Myoglobin rebinding of carbon monoxide and dioxygen after photodissociation has been observed in the temperature range between 40 and 350 K. A system was constructed that records the change in optical absorption at 436 nm smoothly and without break between 2 musec and 1 ksec. Four different rebinding processes have been found. Between 40 and 160 K, a single process is observed. It is not exponential in time, but approximately given by N(t) = (1 + t/to)-n, where to and n are temperature-dependent, ligand-concentration independent, parameters. At about 170 K, a second and at 200 K, a third concentration-independent process emerge. At 210 K, a concentration-dependent process sets in. If myoglobin is embedded in a solid, only the first three can be seen, and they are all nonexponential. In a liquid glycerol-water solvent, rebinding is exponential. To interpret the data, a model is proposed in which the ligand molecule, on its way from the solvent to the binding site at the ferrous heme iron, encounters four barriers in succession. The barriers are tentatively identified with known features of myoglobin. By computer-solving the differential equation for the motion of a ligand molecule over four barriers, the rates for all important steps are obtained. The temperature dependences of the rates yield enthalpy, entropy, and free-energy changes at all barriers. The free-energy barriers at 310 K indicate how myoglobin achieves specificity and order. For carbon monoxide, the heights of these barriers increase toward the inside; carbon monoxide consequently is partially rejected at each of the four barriers. Dioxygen, in contrast, sees barriers of about equal height and moves smoothly toward the binding site. The entropy increases over the first two barriers, indicating a rupturing of bonds or displacement of residues, and then smoothly decreases, reaching a minimum at the binding site. The magnitude of the decrease over the innermost barrier implies participation of heme and/or protein. The nonexponential rebinding observed at low temperatures and in solid samples implies that the innermost barrier has a spectrum of activation energies. The shape of the spectrum has been determined; its existence can be explained by assuming the presence of many conformational states for myoglobin. In a liquid at temperatures above about 230 K, relaxation among conformational states occurs and rebinding becomes exponential.

Dynamics of ligand binding to myoglobin

Publisher Summary The chapter discusses the motions in proteins. Gelation of gelatin or precipitation of casein with mild acid are examples of reversible changes in which structural motility of the protein chains or subunits is recognized as playing a part. The sometimes reversible spreading of monolayers derived from mondisperse proteins provides some of the first evidence for the true plasticity of protein molecules and paved the way for the elegant demonstration of reversible conformational transitions. The tracing of the passage of an unfolded polypeptide chain to the compact, native structure is a primary concern of protein chemistry. One segment of polypeptide chain adapts its backbone and sidechain conformation to the structure of another segment in the process of forming the compact, functional structure of a protein was made particularly vivid by experiments on the reassociation of cleaved fragments. Overall translational and rotational motion is observed with a protein in solution, apart from any intramolecular motions. These overall motions are those that remain if the protein molecule is treated as a rigid matrix. Rotational reorientation of intramolecular components involves rotations about individual interatomic bonds. Concerted motions in proteins involve the movement of groups of side chains or segments of backbone relative to other structures. Motions of interacting ions and small molecules produce fluctuations in protein structure in addition to Brownian transfer of momentum. Time scales of various types of motions are important both for experimental recognition of the time-dependent processes and for analyzing their importance in the functional molecular mechanics. The chapter also discusses the dominant methods of observation that provide information about frequencies and amplitudes of motions in proteins.

Motions in proteins.

The formation of vibrationally excited heme upon photodissociation of carbonmonoxy myoglobin and its subsequent vibrational energy relaxation was monitored by picosecond anti-Stokes resonance Raman spectroscopy. The anti-Stokes intensity of the nu4 band showed immediate generation of vibrationally excited hemes and biphasic decay of the excited populations. The best fit to double exponentials gave time constants of 1.9 +/- 0.6 and 16 +/- 9 picoseconds for vibrational population decay and 3.0 +/- 1.0 and 25 +/- 14 picoseconds for temperature relaxation of the photolyzed heme when a Boltzmann distribution was assumed. The decay of the nu4 anti-Stokes intensity was accompanied by narrowing and frequency upshift of the Stokes counterpart. This direct monitoring of the cooling dynamics of the heme cofactor within the globin matrix allows the characterization of the vibrational energy flow through the protein moiety and to the water bath.

https://science.sciencemag.org/content/sci/278/5337/443.full.pdf

Direct Observation of Cooling of Heme Upon Photodissociation of Carbonmonoxy Myoglobin

Ultrafast absorption spectroscopy is used to study heme-NO recombination at room temperature in aqueous buffer on time scales where the ligand cannot leave its cage environment. While a single barrier is observed for the cage recombination of NO with heme in the absence of globin, recombination in hemoglobin and myoglobin is nonexponential. Examination of hemoglobin with and without inositol hexaphosphate points to proximal constraints as important determinants of the geminate rebinding kinetics. Molecular dynamics simulations of myoglobin and heme-imidazole subsequent to ligand dissociation were used to investigate the transient behavior of the Fe-proximal histidine coordinate and its possible involvement in geminate recombination. The calculations, in the context of the absorption measurements, are used to formulate a distinction between nonexponential rebinding that results from multiple protein conformations (substates) present at equilibrium or from nonequilibrium relaxation of the protein triggered by a perturbation such as ligand dissociation. The importance of these two processes is expected to depend on the time scale of rebinding relative to equilibrium fluctuations and nonequilibrium relaxation. Since NO rebinding occurs on the picosecond time scale of the calculated myoglobin relaxation, a time-dependent barrier is likely to be an important factor in the observed nonexponential kinetics. The general implications of the present results for ligand binding in heme proteins and its time and temperature dependence are discussed. It appears likely that, at low temperatures, inhomogeneous protein populations play an important role and that as the temperature is raised, relaxation effects become significant as well.

https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=1850&context=chem_pubs

Ligand binding and protein relaxation in heme proteins: a room temperature analysis of nitric oxide geminate recombination

Studies on cobalt myoglobins and hemoglobins. I. Preparation and optical properties of myoglobins and hemoglobins containing cobalt proto-, meso-, and deuteroporphyrins and thermodynamic characterization of their reversible oxygenation.

Lumry R

Papers

Studies of heme proteins. II. Preparation and thermodynamic properties of sperm whale myoglobin.