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Schirò G, Weik M. Role of hydration water in the onset of protein structural dynamics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:463002. [PMID: 31382251 DOI: 10.1088/1361-648x/ab388a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Proteins are the molecular workhorses in a living organism. Their 3D structures are animated by a multitude of equilibrium fluctuations and specific out-of-equilibrium motions that are required for proteins to be biologically active. When studied as a function of temperature, functionally relevant dynamics are observed at and above the so-called protein dynamical transition (~240 K) in hydrated, but not in dry proteins. In this review we present and discuss the main experimental and computational results that provided evidence for the dynamical transition, with a focus on the role of hydration water dynamics in sustaining functional protein dynamics. The coupling and mutual influence of hydration water dynamics and protein dynamics are discussed and the hypotheses illustrated that have been put forward to explain the physical origin of their onsets.
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Affiliation(s)
- Giorgio Schirò
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
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Bagchi S, Nebgen BT, Loring RF, Fayer MD. Dynamics of a myoglobin mutant enzyme: 2D IR vibrational echo experiments and simulations. J Am Chem Soc 2010; 132:18367-76. [PMID: 21142083 PMCID: PMC3033732 DOI: 10.1021/ja108491t] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Myoglobin (Mb) double mutant T67R/S92D displays peroxidase enzymatic activity in contrast to the wild type protein. The CO adduct of T67R/S92D shows two CO absorption bands corresponding to the A(1) and A(3) substates. The equilibrium protein dynamics for the two distinct substates of the Mb double mutant are investigated by using two-dimensional infrared (2D IR) vibrational echo spectroscopy and molecular dynamics (MD) simulations. The time-dependent changes in the 2D IR vibrational echo line shapes for both of the substates are analyzed using the center line slope (CLS) method to obtain the frequency-frequency correlation function (FFCF). The results for the double mutant are compared to those from the wild type Mb. The experimentally determined FFCF is compared to the FFCF obtained from molecular dynamics simulations, thereby testing the capacity of a force field to determine the amplitudes and time scales of protein structural fluctuations on fast time scales. The results provide insights into the nature of the energy landscape around the free energy minimum of the folded protein structure.
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Affiliation(s)
- Sayan Bagchi
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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Backus EHG, Bloem R, Pfister R, Moretto A, Crisma M, Toniolo C, Hamm P. Dynamical transition in a small helical peptide and its implication for vibrational energy transport. J Phys Chem B 2009; 113:13405-9. [PMID: 19754080 DOI: 10.1021/jp904905d] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The two-dimensional infrared spectrum of an octameric helical peptide in chloroform was measured as a function of temperature. Isotope labeling of the carbonyl group of one of the amino acids was used to obtain information for an isolated vibration. The antidiagonal width of the 2D-IR signal, which is a measure of the homogeneous dephasing time T(2), is constant from 220 to 260 K (within experimental error), and increases steeply above. The homogeneous dephasing time of the carbonyl vibration is attributed to the flexibility of the system and/or its immediate surrounding. The system undergoes a dynamical transition at about 270 K, with similarities to the protein dynamical transition. Furthermore, the temperature dependence of the antidiagonal width strongly resembles that of the efficiency of vibrational energy transport along the helix, which has been studied in a recent paper (J. Phys. Chem. B 2008, 112, 15487). The connection between the two processes, structural flexibility and energy transport mechanism, is discussed.
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Affiliation(s)
- Ellen H G Backus
- FOM Institute for Atomic and Molecular Physics, 1098 SJ Amsterdam, The Netherlands
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Kim YS, Hochstrasser RM. Applications of 2D IR spectroscopy to peptides, proteins, and hydrogen-bond dynamics. J Phys Chem B 2009; 113:8231-51. [PMID: 19351162 PMCID: PMC2845308 DOI: 10.1021/jp8113978] [Citation(s) in RCA: 245] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Following a survey of 2D IR principles, this article describes recent experiments on the hydrogen-bond dynamics of small ions, amide-I modes, nitrile probes, peptides, reverse transcriptase inhibitors, and amyloid fibrils.
