Effect of solvent viscosity on the heme-pocket dynamics of photolyzed (carbonmonoxy)hemoglobin

Kramers’ Theory and the Dependence of Enzyme Dynamics on Trehalose-Mediated Viscosity

The disaccharide trehalose is accumulated in the cytoplasm of some organisms in response to harsh environmental conditions. Trehalose biosynthesis and accumulation are important for the survival of such organisms by protecting the structure and function of proteins and membranes. Trehalose affects the dynamics of proteins and water molecules in the bulk and the protein hydration shell. Enzyme catalysis and other processes dependent on protein dynamics are affected by the viscosity generated by trehalose, as described by the Kramers’ theory of rate reactions. Enzyme/protein stabilization by trehalose against thermal inactivation/unfolding is also explained by the viscosity mediated hindering of the thermally generated structural dynamics, as described by Kramers’ theory. The analysis of the relationship of viscosity–protein dynamics, and its effects on enzyme/protein function and other processes (thermal inactivation and unfolding/folding), is the focus of the present work regarding the disaccharide trehalose as the viscosity generating solute. Finally, trehalose is widely used (alone or in combination with other compounds) in the stabilization of enzymes in the laboratory and in biotechnological applications; hence, considering the effect of viscosity on catalysis and stability of enzymes may help to improve the results of trehalose in its diverse uses/applications.

Ligand migration through hemeprotein cavities: insights from laser flash photolysis and molecular dynamics simulations

The presence of cavities and tunnels in the interior of proteins, in conjunction with the structural plasticity arising from the coupling to the thermal fluctuations of the protein scaffold, has profound consequences on the pathways followed by ligands moving through the protein matrix. In this perspective we discuss how quantitative analysis of experimental rebinding kinetics from laser flash photolysis, trapping of unstable conformational states by embedding proteins within the nanopores of silica gels, and molecular simulations can synergistically converge to gain insight into the migration mechanism of ligands. We show how the evaluation of the free energy landscape for ligand diffusion based on the outcome of computational techniques can assist the definition of sound reaction schemes, leading to a comprehensive understanding of the broad range of chemical events and time scales that encompass the transport of small ligands in hemeproteins.

Time-resolved methods in Biophysics. 2. Monitoring haem proteins at work with nanosecond laser flash photolysis

Haem proteins have long been the most studied proteins in biophysics, and have become paradigms for the characterization of fundamental biomolecular processes as ligand binding and regulatory conformational transitions. The presence of the haem prosthetic group, the absorbance spectrum of which has a ligation sensitive region conveniently located in the UV-visible range, has offered a powerful and sensitive tool for the investigation of molecular functions. The central Fe atom is capable of reversibly binding diatomic ligands, including O(2), CO, and NO. The Fe-ligand bond is photolabile, and a reactive unligated state can be transiently generated with a pulsed laser. The photodissociated ligands quickly rebind to the haem and the process can be monitored by transient absorbance methods. The ligand rebinding kinetics reflects protein dynamics and ligand migration within the protein inner cavities. The characterization of these processes was done in the past mainly by low temperature experiments. The use of silica gels to trap proteins allows the characterization of internal ligand dynamics at room temperature. In order to show the potential of the laser flash photolysis techniques, combined with modern numerical analysis methods, we report experiments conducted on two non-symbiotic haemoglobins from Arabidopsis thaliana. The comparison between time courses recorded on haemoglobins in solution and encapsulated in silica gels allows for the highlighting of different interplays between protein dynamics and ligand migration.

Application of a universal force field to mixed Fe/Mo-S/Se cubane and heterocubane clusters. 1. Substitution of sulfur by selenium in the series [Fe4X4(YCH3)4]2-; X = S/Se and Y = S/Se

A series of Fe-S and Fe-Se cubane clusters containing all four combinations of the general formula [Fe(4)X(4)(Y-CH(3))(4)](2)(-) (X = S/Se, Y = S/Se) is investigated with FTIR and Raman spectroscopy. The terminally selenolate coordinated clusters (Y = Se) are prepared by a new synthetic route. All four cluster compounds are structurally characterized by X-ray single-crystal structure determination. Infrared and Raman spectra of all compounds are presented and interpreted with normal coordinate analysis. The corresponding force fields are based on that developed for the Fe(4)S(4)-benzyl cluster (Czernuszewicz, R. S.; Macor, K. A.; Johnson, M. K.; Gewirth, A.; Spiro, T. G. J. Am.Chem. Soc. 1987, 109, 7178-7187). An empirical procedure is presented to convert Fe-S into Fe-Se force constants. Only minor changes in force constants are found upon S --> Se exchange, reflecting the similarity of the Fe-S and Fe-Se bonds. The drastic frequency shifts in the metal-ligand region observed upon substitution of sulfur by selenium are, therefore, primarily due to the corresponding mass changes.

