Structure of A 0 , A 1 , and A 3 Conformational Substates of Carbonmonoxy Myoglobin (original) (raw)
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Conformational Dynamics of Heme Pocket in Myoglobin and Hemoglobin
Bulletin of the Korean Chemical Society, 2005
The conformational dynamics of heme pocket, a small vacant site near the binding site of heme proteinsmyoglobin (Mb) and hemoglobin (Hb), was investigated after photolysis of carbon monoxide from MbCO and HbCO in D2O solution at 283 K by probing time-resolved vibrational spectra of photolyzed CO. Two absorption bands, arising from CO in the heme pocket, evolve nonexponentially in time. The band at higher energy side blue shifts and broadens with time and the one at lower energy side narrows significantly with a negligible shift. These spectral evolutions are induced by protein conformational changes following photolysis that modify structure and electric field of heme pocket, and ligand dynamics in it. The conformational changes affecting the spectrum of photolyzed CO in heme pocket likely modulates ligand-binding activity.
Conformational substates and motions in myoglobin. External influences on structure and dynamics
Biophysical Journal, 1990
Myoglobin, a simppe dioxygen-storage protein, is a good laboratory for the investigation of the connection between protein structure, dynamics, and function. Fourier-transform infrared spectroscopy on carbon-monoxymyoglobin (MbCO) shows three major CO bands. These bands are excellent probes for the investigation of the structure-function relationship. They have different CO binding kinetics and their CO dipoles form different angles with respect to the heme normal, implying that MbCO exists in three major conformational substates, AO, A1, and A3. The entropies and enthalpies of these substates depend on temperature above-180 K and are influenced by pH, solvent, and pressure. These results suggest that even a protein as simple as Mb can assume a small number of clearly different structures that perform the same function, but with different rates. Moreover, protein structure and dynamics depend strongly on the interaction of the protein with its environment.
Ligand binding to heme proteins: II. Transitions in the heme pocket of myoglobin
Biophysical Journal, 1993
Phenomena occurring in the heme pocket after photolysis of carbonmonoxymyoglobin (MbCO) below about 100 K are investigated using temperature-derivative spectroscopy of the infrared absorption bands of CO. MbCO exists in three conformations (A substates) that are distinguished by the stretch bands of the bound CO. We establish connections among the A substates and the substates of the photoproduct (B substates) using Fourier-transform infrared spectroscopy together with kinetic experiments on MbCO solution samples at different pH and on orthorhombic crystals. There is no one-to-one mapping between the A and B substates; in some cases, more than one B substate corresponds to a particular A substate. Rebinding is not simply a reversal of dissociation; transitions between B substates occur before rebinding. We measure the nonequilibrium populations of the B substates after photolysis below 25 K and determine the kinetics of B substate transitions leading to equilibrium. Transitions between B substates occur even at 4 K, whereas those between A substates have only been observed above about 160 K. The transitions between the B substates are nonexponential in time, providing evidence for a distribution of substates. The temperature dependence of the B substate transitions implies that they occur mainly by quantum-mechanical tunneling below 10 K. Taken together, the observations suggest that the transitions between the B substates within the same A substate reflect motions of the CO in the heme pocket and not conformational changes. Geminate rebinding of CO to Mb, monitored in the Soret band, depends on pH. Observation of geminate rebinding to the A substates in the infrared indicates that the pH dependence results from a population shift among the substates and not from a change of the rebinding to an individual A substate. INTRODUCTION1 Myoglobin is a globular protein consisting of 153 amino acids and a heme (Fe-protoporphyrin IX) as the prosthetic group. Textbooks state that the function of Mb is the reversible binding of small ligands such as dioxygen (02) and carbon monoxide (CO) at the heme iron (Stryer, 1988). One could expect such a binding process to be simple. It was indeed originally described as a one-step process (Antonini and Brunori, 1971). Flash photolysis experiments performed over wide ranges in time and temperature imply, however, that the binding process is far from simple (Austin et al., 1975). Four phenomena, in particular, produce complexity: 1. multiple wells along the reaction coordinate, 2. confor-mational substates, 3. protein relaxation after photodissociation, and 4. thermal fluctuations. In the following, we briefly describe how these phenomena affect the ligand binding to myoglobin. Multiple wells along the reaction coordinate In the simplest model, CO in the solvent binds to the heme iron in one step. Flash photolysis data, however, show evidence for multiple processes. A model that describes the salient features of the kinetic data uses three wells (states) along the reaction coordinate, A i± B S.