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Affiliation(s)
- Yung Sam Kim
- Department of Chemistry, University of Pennsylvania Philadelphia, Pennsylvania 19104-6323, U.S.A
| | - Robin M. Hochstrasser
- Department of Chemistry, University of Pennsylvania Philadelphia, Pennsylvania 19104-6323, U.S.A
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Kim S, Chung JK, Kwak K, Bowman SEJ, Bren KL, Bagchi B, Fayer MD. Native and unfolded cytochrome c--comparison of dynamics using 2D-IR vibrational echo spectroscopy. J Phys Chem B 2008; 112:10054-63. [PMID: 18646797 PMCID: PMC2671645 DOI: 10.1021/jp802246h] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Unfolded vs native CO-coordinated horse heart cytochrome c (h-cyt c) and a heme axial methionine mutant cyt c552 from Hydrogenobacter thermophilus ( Ht-M61A) are studied by IR absorption spectroscopy and ultrafast 2D-IR vibrational echo spectroscopy of the CO stretching mode. The unfolding is induced by guanidinium hydrochloride (GuHCl). The CO IR absorption spectra for both h-cyt c and Ht-M61A shift to the red as the GuHCl concentration is increased through the concentration region over which unfolding occurs. The spectra for the unfolded state are substantially broader than the spectra for the native proteins. A plot of the CO peak position vs GuHCl concentration produces a sigmoidal curve that overlays the concentration-dependent circular dichroism (CD) data of the CO-coordinated forms of both Ht-M61A and h-cyt c within experimental error. The coincidence of the CO peak shift curve with the CD curves demonstrates that the CO vibrational frequency is sensitive to the structural changes induced by the denaturant. 2D-IR vibrational echo experiments are performed on native Ht-M61A and on the protein in low- and high-concentration GuHCl solutions. The 2D-IR vibrational echo is sensitive to the global protein structural dynamics on time scales from subpicosecond to greater than 100 ps through the change in the shape of the 2D spectrum with time (spectral diffusion). At the high GuHCl concentration (5.1 M), at which Ht-M61A is essentially fully denatured as judged by CD, a very large reduction in dynamics is observed compared to the native protein within the approximately 100 ps time window of the experiment. The results suggest the denatured protein may be in a glassy-like state involving hydrophobic collapse around the heme.
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Affiliation(s)
- Seongheun Kim
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Jean K. Chung
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Kyungwon Kwak
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Sarah E. J. Bowman
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216
| | - Kara L. Bren
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216
| | - Biman Bagchi
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, CA 94305
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Abstract
Spectrally resolved stimulated vibrational echo spectroscopy is used to investigate the dependence of fast protein dynamics on bulk solution viscosity at room temperature in four heme proteins: hemoglobin, myoglobin, a myoglobin mutant with the distal histidine replaced by a valine (H64V), and a cytochrome c552 mutant with the distal methionine replaced by an alanine (M61A). Fructose is added to increase the viscosity of the aqueous protein solutions over many orders of magnitude. The fast dynamics of the four globular proteins were found to be sensitive to solution viscosity and asymptotically approached the dynamical behavior that was previously observed in room temperature sugar glasses. The viscosity-dependent protein dynamics are analyzed in the context of a viscoelastic relaxation model that treats the protein as a deformable breathing sphere. The viscoelastic model is in qualitative agreement with the experimental data but does not capture sufficient system detail to offer a quantitative description of the underlying fluctuation amplitudes and relaxation rates. A calibration method based on the near-infrared spectrum of water overtones was constructed to accurately determine the viscosity of small volumes of protein solutions.
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Finkelstein IJ, Goj A, McClain BL, Massari AM, Merchant KA, Loring RF, Fayer MD. Ultrafast dynamics of myoglobin without the distal histidine: stimulated vibrational echo experiments and molecular dynamics simulations. J Phys Chem B 2007; 109:16959-66. [PMID: 16853158 DOI: 10.1021/jp0517201] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Ultrafast protein dynamics of the CO adduct of a myoglobin mutant with the polar distal histidine replaced by a nonpolar valine (H64V) have been investigated by spectrally resolved infrared stimulated vibrational echo experiments and molecular dynamics (MD) simulations. In aqueous solution at room temperature, the vibrational dephasing rate of CO in the mutant is reduced by approximately 50% relative to the native protein. This finding confirms that the dephasing of the CO vibration in the native protein is sensitive to the interaction between the ligand and the distal histidine. The stimulated vibrational echo observable is calculated from MD simulations of H64V within a model in which vibrational dephasing is driven by electrostatic forces. In agreement with experiment, calculated vibrational echoes show slower dephasing for the mutant than for the native protein. However, vibrational echoes calculated for H64V do not show the quantitative agreement with measurements demonstrated previously for the native protein.
