Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation

Observing ultrafast myoglobin dynamics The oxygen-storage protein myoglobin was the first to have its three-dimensional structure determined and remains a workhorse for understanding how protein structure relates to function. Barends et al. used x-ray free-electron lasers with femtosecond short pulses to directly observe motions that occur within half a picosecond of CO dissociation (see the Perspective by Neutze). Combining the experiments with simulations shows that ultrafast motions of the heme couple to subpicosecond protein motions, which in turn couple to large-scale motions. Science, this issue p. 445, see also p. 381 Time-resolved crystallography at an x-ray laser reveals ultrafast structural changes in myoglobin upon ligand dissociation. [Also see Perspective by Neutze] The hemoprotein myoglobin is a model system for the study of protein dynamics. We used time-resolved serial femtosecond crystallography at an x-ray free-electron laser to resolve the ultrafast structural changes in the carbonmonoxy myoglobin complex upon photolysis of the Fe-CO bond. Structural changes appear throughout the protein within 500 femtoseconds, with the C, F, and H helices moving away from the heme cofactor and the E and A helices moving toward it. These collective movements are predicted by hybrid quantum mechanics/molecular mechanics simulations. Together with the observed oscillations of residues contacting the heme, our calculations support the prediction that an immediate collective response of the protein occurs upon ligand dissociation, as a result of heme vibrational modes coupling to global modes of the protein.

[1]  Victor Guallar,et al.  Modeling of ligation-induced helix/loop displacements in myoglobin: toward an understanding of hemoglobin allostery. , 2006, Journal of the American Chemical Society.

[2]  J. Straub,et al.  Diversity of solvent dependent energy transfer pathways in heme proteins. , 2009, The journal of physical chemistry. B.

[3]  R. Dror,et al.  Improved side-chain torsion potentials for the Amber ff99SB protein force field , 2010, Proteins.

[4]  Parr,et al.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.

[5]  Richard L. Martin NATURAL TRANSITION ORBITALS , 2003 .

[6]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[7]  Garth J. Williams,et al.  Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein , 2014, Science.

[8]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[9]  P. Kozlowski,et al.  Reductive cleavage mechanism of methylcobalamin: elementary steps of Co-C bond breaking. , 2007, The journal of physical chemistry. B.

[10]  D. Barrick,et al.  Investigations of Anharmonic Low-Frequency Oscillations in Heme Proteins † , 2002 .

[11]  Car,et al.  Unified approach for molecular dynamics and density-functional theory. , 1985, Physical review letters.

[12]  D. Houde,et al.  Time-resolved Raman spectroscopy with subpicosecond resolution: vibrational cooling and delocalization of strain energy in photodissociated (carbonmonoxy)hemoglobin. , 1987, Biochemistry.

[13]  J Berendzen,et al.  Crystal structures of myoglobin-ligand complexes at near-atomic resolution. , 1999, Biophysical journal.

[14]  P. Maldivi,et al.  Mössbauer characterization of an unusual high-spin side-on peroxo-Fe3+ species in the active site of superoxide reductase from Desulfoarculus Baarsii. Density functional calculations on related models. , 2004, Biochemistry.

[15]  R. Miller,et al.  Femtosecond Heterodyne-Detected Four-Wave-Mixing Studies of Deterministic Protein Motions. 2. Protein Response , 1999 .

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

[17]  Hans-Joachim Bungartz,et al.  Molecular Dynamics Simulation , 2015 .

[18]  A. Becke,et al.  Density-functional exchange-energy approximation with correct asymptotic behavior. , 1988, Physical review. A, General physics.

[19]  E. Gross,et al.  Density-Functional Theory for Time-Dependent Systems , 1984 .

[20]  I. Schlichting,et al.  Trapping intermediates in the crystal: ligand binding to myoglobin. , 2000, Current opinion in structural biology.

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

[22]  Aleksandr V. Smirnov,et al.  Watching a Protein as it Functions with 150-ps Time-Resolved X-ray Crystallography , 2003, Science.

[23]  R. K. Nesbet,et al.  Self‐Consistent Orbitals for Radicals , 1954 .

[24]  Sébastien Boutet,et al.  The Coherent X-ray Imaging instrument at the Linac Coherent Light Source , 2015, Journal of synchrotron radiation.

[25]  F. van Mourik,et al.  A cascade through spin states in the ultrafast haem relaxation of met-myoglobin. , 2014, The Journal of chemical physics.

[26]  A. Nagy,et al.  Observation of the cascaded atomic-to-global length scales driving protein motion , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[27]  O. Horner,et al.  Mössbauer identification of a protonated ferryl species in catalase from Proteus mirabilis: density functional calculations on related models. , 2006, Journal of inorganic biochemistry.

