Protein hydration dynamics and molecular mechanism of coupled water-protein fluctuations.

Protein surface hydration is fundamental to its structural stability and flexibility, and water-protein fluctuations are essential to biological function. Here, we report a systematic global mapping of water motions in the hydration layer around a model protein of apomyoglobin in both native and molten globule states. With site-directed mutagenesis, we use intrinsic tryptophan as a local optical probe to scan the protein surface one at a time with single-site specificity. With femtosecond resolution, we examined 16 mutants in two states and observed two types of water-network relaxation with distinct energy and time distributions. The first water motion results from the local collective hydrogen-bond network relaxation and occurs in a few picoseconds. The initial hindered motions, observed in bulk water in femtoseconds, are highly suppressed and drastically slow down due to structured water-network collectivity in the layer. The second water-network relaxation unambiguously results from the lateral cooperative rearrangements in the inner hydration shell and occurs in tens to hundreds of picoseconds. Significantly, this longtime dynamics is the coupled interfacial water-protein motions and is the direct measurement of such cooperative fluctuations. These local protein motions, although highly constrained, are necessary to assist the longtime water-network relaxation. A series of correlations of hydrating water dynamics and coupled fluctuations with local protein's chemical and structural properties were observed. These results are significant and reveal various water behaviors in the hydration layer with wide heterogeneity. We defined a solvation speed and an angular speed to quantify the water-network rigidity and local protein flexibility, respectively. We also observed that the dynamic hydration layer extends to more than 10 A. Finally, from native to molten globule states, the hydration water networks loosen up, and the protein locally becomes more flexible with larger global plasticity and partial unfolding.

[1]  Tarun Jain,et al.  The role of water in protein-DNA recognition. , 2004, Annual review of biophysics and biomolecular structure.

[2]  Alan E. Johnson,et al.  Femtosecond microscopic solvation dynamics of aqueous solutions , 1988 .

[3]  Y. Pocker.  Water in enzyme reactions: biophysical aspects of hydration-dehydration processes , 2000, Cellular and Molecular Life Sciences CMLS.

[4]  Andrea Amadei,et al.  Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding , 2007, Proceedings of the National Academy of Sciences.

[5]  H. Frauenfelder,et al.  A unified model of protein dynamics , 2009, Proceedings of the National Academy of Sciences.

[6]  S. Boxer,et al.  Dynamic Stokes shift in green fluorescent protein variants , 2007, Proceedings of the National Academy of Sciences.

[7]  Biman Bagchi,et al.  Water dynamics in the hydration layer around proteins and micelles. , 2005, Chemical reviews.

[8]  B. Valeur,et al.  RESOLUTION OF THE FLUORESCENCE EXCITATION SPECTRUM OF INDOLE INTO THE 1La AND 1Lb EXCITATION BANDS * , 1977, Photochemistry and photobiology.

[9]  D. Zhong,et al.  Femtosecond studies of tryptophan solvation: correlation function and water dynamics at lipid surfaces , 2004 .

[10]  A. Zewail,et al.  Ordered water structure at hydrophobic graphite interfaces observed by 4D, ultrafast electron crystallography , 2009, Proceedings of the National Academy of Sciences.

[11]  B. Cohen,et al.  Measurement of solvation responses at multiple sites in a globular protein. , 2007, The journal of physical chemistry. B.

[12]  Luyuan Zhang,et al.  Mapping hydration dynamics around a protein surface , 2007, Proceedings of the National Academy of Sciences.

[13]  M. Maroncelli,et al.  Subpicosecond Measurements of Polar Solvation Dynamics: Coumarin 153 Revisited , 1995 .

[14]  Chandra S Verma,et al.  Prion and water: tight and dynamical hydration sites have a key role in structural stability. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[15]  B M Pettitt,et al.  Residence times of water molecules in the hydration sites of myoglobin. , 2000, Biophysical journal.

[16]  S. H. A. Chen,et al.  Observation of fragile-to-strong dynamic crossover in protein hydration water. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[17]  P E Wright,et al.  Native and non-native secondary structure and dynamics in the pH 4 intermediate of apomyoglobin. , 2000, Biochemistry.

[18]  A. Zewail,et al.  Biological water: femtosecond dynamics of macromolecular hydration , 2002 .

[19]  D. Tobias,et al.  Role of protein-water hydrogen bond dynamics in the protein dynamical transition. , 2002, Physical review letters.

[20]  Martin Gruebele,et al.  Protein sequence- and pH-dependent hydration probed by terahertz spectroscopy. , 2008, Journal of the American Chemical Society.