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Affiliation(s)
- Ilya J Finkelstein
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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Edwards GS, Allen SJ, Haglund RF, Nemanich RJ, Redlich B, Simon JD, Yang WC. Applications of Free-Electron Lasers in the Biological and Material Sciences¶. Photochem Photobiol 2007. [DOI: 10.1111/j.1751-1097.2005.tb01437.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Finkelstein IJ, Zheng J, Ishikawa H, Kim S, Kwak K, Fayer MD. Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy. Phys Chem Chem Phys 2007; 9:1533-49. [PMID: 17429547 DOI: 10.1039/b618158a] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultrafast 2D IR vibrational echo spectroscopy is described and a number of experimental examples are given. Details of the experimental method including the pulse sequence, heterodyne detection, and determination of the absorptive component of the 2D spectrum are outlined. As an initial example, the 2D spectrum of the stretching mode of CO bound to the protein myoglobin (MbCO) is presented. The time dependence of the 2D spectrum of MbCO, which is caused by protein structural evolution, is presented and its relationship to the frequency-frequency correlation function is described and used to make protein structural assignments based on comparisons to molecular dynamics simulations. The 2D vibrational echo experiments on the protein horseradish peroxidase are presented. The time dependence of the 2D spectra of the enzyme in the free form and with a substrate bound at the active site are compared and used to examine the influence of substrate binding on the protein's structural dynamics. The application of 2D vibrational echo spectroscopy to the study of chemical exchange under thermal equilibrium conditions is described. 2D vibrational echo chemical exchange spectroscopy is applied to the study of formation and dissociation of organic solute-solvent complexes and to the isomerization around a carbon-carbon single bond of an ethane derivative.
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Massari AM, Finkelstein IJ, McClain BL, Goj A, Wen X, Bren KL, Loring RF, Fayer MD. The Influence of Aqueous versus Glassy Solvents on Protein Dynamics: Vibrational Echo Experiments and Molecular Dynamics Simulations. J Am Chem Soc 2005; 127:14279-89. [PMID: 16218622 DOI: 10.1021/ja053627w] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spectrally resolved infrared stimulated vibrational echo measurements are used to measure the vibrational dephasing of the CO stretching mode of carbonmonoxy-hemoglobin (HbCO), a myoglobin mutant (H64V), and a bacterial cytochrome c(552) mutant (Ht-M61A) in aqueous solution and trehalose glasses. The vibrational dephasing of the heme-bound CO is significantly slower for all three proteins embedded in trehalose glasses compared to that of aqueous protein solutions. All three proteins exhibit persistent but notably slower spectral diffusion when the protein surface is fixed by the glassy solvent. Frequency-frequency correlation functions (FFCFs) of the CO are extracted from the vibrational echo data to reveal that the structural dynamics, as sensed by the CO, of the three proteins in trehalose and aqueous solution are dominated by fast (tens of femtoseconds), motionally narrowed fluctuations. MD simulations of H64V in dynamic and "static" water are presented as models of the aqueous and glassy environments. FFCFs are calculated from the H64V simulations and qualitatively reproduce the important features of the experimentally extracted FFCFs. The suppression of long time scale (picoseconds to tens of picoseconds) frequency fluctuations (spectral diffusion) in the glassy solvent is the result of a damping of atomic displacements throughout the protein structure and is not limited to structural dynamics that occur only at the protein surface. The analysis provides evidence that some dynamics are coupled to the hydration shell of water, supporting the idea that the bioprotection offered by trehalose is due to its ability to immobilize the protein surface through a thin, constrained layer of water.
