Ultrafast Dynamics of Myoglobin without the Distal Histidine:  Stimulated Vibrational Echo Experiments and Molecular Dynamics Simulations

Finkelstein, Ilya J.; Goj, Anne; McClain, Brian L.; Massari, Aaron M.; Merchant, Kusai A.; Loring, Roger F.; Fayer, M. D.

doi:10.1021/jp0517201

Cited by 55 publications

(118 citation statements)

References 63 publications

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“…Carbonmonoxy-myoglobin (MbCO) has been extensively studied both experimentally [47][48][49][50][51][52][53][54][55][56] and computationally. [57][58][59][60] Myoglobin (Mb) is a small globular heme protein weighing approximately 17 kDa that is found in mammalian muscle tissue.…”

Section: D Vibrational Echo Experiments a Illustration Of The mentioning

confidence: 99%

“…55,64,[67][68][69][70] Structural fluctuations give rise to frequency fluctuations. The FFCF is the probability that a molecule with frequency o at time t = 0, still has frequency o at some later time averaged over the complete ensemble of molecules.…”

Section: D Vibrational Echo Experiments a Illustration Of The mentioning

confidence: 99%

“…6) that participates in the enzymatic catalysis cycle. 85,86 The heme can bind carbon monoxide (CO), which has been frequently exploited as a site specific reporter of protein structure 55,64,66,87 and dynamics. 64,70,88 As in the MbCO experiments discussed above, the time dependence of the CO transition frequency is a spectroscopic reporter of protein structural fluctuations.…”

Section: B the Influence Of Substrate Binding Of Enzyme Dynamicsmentioning

confidence: 99%

“…64,70,88 As in the MbCO experiments discussed above, the time dependence of the CO transition frequency is a spectroscopic reporter of protein structural fluctuations. 55,64,70 Like MbCO, the CO transition frequency of HRP is highly sensitive to electric fields. [87][88][89] Five small molecule substrates that are benzhydroxamic acid (BHA) analogs have been studied with 2D vibrational echoes.…”

Section: B the Influence Of Substrate Binding Of Enzyme Dynamicsmentioning

confidence: 99%

“…The H64V mutant (the distal histidine is replaced by a non-polar valine) displays significantly decreased vibrational dephasing because of the elimination of this polar group. 55,64 It is instructive to compare the dynamics of free HRP to that of wild-type myoglobin and substrate-bound HRP with H64V. When this is done, it is found that the dynamics of the A 1 state of MbCO are very similar to the free HRP red state while the HRP-substrate dynamics are very similar to those of H64V.…”

Section: B the Influence Of Substrate Binding Of Enzyme Dynamicsmentioning

confidence: 99%

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Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy

Finkelstein

Zheng

Ishikawa

et al. 2007

Phys. Chem. Chem. Phys.

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148

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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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Section: D Vibrational Echo Experiments a Illustration Of The mentioning

confidence: 99%

Section: D Vibrational Echo Experiments a Illustration Of The mentioning

confidence: 99%

Section: B the Influence Of Substrate Binding Of Enzyme Dynamicsmentioning

confidence: 99%

Section: B the Influence Of Substrate Binding Of Enzyme Dynamicsmentioning

confidence: 99%

Section: B the Influence Of Substrate Binding Of Enzyme Dynamicsmentioning

confidence: 99%

See 3 more Smart Citations

Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy

Finkelstein

Zheng

Ishikawa

et al. 2007

Phys. Chem. Chem. Phys.

Self Cite

148

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Two‐dimensional Optical Spectroscopy: Theory and Experiment

Jeon

Park

2010

Encyclopedia of Analytical Chemistry

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Two‐dimensional (2D) optical spectroscopy, despite its short history, has emerged as a promising technique to study the structure and dynamics of complex molecular systems in condensed phases. This article reviews the basic principles, implementation, and application of this spectroscopic technique. 2D optical spectroscopy employs multiple femtosecond laser pulses in the infrared (IR) or visible frequency range to induce multiple quantum transitions and displays the detected signal in a 2D frequency space. This enables a natural resolution of congested and averaged spectral features often found in condensed‐phase 1D spectra. Coupled multichromophore systems exhibit off‐diagonal cross peaks reflecting their coupling strengths, which can be monitored in time to extract information on the system dynamics. To provide a perspective on the development of 2D optical spectroscopy, we discuss its brief history. Since 2D spectroscopic features arise from multiple nonlinear optical transitions, their interpretation requires the knowledge of nonlinear response properties of molecular systems. This theoretical background is presented in some detail together with working formulas for two of the most popular techniques, 2D pump‐probe and 2D photon echo spectroscopy. Technically, 2D optical spectroscopy has been made possible by the availability of ultrafast femtosecond laser pulses and the spectral interferometric detection method to detect weak signals. The experimental setup of 2D spectrometer is, therefore, described with brief introductions to recent technological developments in instrumentation. Computational methods to simulate 2D optical spectra are also described, which play a vital role in the interpretation of the experimental spectra. General features of 2D spectra and their relations to underlying physical processes are important for proper application of the technique and they are discussed separately. 2D optical spectroscopy has the unique advantage of ultrafast time resolution in addition to spectral resolution in 2D frequency space. It will therefore continue to evolve with technical refinement and provide incisive analytical means to study structure and dynamics of chemical and biological systems.

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Fine Sampling of the R→T Quaternary‐Structure Transition of a Tetrameric Hemoglobin

Vitagliano

Mazzarella

Merlino

et al. 2016

Chemistry A European J

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Although the end points of the functional transitions of tetrameric hemoglobins (Hbs) have been well characterized, atomic-resolution data on R-T intermediate states are extremely limited. Herein, the X-ray structures of two independent tetramers of the fully ligated carbomonoxy form of Trematomus newnesi hemoglobin (Hb1Tn) within the same crystal are described. These structures show peculiar features in the heme pocket, EF corner, and tertiary/quaternary structure. Distal histidine side chains have a propensity to swing out of the heme pocket and thus allow compression of the EF corner. In this rotameric state, the distal His group does not interact with the CO ligand, consistent with FTIR spectra recorded in solution. At the quaternary-structure level, one tetramer is an intermediate R-T state, whereas the other assumes a T-like structure. Altogether, the structures of these tetramers provide the best available atomic-level picture of the R→T transition of vertebrate Hbs.

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Ultrafast Dynamics of Myoglobin without the Distal Histidine: Stimulated Vibrational Echo Experiments and Molecular Dynamics Simulations

Cited by 55 publications

References 63 publications

Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy

Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy

Two‐dimensional Optical Spectroscopy: Theory and Experiment

Fine Sampling of the R→T Quaternary‐Structure Transition of a Tetrameric Hemoglobin

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