[21]  G. Fleming,et al.  Solvation Dynamics in Protein Environments Studied by Photon Echo Spectroscopy , 1999 .

[22]  Salvatore Cannistraro,et al.  Molecular Dynamics of Water at the Protein-Solvent Interface , 2002 .

[23]  David N. Beratan,et al.  The Nature of Aqueous Tunneling Pathways Between Electron-Transfer Proteins , 2005, Science.

[24]  C. Viappiani,et al.  Fast events in protein folding: structural volume changes accompanying the early events in the N-->I transition of apomyoglobin induced by ultrafast pH jump. , 2000, Biophysical journal.

[25]  M. Gruebele,et al.  Direct observation of fast protein folding: the initial collapse of apomyoglobin. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Nokyoung Park,et al.  Structural characterization of the molten globule state of apomyoglobin by limited proteolysis and HPLC-mass spectrometry. , 2005, Biochemistry.

[27]  Y. Jan,et al.  Probing Protein Electrostatics with a Synthetic Fluorescent Amino Acid , 2002, Science.

[28]  Ruhong Zhou,et al.  Hydrophobic Collapse in Multidomain Protein Folding , 2004, Science.

[29]  W. Lu,et al.  Ultrafast hydration dynamics in melittin folding and aggregation: helix formation and tetramer self-assembly. , 2005, The journal of physical chemistry. B.

[30]  P E Wright,et al.  Structural characterization of a partly folded apomyoglobin intermediate. , 1990, Science.

[31]  Philip Ball,et al.  Water as a biomolecule. , 2008, Chemphyschem : a European journal of chemical physics and physical chemistry.

[32]  Martin Gruebele,et al.  An extended dynamical hydration shell around proteins , 2007, Proceedings of the National Academy of Sciences.

[33]  H. Frauenfelder,et al.  Protein folding is slaved to solvent motions , 2006, Proceedings of the National Academy of Sciences.

[34]  S. J. Singer,et al.  Origin of slow relaxation following photoexcitation of W7 in myoglobin and the dynamics of its hydration layer. , 2008, The journal of physical chemistry. B.

[35]  C. Ruan,et al.  Ultrafast Electron Crystallography of Interfacial Water , 2004, Science.

[36]  Margaret E. Johnson,et al.  Hydration water dynamics near biological interfaces. , 2009, The journal of physical chemistry. B.

[37]  J. Finney.  Overview lecture. Hydration processes in biological and macromolecular systems. , 1996, Faraday discussions.

[38]  Klaus Gerwert,et al.  Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy , 2006, Nature.

[39]  Graham R. Fleming,et al.  Femtosecond solvation dynamics of water , 1994, Nature.

[40]  Kurt Wüthrich,et al.  Hydration and DNA Recognition by Homeodomains , 1996, Cell.

[41]  A. Zewail,et al.  Protein surface hydration mapped by site-specific mutations , 2006, Proceedings of the National Academy of Sciences.

[42]  M. Barkley,et al.  Toward understanding tryptophan fluorescence in proteins. , 1998, Biochemistry.

[43]  R. Dyer,et al.  Fast events in protein folding: relaxation dynamics of secondary and tertiary structure in native apomyoglobin. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[44]  Greg L. Hura,et al.  Hydration dynamics near a model protein surface. , 2004, Biophysical journal.

[45]  R. Allemann,et al.  Role of water in the catalytic cycle of E. coli dihydrofolate reductase , 2002, Protein science : a publication of the Protein Society.

[46]  P. Rossky,et al.  How protein surfaces induce anomalous dynamics of hydration water. , 2007, The journal of physical chemistry. B.

[47]  A. Zewail,et al.  Femtosecond studies of protein-DNA binding and dynamics: histone I. , 2001, Chemphyschem : a European journal of chemical physics and physical chemistry.

[48]  Martin Caffrey,et al.  Ultrafast hydration dynamics in the lipidic cubic phase: Discrete water structures in nanochannels. , 2006, The journal of physical chemistry. B.

[49]  M. Karplus,et al.  Probing polar solvation dynamics in proteins: a molecular dynamics simulation analysis. , 2007, The journal of physical chemistry. B.

[50]  S. Sukits,et al.  Conformational properties of native sperm whale apomyoglobin in solution , 1999, Protein science : a publication of the Protein Society.

[51]  Luyuan Zhang,et al.  Femtosecond studies of tryptophan fluorescence dynamics in proteins: local solvation and electronic quenching. , 2006, The journal of physical chemistry. B.