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Affiliation(s)
- Aaron M Massari
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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13
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Londergan CH, Sam Kim Y, Hochstrasser * RM. Two-dimensional infrared spectroscopy of dipeptides in trehalose glass. Mol Phys 2005. [DOI: 10.1080/00268970500095600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Kurkal V, Daniel RM, Finney JL, Tehei M, Dunn RV, Smith JC. Enzyme activity and flexibility at very low hydration. Biophys J 2005; 89:1282-7. [PMID: 15894640 PMCID: PMC1366612 DOI: 10.1529/biophysj.104.058677] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent measurements have demonstrated enzyme activity at hydrations as low as 3%. This raises the question of whether hydration-induced enzyme flexibility is important for activity. Here, to address this, picosecond dynamic neutron scattering experiments are performed on pig liver esterase powders at 0%, 3%, 12%, and 50% hydration by weight and at temperatures ranging from 120 to 300 K. At all temperatures and hydrations, significant quasielastic scattering intensity is found in the protein, indicating the presence of anharmonic, diffusive motion. As the hydration increases, a temperature-dependent dynamical transition appears and strengthens involving additional diffusive motion. The implication of these results is that, although the additional hydration-induced diffusive motion in the protein detected here may be related to increased activity, it is not required for the enzyme to function.
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Affiliation(s)
- V Kurkal
- Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Germany
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15
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Edwards GS, Allen SJ, Haglund RF, Nemanich RJ, Redlich B, Simon JD, Yang WC. Applications of Free-Electron Lasers in the Biological and Material Sciences¶. Photochem Photobiol 2005. [DOI: 10.1562/2004-11-08-ir-363r.1] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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Fenimore PW, Frauenfelder H, McMahon BH, Young RD. Bulk-solvent and hydration-shell fluctuations, similar to alpha- and beta-fluctuations in glasses, control protein motions and functions. Proc Natl Acad Sci U S A 2004; 101:14408-13. [PMID: 15448207 PMCID: PMC521939 DOI: 10.1073/pnas.0405573101] [Citation(s) in RCA: 405] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The concept that proteins exist in numerous different conformations or conformational substates, described by an energy landscape, is now accepted, but the dynamics is incompletely explored. We have previously shown that large-scale protein motions, such as the exit of a ligand from the protein interior, follow the dielectric fluctuations in the bulk solvent. Here, we demonstrate, by using mean-square displacements (msd) from Mossbauer and neutron-scattering experiments, that fluctuations in the hydration shell control fast fluctuations in the protein. We call the first type solvent-slaved or alpha-fluctuations and the second type hydration-shell-coupled or beta-fluctuations. Solvent-slaved motions are similar to the alpha-fluctuations in glasses. Their temperature dependence can be approximated by a Vogel-Tammann-Fulcher relation and they are absent in a solid environment. Hydration-shell-coupled fluctuations are similar to the beta-relaxation in glasses. They can be approximated by a Ferry or an Arrhenius relation, are much reduced or absent in dehydrated proteins, and occur in hydrated proteins even if embedded in a solid. They can be responsible for internal processes such as the migration of ligands within myoglobin. The existence of two functionally important fluctuations in proteins, one slaved to bulk motions and the other coupled to hydration-shell fluctuations, implies that the environment can control protein functions through different avenues and that no real protein transition occurs at approximately 200 K. The large number of conformational substates is essential; proteins cannot function without this reservoir of entropy, which resides mainly in the hydration shell.
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Affiliation(s)
- P W Fenimore
- Theory Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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Asbury JB, Steinel T, Fayer MD. Vibrational echo correlation spectroscopy probes of hydrogen bond dynamics in water and methanol. JOURNAL OF LUMINESCENCE 2004; 107:271-286. [PMID: 19180255 PMCID: PMC2632596 DOI: 10.1016/j.jlumin.2003.12.035] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Multidimensional vibrational echo correlation spectroscopy with full phase resolution is used to measure hydrogen bond dynamics in water and methanol. The OD hydroxyl stretches of methanol-OD oligomers in CCl(4) and HOD in H(2)O are studied using the shortest mid-IR pulses (<50 fs, <4 cycles of light) produced to date. The pulses have sufficient spectral bandwidth to span the very broad (>400 cm(-1)) spectrum of the 0-1 and 1-2 transitions. Hydrogen bond population dynamics are extricated with exceptional detail in MeOD oligomers because the different hydrogen bonded species are spectrally distinct. The experimental results along with detailed calculations indicate the strongest hydrogen bonds are selectively broken through a non-equilibrium relaxation pathway following vibrational relaxation of the hydroxyl stretch. The correlation spectra are also a sensitive probe of the fluctuations in water and provide a stringent test of water models that are widely used in simulations of aqueous systems. The analysis of the 2D band shapes demonstrates that different hydrogen bonded species are subject to distinct (wavelength dependent) ultrafast (~100 fs) local fluctuations and essentially identical slow (0.4 and ~2 ps) structural rearrangements. Observation of wavelength dependent dynamics demonstrates that standard theoretical approaches assuming Gaussian fluctuations cannot adequately describe water dynamics.
