Protein Conformational Fluctuations Research Articles

Single-particle survival in gated trapping.

Any chemical reaction A*+B\ensuremath{\rightarrow}C whose progress is modulated by another reaction of the form A*\ensuremath{\rightleftarrows}A is said to be gated. The gating reaction A*\ensuremath{\rightleftarrows}A represents a reversible fluctuation from a active state A* to an inactive state A that does not react with B. Reversibly blocked chemical reactions, conformational fluctuations in proteins, and reactions occurring within biomembranes or involving biological molecules have all been studied recently in contexts related to gating. This paper gives a unified, general formalism for calculating trapping rates and mean survival times of gated reactions. It also presents and solves some gating models. Although most of its explicit formulas are for problems with a single particle moving in the presence of a single gated, static trap, the method of solution is formally applicable to problems involving several particles and several point traps, even when the gating kinetics are non-Markovian. Those cases give integral equations that cannot be solved in closed form, however. This paper's results also include the bimolecular rate constant for a gated ligand binding to a gated protein.

Using buried water molecules to explore the energy landscape of proteins.

Buried water molecules constitute a highly conserved, integral part of nearly all known protein structures. Such water molecules exchange with external solvent as a result of protein conformational fluctuations. We report here the results of water (17)O and (2)H magnetic relaxation dispersion measurements on wild-type and mutant bovine pancreatic trypsin inhibitor in aqueous solution at 4-80 degrees C. These data lead to the first determination of the exchange rate of a water molecule buried in a protein. The strong temperature dependence of this rate is ascribed to large-scale conformational fluctuations in an energy landscape with a statistical ruggedness of approximately 10 kJ mol(-1).

Reaction–diffusion description of biological transport processes in general dimension

We introduce a reaction–diffusion system capable of modeling ligand migration inside of proteins as well as conformational fluctuations of proteins, and present a detailed analytical and numerical analysis of this system in general dimension. The main observable, the probability of finding the system in the starting state, exhibits dimension-dependent as well as dimension-independent properties, allowing for sharp experimental tests of the effective dimension of the process in question. We discuss the application of this theory to ligand migration in myoglobin and to the description of gating fluctuations of ion channel proteins.

Evidence for Damped Hemoglobin Dynamics in a Room Temperature Trehalose Glass

Upon photodissociation of its ligand, COHbA exhibits a wide range of nonequilibrium relaxation phenomena that start within a fraction of a picosecond and extend out to tens of microseconds. In addition, equilibrium fluctuations of the protein result in conformational averaging. All of these dynamics can have an impact on ligand rebinding. In an effort to better understand the relationship between conformational dynamics and ligand-binding reactivity, COHbA was embedded in a room temperature trehalose sugar glass (Hagen et al. Science 1995, 269, 959) in order to uncouple solvent motions from protein dynamics as well as reduce the amplitude of large-scale protein conformational fluctuations. Time-resolved resonance Raman spectroscopy and ligand-rebinding kinetics show that the trehalose glass does not impede the initial fast relaxation of the iron−histidine linkage, but does dramatically impede conformational averaging and completely eliminates ligand escape at all temperatures from 140 K to room temperature. Fluorescence measurements indicate that in the trehalose glass the picosecond tryptophan lifetimes are nearly unchanged, but there is a complete absence of the nanosecond fluorescence decay (observed in aqueous solutions), which is replaced by a decay of ∼700 ps. This change in the fluorescence decay is ascribed to a significant decrease in the structural dynamics that normally allow transient opening of the distal heme pocket.

My life in and beyond the laboratory.

Ephraim Katchalski-Katzir grew up in Israel at a time when the State was coming into being, and like many of those of his generation, participated in its creation and defense. He received his scientific education at the Hebrew University of Jerusalem and thereafter at the Polytechnic Institute of Brooklyn, Columbia University, and Harvard University. During and after the establishment of the State, he acted as scientific consultant to the defense leadership, and continued throughout his career to advise the Government of Israel on research and development. His public activities culminated in his election in 1973 as President of the State of Israel. As one of the founders of the Weizmann Institute of Science, he headed the Department of Biophysics for many years. His research included the study of poly-alpha-amino acids as protein models, immobilized enzymes, and polymers as chemical reagents. He also carried out theoretical and experimental work on the determination of distance distributions and conformational fluctuations in proteins by nonradiative energy-transfer techniques.

Pressure effects on carbon monoxide rebinding to the isolated .alpha. and .beta. chains of human hemoglobin

The effects of pressure on the recombination kinetics of carbon monoxide binding to the isolated alpha and beta chains of human adult hemoglobin at pH 7, approximately 20 degrees C, were studied by the use of millisecond and nanosecond laser photolyses. The kinetic data were analyzed on the basis of a simple three-species model, which assumes two elementary reaction processes of bond formation and ligand migration steps. The activation volume for each elementary step was obtained from the pressure dependence of the rate constants. A pressure-dependent activation volume change from negative to positive values in the bimolecular carbon monoxide association reaction was observed for both of the isolated chains. This finding is attributed to a change of the rate-limiting step from the bond formation step to the ligand migration step. For both of the isolated chains, the activation volumes for ligand migration into and from the protein were estimated as +12-16 and +7-11 cm3 mol-1, respectively. These positive activation volumes for the ligand migration process may be caused by conformational fluctuations of proteins, that is, the conformational changes from "closed" to "open" structure. In the iron-ligand bond formation process, the activation volumes are -15 to -22 cm3 mol-1, which are almost identical to that for the model heme complexes [Taube, D. J., Projahn, H.-D., van Eldik, R., Magde, D., & Traylor, T. G. (1990) J. Am. Chem. Soc. 112, 6880-6886]. Accordingly, the surrounding protein contributions to the activation volumes for the bond formation process could be small.(ABSTRACT TRUNCATED AT 250 WORDS)

Electrostatic field around cytochrome c: theory and energy transfer experiment.