[52]  Jeremy C. Smith,et al.  Translational hydration water dynamics drives the protein glass transition. , 2003, Biophysical journal.

[53]  Richard K Darst,et al.  Mechanistic elements of protein cold denaturation. , 2008, The journal of physical chemistry. B.

[54]  D. Zhong.  Hydration Dynamics and Coupled Water–Protein Fluctuations Probed by Intrinsic Tryptophan , 2009 .

[55]  J. Onuchic,et al.  Water mediation in protein folding and molecular recognition. , 2006, Annual review of biophysics and biomolecular structure.

[56]  Gerhard Hummer,et al.  Water in nonpolar confinement: from nanotubes to proteins and beyond. , 2008, Annual review of physical chemistry.

[57]  B. Pettitt,et al.  Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment. , 2002, Accounts of chemical research.

[58]  H. Frauenfelder,et al.  Slaving: Solvent fluctuations dominate protein dynamics and functions , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[59]  S. Buldyrev,et al.  Glass transition in biomolecules and the liquid-liquid critical point of water. , 2006, Physical Review Letters.

[60]  S. Mukamel,et al.  Influence of medium dynamics on solvation and charge separation reactions: comparison of a simple alcohol and a protein "solvent" , 1990 .

[61]  P. Callis,et al.  Mechanisms of tryptophan fluorescence shifts in proteins. , 2001, Biophysical journal.

[62]  P. Ball.  Water as an active constituent in cell biology. , 2008, Chemical reviews.

[63]  Vijay S Pande,et al.  Protein folding under confinement: A role for solvent , 2007, Proceedings of the National Academy of Sciences.

[64]  H. Jane Dyson,et al.  Structural and dynamic characterization of partially folded states of apomyoglobin and implications for protein folding , 1998, Nature Structural Biology.

[65]  Martin Gruebele,et al.  Real-time detection of protein-water dynamics upon protein folding by terahertz absorption spectroscopy. , 2008, Angewandte Chemie.

[66]  J. Knutson,et al.  Subpicosecond Fluorescence Spectra of Tryptophan in Water , 2001 .

[67]  Martin Chaplin,et al.  Do we underestimate the importance of water in cell biology? , 2006, Nature Reviews Molecular Cell Biology.

[68]  Volkhard Helms,et al.  Protein dynamics tightly connected to the dynamics of surrounding and internal water molecules. , 2007, Chemphyschem : a European journal of chemical physics and physical chemistry.

[69]  W. F. Beck,et al.  Protein-Matrix Solvation Dynamics in the α Subunit of C-Phycocyanin , 1996 .

[70]  Satoshi Takahashi,et al.  Collapse and search dynamics of apomyoglobin folding revealed by submillisecond observations of alpha-helical content and compactness. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[71]  Luyuan Zhang,et al.  Ultrafast quenching of tryptophan fluorescence in proteins: Interresidue and intrahelical electron transfer , 2008 .

[72]  R. L. Baldwin,et al.  Probing the stability of a partly folded apomyoglobin intermediate by site-directed mutagenesis. , 1991, Biochemistry.

[73]  S. Sligar,et al.  The role of Val68(E11) in ligand binding to sperm whale myoglobin. Site-directed mutagenesis of a synthetic gene. , 1990, The Journal of biological chemistry.

[74]  R. Winter,et al.  Molecular Dynamics Simulations of Staphylococcal Nuclease: Properties of Water at the Protein Surface , 2004 .

[75]  Dagmar Ringe,et al.  Solvent mobility and the protein 'glass' transition , 2000, Nature Structural Biology.

[76]  B. Schoenborn,et al.  Molecular dynamics simulation of hydration in myoglobin , 1995, Proteins.

[77]  Samir Kumar Pal,et al.  Biological water at the protein surface: Dynamical solvation probed directly with femtosecond resolution , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[78]  A. Sancar,et al.  Femtosecond Dynamics of DNA Photolyase: Energy Transfer of Antenna Initiation and Electron Transfer of Cofactor Reduction , 2004 .

[79]  Dongping Zhong,et al.  Hydration dynamics and time scales of coupled water-protein fluctuations. , 2007, Journal of the American Chemical Society.

[80]  J. Gilmore,et al.  Quantum dynamics of electronic excitations in biomolecular chromophores: role of the protein environment and solvent. , 2006, Journal of Physical Chemistry A.

[81]  S. Boxer,et al.  Dielectric relaxation in a protein matrix , 1992 .

