Control and pH dependence of ligand binding to heme proteins

Doster, Wolfgang; Beece, D.; Bowne, Samuel F.; DiIorio, Ernesto E.; Eisenstein, L.; Frauenfelder, Hans; Reinisch, Lou; Erramilli, Shyamsunder; Winterhalter, Kaspar H.; Yue, Kwok To

doi:10.1021/bi00263a001

Cited by 169 publications

(143 citation statements)

References 47 publications

(64 reference statements)

Supporting

Mentioning

138

Contrasting

Order By: Relevance

“…At higher temperatures the ligand wanders off into the protein matrix (processes II and higher), and this diffusion process is also reflected in the rebinding curve. The time dependence of the curve that results from this diffusion is typically seen to exhibit a t-F12 behavior within a certain range oftemperatures and time scales, crossing over to an exponential at longer times (2,4,5). This behavior is often taken as evidence that the diffusion regime is effectively a one-dimensional process; however, we will show that this conclusion is incorrect.…”

mentioning

confidence: 74%

“…Nld(t) = exp(t/Tr)erfc(\/7r), 0 [5] There it can either rebind with a rate 'y to the active site or diffuse into the protein matrix and be rebound later.…”

Section: Ligand Migrationmentioning

confidence: 99%

“…Our attention was drawn to this problem while investigating ligand migration through protein matter. Consider, for example, the most thoroughly researched case: ligand migration through myoglobin (Mb) (2)(3)(4)(5)(6)(7)(8)(9). Because no channel of sufficient size is available in the averaged static conformation of the protein (10), diffusion of ligand molecules (CO or 02) through the protein matrix cannot occur in the absence of conformational fluctuations (4,11,12).…”

mentioning

confidence: 99%

See 2 more Smart Citations

Biological transport processes and space dimension.

Nadler

Stein

1991

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

We discuss the generic time behavior of reaction-diffusion processes capable of modeling various types of biological transport processes, such as ligand migration in proteins and gating fluctuations in ion channel proteins. The main observable in these two cases, the fraction of unbound ligands and the probability of finding the channel in the closed state, respectively, exhibits an algebraic t-F/2 decay at intermediate times, followed by an exponential cutoff. We provide a simple framework for understanding these observations and explain their ubiquity by showing that these qualitative results are independent of space dimension. We also derive an experimental criterion to dis h between a one-dimensional process and one whose effective dimension is higher.Transport processes in biological systems can often be described as reaction-diffusion processes either in real space or in a configuration space of some appropriate dimension. A prominent example of the former is the diffusive transport of biological molecules through the cell protoplasm from the site where they are produced or incorporated to the location where they are needed and absorbed. Adam and Delbruck (1) pointed out the importance of dimensionality in such processes, by observing that an effective reduction of the dimension of the diffusion space-e.g., by restricting the motion of those molecules to certain network structures that pervade the cell-can be utilized to speed up this transport. In this paper we will be concerned with a different question: How does the time behavior of such transport processes depend on the space dimension involved, and, consequently, can experimental observation give any information on it? Our attention was drawn to this problem while investigating ligand migration through protein matter. Consider, for example, the most thoroughly researched case: ligand migration through myoglobin (Mb) (2-9). Because no channel of sufficient size is available in the averaged static conformation of the protein (10), diffusion of ligand molecules (CO or 02) through the protein matrix cannot occur in the absence of conformational fluctuations (4,11,12). The question then arises whether the ligand motion through the protein matrix is effectively three-dimensional or whether the necessary protein fluctuations occur only within a lower-dimensional subspace (the single-channel hypothesis) (4, 13).Usually, the ligand diffusion process can be experimentally studied only indirectly: bound ligands are separated from the active site by flash photolysis and the fraction of unbound ligands after a time t is monitored (2). The nonexponential rebinding kinetics then observed at low temperatures (process I, below 170 K) is commonly ascribed to a distribution of reaction barriers (2). At higher temperatures the ligand wanders off into the protein matrix (processes II and higher), and this diffusion process is also reflected in the rebinding curve. The time dependence of the curve that results from this diffusion is typically seen to exhibit a t-...

show abstract

mentioning

confidence: 74%

“…Nld(t) = exp(t/Tr)erfc(\/7r), 0 [5] There it can either rebind with a rate 'y to the active site or diffuse into the protein matrix and be rebound later.…”

Section: Ligand Migrationmentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Biological transport processes and space dimension.

