Conical intersection dynamics in solution: the chromophore of Green Fluorescent Protein.

We use ab initio results to reparameterize a multi-reference semiempirical method to reproduce the ground and excited state potential energy surfaces (PESs) for the chromophore of Green Fluorescent Protein (GFP). The validity of the new parameter set is tested, and the new method is combined with a quantum mechanical/molecular mechanical (QM/MM) treatment so that it can be applied in the solution phase. Solvent effects on the energetics of the relevant conical intersections are explored. We then combine this representation of the ground and excited state PESs with the full multiple spawning (FMS) nonadiabatic wavepacket dynamics method to simulate the photodynamics of the neutral GFP chromophore in both gas and solution phases. In these calculations, the PESs and their nonadiabatic couplings are evaluated simultaneously with the nuclear dynamics, ie. "on-the-fly". The effect of solvation is seen to be quite dramatic, resulting in an order of magnitude decrease in the excited state lifetime. We observe a correlated torsion about a double bond and its adjacent single bond in both gas and solution phases. This is discussed in the context of previous proposals about minimal volume isomerization mechanisms in protein environments.

[1]  Bjoern O. Roos.  Theoretical Studies of Electronically Excited States of Molecular Systems Using Multiconfigurational Perturbation Theory , 1999 .

[2]  F. Gubler,et al.  Use of the green fluorescent protein to locate α-amylase gene expression in barley grains. , 2002, Functional plant biology : FPB.

[3]  Hollis T. Cline,et al.  Multiphoton Imaging of Neurons in Living Tissue: Acquisition and Analysis of Time-Lapse Morphological Data , 2002, Real Time Imaging.

[4]  H. C. Longuet-Higgins.  The symmetry groups of non-rigid molecules , 1963 .

[5]  M. Zimmer,et al.  Green fluorescent protein (GFP): applications, structure, and related photophysical behavior. , 2002, Chemical reviews.

[6]  D. Yarkony.  Nuclear dynamics near conical intersections in the adiabatic representation: I. The effects of local topography on interstate transitions , 2001 .

[7]  G. Segal.  Semiempirical Methods of Electronic Structure Calculation , 1977 .

[8]  W. Almers,et al.  Targeting of green fluorescent protein to neuroendocrine secretory granules: a new tool for real time studies of regulated protein secretion. , 1997, European journal of cell biology.

[9]  Charles H. Martin,et al.  Abinitio computation of semiempirical π‐electron methods. V. Geometry dependence of Hν π‐electron effective integrals , 1996 .

[10]  M. Ikawa,et al.  `Green mice' and their potential usage in biological research , 1998, FEBS letters.

[11]  Kazuo Kobayashi,et al.  High-level expression of a sweet protein, monellin, in the food yeast Candida utilis , 1997, Nature Biotechnology.

[12]  M. Karplus,et al.  A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations , 1990 .

[13]  E. Suzuki,et al.  Postsynaptic filopodia in muscle cells interact with innervating motoneuron axons , 2000, Nature Neuroscience.

[14]  E. Teller.  Internal Conversion in Polyatomic Molecules , 1969 .

[15]  Jacques Haiech,et al.  Fluorescent derivatives of the GFP chromophore give a new insight into the GFP fluorescence process. , 2003, Biophysical journal.

[16]  Haruki Niwa,et al.  Fluorescent properties of model chromophores of tyrosine-66 substituted mutants of Aequorea green fluorescent protein (GEP) , 1998 .

[17]  P. Tonge,et al.  Probing the ground state structure of the green fluorescent protein chromophore using Raman spectroscopy. , 2000, Biochemistry.

[18]  S. Inouye,et al.  Mechanism of the redox reaction of the Aequorea green fluorescent protein (GFP) , 1997 .

[19]  T. Martínez,et al.  Conical Intersections in Solution: A QM/MM Study Using Floating Occupation Semiempirical Configuration Interaction Wave Functions , 2003 .

[20]  Hans-Joachim Werner,et al.  Ab initio excited-state dynamics of the photoactive yellow protein chromophore. , 2003, Journal of the American Chemical Society.

[21]  R. Tsien,et al.  green fluorescent protein , 2020, Catalysis from A to Z.

[22]  U. Singh,et al.  A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl− exchange reaction and gas phase protonation of polyethers , 1986 .

[23]  R. Levine,et al.  First‐principles molecular dynamics on multiple electronic states: A case study of NaI , 1996 .

[24]  Massimo Olivucci,et al.  Relationship between photoisomerization path and intersection space in a retinal chromophore model. , 2003, Journal of the American Chemical Society.

[25]  Hans-Joachim Werner,et al.  Multireference perturbation theory for large restricted and selected active space reference wave functions , 2000 .

[26]  A. Warshel,et al.  A new view of the dynamics of singlet cis-trans photoisomerization , 1979 .

[27]  Robert S. H. Liu,et al.  Photochemistry of polyenes. 23. Application of the H.T.-n mechanism of photoisomerization to the photocycles of bacteriorhodopsin. A model study , 1985 .

[28]  William H. Press,et al.  Numerical recipes , 1990 .

