Glassy behavior of a protein

Biophysical aspects of neutron scattering from vibrational modes of proteins

This review describes a major portion of the published work on neutron scattering experiments aimed at measuring large scale motions in proteins. The importance of these motions for enzyme function and oxygen transport is indicated. The theory applicable to each type of neuron scattering measurement is given and results are discussed with a view to biological relevance. New experiments are suggested and a comparison of neutron scattering data is made with results from other techniques such as raman scattering, infrared absorption, photolysis and molecular dynamics simulations.

Solvent effects on myoglobin conformational substates as studied by electron paramagnetic resonance

Electronic paramagnetic resonance spectra of frozen horse myoglobin solutions at two different pH values and with different added organic solvents are analyzed by computer simulation in terms of Gaussian distributions of some ferric ion crystal field parameters. The mean values and the corresponding variances of these distributions, thought as arising from a distribution of the protein conformational substates, are found to be affected by both the pH and the addition of organic solvents. The significant narrowing of the conformational substate distribution, induced by large addition of glycerol, is discussed.

The energy landscapes and motions of proteins

Recent experiments, advances in theory, and analogies to other complex systems such as glasses and spin glasses yield insight into protein dynamics. The basis of the understanding is the observation that the energy landscape is complex: Proteins can assume a large number of nearly isoenergetic conformations (conformational substates). The concepts that emerge from studies of the conformational substates and the motions between them permit a quantitative discussion of one simple reaction, the binding of small ligands such as carbon monoxide to myoglobin.

Gd3+ vibronic side band spectroscopy. New optical probe of Ca2+ binding sites applied to biological macromolecules

A new spectroscopic technique is presented for obtaining infraredlike spectra of the binding sites of Ca2+ and other metals in biological macromolecules. The technique, based on the Ca(2+)-like binding properties of Gd3+, utilizes vibronic side bands (VSB) that appear in Gd3+ fluorescence. In the fluorescence spectrum of Gd3+, the separation in photon frequency between a VSB and its electronic origin at approximately 32,150 cm-1 (approximately 311 nm) is a direct measure of the vibrational frequency of a ligand coordinated to Gd3+ ion. As a consequence, the VSB are uncomplicated by molecular vibrations distant from the Gd3+ binding site. The vibrational spectra resulting from the VSB of Gd3+ coordinated to a Ca2+ binding protein, a phospholipid, and DNA are presented.

Conformational fluctuations and protein reactivity. Determination of the rate-constant spectrum and consequences in elementary biochemical processes

When a protein's active site happens to be strongly coupled with the protein structure, the rate constant of the reaction may eventually be modulated by the conformational fluctuations. Evidence for this effect has long been provided by extensive flash photolysis investigations of liganded hemoproteins and more recently of the non-heme respiratory protein hemerythrin in hydro-organic solvents. Within a given protein conformational substate, an elementary reaction step is characterized by one single free energy barrier and by a first-order rate constant, k, which changes with temperature according to an Arrhenius law. At physiological temperature and low viscosity, ultrafast conformational relaxation causes efficient averaging of the reaction rates and the protein displays exponential kinetics with an average rate constant (k). Under sufficiently general conditions, it can be shown that (k) also follows a simple Arrhenius law with 'effective' values of the pre-exponential factor Aeff and activation enthalpy Heff. It is found that Aeff strongly depends on the overall shape of the rate constant distribution and that Heff actually corresponds to the lower limit of the enthalpy of activation, i.e. the value associated with the highest possible reaction rate. The underlying distribution of rate constants can be reconstructed from a set of experiments in which the kinetics depart from an exponential, i.e. at low temperature and high viscosity. The most probable distribution of exponentials consistent with the observed kinetics of the geminate recombinations of oxygen with photodissociated hemerythrin has been determined by using a new approach, known as the maximum entropy method. The results are consistent with a single pre-exponential value and a distributed enthalpy spectrum. As expected, Heff does not coincide either with the most probable nor with the average value of the enthalpy. The most salient findings are that the probability for any protein molecule to have an enthalpy of activation equal to the effective value Heff vanishes and that Aeff differs by nearly three orders of magnitude from the true value A0. Biochemical reaction rates are actually average values, since protein reactions are measured under physiological conditions, where conformational relaxation is always fast. Our understanding of the significance of Aeff and Heff is therefore entirely dependent on the knowledge of the distribution function of the rate constants. In particular, enthalpy and entropy terms of similar reactions performed by different proteins cannot be compared as long as the distribution of the rate constants remains unknown.

