Dòng chảy năng lượng dao động qua các giao diện heme–cytochrome c và cytochrome c–nước

Leitner DM, Straub JE (2009) Proteins: energy, heat and signal flow. Taylor and Francis Press, New York Smock RG, Gierasch LM (2009) Sending signals dynamically. Science 324:198–203 Fujisaki H, Straub JE (2005) Vibrational energy relaxation in proteins. Proc Natl Acad Sci (USA) 102:7626–7631 Leitner DM (2008) Energy flow in proteins. Ann Rev Phys Chem 59:233–259 Gunasekaran K, Ma B, Nussinov R (2004) Is allostery an intrinsic property of all dynamic proteins? Proteins Struct Func Bioinform 57:433–443 Nussinov R, Tsai C-J (2012) Allostery in disease and in drug discovery. Cell 153:293–305 Agarwal PK (2005) Role of protein dynamics in reaction rate enhancement by enzymes. J Am Chem Soc 127:15248–15256 Fang C, Frontiera RR, Tran R, Mathies RA (2009) Mapping GFP structure evolution during proton transfer with femtosecond Raman spectroscopy. Nature 462:200–205 Buchli B, Waldauer SA, Walser R, Donten ML, Pfister R, Bloechliger N, Steiner S, Caflisch A, Zerbe O, Hamm P (2013) Kinetic response of a photoperturbed allosteric protein. Proc Natl Acad Sci USA 110:11725–11730 Nagy AM, Raicu V, Miller RJD (2005) Nonlinear optical studies of heme protein dynamics: implications for proteins as hybrid states of matter. Biochim Biophys Acta 1749:148–172 Sagnella DE, Straub JE, Jackson TA, Lim M, Anfinrud PA (1999) Vibrational population relaxation of carbon monoxide in the heme pocket of carbonmonoxy myoglobin: comparison of time-resolved mid-IR absorbance experiments and molecular dynamics simulations. Proc Natl Acad Sci USA 96:14324–14329 Henry ER, Eaton WA, Hochstrasser RM (1986) Molecular dynamics simulations of cooling in laser-excited heme proteins. Proc Natl Acad Sci USA 83:8982–8986 Lian T, Locke B, Kholodenko Y, Hochstrasser RM (1994) Energy flow from solute to solvent probed by femtosecond ir spectroscopy: malachite green and heme protein solutions. J Phys Chem 98:11648–11656 Gnanasekaran R, Agbo JK, Leitner DM (2011) Communication maps computed for homodimeric hemoglobin: computational study of water-mediated energy transport in proteins. J Chem Phys 135:065103 Champion PM (2005) Following the flow of energy in biomolecules. Science 310:980–982 Sagnella DE, Straub JE (2001) Directed energy “funneling” mechanism for heme cooling following ligand photolysis or direct excitation in solvated carbonmonoxy myoglobin. J Phys Chem B 105:7057–7063 Takayanagi M, Okumura H, Nagaoka M (2007) Anisotropic structural relaxation and its correlation with the excess energy diffusion in the incipient process of photodissociated MbCO: high-resolution analysis via ensemble perturbation method. J Phys Chem B 111:864–869 Nagaoka M, Yu I, Takayanagi M (2009) Energy flow analysis in proteins via ensemble molecular dynamics simulations: time-resolved vibrational analysis and surficial Kirkwood-Buff Theory. In: Leitner DM, Straub JE (eds) Proteins: energy, heat and signal flow. Taylor & Francis Group, CRC Press, Boca Raton, pp 169–196 Mizutani Y, Kitagawa T (1997) Direct observation of cooling of heme upon photodissociation of carbonmonoxy myoglobin. Science 278:443–446 Koyama M, Neya S, Mizutani Y (2006) Role of heme propionates of myoglobin in vibrational energy relaxation. Chem Phys Lett 430:404–408 Sato A, Mizutani Y (2005) Picosecond structural dynamics of myoglobin following photodissociation of carbon monoxide as revealed by ultraviolet time-resolved resonance Raman spectroscopy. Biochem 44:14709–14714 Ye X, Demidov A, Champion PM (2002) Measurements of the photodissociation quantum yields of MbNO and MbO2 and the vibrational relaxation of the six-coordinate heme species. J Am Chem Soc 124:5914–5924 Ow Y-LP, Green DR, Hao Z, Mak TW (2008) Cytochrome c: functions beyond respiration. Nat Rev Mol Cell Biol 9:532–542 Vos MH (2008) Ultrafast dynamics of ligands within heme proteins. Biochim Biophys Acta 1777:15–31 Zang C, Stevens JA, Link JJ, Guo L, Wang L, Zhong D (2009) Ultrafast proteinquake dynamics in cytochrome c. J Am Chem Soc 131:2846–2852 Fujii N, Mizuno M, Mizutani Y (2011) Direct observation of vibrational energy flow in cytochrome c. J Phys Chem B 115:13057–13064 Zhang P, Malolepsza