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Affiliation(s)
- John B Asbury
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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Asbury JB, Steinel T, Fayer MD. Hydrogen Bond Networks: Structure and Evolution after Hydrogen Bond Breaking. J Phys Chem B 2004. [DOI: 10.1021/jp036600c] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- John B. Asbury
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Tobias Steinel
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305
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19
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Asbury JB, Steinel T, Stromberg C, Gaffney KJ, Piletic IR, Fayer MD. Hydrogen bond breaking probed with multidimensional stimulated vibrational echo correlation spectroscopy. J Chem Phys 2003. [DOI: 10.1063/1.1627762] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Merchant KA, Noid WG, Akiyama R, Finkelstein IJ, Goun A, McClain BL, Loring RF, Fayer MD. Myoglobin-CO substate structures and dynamics: multidimensional vibrational echoes and molecular dynamics simulations. J Am Chem Soc 2003; 125:13804-18. [PMID: 14599220 PMCID: PMC2435512 DOI: 10.1021/ja035654x] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spectrally resolved infrared stimulated vibrational echo data were obtained for sperm whale carbonmonoxymyoglobin (MbCO) at 300 K. The measured dephasing dynamics of the CO ligand are in agreement with dephasing dynamics calculated with molecular dynamics (MD) simulations for MbCO with the residue histidine-64 (His64) having its imidazole epsilon nitrogen protonated (N(epsilon)-H). The two conformational substate structures B(epsilon) and R(epsilon) observed in the MD simulations are assigned to the spectroscopic A(1) and A(3) conformational substates of MbCO, respectively, based on the agreement between the experimentally measured and calculated dephasing dynamics for these substates. In the A(1) substate, the N(epsilon)-H proton and N(delta) of His64 are approximately equidistant from the CO ligand, while in the A(3) substate, the N(epsilon)-H of His64 is oriented toward the CO, and the N(delta) is on the surface of the protein. The MD simulations show that dynamics of His64 represent the major source of vibrational dephasing of the CO ligand in the A(3) state on both femtosecond and picosecond time scales. Dephasing in the A(1) state is controlled by His64 on femtosecond time scales, and by the rest of the protein and the water solvent on longer time scales.
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Affiliation(s)
- Kusai A Merchant
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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Borovykh I, Kulik L, Gast P, Dzuba S. Conformation transition in the protein of a photosynthetic reaction center observed at the nanometer range of distances at cryogenic temperatures. Chem Phys 2003. [DOI: 10.1016/s0301-0104(03)00323-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Asbury JB, Steinel T, Fayer M. Using ultrafast infrared multidimensional correlation spectroscopy to aid in vibrational spectral peak assignments. Chem Phys Lett 2003. [DOI: 10.1016/j.cplett.2003.09.113] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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23
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Bredenbeck J, Helbing J, Behrendt R, Renner C, Moroder L, Wachtveitl J, Hamm P. Transient 2D-IR Spectroscopy: Snapshots of the Nonequilibrium Ensemble during the Picosecond Conformational Transition of a Small Peptide. J Phys Chem B 2003. [DOI: 10.1021/jp034552q] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jens Bredenbeck
- Universität Zürich, Physikalisch Chemisches Institut, Winterthurer Strasse 190, CH-8057 Zürich, Switzerland, Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, D-82152 Martinsried, Germany, and Johann Wolfgang Goethe Universität Frankfurt am Main, Institut für Physikalische und Theoretische Chemie, Marie-Curie-Strasse 11, D-60439 Frankfurt am Main, Germany
| | - Jan Helbing
- Universität Zürich, Physikalisch Chemisches Institut, Winterthurer Strasse 190, CH-8057 Zürich, Switzerland, Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, D-82152 Martinsried, Germany, and Johann Wolfgang Goethe Universität Frankfurt am Main, Institut für Physikalische und Theoretische Chemie, Marie-Curie-Strasse 11, D-60439 Frankfurt am Main, Germany
| | - Raymond Behrendt
