Ligand binding to heme proteins: III. FTIR studies of His-E7 and Val-E11 mutants of carbonmonoxymyoglobin

Braunstein, D.; Chu, K.R.; Egeberg, Karen D.; Frauenfelder, Hans; Mourant, Judith R.; Nienhaus, G. Ulrich; Ormos, Pál; Sligar, Stephen G.; Springer, Barry A.; Young, Robert D.

doi:10.1016/s0006-3495(93)81310-9

Cited by 90 publications

(118 citation statements)

References 42 publications

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“…32,35,36,42 The vibrational echo measurements reported here confirm that H64 plays a significant role in dephasing of the CO vibration in myoglobin. Vibrational echo decays measured in H64V are considerably slower than those in wtMbCO.…”

Section: Discussionsupporting

confidence: 61%

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

et al. 2005

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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 ∼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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Section: Discussionsupporting

confidence: 61%

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

et al. 2005

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“…The A band at 1948 cm -1 can be associated with the conformation seen in the high-resolution crystal structure of wild-type HbICO determined at pH 7.5, in which the His-69 imidazole side chain resides within the distal heme pocket (48). The frequency of this band is similar to the one of the A 1 substate at 1945 cm -1 in MbCO, which suggests that a weak hydrogen bond exists between His-69-Nε H and the CO oxygen (68,73,74). For the H69Q HbICO mutant, we find an asymmetric band at 1957 cm -1 with broad tails that can be modeled by additional bands at 1945 cm -1 and 1971 cm -1 , indicating that the glutamine side chain adopts different conformations and is also involved in hydrogen bonding interactions with the bound CO.…”

Section: The Active Site Of Wild-type Hbimentioning

confidence: 72%

“…Here, we merely present the integrated absorption changes as solid lines in Figure 6, which allow for convenient comparison of ligand rebinding between the different samples. For most samples, the population with the lowest rebinding temperatures (site B) is found to peak in the range 30 -50 K. Replacement of His-69 by aliphatic amino acids clearly shifts the rebinding maximum to <20 K, which indicates that His-69 contributes significantly to the overall rebinding barrier, as is also the case for MbCO (23,24,73). For H69Q, there is a tail extending up to 75 K in addition to the peak at 20 K. This observation suggests that the glutamine side chain assumes multiple conformations, as was also observed for the corresponding mutant Mb H64Q (26,(90)(91)(92).…”

mentioning

confidence: 74%

Ligand Migration and Binding in the Dimeric Hemoglobin ofScapharca inaequivalvis^,

et al. 2007

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Using Fourier transform infrared (FTIR) spectroscopy combined with temperature derivative spectroscopy (TDS) at cryogenic temperatures, we have studied CO binding to the heme and CO migration among cavities in the interior of the dimeric hemoglobin of Scapharca inaequivalvis (HbI) after photodissociation. By combining these studies with x-ray crystallography, three transient ligand docking sites were identified: a primary docking site B in close vicinity to the heme iron, and two secondary docking sites C and D corresponding to the Xe4 and Xe2 cavities of myoglobin. To assess the relevance of these findings for physiological binding, we also performed flash photolysis experiments on HbICO at room temperature and equilibrium binding studies with dioxygen. Our results show that the Xe4 and Xe2 cavities serve as transient docking sites for unbound ligands in the protein, but not as way stations on the entry/exit pathway. For HbI, the so-called histidine gate mechanism proposed for other globins appears as a plausible entry/exit route as well.The globin superfamily of proteins includes vertebrate hemoglobins (Hb), vertebrate myoglobins (Mb), invertebrate globins, plant globins, and bacterial and fungal flavohemoproteins (1). These proteins all bind oxygen and a variety of other small molecules at the central iron of a heme group enwrapped by the polypeptide chain in its characteristic 'globin' fold. Yet they are structurally highly diverse, ranging in size from the small monomeric mini-hemoglobin of the nemertean worm Cerebratulus lacteus with only 109 amino acid residues (2) to the giant erythrocruorin protein found in the annelid Lumbricus terrestris that consists of 144 hemoglobin subunits held together by 36 linker proteins (3). Globins perform a multitude of tasks in biological systems, including oxygen storage and transport, NO scavenging, enzyme action and small-molecule sensor function (4,5).The monomeric Mb is arguably the best studied member of the globin family. For many years, Mb has served as a model system for protein structural dynamics (6-13). A surprising complexity was discovered in its seemingly simple ligand binding reaction, which involves Address correspondence to G. Ulrich Nienhaus, Institute of Biophysics, University of Ulm, 89069 Ulm, Germany, Tel.: +49 731 5023050, Fax.: +49 731 5023059, Email: uli@uiuc.edu. ∥ Current Address: Department of Biochemistry and Molecular Biology, University of Texas, Medical Branch at Galveston, 301 University Blvd, Galveston, TX 77551-1055, USA * The first two authors contributed equally. † G.U.N. was supported by the Deutsche Forschungsgemeinschaft (grant Ni 291/3) and the Fonds der Chemischen Industrie. W.E.R. was supported by the National Institutes of Health (grants DK43323 and GM66756). NIH Public Access Author ManuscriptBiochemistry. Author manuscript; available in PMC 2008 December 11. Published in final edited form as:Biochemistry. (FTIR) cryospectroscopy to study the migration of carbon monoxide (CO) among cavities within the protein interio...

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“…40,64 It has been well documented that the A 0 state has the distal histidine swung out of pocket that contains the active iron heme site. 75,76 It was also known that the A 1 and A 3 states have the distal histidine in the pocket. However, these structures interconvert too fast to be amenable to study using other techniques such as NMR.…”

Section: D Vibrational Echo Experiments a Illustration Of The mentioning

confidence: 99%

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

Finkelstein

Zheng

Ishikawa

et al. 2007

Phys. Chem. Chem. Phys.

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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Ligand binding to heme proteins: III. FTIR studies of His-E7 and Val-E11 mutants of carbonmonoxymyoglobin

Cited by 90 publications

References 42 publications

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

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

Ligand Migration and Binding in the Dimeric Hemoglobin ofScapharca inaequivalvis^,

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

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Ligand binding to heme proteins: III. FTIR studies of His-E7 and Val-E11 mutants of carbonmonoxymyoglobin

Cited by 90 publications

References 42 publications

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

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

Ligand Migration and Binding in the Dimeric Hemoglobin ofScapharca inaequivalvis,

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

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Product

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Ligand Migration and Binding in the Dimeric Hemoglobin ofScapharca inaequivalvis^,