E, Straub JE (2012) Dynamics of methionine ligand rebinding in cytochrome c. J Phys Chem B 116:6980–6990 Zhang P, Ahn SW, Straub JE (2013) “Strange kinetics” in the temperature dependence of methionine ligand rebinding dynamics in cytochrome c. J Phys Chem B 117:7190–7202 Bu L, Straub JE (2003) Simulating vibrational energy flow in proteins: relaxation rate and mechanism for heme cooling in cytochrome c. J Phys Chem B 107:12339–12345 Zhang Y, Fujisaki H, Straub JE (2009) Mode specific vibrational energy relaxation of amide I and II modes in N-methylacetamide/water clusters: the intra- and inter-molecular energy transfer mechanisms. J Phys Chem A 113:3051–3060 Zhang Y, Fujisaki H, Straub JE (2009) Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. I. Five-coordinate ferrous iron porphydin model. J Chem Phys 130:025102 Leitner DM (2001) Vibrational energy transfer in helices. Phys Rev Lett 87:188102 Leitner DM, Wolynes PG (1996) Statistical properties of localized vibrational eigenstates. Chem Phys Lett 258:18–24 Leitner DM, Wolynes PG (1997) Vibrational mixing and energy flow in polyatomic molecules: quantitative prediction using local random matrix theory. J Phys Chem A 101:541–548 Keshavamurthy S (2013) Scaling perspective on intramolecular vibrational energy flow: analogies, insights and challenges. Adv Chem Phys 153:43–110 Semparithi A, Keshavamurthy S (2006) Intramolecular vibrational energy redistributions as diffusion in state space: classical-quantum correspondence. J Chem Phys 125:141101 Leitner DM, Gruebele M (2008) A quantum model of restricted vibrational energy flow on the way to the transition state in unimolecular reactions. Mol Phys 106:433–442 Gruebele M, Bigwood R (1998) Molecular vibrational energy flow: beyond the golden rule. Int Rev Phys Chem 17:91–145 Bu L, Straub JE (2003) Vibrational energy relaxation of ‘tailored’ hemes in myoglobin following ligand photolysis supports energy funneling mechanism of heme ‘cooling’. J Phys Chem B 107:10634–10639 Lervik A, Bresme F, Kjelstrup S, Bedeaux D, Rubi JM (2010) Heat transfer in protein–water interfaces. Phys Chem Chem Phys 12:1610–1617 Leitner DM (2013) Thermal boundary conductance and rectification in molecules. J Phys Chem B 117:12820–12828 Xu Y, Leitner DM (2014) Vibrational energy flow through the green fluorescent protein water interface: communication maps and thermal boundary conductance. J Phys Chem B. doi:10.1021/jp412141z Leitner DM (2009) Frequency resolved communication maps for proteins and other nanoscale materials. J Chem Phys 130:195101 Berne BJ, Borkovec M, Straub JE (1988) Classical and modern methods in reaction rate theory. J Phys Chem 92:3711–3725 Leitner DM (2005) Heat transport in molecules and reaction kinetics: the role of quantum energy flow and localization. Adv Chem Phys 130B:205–256 Komatsuzaki T, Baba A, Kawai S, Toda M, Straub JE, Berry RS (2011) Ergodic problems for real complex systems in chemical physics. Adv Chem Phys 145:171–220 Leitner DM, Matsunaga Y, Li C-B, Komatsuzaki T, Shojiguchi A, Toda M (2011) Non-brownian phase space dynamics of molecules, the nature of their vibrational states, and non-RRKM kinetics. Adv Chem Phys 145:83–122 Li CB, Matsunaga Y, Toda M, Komatsuzaki T (2005) Phase space reaction network on a multisaddle energy landscape: HCN isomerization. J Chem Phys 123:184301 Shojiguchi A, Li CB, Komatsuzaki T, Toda M (2007) Fractional behavior in multi-dimensional Hamiltonian systems describing reactions. Phys Rev E 76:056205 Toda M (2005) Global aspects of chemical reactions in multidimensional phase space. Adv Chem Phys 130A:337–399 Ezra GS, Martens CC, Fried LE (1987) Semiclassical quantization of polyatomic molecules: some recent developments. J Phys Chem 91:3721–3730 Uzer T (1991) Theories of intramolecular vibrational energy transfer. Phys Rep 199(2):73–146 Keshavamurthy S, Ezra GS (1997) Eigenstate assignments and the quantum-classical correspondence for highly-excited vibrational states of the Baggot H2O Hamiltonian. J Chem Phys 107:156–179 Leitner DM, Wolynes PG (1996) Vibrational relaxation and energy localization in polyatomics: effects of high-order resonances on flow rates and the quantum ergodicity transition. J Chem Phys 