Nadler

Stein

1991

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…In heme proteins such as myoglobin, the internal motions have been shown to have an essential role in ligand binding (1)(2)(3)(4)(5)(6)(7)(8)(9). Two extreme models for the internal motions have been considered.…”

mentioning

confidence: 99%

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

Smith

Kuczera

Karplus

1990

Proc. Natl. Acad. Sci. U.S.A.

156

View full text Add to dashboard Cite

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-'). 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.Experimental and theoretical studies ofthe internal dynamics of proteins can provide insight into the atomic interactions determining their structure and function (1). In heme proteins such as myoglobin, the internal motions have been shown to have an essential role in ligand binding (1-9). Two extreme models for the internal motions have been considered. In one the fluctuations are assumed to occur within a single multidimensional well that is harmonic or quasiharmonic (10). The other model assumes that there exist multiple minima or substates on the protein potential surface (2, 5, 11, 12); the internal motions correspond to a superposition of oscillations within the wells and transitions among them (11). Photolysis rebinding studies (2, 5, 12) and simulations (11) of myoglobin provide strong evidence for the substate model, which may be generally applicable to globular proteins (12). The simulations have shown that structures associated with different substates are similar but differ in detail; for myoglobin the differences can be described in terms of rigid body displacements of the helices with rearrangements of the connecting loops and reorientation of the side chains involved in helix contacts. At low temperatures individual protein molecules are trapped in local regions of conformational space and static disorder, corresponding to an inhomogeneous macroscopic system, results; at higher temperatures transitions between the substates, which involve the crossing of energy barriers, are possible. Such behavior is analogous to that found in other complex systems (13).Although much has been learned about protein motions from simulations, detailed experimental tests have been limited by the accessible time scales. Comparisons with x-ray, NMR, and fluorescence depolarization data have provided evidence that supports the simulation results (1), although it was suggested on the basis of the Mossbauer spectrum of myoglobin that the time scale of the simulated atomic fluctuations is two orders of magnitude too short (14); a reinterpretation of the results shows there is no inconsistency between the Mossbauer and simulation dynamics (15).Incoherent neu...

show abstract

“…Given such a set, and applying Eqn (2), the calculated kinetics Ncalc(t) are compared to the data points NeXp(t). The weights of the ki values are iteratively adjusted subject to the dual constraints of minimizing a x2 statistic (3) (where o2 is the variance of the data points), and simultaneously maximizing S, the entropy of thef(ki) probability set:…”

Section: Use Of the Maximum Entropy Methodsmentioning

confidence: 99%

Conformational fluctuations and protein reactivity

Lavalette

Tétreau

Brochon

et al. 1991

European Journal of Biochemistry

View full text Add to dashboard Cite

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 nonheme 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 He,,. It is found that Aeff strongly depends on the overall shape of the rate constant distribution and that He,, 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, He,, 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 He,, vanishes and that Aeff differs by nearly three orders of magnitude from the true value Ao.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.Conformational fluctuations of proteins can modulate the rate of simple reactions such as, for instance, the internal binding of oxygen with respiratory proteins. Extensive flash photolysis investigations of liganded hemoproteins have provided evidence that the kinetics of geminate recombinations (i.e. the rebinding of the photodissociated ligand with its original site), are strongly non-exponential and...

show abstract

Control and pH dependence of ligand binding to heme proteins

Cited by 169 publications

References 47 publications

Biological transport processes and space dimension.

Biological transport processes and space dimension.

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

Conformational fluctuations and protein reactivity

Contact Info

Product

Resources

About