishnan V (2004) Cytochrome c: the effect of temperature and pressure from molecular dynamics simulations. J Phys Chem Solids 65:1615–1622 Price DL, Sköld K (1986) Introduction to neutron scattering. In: Celotta R, Levine J (eds) Methods of experimental physics. Academic Press, London, pp 1–98 Renugopalakrishnan V, Bhatnagar RS (1984) Fourier transform infrared photoacoustic spectroscopy: a novel conformational probe. Demonstration of α-helical conformation of poly (γ-benzyl glutamate). J Am Chem Soc 106:2217–2219 Renugopalakrishnan V, Collette TW, Carreira LA, Bhatnagar RS (1985) Low-frequency Raman spectra as a conformational probe for polypeptides and proteins. Macromolecules 18:1786–1788 Renugopalakrishnan V, Ortiz-Lombardia M, Verma CJ (2005) Electrostatics of cytochrome-c assemblies. J Mol Model 11:265–270 Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23:327–341 Simonson T (2002) Gaussian fluctuations and linear response in an electron transfer protein. Proc Natl Acad Sci USA 99:6544–6549 Singh SR, Prakash S, Vasu V, Karunakaran C (2009) Conformational flexibility decreased due to Y67F and F82H mutations in cytochrome c: molecular dynamics simulation studies. J Mol Graphics Model 28:270–277 Smith JC (2000) Inelastic and quasielastic neutron scattering: complementarity with biomolecular simulation. In: Fanchon E (ed) Structure and dynamics of biomolecules. Oxford University Press, Oxford, pp 161–180 Tarek M, Tobias DJ (2000) The dynamics of protein hydration water: a quantitative comparison of molecular dynamics simulations and neutron-scattering experiments. Biophys J 79:3244–3257 Tarek M, Tobias DJ (2001) Effects of solvent damping on side chain and backbone contributions to the protein boson peak. J Chem Phys 115:1607–1612 Tarek M, Tobias DJ (2002) Role of protein-water hydrogen bond dynamics in the protein dynamical transition. Phys Rev Lett 88:138101 van Gunsteren WF, Berendsen HJC (1988) A leap-frog algorithm for stochastic dynamics. Mol Simul 1:173–185 Verma CS, Renugopalakrishnan V (2004) Computer experiments in the design of bionanodevices, modeling and simulating materials nanoworld. In: Vincenzini P, Zerbetto F (eds) Advances in science and technology. Techna Group Srl., Faenza, pp 321–328 Zaccai G (2004) The effect of water on protein dynamics. Philos Trans R Soc London A 359:1269–1275