Energy transfer in the "rapid diffusion" limit from electronically excited terbium(III) chelates in three different charge states to horse heart ferricytochrome c was measured as a function of ionic strength. Theoretical rate constants calculated by numerical integration of the Forster integral (containing the Poisson-Boltzmann-generated protein electrostatic potential) were compared with the experimental data to evaluate the accuracy of protein electrostatic field calculations at the protein/solvent interface. Two dielectric formalisms were used: a simple coulombic/Debye-Hückel procedure and a finite difference method [Warwicker, J. & Watson, H. C. (1982) J. Mol. Biol. 157, 671-679] that accounts for the low-dielectric protein interior and the irregular protein/solvent boundary. Good agreement with experiment was obtained and the ionic-strength dependence of the reaction was successfully reproduced. The sensitivity of theoretical rate constants to the choices of effective donor sphere size and the energy transfer distance criterion was analyzed. Electrostatic potential and rate-constant calculations were carried out on sets of structures collected along two molecular dynamics trajectories of cytochrome c. Protein conformational fluctuations were shown to produce large variations in the calculated energy transfer rate constant. We conclude that protein fluctuations and the resulting transient structures can play significant roles in biological or catalytic activities that are not apparent from examination of a static structure. For calculating protein electrostatics, large-scale low-frequency conformational fluctuations, such as charged side-chain reorientation, are established to be as important as the computational method for incorporating dielectric boundary effects.

Dynamical factors in protein-protein association

Although the conformational fluctuations of proteins in solution are not yet well characterized, there is ample evidence that some have amplitudes signficant with respect to the surface roughness of proteins and the distance-dependence of van der Waals potential-energy functions. It thus becomes necessary to examine the ways fluctuations may influence protein-protein association processes and the communication between associated proteins which makes free-energy management possible. This contribution is a first step in this examination. The dynamical possibilities are grouped into two dynamical factors both of which are sensitive to the degree of matching of the dynamical spectra of the associated proteins. A mechanism for free-energy storage and redistribution based on alterations of dynamic spectra is elaborated in some detail using hemoglobin as a model, since the mechanism appears to be responsible for linkage in that protein. However, hemoglobin may not be an entirely satisfactory prototype for some other kinds of proteins, e.g., enzymes, which are built using the knot-matrix principle, since there are good reasons for suspecting that hemoglobin folding is based on a different construction principle. Some consequences of the two principles for fluctuation behavior are discussed particularly as they influence activated free-volume rearrangements, which appear to form the most important class of fluctuation phenomena. Knot-matrix proteins probably have fewer substates and fewer large-amplitude fluctuations, but the limited experimental information suggests that the dynamical factors are important for this class as well.

Dynamics of protein conformational fluctuation in enzyme catalysis with special attention to proton transfers in serine proteinases

We have provided a quantum mechanical model for proteinase-catalyzed peptide, amide and ester hydrolysis. The model rests on electron and atom transfer theory, but incorporates the dynamics of conformational nuclear modes as a new element. The model is applied to acylation, but can straightaway be extended to deacylation, and is substantiated by recent structural and kinetic data for proteinase enzyme catalysis. The role of the conformational modes is found to be two-fold. First, the crystallographic distances for the proton transfers involved are far too large for direct transfer. His-57 mobility, handled stochastically, to bring the donor and acceptor groups within suitable reach, is therefore a crucial element of the theory. Secondly, the charge alignment in the Asp-102/His-57/tetrahedral intermediate system implies that the curvature of the potential surface along the conformational coordinates in this state is much lower than in the initial enzyme-substrate and final acyl states. A consequence of this is that the activation energy liberated after the first proton transfer is not dissipated, but stored in the conformational system and used in the second proton transfer step.

Fluctuations of protein structure as expressed in the distribution of hydrogen exchange rate constants.

AbstractHydrogen exchange kinetics of proteins provide information about the dynamics of their structure. The interpretation of experiments has been limited by difficulty in identifying individual rate constants. In order to invert the kinetic data, and to gain information about the individual reacting sites, we introduce a Laplace inversion technique and obtain the distribution function of rate constants by which the intricate reaction proceeds. A series of carefully overlapped experiments were performed on lysozyme at 25°C, an exchange profile obtained, and a distribution function extracted. This function was composed of a product of two terms, indicating two parallel pathways. The first, a power‐law term, was attributed to exchange from the native state. This part of the distribution function thus describes the scope of the conformational fluctuations in proteins at constant temperature and pressure. The second, an exponential, was seen to be associated with the pathway involving thermal unfolding and subsequent free exchange with the solvent. The influence of trichlorethanol and glycerol on the total distribution function was measured. Trichloroethanol selectively increased the contribution from the thermal unfolding pathway, whereas glycerol, besides decreasing this type of contribution, increased the width of the distribution function attributed to structural fluctuations.