[29]  Stewart Cn,et al.  The Utility of Green Fluorescent Protein in Transgenic Plants , 2001 .

[30]  T. Martínez,et al.  Ab Initio Multiple Spawning: Photochemistry from First Principles Quantum Molecular Dynamics , 2000 .

[31]  R. Tsien,et al.  Fluorescent indicators for Ca2+based on green fluorescent proteins and calmodulin , 1997, Nature.

[32]  T. Martínez,et al.  Nonadiabatic molecular dynamics: Validation of the multiple spawning method for a multidimensional problem , 1998 .

[33]  V. Subramaniam,et al.  Three photoconvertible forms of green fluorescent protein identified by spectral hole-burning , 1999, Nature Structural Biology.

[34]  Robert S. H. Liu,et al.  Photoisomerization by hula-twist: a fundamental supramolecular photochemical reaction. , 2001, Accounts of chemical research.

[35]  B. Reid,et al.  Chromophore formation in green fluorescent protein. , 1997, Biochemistry.

[36]  Stephen R. Meech,et al.  An ultrafast polarisation spectroscopy study of internal conversion and orientational relaxation of the chromophore of the green fluorescent protein , 2001 .

[37]  Albert Stolow,et al.  Mechanism and dynamics of azobenzene photoisomerization. , 2003, Journal of the American Chemical Society.

[38]  Functional expression of green fluorescent protein derivatives in Halobacterium salinarum. , 1998, FEMS microbiology letters.

[39]  Giovanni Granucci,et al.  Molecular gradients for semiempirical CI wavefunctions with floating occupation molecular orbitals , 2000 .

[40]  S. Forrest,et al.  Fluorophores Related to the Green Fluorescent Protein and Their Use in Optoelectronic Devices , 2000 .

[41]  T. Carrington.  Geometry of intersecting potential surfaces , 1974 .

[42]  Todd J. Martínez,et al.  Photodynamics of ethylene: ab initio studies of conical intersections , 2000 .

[43]  A molecular mechanics and database analysis of the structural preorganization and activation of the chromophore-containing hexapeptide fragment in green fluorescent protein. , 1997, Journal of biomolecular structure & dynamics.

[44]  J. Hynes,et al.  On the Dissociation of Aromatic Radical Anions in Solution , 2003 .

[45]  George H. Patterson,et al.  A Photoactivatable GFP for Selective Photolabeling of Proteins and Cells , 2002, Science.

[46]  Stephen R. Meech,et al.  Radiationless relaxation in a synthetic analogue of the green fluorescent protein chromophore , 2001 .

[47]  Volkhard Helms,et al.  Low-lying electronic excitations of the green fluorescent protein chromophore , 2000 .

[48]  T. Martínez,et al.  Optimization of Conical Intersections with Floating Occupation Semiempirical Configuration Interaction Wave Functions , 2002 .

[49]  A. Asato,et al.  The primary process of vision and the structure of bathorhodopsin: a mechanism for photoisomerization of polyenes. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[50]  T. Martínez,et al.  Classical/quantal method for multistate dynamics: A computational study , 1996 .

[51]  F. Bernardi,et al.  Conical intersections as a mechanistic feature of organic photochemistry , 1995 .

[52]  Eric J. Heller,et al.  Frozen Gaussians: A very simple semiclassical approximation , 1981 .

[53]  Eamonn F. Healy,et al.  Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model , 1985 .

[54]  S. Meech,et al.  Ultrafast fluorescence of the chromophore of the green fluorescent protein in alcohol solutions , 2002 .

[55]  Notker Rösch,et al.  Structure and rotation barriers for ground and excited states of the isolated chromophore of the green fluorescent protein , 1998 .

[56]  Steen Brøndsted Nielsen,et al.  Chromophores of the green fluorescent protein studied in the gas phase , 2002 .

[57]  T. Laino,et al.  Semiclassical simulation of photochemical reactions in condensed phase , 2003 .

[58]  D. Yarkony.  Conical Intersections: The New Conventional Wisdom , 2001 .

[59]  T. Martínez,et al.  Direct Observation of Disrotatory Ring-Opening in Photoexcited Cyclobutene Using ab Initio Molecular Dynamics , 2000 .

[60]  J. Pople,et al.  Approximate Self-Consistent Molecular Orbital Theory. I. Invariant Procedures , 1965 .

[61]  R. Levine,et al.  Dynamics of the collisional electron transfer and femtosecond photodissociation of NaI on ab initio electronic energy curves , 1996 .

[62]  Robert S. H. Liu,et al.  A bioorganic view of the chemistry of vision: H.T.-n and B.P.-m,n mechanisms for reactions of confined, anchored polyenes , 1986 .

[63]  T. Martínez.  Ab initio molecular dynamics around a conical intersection: Li(2p) + H2 , 1997 .

[64]  Ab initio molecular dynamics with equation-of-motion coupled-cluster theory: electronic absorption spectrum of ethylene , 2003 .

[65]  R. Levine,et al.  Multi-Electronic-State Molecular Dynamics: A Wave Function Approach with Applications , 1996 .

