The rate of entry of dioxygen and carbon monoxide into myoglobin

Extraction of Protein Conformational Modes from Distance Distributions Using Structurally Imputed Bayesian Data Augmentation

Protein conformational changes are known to play important roles in assorted biochemical and biological processes. Driven by thermal motions of surrounding solvent molecules, such a structural remodeling often occurs stochastically. Yet, regardless of how random the conformational reconfiguration may appear, it could in principle be described by a linear combination of a set of orthogonal modes which, in turn, are contained in the intramolecular distance distributions. The central challenge is how to obtain the distribution. This contribution proposes a Bayesian data-augmentation scheme to extract the predominant modes from only few distance distributions, be they from computational sampling or directly from experiments such as single-molecule Förster-type resonance energy transfer (smFRET). The inference of the complete protein structure from insufficient data was recognized as isomorphic to the missing-data problem in Bayesian statistical learning. Using smFRET data as an example, the missing coordinates were deduced, given protein structural constraints and multiple but limited number of smFRET distances; the Boltzmann weighing of each inferred protein structure was then evaluated using computational modeling to numerically construct the posterior density for the global protein conformation. The conformational modes were then determined from the iteratively converged overall conformational distribution using principal component analysis. Two examples were presented to illustrate these basic ideas as well as their practical implementation. The scheme described herein was based on the theory behind the powerful Tanner-Wang algorithm that guarantees convergence to the true posterior density. However, instead of assuming a mathematical model to calculate the likelihood as in conventional statistical inference, here the protein structure was treated as a statistical parameter and was imputed from the numerical likelihood function based on structural information, a probability model-free method. The framework put forth here is anticipated to be generally applicable, offering a new way to articulate protein conformational changes in a quantifiable manner.

Dynamics of structure and energy of horse carboxymyoglobin after photodissociation of carbon monoxide

The energetics and structural volume changes after photodissociation of carboxymyoglobin are quantitatively investigated by laser-induced transient grating (TG) and photoacoustic calorimetric techniques. Various origins of the TG signal are distinguished: the phase grating signals due to temperature change, due to absorption spectrum change, and due to volume change. We found a new kinetics of approximately 700 ns (at room temperature), which was not observed by the flash photolysis technique. This kinetics should be attributed to the intermediate between the geminate pair and the fully dissociated state. The enthalpy of an intermediate species is determined to be 61 +/- 10 kJ/mol, which is smaller than the expected Fe-CO bond energy. The volume of MbCO slightly contracts (5 +/- 3 cm(3)/mol) during this process. CO is fully released from the protein by an exponential kinetics from 25 to -2 degrees C. During this escaping process, the volume expands by 14.7 +/- 2 cm(3)/mol at room temperature and 14 +/- 10 kJ/mol is released, which should represent the protein relaxation and the solvation of the CO (the enthalpy of this final state is 47 +/- 10 kJ/mol). A potential barrier between the intermediate and the fully dissociated state is DeltaH(*) = 41.3 kJ/mol and DeltaS(*) = 13.6 J mol(-1) K(-1). The TG experiment under a high wavenumber reveals that the volume expansion depends on the temperature from 25 to -2 degrees C. The volume changes and the energies of the intermediate species are discussed.

Reactions of excited triplet states of metal substituted myoglobin with dioxygen and quinone

The triplet state absorption and phosphorescence of Zn and Pd derivatives of myoglobin were compared. Both metal derivatives exhibit long triplet state lifetimes at room temperature, but whereas the Pd derivative showed exponential decay and an isosbestic point in the transient absorption spectra, the decay of the Zn derivative was nonsingle exponential and the transient absorption spectra showed evidence of more than one excited state species. No difference was seen in triplet quenching by oxygen for either derivative, indicating that differences in the polypeptide chain between the two derivatives are not large enough to affect oxygen penetrability. Quenching was also observed by anthraquinone sulfonate. In this case, the possibility of long-range transfer by an exchange mechanism is considered.

Pulse radiolysis kinetics of the reaction of hydrated electrons with ferric-, ferrous-, protoporphyrin IX- and apo-myoglobin

The kinetics of the reaction of hydrated electron (e-aq) with ferric-, ferrous-, metal-free protoporphyrin IX-and apo-myoglobin have been studied by pulse radiolysis so that a direct kinetic measure of the relative reactivities of the heme and the protein part of myoglobin can be made. The second-order association rate constant with ferric Mb is about 3-times that for ApoMb, while ferric Mb, ferrous Mb and protoporphyrin IX-Mb all react at about the same rate, indicating that it is mainly the porphyrin that is the electron-attracting site. The magnitude of the rate constants (8-25 nM-1 X S-1) indicates that the encounter of e-aq with the protein is almost certainly diffusion-controlled. The initial encounter is probably followed by electron migration along parallel paths to the heme and most likely several of the 12 histidine residues. The heme competes very effectively (approx. 70%) with these other sites. The kinetically measured reduction yield of heme is consistent with that found spectrally, indicating that a histidine radical on the protein does not effectively transfer an electron intramolecularly to the heme. The spectral changes found upon the completion of the fast reaction (approx. 40 microseconds) for protoporphyrin IX-Mb and ferrous Mb are consistent with the formation of a porphyrin anion radical. For ApoMb the spectral changes are consistent with the formation of a histidine free radical.

Hemerythrin's oxygen-binding reaction studied by laser photolysis

The dioxygen--iron bond in oxyhemerythrin is shown to be photosensitive. The recombination reaction after photodissociation depends strongly on solvent viscosity. In water (eta = 1 centipoise or 1 x 10(-3) Pa . s) the recombination is monophasic and second-order in solvent oxygen concentration, with a bimolecular rate coefficient of 2.9 x 10(7) M-1 s-1. In a glycerol/water mixture (eta = 180 centipoise) a concentration-dependent geminate recombination process is also seen. This opens a class of proteins to study by flash photolysis.

Flash photolysis study of ligand binding by modified myoglobins at low temperatures

The CO-binding kinetics of myoglobin containing proto-, meso- and deutero-hemes were studied by flash photolysis over the temperature range 50-300 K. Results recorded over a large dynamic range of time (microseconds to many seconds) reveal processes that are non-exponential in time and multiphasic. The data are explained by a model in which the CO molecule must surmount four barriers in migrating from the solvent to the heme iron. At least two of these barriers have heights that vary from one molecule to another. Varying the nature of the heme group affects mainly the innermost of these barriers and, to a lesser degree, the second-outermost barrier.

The rotational diffusion of cytochrome b5 in lipid bilayer membranes. Influence of the lipid physical state

A derivative of the integral membranes protein, cytochrome b5, has been prepared in which the native heme group has been replaced by the structurally similar rhodium(III)-protoporphyrin IX. This metalloporphyrin has a finite triplet yield with a single exponential decay time of 22 microsecond in water. After insertion of the metalloporphyrin into the protein, its triplet-state decay becomes strongly nonexponential with at least three equal amplitude components with time constants varying over a range of 100. The derivatized protein has been incorporated into unilamellar liposomes prepared from dimyristoyllecithin, and the rotational diffusion of the protein in the lipid bilayer has been studied at temperatures above and below the lipid phase transition temperature via triplet absorbance anisotropy decay. The anisotropy decay curves are biphasic both above and below the lipid phase transition. The rotational diffusion constant is found to be 2.4 X 10(5) s-1 at 35 degrees C, and 1.1 X 10(4) s-1 at 10 degrees C, both being calculated from the fast decay component. The ratio of the limiting anisotropy to the initial anisotropy is 0.6 at both temperatures. This implies a cone of restricted motion of 34 degrees for the protein in the bilayer.