Spectroscopically and kinetically distinct conformational populations of sol-gel-encapsulated carbonmonoxy myoglobin. A comparison with hemoglobin

We have used sol-gel encapsulation protocols to trap kinetically and spectroscopically distinct conformational populations of native horse carbonmonoxy myoglobin. The method allows for direct comparison of functional and spectroscopic properties of equilibrium and non-equilibrium populations under the same temperature and viscosity conditions. The results implicate tertiary structure changes that include the proximal heme environment in the mechanism for population-specific differences in the observed rebinding kinetics. Differences in the resonance Raman frequency of nu(Fe-His), the iron-proximal histidine stretching mode, are attributed to differences in the positioning of the F helix. For myoglobin, the degree of separation between the F helix and the heme is assigned as the conformational coordinate that modulates both this frequency and the innermost barrier controlling CO rebinding. A comparison with the behavior of encapsulated derivatives of human adult hemoglobin indicates that these CO binding-induced conformational changes are qualitatively similar to the tertiary changes that occur within both the R and T quaternary states. Protein-specific differences in the time scale for the proposed F helix relaxation are attributed to variations in the intra-helical hydrogen bonding patterns that help stabilize the position of the F helix.

The effect of water on the rate of conformational change in protein allostery

The influence of solvation on the rate of quaternary structural change is investigated in human hemoglobin, an allosteric protein in which reduced water activity destabilizes the R state relative to T. Nanosecond absorption spectroscopy of the heme Soret band was used to monitor protein relaxation after photodissociation of aqueous HbCO complex under osmotic stress induced by the nonbinding cosolute poly(ethylene glycol) (PEG). Photolysis data were analyzed globally for six exponential time constants and amplitudes as a function of osmotic stress and viscosity. Increases in time constants associated with geminate rebinding, tertiary relaxation, and quaternary relaxation were observed in the presence of PEG, along with a decrease in the fraction of hemes rebinding CO with the slow rate constant characteristic of the T state. An analysis of these results along with those obtained by others for small cosolutes showed that both osmotic stress and solvent viscosity are important determinants of the microscopic R --> T rate constant. The size and direction of the osmotic stress effect suggests that at least nine additional water molecules are required to solvate the allosteric transition state relative to the R-state hydration, implying that the transition state has a greater solvent-exposed area than either end state.

Temperature dependent quaternary state relaxation in sol-gel encapsulated hemoglobin

Samples of human adult hemoglobin (HbA) encapsulated in a wet porous sol-gel are prepared under aerobic and anaerobic conditions. Resonance Raman spectroscopy is used to compare equilibrium deoxyHbA to the nonequilibrium deoxy species generated by deoxygenating an encapsulated oxyHbA sample. The spectra of the deoxygenated samples as a function of delay subsequent to deoxygenation reveal a marked slow down by the gel of the two phases of relaxation: the tertiary relaxation associated with the transition from the liganded R to deoxy R conformations and the quaternary relaxation associated with the deoxy R to deoxy T transition. The temperature dependence (4-80 degrees C) of the relaxation indicates that the internal viscosity of the gel is greatly enhanced at the lower temperatures. At 80 degrees C the tertiary and quaternary relaxations occur over minutes to hours, respectively, whereas at 4 degrees C both relaxations are essentially frozen. These results demonstrate the impressive potential of using sol-gel encapsulation as a means of studying substrate binding induced conformational changes in proteins.