[82]  P. Wolynes,et al.  Water in protein structure prediction. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[83]  Joan-Emma Shea,et al.  Probing the folding free energy landscape of the src-SH3 protein domain , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[84]  R. Casadio,et al.  The effect of tryptophanyl substitution on folding and structure of myoglobin. , 2000, European journal of biochemistry.

[85]  S. Sligar,et al.  The effects of amino acid substitution at position E7 (residue 64) on the kinetics of ligand binding to sperm whale myoglobin. , 1990, The Journal of biological chemistry.

[86]  S. J. Singer,et al.  A molecular dynamics study of Lys-Trp-Lys: structure and dynamics in solution following photoexcitation. , 2006, Journal of Physical Chemistry B.

[87]  A. Zewail,et al.  Femtosecond studies of protein-ligand hydrophobic binding and dynamics: human serum albumin. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[88]  Lijuan Wang,et al.  Dissection of complex protein dynamics in human thioredoxin , 2007, Proceedings of the National Academy of Sciences.

[89]  F. Gai,et al.  Infrared study of the effect of hydration on the amide I band and aggregation properties of helical peptides. , 2007, The journal of physical chemistry. B.

[90]  Carla Mattos,et al.  Protein-water interactions in a dynamic world. , 2002, Trends in biochemical sciences.

[91]  J. Olson,et al.  Solution and Crystal Structures of a Sperm Whale Myoglobin Triple Mutant That Mimics the Sulfide-binding Hemoglobin fromLucina pectinata * , 1998, The Journal of Biological Chemistry.

[92]  Luyuan Zhang,et al.  Ultrafast solvation dynamics of human serum albumin: correlations with conformational transitions and site-selected recognition. , 2006, The journal of physical chemistry. B.

[93]  R. Dyer,et al.  Primary folding dynamics of sperm whale apomyoglobin: core formation. , 2003, Biophysical journal.

[94]  Samir Kumar Pal,et al.  Dynamics of water in biological recognition. , 2004, Chemical reviews.

[95]  P E Wright,et al.  Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin. , 1993, Science.

[96]  A. Zewail,et al.  Hydration at the surface of the protein Monellin: Dynamics with femtosecond resolution , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[97]  Samir Kumar Pal,et al.  Femtosecond dynamics of rubredoxin: Tryptophan solvation and resonance energy transfer in the protein , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[98]  F. Teale,et al.  Cleavage of the haem-protein link by acid methylethylketone. , 1959, Biochimica et biophysica acta.

[99]  Kurt Wüthrich,et al.  NMR studies of structure and function of biological macromolecules (Nobel lecture). , 2003, Angewandte Chemie.

[100]  H. Stanley,et al.  Solvent and mutation effects on the nucleation of amyloid beta-protein folding. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[101]  S. Sligar,et al.  High-level expression of sperm whale myoglobin in Escherichia coli. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[102]  R. Murarka,et al.  Molecular view of water dynamics near model peptides. , 2005, The journal of physical chemistry. B.

[103]  Feng Gai,et al.  Effect of dehydration on the aggregation kinetics of two amyloid peptides. , 2009, The journal of physical chemistry. B.

[104]  Benno P. Schoenborn,et al.  Neutron diffraction reveals oxygen–histidine hydrogen bond in oxymyoglobin , 1981, Nature.

[105]  Robin M. Hochstrasser,et al.  Ultrafast Dielectric Response of Proteins from Dynamics Stokes Shifting of Coumarin in Calmodulin , 2000 .

[106]  M. Hennig,et al.  Direct Detection of a Histidine−Histidine Side Chain Hydrogen Bond Important for Folding of Apomyoglobin , 1999 .

[107]  Satoshi Takahashi,et al.  Dehydration of main-chain amides in the final folding step of single-chain monellin revealed by time-resolved infrared spectroscopy , 2008, Proceedings of the National Academy of Sciences.

[108]  J. Onuchic,et al.  Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[109]  Carlos F. Lopez,et al.  Hydrophobicity of protein surfaces: Separating geometry from chemistry , 2008, Proceedings of the National Academy of Sciences.

[110]  Lennart Nilsson,et al.  Molecular origin of time-dependent fluorescence shifts in proteins. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[111]  Tiqing Liu,et al.  Quantitative Prediction of Fluorescence Quantum Yields for Tryptophan in Proteins , 2004 .

[112]  Hans Frauenfelder,et al.  Bulk-solvent and hydration-shell fluctuations, similar to α- and β-fluctuations in glasses, control protein motions and functions , 2004 .