- Universität Zürich, Physikalisch Chemisches Institut, Winterthurer Strasse 190, CH-8057 Zürich, Switzerland, Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, D-82152 Martinsried, Germany, and Johann Wolfgang Goethe Universität Frankfurt am Main, Institut für Physikalische und Theoretische Chemie, Marie-Curie-Strasse 11, D-60439 Frankfurt am Main, Germany
| | - Christian Renner
- Universität Zürich, Physikalisch Chemisches Institut, Winterthurer Strasse 190, CH-8057 Zürich, Switzerland, Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, D-82152 Martinsried, Germany, and Johann Wolfgang Goethe Universität Frankfurt am Main, Institut für Physikalische und Theoretische Chemie, Marie-Curie-Strasse 11, D-60439 Frankfurt am Main, Germany
| | - Luis Moroder
- Universität Zürich, Physikalisch Chemisches Institut, Winterthurer Strasse 190, CH-8057 Zürich, Switzerland, Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, D-82152 Martinsried, Germany, and Johann Wolfgang Goethe Universität Frankfurt am Main, Institut für Physikalische und Theoretische Chemie, Marie-Curie-Strasse 11, D-60439 Frankfurt am Main, Germany
| | - Josef Wachtveitl
- Universität Zürich, Physikalisch Chemisches Institut, Winterthurer Strasse 190, CH-8057 Zürich, Switzerland, Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, D-82152 Martinsried, Germany, and Johann Wolfgang Goethe Universität Frankfurt am Main, Institut für Physikalische und Theoretische Chemie, Marie-Curie-Strasse 11, D-60439 Frankfurt am Main, Germany
| | - Peter Hamm
- Universität Zürich, Physikalisch Chemisches Institut, Winterthurer Strasse 190, CH-8057 Zürich, Switzerland, Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, D-82152 Martinsried, Germany, and Johann Wolfgang Goethe Universität Frankfurt am Main, Institut für Physikalische und Theoretische Chemie, Marie-Curie-Strasse 11, D-60439 Frankfurt am Main, Germany
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24
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Ultrafast heterodyne detected infrared multidimensional vibrational stimulated echo studies of hydrogen bond dynamics. Chem Phys Lett 2003. [DOI: 10.1016/s0009-2614(03)00643-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Merchant KA, Noid WG, Thompson DE, Akiyama R, Loring RF, Fayer MD. Structural Assignments and Dynamics of the A Substates of MbCO: Spectrally Resolved Vibrational Echo Experiments and Molecular Dynamics Simulations. J Phys Chem B 2002. [DOI: 10.1021/jp026793o] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kusai A. Merchant
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853
| | - W. G. Noid
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853
| | - David E. Thompson
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853
| | - Ryo Akiyama
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853
| | - Roger F. Loring
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853
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Merchant KA, Xu QH, Thompson DE, Fayer MD. Frequency Selected Ultrafast Infrared Vibrational Echo Studies of Liquids, Glasses, and Proteins. J Phys Chem A 2002. [DOI: 10.1021/jp021145q] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- K. A. Merchant
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Qing-Hua Xu
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - David E. Thompson
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305
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Merchant KA, Thompson DE, Xu QH, Williams RB, Loring RF, Fayer MD. Myoglobin-CO conformational substate dynamics: 2D vibrational echoes and MD simulations. Biophys J 2002; 82:3277-88. [PMID: 12023251 PMCID: PMC1302116 DOI: 10.1016/s0006-3495(02)75669-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Two-dimensional (2D) infrared vibrational echoes were performed on horse heart carbonmonoxymyoglobin (MbCO) in water over a range of temperatures. The A(1) and A(3) conformational substates of MbCO are found to have different dephasing rates with different temperature dependences. A frequency-frequency correlation function derived from molecular dynamics simulations on MbCO at 298 K is used to calculate the vibrational echo decay. The calculated decay shows substantial agreement with the experimentally measured decays. The 2D vibrational echo probes protein dynamics and provides an observable that can be used to test structural assignments for the MbCO conformational substates.