Transient and time-resolved resonance Raman investigation of photoinitiated electron transfer in ruthenated cytochromes c

Ruthenation of exterior amino acid residues of heme proteins provides an effective means by which biological ET reactions can be studied within the context of highly complex protein environments. Resonance Raman spectroscopy can probe both ET kinetics and structural dynamics at the molecular level. Here we present the first comprehensive use of time-resolved and transient resonance Raman spectroscopies to examine photoinduced ET in cytochromes. Two ruthenated cytochromes c, Ru(lys72)-cyt.c and Ru(cyt102)cyt.c, were studied with TRRS using 10 ns laser pulses and with TRRRS on a 10 ns to 10 ms time scale. It was found that resonance Raman protocols can effectively trace ET kinetics and associated heme--protein structural dynamics. Care must be exercised, however, when drawing comparisons to measurements made by other methods (i.e., transient absorbance). The TRRS studies directly probe the heme and its local environment and reveal that the heme dynamics accompanying ET are very rapid relative to phenomenological ET kinetics. The heme and its local environment evolve to their equilibrium (ferrous) structure in less than 10 ns subsequent to ET, with no evidence for the existence of metastable heme pocket geometries analogous to those observed in the dynamic response of hemoglobins and oxidases. Finally, species-specific differences are observed in the photoinduced ET kinetics and heme structural dynamics. However, these differences are confined to nanosecond or faster time scales.

Hydrogen bonding of tyrosine B10 to heme-bound oxygen in Ascaris hemoglobin. Direct evidence from UV resonance Raman spectroscopy

The hemoglobin from Ascaris suum, a parasitic nematode, has a spontaneous dissociation rate for the dioxygen ligand that is 3 orders of magnitude less than for mammalian myoglobins or hemoglobins. In this hemoglobin, the distal histidine is replaced with a glutamine which is capable of forming a stabilizing hydrogen bond to the bound dioxygen. A single hydrogen bond from a glutamine is, under typical circumstances, not sufficient to account for the low off rate for oxygen. Several studies point to a second hydrogen bond to the heme-bound dioxygen originating from tyrosine B10 as the source of this unusual reactivity. In this study ultraviolet (UV) resonance Raman spectroscopy is used to directly observe the formation of this hydrogen bond upon oxygen binding. The study reveals that both oxygen and carbon monoxide induce similar conformational changes in the globin upon binding to the heme; however, in the case of oxygen, a strong hydrogen bond involving a tyrosine is also observed. Similar studies on the QE7L mutant of this Hb suggest that the glutamine plays a role in stabilizing a rigid tertiary structure associated with the distal heme pocket. This conformation maintains the tyrosine in an orientation conducive to hydrogen bond formation with a heme-bound dioxygen ligand.

Effects of intra- and intersubunit hydrogen bonds on the R-T transition in human hemoglobin as studied with alpha 42(C7) and beta 145(HC2) mutations

To clarify the effects of specific inter- and intrasubunit hydrogen bonds on the R-T transition in human hemoglobin (Hb A), the recombination reaction of carbon monoxide with artificial mutant Hbs was measured and analyzed. One of the hydrogen bonds we focused on is formed between Tyr-42 alpha and Asp-99 beta in the alpha 1-beta 2 interface of Hb A, which is one of the hydrogen bonds characteristic of the T state. Hb His-42 alpha, in which Tyr-42 alpha is replaced by His to perturb this hydrogen bond, showed that the ligand-free R to T transition rate was decreased by 20-fold compared with that for Hb A. This mutation caused the destabilization of the transition state in the R to T quaternary structure change by about 7 kJ mol-1, indicating that the hydrogen bond between Tyr-42 alpha and Asp-99 beta plays a definite role in the R-T transition as well as in stabilization of the equilibrium T state. Hb Phe-145 beta, in which Tyr-145 beta is replaced by Phe and the intrasubunit hydrogen bond between Tyr-145 beta and Val-98 beta is lacking, also showed a slow R-T transition rate as observed in Hb His-42 alpha. The published crystallographic data suggest that this intrasubunit hydrogen bond stabilizes the transition state by reducing the freedom of motion of the C-terminus of the beta subunit and, thereby, facilitates the R-T transition.

Solvent damping of internal processes in myoglobin studied by specific heat spectroscopy and flash photolysis

We address the question of dynamic coupling between protein and solvent by comparing the enthalpy relaxation of the solvent (75% v/v glycerol-water) to internal ligand binding in myoglobin. When the solvent relaxation is slow compared to intramolecular events we observe decoupling of protein motions from the solvent. In the opposite limit there is a significant contribution of the solvent to internal friction. The solvent enhances the apparent activation energy of transitions in myoglobin. This result is discussed in terms of a generalized Kramer's law involving a dynamic friction coefficient.