[66]  Michael J. Bearpark,et al.  A direct method for the location of the lowest energy point on a potential surface crossing , 1994 .

[67]  G. Striker,et al.  Photochromicity and fluorescence lifetimes of green fluorescent protein , 1999 .

[68]  T. Martínez,et al.  Ab initio molecular dynamics study of cis–trans photoisomerization in ethylene , 1998 .

[69]  J. Hynes,et al.  On the dissociation of aromatic radical anions in solution. , 2003, Chemphyschem : a European journal of chemical physics and physical chemistry.

[70]  H. C. Longuet-Higgins,et al.  Intersection of potential energy surfaces in polyatomic molecules , 1963 .

[71]  Todd J Martinez,et al.  The role of intersection topography in bond selectivity of cis-trans photoisomerization , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[72]  Arieh Warshel,et al.  Bicycle-pedal model for the first step in the vision process , 1976, Nature.

[73]  Todd J. Martínez,et al.  Photochemistry from first principles — advances and future prospects , 2001 .

[74]  Thom Vreven,et al.  Potential-energy surfaces for ultrafast photochemistry Static and dynamic aspects , 1998 .

[75]  John F. Stanton,et al.  The equation of motion coupled‐cluster method. A systematic biorthogonal approach to molecular excitation energies, transition probabilities, and excited state properties , 1993 .

[76]  Vladislav V. Yakovlev,et al.  Quantum Control of Population Transfer in Green Fluorescent Protein by Using Chirped Femtosecond Pulses , 1998 .

[77]  Green fluorescent proteins as optically controllable elements in bioelectronics , 2001, cond-mat/0107576.

[78]  Martin Klessinger,et al.  Excited states and photochemistry of organic molecules , 1995 .

[79]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[80]  Y. Wang,et al.  Visualizing and quantifying protein secretion using a Renilla luciferase-GFP fusion protein. , 2000, Luminescence : the journal of biological and chemical luminescence.

[81]  S. Boxer,et al.  Ultra-fast excited state dynamics in green fluorescent protein: multiple states and proton transfer. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[82]  Andrew Gilbert,et al.  Essentials of Molecular Photochemistry , 1991 .

[83]  J. Pople,et al.  Self—Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian—Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules , 1972 .

[84]  F. Dudek,et al.  Pseudorabies virus expressing enhanced green fluorescent protein: A tool for in vitro electrophysiological analysis of transsynaptically labeled neurons in identified central nervous system circuits. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[85]  S. Inouye,et al.  Chemical nature of the light emitter of the Aequorea green fluorescent protein. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[86]  Todd J. Martínez,et al.  Ab Initio Quantum Molecular Dynamics , 2002 .

[87]  Jiali Gao,et al.  Hybrid Quantum and Molecular Mechanical Simulations: An Alternative Avenue to Solvent Effects in Organic Chemistry , 1996 .

[88]  T. Martínez,et al.  Ab Initio Study of Cis−Trans Photoisomerization in Stilbene and Ethylene , 2003 .

[89]  N. Turro.  Modern Molecular Photochemistry , 1978 .

[90]  Edward Teller,et al.  The Crossing of Potential Surfaces. , 1937 .

[91]  George C. Schatz,et al.  The analytical representation of electronic potential-energy surfaces , 1989 .

[92]  Gero Miesenböck,et al.  Visualizing secretion and synaptic transmission with pH-sensitive green fluorescent proteins , 1998, Nature.

[93]  R. Robey,et al.  pH-dependent fluorescence of a heterologously expressed Aequorea green fluorescent protein mutant: in situ spectral characteristics and applicability to intracellular pH estimation. , 1998, Biochemistry.

[94]  J A McCammon,et al.  Shedding light on the dark and weakly fluorescent states of green fluorescent proteins. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[95]  W. M. Westler,et al.  Chemical structure of the hexapeptide chromophore of the Aequorea green-fluorescent protein. , 1993, Biochemistry.

[96]  A S Verkman,et al.  Green fluorescent protein as a noninvasive intracellular pH indicator. , 1998, Biophysical journal.

[97]  D. Yarkony,et al.  On the intersection of two potential energy surfaces of the same symmetry. Systematic characterization using a Lagrange multiplier constrained procedure , 1993 .

[98]  M. Levitt,et al.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.

[99]  W. Ward,et al.  Reversible denaturation of Aequorea green-fluorescent protein: physical separation and characterization of the renatured protein. , 1982, Biochemistry.

[100]  William W. Ward,et al.  SPECTRAL PERTURBATIONS OF THE AEQUOREA GREEN‐FLUORESCENT PROTEIN , 1982 .

[101]  M. Dewar,et al.  Ground States of Molecules. 38. The MNDO Method. Approximations and Parameters , 1977 .

[102]  B. Montgomery Pettitt,et al.  Simple intramolecular model potentials for water , 1987 .

[103]  J. Lippincott-Schwartz,et al.  Studying protein dynamics in living cells , 2001, Nature Reviews Molecular Cell Biology.

[104]  M. Chalfie,et al.  Green fluorescent protein as a marker for gene expression. , 1994, Science.