Conformational substates and dynamic properties of carbonmonoxy hemoglobin
Biophysical Chemistry, 2003
Heme pocket dynamics of human carbonmonoxy hemoglobin (HbCO) is studied by Fourier transform infrared spectroscopy. The CO stretching band at various temperatures in the interval 300-10 K is analyzed in terms of three taxonomic A substates; however, in HbCO the band attributed to the A taxonomic substate accounts for f90% of 1 the total intensity in the pH range 8.8-4.5. Two different regimes as a function of temperature are observed: below 160 K, the peak frequency and the bandwidth of the A band have constant values whereas, above this temperature, 1 a linear temperature dependence is observed, suggesting the occurrence of transitions between statistical substates within the A taxonomic substate in this protein. The relationship between the heme pocket dynamics (as monitored 1 by the thermal behavior of the CO stretching band), the overall dynamic properties of the protein matrix (as monitored by the thermal behavior of Amide II and Amide I9 bands) and the glass transition of the solvent (as monitored by the thermal behavior of the bending band of water) is also investigated. From this analysis, we derive the picture of a very soft heme pocket of hemoglobin characterized by rather large anharmonic terms and strongly coupled to the dynamic properties of the solvent. ᮊ
The Journal of Physical Chemistry B, 2005
Control of O 2 versus CO binding in myoglobin (Mb) is tuned by a distal histidine residue through steric and H-bonding interactions. These interactions have been evaluated via Car-Parrinello DFT calculations, whose efficiency allows full quantum mechanical treatment of the 13 closest residues surrounding the heme. The small (8°) deviation of the Fe-C-O bond angle from linearity results from the steric influence of a distal valine residue and not the distal histidine. H-bond energies were evaluated by replacing the distal histidine with the non-H-bonding residue isoleucine. Binding energies for CO and O 2 decreased by 0.8 and 4.1 kcal/ mol for MbCO and MbO 2 , in good agreement with experimental H-bond estimates. Ligand discrimination is dominated by distal histidine H-bonding, which is also found to stabilize a metastable side-on isomer of MbO 2 that may play a key role in MbO 2 photodynamics. Figure 1. Overlay of residues and heme positions for the Mb(His64)-CO model calculation (gray) and X-ray (ref 10) coordinates (green).
MD Simulations of Carbonmonoxy Myoglobin and Calculations of Heme CD
2000
i The Soret circular dichroism (CD) spectrum of carbonmonoxy myoglobin dtifers strikingly for the two heme isomers: Aqzl =+90 M-'cm-' for isomer A, AQ21 =-7 M-'cm-' for isomer B (Aojula et al., BiochemJ. 250, 853(1988)). This observation implies significant differences in the protein conformation andlor distortions of the heme from planarity between the two isomers. Molecular dynamics simulations of the two isomers have been performed, using both neutron diffraction (ND) and NMR structures for stwting geometries. The geometry for isomer B was generated from the isomer A geometry by rotation of the heme by 180°about the a-y methine carbon axis. Four ND-based trajectories for isomer A, each of 600 ps duration, gave average CD spectra that reproduced the strong positive Soret CD inferred for isomer from experiment. Four such trajectories for isomer B gave results similar to those for isomer A, and therefore disagreed with the weak negative Soret CD band inferred from experiment for isomer B. The two NMR-based hajectories for each isomer gave poor agreement with experiment. We attribute the failure of the calculations for isomer B to a poor starting structure for this isomer, and we are conducting further studies to overcome this problem. In the successful calculations for isomer A, heme-aromatic side chain coupling accounts for 1
Structural and dynamic properties of the heme pocket in myoglobin probed by optical spectroscopy
Biopolymers, 1988
We report the optical absorption spectra of sperm whale deoxy-, oxy-, and carbonmonoxymyoglobin in the temperature range 300-20 K and in &5' % glycerol or ethylene glycol-water mixtures. By lowering the temperature, all bands exhibit half-width narrowing and peak frequency shift; moreover, the near-ir bands of deoxymyoglobin show a marked increase of the integrated intensities. Opposed to what has already been reported for human hemoglobin, the temperature dependence of the first moment of the investigated bands does not follow the behavior predicted by the harmonic Franck-Condon approximation and is sizably affected by the solvent composition; this solvent effect is larger in liganded than in nonligmded myoglobin. However, for all the observed bands the behavior of the second moment can be quite well rationalized in terms of the harmonic Ranck-Condon approximation and is not dependent on solvent composition. On the basis of these data we put forward some suggestions concerning the structural and dynamic properties of the heme pocket in myoglobin and their dependence upon solvent composition. We also discuss the different behaviok of myoglobin and hemoglobin in terms of the different heme pocket structures and deformabilities of the two proteins.
Inorganic chemistry, 2016
We analyzed the oxygen (O2) and carbon monoxide (CO) binding properties, autoxidation reaction rate, and FeO2 and FeCO vibrational frequencies of the H64Q mutant of sperm whale myoglobin (Mb) reconstituted with chemically modified heme cofactors possessing a variety of heme Fe electron densities (ρFe), and the results were compared with those for the previously studied native [Shibata, T. et al. J. Am. Chem. Soc. 2010 , 132 , 6091 - 6098 ], and H64L [Nishimura, R. et al. Inorg. Chem. 2014 , 53 , 1091 - 1099 ], and L29F [Nishimura, R. et al. Inorg. Chem. 2014 , 53 , 9156 - 9165 ] mutants in order to elucidate the effect of changes in the heme electronic structure and distal polar interaction contributing to stabilization of the Fe-bound ligand on the functional and vibrational properties of the protein. The study revealed that, as in the cases of the previously studied native protein [Shibata, T. et al. Inorg. Chem. 2012 , 51 , 11955 - 11960 ], the O2 affinity and autoxidation reacti...