[28]  Y Lecarpentier,et al.  Spectral evidence for sub‐picosecond iron displacement after ligand detachment from hemoproteins by femtosecond light pulses. , 1983, The EMBO journal.

[29]  S. Franzen,et al.  Evidence for sub-picosecond heme doming in hemoglobin and myoglobin: a time-resolved resonance Raman comparison of carbonmonoxy and deoxy species. , 1995, Biochemistry.

[30]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[31]  Berk Hess,et al.  GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .

[32]  Carsten Kutzner,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[33]  Andrew E. Torda,et al.  The GROMOS biomolecular simulation program package , 1999 .

[34]  B. Soep,et al.  First observation in the gas phase of the ultrafast electronic relaxation pathways of the S(2) states of heme and hemin. , 2010, Physical chemistry chemical physics : PCCP.

[35]  M. Klein,et al.  Nosé-Hoover chains : the canonical ensemble via continuous dynamics , 1992 .

[36]  G. Kachalova,et al.  A steric mechanism for inhibition of CO binding to heme proteins. , 1999, Science.

[37]  Martins,et al.  Efficient pseudopotentials for plane-wave calculations. , 1991, Physical review. B, Condensed matter.

[38]  S. Nosé A molecular dynamics method for simulations in the canonical ensemble , 1984 .

[39]  C. Bostedt,et al.  Spectral encoding of x-ray/optical relative delay. , 2011, Optics express.

[40]  C. Rovira Structure, protonation state and dynamics of catalase compound II. , 2005, Chemphyschem : a European journal of chemical physics and physical chemistry.

[41]  Donny Magana,et al.  Anisotropic energy flow and allosteric ligand binding in albumin , 2014, Nature Communications.

[42]  W. R. Wadt,et al.  Ab initio effective core potentials for molecular calculations , 1984 .

[43]  《中华放射肿瘤学杂志》编辑部 Medline , 2001, Current Biology.

[44]  N Go,et al.  Deoxymyoglobin studied by the conformational normal mode analysis. I. Dynamics of globin and the heme-globin interaction. , 1990, Journal of molecular biology.

[45]  M Eichinger,et al.  Influence of the heme pocket conformation on the structure and vibrations of the Fe-CO bond in myoglobin: a QM/MM density functional study. , 2001, Biophysical journal.

[46]  M. Alfonso-Prieto,et al.  Electronic state of the molecular oxygen released by catalase. , 2008, The journal of physical chemistry. A.

[47]  J. Perdew,et al.  Density-functional approximation for the correlation energy of the inhomogeneous electron gas. , 1986, Physical review. B, Condensed matter.

[48]  Anton Barty,et al.  Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser , 2014, Nature Methods.

[49]  V. Hornak,et al.  Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.

[50]  F. Schotte,et al.  Time-dependent atomic coordinates for the dissociation of carbon monoxide from myoglobin. , 2006, Acta crystallographica. Section D, Biological crystallography.

[51]  M. Karplus,et al.  Nonexponential relaxation after ligand dissociation from myoglobin: a molecular dynamics simulation. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[52]  V. Raicu,et al.  Nonlinear optical studies of heme protein dynamics: implications for proteins as hybrid states of matter. , 2005, Biochimica et biophysica acta.

[53]  Pietro Vidossich,et al.  The molecular mechanism of the catalase reaction. , 2009, Journal of the American Chemical Society.

[54]  L. Zhu,et al.  Observation of coherent reaction dynamics in heme proteins. , 1994, Science.

[55]  J. Straub,et al.  Vibrational energy relaxation in proteins. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[56]  R. Hochstrasser,et al.  Spectroscopic studies of oxy- and carbonmonoxyhemoglobin after pulsed optical excitation. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[57]  N Go,et al.  Deoxymyoglobin studied by the conformational normal mode analysis. II. The conformational change upon oxygenation. , 1990, Journal of molecular biology.

[58]  Tai-Sung Lee,et al.  A pseudobond approach to combining quantum mechanical and molecular mechanical methods , 1999 .

[59]  Hoover,et al.  Canonical dynamics: Equilibrium phase-space distributions. , 1985, Physical review. A, General physics.

[60]  Philippe H. Hünenberger,et al.  Optimal charge-shaping functions for the particle–particle—particle–mesh (P3M) method for computing electrostatic interactions in molecular simulations , 2000 .

[61]  G. Sciara,et al.  Extended subnanosecond structural dynamics of myoglobin revealed by Laue crystallography. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[62]  Anton Barty,et al.  Crystallographic data processing for free-electron laser sources , 2013, Acta crystallographica. Section D, Biological crystallography.