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Affiliation(s)
- Kusai A Merchant
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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Asbury JB, Wang Y, Lian T. Time-Dependent Vibration Stokes Shift during Solvation: Experiment and Theory. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2002. [DOI: 10.1246/bcsj.75.973] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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29
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Xu QH, Thompson DE, Merchant K, Fayer M. Separation of contributions to the third-order signal: ultrafast frequency-selected vibrational echo experiments on a metalloporphyrin-CO. Chem Phys Lett 2002. [DOI: 10.1016/s0009-2614(02)00197-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Abstract
IR vibrational echo experiments are used to study dynamics in myoglobin (Mb) by investigating the dephasing of the CO-stretching mode of CO bound at the active site of the protein (Mb-CO). The temperature dependence and the viscosity dependence of Mb-CO pure dephasing have been measured in several solvents. In low-temperature, glassy solvents, the pure dephasing has a power law temperature dependence, T(1.3), that reflects glasslike protein dynamics. In liquids, the temperature dependence is much steeper and arises from a combination of pure temperature dependence and the influence of decreasing solvent viscosity with increasing temperature. As the solvent viscosity decreases, the ability of the protein's surface to undergo topological fluctuations increases, which in turn increases the internal protein-structural fluctuations. The protein-structural motions are coupled to the CO bound at the active site by electric field fluctuations that accompany movements of polar residues. The dynamic electric field-coupling mechanism is tested by observing differences in the temperature dependence of the pure dephasing of Mb-CO mutations.
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Affiliation(s)
- M D Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA.
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31
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Yang S, Cao J. Two-Event Echos in Single-Molecule Kinetics: A Signature of Conformational Fluctuations. J Phys Chem B 2001. [DOI: 10.1021/jp004349k] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shilong Yang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Jianshu Cao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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32
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Williams RB, Loring RF. Crossover from dynamic towards static line broadening in the classical mechanical vibrational photon echo. Chem Phys 2001. [DOI: 10.1016/s0301-0104(01)00226-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Affiliation(s)
- Ryan B. Williams
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853
| | - Roger F. Loring
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305
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Rector KD, Jiang J, Berg MA, Fayer MD. Effects of Solvent Viscosity on Protein Dynamics: Infrared Vibrational Echo Experiments and Theory. J Phys Chem B 2001. [DOI: 10.1021/jp0023563] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- K. D. Rector
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Jianwen Jiang
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - Mark A. Berg
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | - M. D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, and Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
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Dvorsky R, Sevcik J, Caves LSD, Hubbard RE, Verma CS. Temperature Effects on Protein Motions: A Molecular Dynamics Study of RNase-Sa. J Phys Chem B 2000. [DOI: 10.1021/jp001933k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Mukamel S. Multidimensional femtosecond correlation spectroscopies of electronic and vibrational excitations. Annu Rev Phys Chem 2000; 51:691-729. [PMID: 11031297 DOI: 10.1146/annurev.physchem.51.1.691] [Citation(s) in RCA: 545] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Femtosecond visible and infrared analogues of multiple-pulse nuclear magnetic resonance techniques provide novel snapshot probes into the structure and electronic and vibrational dynamics of complex molecular assemblies such as photosynthetic antennae, proteins, and hydrogen-bonded liquids. A classical-oscillator description of these spectroscopies in terms of interacting quasiparticles (rather than transitions among global eigenstates) is developed and sets the stage for designing new pulse sequences and inverting the multidimensional signals to yield molecular structures. Considerable computational advantages and a clear physical insight into the origin of the response and the relevant coherence sizes are provided by a real-space analysis of the underlying coherence-transfer pathways in Liouville space.
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Affiliation(s)
- S Mukamel
- Department of Chemistry, University of Rochester, PO Box 270216, Rochester, New York 14627-0216, USA.
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Berg MA, Rector KD, Fayer MD. Two-pulse echo experiments in the spectral diffusion regime. J Chem Phys 2000. [DOI: 10.1063/1.1287172] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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