Infrared spectroscopic demonstration of a conformational change in bacteriorhodopsin involved in proton pumping

Infrared spectral changes in bacteriorhodopsin (bR) were followed during the slow decay of the M intermediate in the temperature region 240-260 K. The decay of the M form is characterized by the disappearance of the ethylenic bands and the bands indicating the reprotonation of the Schiff base. The route of Schiff-base reprotonation completely changes between 240 K and 260 K. At 240 K reprotonation occurs from Asp-85, the group to which the proton was released during M formation, and there is no pumping. At 260 K Schiff-base reprotonation takes place through Asp-96 from the cytoplasmic side, in the normal sequence assumed for proton pumping. The dramatic change in the route of Schiff-base reprotonation is coupled to a protein conformational change characterized by the change of the ratio of the two amide I bands at 1658 cm-1 and 1669 cm-1. This conformational change is interpreted as the conformational switch crucial for proton pumping: a protein relaxation following M formation results in a local rearrangement of the group, in the vicinity of the Schiff base. The rearrangement changes the accessibility of the Schiff base and provides that its deprotonation and reprotonation occur on different sides. The conformational change has characteristics typical for relaxations in proteins. In addition, it is shown that at 260 K an equilibrium exists between the M and N forms.

Proton tunneling in hydrated biological tissues near 200 K

We measure the protonic conductivity in water clusters adsorbed on intact samples of viable biological samples (corn embryo and endosperm, Artemia cysts, and Typha pollen) below room temperature. In the low-temperature region, the conductivity increases with temperature as exp T6, in agreement with prediction by the theory of dissipative quantum tunneling. We detect the onset of this effect near 180 K, where a glass transition in the hydrated protein matrix is known to take place. Above 220 K other transitions are superimposed onto this simple behavior.

Conformational substates and motions in myoglobin. External influences on structure and dynamics

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, A0, A1, and A3. The entropies and enthalpies of these substates depend on temperature above approximately 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.

Percolation model of ionic channel dynamics

The nonexponential closed-time distributions observed for ionic channels have been explained recently by quasi-one-dimensional models of structural diffusion (Millhauser, G. L., E. E. Salpeter, and R. E. Oswald. 1988. Proc. Natl. Acad. Sci. USA. 85: 1503-1507; Condat, C. A., and J. Jäckle. 1989. Biophys. J. 55: 915-925; Levitt, D. G. 1989. Biophys. J. 55: 489-498). We generalize this treatment by allowing for more complex trajectories using percolation theory. We assume that the gating transition depends on marginally connected conformational states leading to the observed spread in time scales.

Dynamics of myoglobin: comparison of simulation results with neutron scattering spectra

Molecular dynamics simulations are used to calculate the incoherent neutron scattering spectra of myoglobin between 80 K and 325 K and compared with experimental data. There is good agreement over the entire temperature range for the elastic, quasi-elastic, and inelastic components of the scattering. This provides support for the accuracy of the simulations of the internal motions that make the dominant contributions to the atomic displacements on a time scale of 0.3-100 ps (100-0.3 cm-1). Analysis of the simulations shows that at low temperatures a harmonic description of the molecule is appropriate and that the molecule is trapped in localized regions of conformational space. At higher temperatures the scattering arises from a combination of vibrations within wells (substates) and transitions between them; the latter contribute to the quasi-elastic scattering.

Inhomogeneous broadening in spectral bands of carbonmonoxymyoglobin. The connection between spectral and functional heterogeneity

The rebinding kinetics of CO to myoglobin after flash photolysis is nonexponential in time below approximately 180 K; the kinetics is governed by a distribution of enthalpic barriers. This distribution results from inhomogeneities in the protein conformation, referred to as conformational substates. Hole-burning experiments on the Soret and IR CO-stretch bands test the assumption that an inhomogeneous distribution of conformational substates results in inhomogeneously broadened spectra. CO was slowly photolyzed at different wavelengths in the Soret band at 10 K. Both the Soret band and the CO-stretch band A1, centered at 1,945 cm-1, shift during photolysis, demonstrating that different wavelengths excite different parts of the distributed population. We have also done kinetic hole-burning experiments by measuring peak shifts in the Soret and A1 bands as the CO molecules rebind. The shifts indicate that the spectral and enthalpic distributions are correlated. In the A1 band, the spectral and enthalpic distributions are highly correlated while in the Soret the correlation is weak. From the peak shifts in the spectral and kinetic hole-burning experiments the inhomogeneous broadening is estimated to be approximately 15% of the total width in the Soret band and approximately 60% in A1. We have previously measured the tilt angle alpha between the bound CO and the heme normal (Ormos, P., D. Braunstein, H. Frauenfelder, M. K. Hong, S.-L. Lin, T. B. Sauke, and R. D. Young. 1988. Proc. Natl. Acad. Sci. USA. 85:8492-8496) and observed a wave number dependence of the tilt angles within the CO-stretch A bands. Thus the spectral and enthalpic distributions of the A bands are coupled to a heterogeneity of the structure.

Temperature-derivative spectroscopy: a tool for protein dynamics

A relaxation method that measures the derivative of a population with respect to temperature is introduced and used to study the recombination of CO to sperm whale myoglobin after a photolyzing flash. Measurement of the geminate process in the infrared CO-stretch bands shows distributed activation enthalpies with different distributions for each band, transitions between two bands that correspond to photolyzed ligands, and kinetic hole burning. The data are well described by gaussian enthalpy distributions; the results match and complement those of isothermal methods. The temperature-derivative technique is further used to explore the recombination of CO from outside the heme pocket.