Heat transfer in protein-water interfaces.

We investigate using transient non-equilibrum molecular dynamics simulation the temperature relaxation process of three structurally different proteins in water, namely; myoglobin, green fluorescence protein (GFP) and two conformations of the Ca(2+)-ATPase protein. By modeling the temperature relaxation process using the solution of the heat diffusion equation we compute the thermal conductivity and thermal diffusivity of the proteins, as well as the thermal conductance of the protein-water interface. Our results indicate that the temperature relaxation of the protein can be described using a macroscopic approach. The protein-water interface has a thermal conductance of the order of 100-270 MW K(-1) m(-2), characteristic of water-hydrophilic interfaces. The thermal conductivity of the proteins is of the order of 0.1-0.2 W K(-1) m(-1) as compared with approximately 0.6 W K(-1) m(-1) for water, suggesting that these proteins can develop temperature gradients within the biomolecular structures that are larger than those of aqueous solutions. We find that the thermal diffusivity of the transmembrane protein, Ca(2+)-ATPase is about three times larger than that of myoglobin or GFP. Our simulation shows that the Kapitza length of these structurally different proteins is of the order of 1 nm, showing that the protein-water interface should play a major role in defining the thermal relaxation of biomolecules.

[1]  M. Nadeau Proteins : Structure , Function , and Genetics , 2022 .

[2]  M. Nakasako,et al.  Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 Å resolution , 2000, Nature.

[3]  D. Bedeaux,et al.  Energy dissipation in slipping biological pumps. , 2005, Physical chemistry chemical physics : PCCP.

[4]  D. Bedeaux,et al.  Coefficients for active transport and thermogenesis of Ca2+-ATPase isoforms. , 2009, Biophysical journal.

[5]  A. Kidera,et al.  Temperature Dependence of Vibrational Energy Transfer in a Protein Molecule , 2003 .

[6]  D. Leitner Energy flow in proteins. , 2008, Annual review of physical chemistry.

[7]  E. Grant,et al.  Dielectric dispersion and dipole moment of myoglobin in water , 1972, Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences.

[8]  P. Mazur,et al.  Non-equilibrium thermodynamics, , 1963 .

[9]  D. Bedeaux,et al.  Non-equilibrium Thermodynamics of Heterogeneous Systems , 2008, Series on Advances in Statistical Mechanics.

[10]  K. Bugaev,et al.  On Thermodynamics of Small Systems , 2005 .

[11]  B. Hafskjold,et al.  NONEQUILIBRIUM MOLECULAR DYNAMICS STUDY OF HEAT CONDUCTION IN IONIC SYSTEMS , 1996 .

[12]  Marc J. Assael,et al.  The thermal conductivity of n-hexane, n-heptane, and n-decane by the transient hot-wire method , 1987 .

[13]  David M. Leitner,et al.  Vibrational Energy Transfer and Heat Conduction in a Protein , 2003 .

[14]  S. Brereton Life , 1876, The Indian medical gazette.

[15]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[16]  S. Harvey,et al.  The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition , 1998, J. Comput. Chem..

[17]  Y. S. Touloukian Thermophysical properties of matter , 1970 .

[18]  E N Baker,et al.  X-ray crystallographic studies of seal myoglobin. The molecule at 2.5 A resolution. , 1969, Journal of molecular biology.

[19]  A. Abdel-azim Fundamentals of Heat and Mass Transfer , 2011 .

[20]  H. Frauenfelder,et al.  Picosecond thermometer in the amide I band of myoglobin. , 2005, Physical review letters.

[21]  David A Agard,et al.  Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion. , 2005, Journal of molecular biology.

[22]  Paul V Braun,et al.  Thermal conductance of hydrophilic and hydrophobic interfaces. , 2006, Physical review letters.

[23]  V. Hilser,et al.  The heat capacity of proteins , 1995, Proteins.

[24]  Lila M Gierasch,et al.  The changing landscape of protein allostery. , 2006, Current opinion in structural biology.

[25]  Chen Xu,et al.  A structural model for the catalytic cycle of Ca(2+)-ATPase. , 2002, Journal of molecular biology.

[26]  I. Muegge,et al.  Diffusion of two different water models and thermal conductivity in a protein—water system , 1996 .

[27]  T. Straatsma,et al.  THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS , 1987 .

[28]  P. Champion,et al.  Investigations of the thermal response of laser-excited biomolecules. , 1994, Biophysical journal.