[63]  Y. Mizutani,et al.  Time-resolved resonance Raman study on ultrafast structural relaxation and vibrational cooling of photodissociated carbonmonoxy myoglobin. , 2002, Biopolymers.

[64]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[65]  Michele Parrinello,et al.  Equilibrium Geometries and Electronic Structure of Iron−Porphyrin Complexes: A Density Functional Study , 1997 .

[66]  Anton Barty,et al.  CASS - CFEL-ASG software suite , 2012, Comput. Phys. Commun..

[67]  Elspeth F. Garman,et al.  RADDOSE-3D: time- and space-resolved modelling of dose in macromolecular crystallography , 2013 .

[68]  Garth J. Williams,et al.  High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography , 2012, Science.

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

[70]  E. Henry,et al.  Simulation of the kinetics of ligand binding to a protein by molecular dynamics: geminate rebinding of nitric oxide to myoglobin. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[71]  M. Karplus,et al.  Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin , 1990 .

[72]  E. Alp,et al.  Long-range reactive dynamics in myoglobin. , 2001, Physical review letters.

[73]  R. Hochstrasser,et al.  Energy dissipation and relaxation processes in deoxy myoglobin after photoexcitation in the Soret region , 2000 .

[74]  Robert M. Sweet,et al.  Structure of a ligand-binding intermediate in wild-type carbonmonoxy myoglobin , 2000, Nature.

[75]  Sébastien Boutet,et al.  The CSPAD megapixel x-ray camera at LCLS , 2012, Other Conferences.

[76]  A. Becke Density-functional thermochemistry. III. The role of exact exchange , 1993 .

[77]  Steven G. Louie,et al.  Nonlinear ionic pseudopotentials in spin-density-functional calculations , 1982 .

[78]  Teizo Kitagawa,et al.  Primary protein response after ligand photodissociation in carbonmonoxy myoglobin , 2007, Proceedings of the National Academy of Sciences.

[79]  U Weierstall,et al.  Injector for scattering measurements on fully solvated biospecies. , 2012, The Review of scientific instruments.

[80]  S. Nosé A unified formulation of the constant temperature molecular dynamics methods , 1984 .

[81]  N. Pannu,et al.  REFMAC5 for the refinement of macromolecular crystal structures , 2011, Acta crystallographica. Section D, Biological crystallography.

[82]  V. Schramm Transition States and transition state analogue interactions with enzymes. , 2015, Accounts of chemical research.

[83]  R. J. Dwayne Miller,et al.  Ultrafast Phase Grating Studies of Heme Proteins: Observation of the Low-Frequency Modes Directing Functionally Important Protein Motions , 1998 .

[84]  R D Young,et al.  Protein states and proteinquakes. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[85]  C. de Graaf,et al.  Ultrafast deactivation mechanism of the excited singlet in the light-induced spin crossover of [Fe(2,2'-bipyridine)3]2+. , 2013, Chemistry.

[86]  R. Hochstrasser,et al.  ENERGY FLOW FROM SOLUTE TO SOLVENT PROBED BY FEMTOSECOND IR SPECTROSCOPY :MALACHITE GREEN AND HEME PROTEIN SOLUTIONS , 1994 .

[87]  M. Levitt,et al.  Molecular dynamics simulation of photodissociation of carbon monoxide from hemoglobin. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[88]  G. Schirò,et al.  Observing heme doming in myoglobin with femtosecond X-ray absorption spectroscopya) , 2015, Structural dynamics.

[89]  M. Head‐Gordon,et al.  Initial Steps of the Photodissociation of the CO Ligated Heme Group , 2003 .

[90]  W. Cao,et al.  Rapid timescale processes and the role of electronic surface coupling in the photolysis of diatomic ligands from heme proteins. , 2004, Faraday discussions.

[91]  S. Boxer,et al.  Functional Aspects of Ultra-rapid Heme Doming in Hemoglobin, Myoglobin, and the Myoglobin Mutant H93G (*) , 1995, The Journal of Biological Chemistry.

[92]  J. Petrich,et al.  Photophysics and reactivity of heme proteins: a femtosecond absorption study of hemoglobin, myoglobin, and protoheme. , 1988, Biochemistry.

[93]  R. J. Dwayne Miller,et al.  ENERGETICS AND DYNAMICS OF DETERMINISTIC PROTEIN MOTION , 1994 .

[94]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[95]  P. Champion,et al.  Investigations of Coherent Vibrational Oscillations in Myoglobin , 2000 .

[96]  Alessandro Laio,et al.  A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations , 2002 .

[97]  Matteo Levantino,et al.  Ultrafast myoglobin structural dynamics observed with an X-ray free-electron laser , 2015, Nature Communications.