105:11226–11236 Logan DE, Wolynes PG (1990) Quantum localization and energy flow in many-dimensional Fermi resonant systems. J Chem Phys 93:4994–5012 Lervik A, Bresme F, Kjelstrup S (2009) Heat transfer in soft nanoscale interfaces: the influence of interface curvature. Soft Matter 5:2407–2414 Nguyen PH, Park SM, Stock G (2010) Nonequilibrium molecular dynamics simulation of the energy transfer through a peptide helix. J Chem Phys 132:025102 Nguyen PH, Hamm P, Stock G (2009) Nonequilibrium molecular dynamics simulation of photoinduced energy flow in peptides: theory meets experiment. In: Leitner DM, Straub JE (eds) Proteins: energy, heat and signal flow. Taylor & Francis Group, CRC Press, Boca Raton, pp 149–168 Yu X, Leitner DM (2003) Vibrational energy transfer and heat conduction in a protein. J Phys Chem B 107:1698–1707 Yu X, Leitner DM (2005) Heat flow in proteins: computation of thermal transport coefficients. J Chem Phys 122:054902 Botan V, Backus EHG, Pfister R, Moretto A, Crisma M, Toniolo C, Nguyen PH, Stock G, Hamm P (2007) Energy transport in peptide helices. Proc Natl Acad Sci USA 104:12749–12754 Kholodenko Y, Volk M, Gooding E, Hochstrasser RM (2000) Energy dissipation and relaxation processes in deoxymyoglobin after photoexcitation in the Soret region. Chem Phys 259:71–87 Helbing J, Devereux M, Nienhaus K, Nienhaus GU, Hamm P, Meuwly M (2012) Temperature dependence of the heat diffusivity of proteins. J Phys Chem A 116:2620–2628 Müller-Werkmeister HM, Bredenbeck J (2014) A donor-acceptor pair for the real time study of vibrational energy transfer in proteins. Phys Chem Chem Phys 16:3261–3266 Hopkins PE (2013) Thermal transport across solid interfaces with nanoscale imperfections: effects of roughness, disorder, dislocations and bonding on thermal boundary conductance (Review Article). ISRN Mech Eng, 2013: 682586 Buldum A, Leitner DM, Ciraci S (1999) Thermal conduction through a molecule. Europhys Lett 47:208–212 Segal D, Nitzan A, Hänggi P (2003) Thermal conductance through molecular wires. J Chem Phys 119:6840–6855 Leitner DM, Wolynes PG (2000) Heat flow through an insulating nanocrystal. Phys Rev E 61:2902–2908 Allen PB, Feldman JL (1993) Thermal conductivity of disordered harmonic solids. Phys Rev B 48:12581–12588 Xu Y, Leitner DM (2014) Communication maps of vibrational energy transport in photoactive yellow protein. J Phys Chem A. doi:10.1021/jp411281y Ishikura T, Yamato T (2006) Energy transfer pathways relevant for long-range intramolecular signaling of photosensory protein revealed by microscopic energy conductivity analysis. Chem Phys Lett 432:533–537 Ota N, Agard DA (2005) Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion. J Mol Biol 351:345–354 Gnanasekaran R, Xu Y, Leitner DM (2010) Dynamics of water clusters confined in proteins: a molecular dynamics simulation study of interfacial waters in a dimeric hemoglobin. J Phys Chem B 114:16989–16996 Yu X, Leitner DM (2003) Anomalous diffusion of vibrational energy in proteins. J Chem Phys 119:12673–12679 Yu X, Leitner DM (2006) Thermal conductivity computed for vitreous silica and methyl-doped silica above the plateau. Phys Rev B 74:184305 Swartz ET, Pohl RO (1989) Thermal boundary resistance. Rev Mod Phys 61:605–668 Yu X, Leitner DM (2005) Thermal transport coefficients for liquid and glassy water computer from a harmonic aqueous glass. J Chem Phys 123:104503 Bigwood R, Gruebele M, Leitner DM, Wolynes PG (1998) The vibrational energy flow transition in organic molecules: theory meets experiment. Proc Natl Acad Sci USA 95:5960–5967 Agbo JK, Leitner DM, Myshakin EM, Jordan KD (2007) Quantum energy flow and the kinetics of water shuttling between hydrogen bonding sites on trans-formanilide (TFA). J Chem Phys 127:064315 Acharya H, Mozdzierz NJ, Keblinski P, Garde S (2012) How chemistry, nanoscale roughness, and the direction of heat flow affect thermal conductance of solid–water interfaces. Ind Eng Chem Res 51:1767–1773 Agbo JK, Gnanasekaran R, Leitner DM (2014) Communication maps: exploring energy transport through proteins and water. Isr J Chem. doi:10.1002/ijch.201300139 Volkov AM, vanNuland NAJ (2012) Electron transfer interactome of cytochrome c. PLoS Comput Biol 8:e1002807