On the Influence of the Local Environment on the CO Stretching Frequencies in Native Myoglobin: Assignment of the B‐States in MbCO

Meuwly, Markus

doi:10.1002/cphc.200600304

Cited by 48 publications

(61 citation statements)

References 54 publications

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“…Concerning the assignment of the two CO orientations to the B substates, we have proposed that the high-frequency photoproduct species absorbing at 2131 cm -1 in MbCO points its carbon atom towards the heme iron (70), which was independently supported by combining MD and QM/MM calculations (84). (Interestingly, Anselmi et al (86) recently arrived at the opposite assignment based on their computational data for unknown reasons.)…”

Section: The Primary Ligand Docking Site Bmentioning

confidence: 96%

“…This doublet has been assigned to photolyzed ligands in the primary docking site B on top of pyrrole C in two opposing orientations (70,83,84). Comparison of active-site mutants of MbCO has revealed that the distal histidine is mainly responsible for the splitting (70).…”

Section: The Primary Ligand Docking Site Bmentioning

confidence: 99%

“…This doublet has been assigned to photolyzed ligands in the primary docking site B on top of pyrrole C in two opposing orientations (70,83,84).…”

Section: The Primary Ligand Docking Site Bmentioning

confidence: 99%

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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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Section: The Primary Ligand Docking Site Bmentioning

confidence: 96%

Section: The Primary Ligand Docking Site Bmentioning

confidence: 99%

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

et al. 2007

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“…However, there is increasing evidence that in Mb the alternative e tautomer is present. [22,[39][40][41] Thus, additional calculations with His64 e were carried out. The corresponding IR spectra are shown in Figure 8.…”

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confidence: 99%

Ferric and Ferrous Iron in Nitroso‐Myoglobin: Computer Simulations of Stable and Metastable States and Their Infrared Spectra

Nutt

Meuwly

2007

ChemPhysChem

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The binding of NO to iron is involved in the biological function of many heme proteins. Contrary to ligands like CO and O(2), which only bind to ferrous (Fe(II)) iron, NO binds to both ferrous and ferric (Fe(III)) iron. In a particular protein, the natural oxidation state can therefore be expected to be tailored to the required function. Herein, we present an ab initio potential-energy surface for ferric iron interacting with NO. This potential-energy surface exhibits three minima corresponding to eta(1)-NO coordination (the global minimum), eta(1)-ON coordination and eta(2) coordination. This contrasts with the potential-energy surface for Fe(II)-NO, which exhibits only two minima (the eta(2) coordination mode for Fe(II) is a transition state, not a minimum). In addition, the binding energies of NO are substantially larger for Fe(III) than for Fe(II). We have performed molecular dynamics simulations for NO bound to ferric myoglobin (Mb(III)) and compare these with results obtained for Mb(II). Over the duration of our simulations (1.5 ns), all three binding modes are found to be stable at 200 K and transiently stable at 300 K, with eventual transformation to the eta(1)-NO global-minimum conformation. We discuss the implication of these results related to studies of rebinding processes in myoglobin.

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“…Simulations were carried out for both, His δ 64 and His ϵ 64 protonation, with the latter being the more likely state. [49][50][51][52][53] Contrary to the previous work which employed stochastic boundaries, in the present work, the protein was solvated in a periodic, pre equilibrated waterbox 62.0864 × 62.0864 × 62.0864 Å 3 . The final system contains 23 711 atoms.…”

Section: B Molecular Dynamics Simulationsmentioning

confidence: 99%

Reproducing kernel potential energy surfaces in biomolecular simulations: Nitric oxide binding to myoglobin

Soloviov

Meuwly

2015

The Journal of Chemical Physics

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A line integral reaction path approximation for large systems via nonlinear constrained optimization: Application to alanine dipeptide and the β hairpin of protein G J. Chem. Phys. 124, 194903 (2006) Multidimensional potential energy surfaces based on reproducing kernel-interpolation are employed to explore the energetics and dynamics of free and bound nitric oxide in myoglobin (Mb). Combining a force field description for the majority of degrees of freedom and the higher-accuracy representation for the NO ligand and the Fe out-of-plane motion allows for a simulation approach akin to a mixed quantum mechanics/molecular mechanics treatment. However, the kernel-representation can be evaluated at conventional force-field speed. With the explicit inclusion of the Fe-out-of-plane (Fe-oop) coordinate, the dynamics and structural equilibrium after photodissociation of the ligand are correctly described compared to experiment. Experimentally, the Fe-oop coordinate plays an important role for the ligand dynamics. This is also found here where the isomerization dynamics between the Fe-ON and Fe-NO state is significantly affected whether or not this co-ordinate is explicitly included.

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On the Influence of the Local Environment on the CO Stretching Frequencies in Native Myoglobin: Assignment of the B‐States in MbCO

Cited by 48 publications

References 54 publications

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

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

Ferric and Ferrous Iron in Nitroso‐Myoglobin: Computer Simulations of Stable and Metastable States and Their Infrared Spectra

Reproducing kernel potential energy surfaces in biomolecular simulations: Nitric oxide binding to myoglobin

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On the Influence of the Local Environment on the CO Stretching Frequencies in Native Myoglobin: Assignment of the B‐States in MbCO

Cited by 48 publications

References 54 publications

Ligand Migration and Binding in the Dimeric Hemoglobin ofScapharca inaequivalvis,

Ligand Migration and Binding in the Dimeric Hemoglobin ofScapharca inaequivalvis,

Ferric and Ferrous Iron in Nitroso‐Myoglobin: Computer Simulations of Stable and Metastable States and Their Infrared Spectra

Reproducing kernel potential energy surfaces in biomolecular simulations: Nitric oxide binding to myoglobin

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

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