[29]  Kotaro Oyama,et al.  Microscopic detection of thermogenesis in a single HeLa cell. , 2007, Biophysical journal.

[30]  K. Pearson,et al.  Biometrika , 1902, The American Naturalist.

[31]  R. Ranganathan,et al.  Evolutionarily conserved pathways of energetic connectivity in protein families. , 1999, Science.

[32]  Ernesto Carafoli,et al.  Calcium pump of the plasma membrane , 1991 .

[33]  R. Rosenfeld Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[34]  宁北芳,et al.  疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A , 2005 .

[35]  P. Agarwal Role of protein dynamics in reaction rate enhancement by enzymes. , 2005, Journal of the American Chemical Society.

[36]  J. Ross Energy transfer from adenosine triphosphate. , 2006, The journal of physical chemistry. B.

[37]  D. Leitner,et al.  Heat flow in proteins: computation of thermal transport coefficients. , 2005, The Journal of chemical physics.

[38]  M. Nagaoka,et al.  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. , 2007, The journal of physical chemistry. B.

[39]  T. L. Hill,et al.  Thermodynamics of Small Systems , 2002 .

[40]  P. Privalov,et al.  Heat capacity of proteins. II. Partial molar heat capacity of the unfolded polypeptide chain of proteins: protein unfolding effects. , 1990, Journal of molecular biology.

[41]  K. Sharp,et al.  Pump‐probe molecular dynamics as a tool for studying protein motion and long range coupling , 2006, Proteins.

[42]  S. Garde,et al.  Strong frequency dependence of dynamical coupling between protein and water. , 2008, The Journal of chemical physics.

[43]  Takahisa Yamato,et al.  Energy transfer pathways relevant for long-range intramolecular signaling of photosensory protein revealed by microscopic energy conductivity analysis , 2006 .

[44]  D. Bedeaux,et al.  The measurable heat flux that accompanies active transport by Ca2+-ATPase. , 2008, Physical chemistry chemical physics : PCCP.

[45]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[46]  T. Ikeshoji,et al.  Non-equilibrium molecular dynamics calculation of heat conduction in liquid and through liquid-gas interface , 1994 .

[47]  S. Shapiro,et al.  An Analysis of Variance Test for Normality (Complete Samples) , 1965 .

[48]  Fernando Bresme,et al.  Water polarization under thermal gradients. , 2008, Physical review letters.

[49]  S. Garde,et al.  Thermal resistance of nanoscopic liquid-liquid interfaces: dependence on chemistry and molecular architecture. , 2005, Nano letters.

[50]  K. Schulten,et al.  A simulated cooling process for proteins , 1990 .

[51]  D. Leitner Vibrational Energy Transfer in Helices , 2001 .

[52]  F. Bresme Equilibrium and nonequilibrium molecular-dynamics simulations of the central force model of water , 2001 .

[53]  Claudio Toniolo,et al.  Energy transport in peptide helices , 2007, Proceedings of the National Academy of Sciences.

[54]  A. Kidera,et al.  Vibrational energy transfer in a protein molecule. , 2000, Physical review letters.

[55]  J. Tainer,et al.  Mechanism and energetics of green fluorescent protein chromophore synthesis revealed by trapped intermediate structures , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[56]  R. Hochstrasser,et al.  Molecular dynamics simulations of cooling in laser-excited heme proteins. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[57]  S. Schultz,et al.  Physiological Reviews , 1941 .

[58]  S. Kjelstrup,et al.  Heat transfer in soft nanoscale interfaces: the influence of interface curvature , 2009 .

[59]  Y. Mizutani,et al.  Direct observation of cooling of heme upon photodissociation of carbonmonoxy myoglobin. , 1997, Science.

[60]  Wilfred F. van Gunsteren,et al.  An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase , 2001, J. Comput. Chem..

[61]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997 .

[62]  R. Miller,et al.  Vibrational energy relaxation and structural dynamics of heme proteins. , 1991, Annual review of physical chemistry.

[63]  John E. Straub,et al.  Time scales and pathways for kinetic energy relaxation in solvated proteins: Application to carbonmonoxy myoglobin , 2000 .

[64]  J. Straub,et al.  Directed Energy "Funneling" Mechanism for Heme Cooling Following Ligand Photolysis or Direct Excitation in Solvated Carbonmonoxy Myoglobin , 2001 .