Kinetics of histidine deligation from the heme in GuHCl-unfolded Fe(III) cytochrome C studied by a laser-induced pH-jump technique.

We have developed an instrumental setup that uses transient absorption to monitor protein folding/unfolding processes following a laser-induced, ultrafast release of protons from o-nitrobenzaldehyde. The resulting increase in [H(+)], which can be more than 100 microM, is complete within a few nanoseconds. The increase in [H(+)] lowers the pH of the solution from neutrality to approximately 4 at the highest laser pulse energy used. Protein structural rearrangements can be followed by transient absorption, with kinetic monitoring over a broad time range (approximately 10 ns to 500 ms). Using this pH-jump/transient absorption technique, we have examined the dissociation kinetics of non-native axial heme ligands (either histidine His26 or His33) in GuHCl-unfolded Fe(III) cytochrome c (cyt c). Deligation of the non-native ligands following the acidic pH-jump occurs as a biexponential process with different pre-exponential factors. The pre-exponential factors markedly depend on the extent of the pH-jump, as expected from differences in the pK(a) values of His26 and His33. The two lifetimes were found to depend on temperature but were not functions of either the magnitude of the pH-jump or the pre-pulse pH of the solution. The activation energies of the deligation processes support the suggestion that GuHCl-unfolded cyt c structures with non-native histidine axial ligands represent kinetic traps in unfolding.

Kinetics of local helix formation in poly-L-glutamic acid studied by time-resolved photoacoustics: neutralization reactions of carboxylates in aqueous solutions and their relevance to the problem of protein folding.

Photoactivatable caged protons have been used to trigger proton transfer reactions in aqueous solutions of acetate, glutamate, and poly-L-glutamic acid, and the volumetric and enthalpic changes have been detected and characterized by means of time-resolved photoacoustics. Neutralization of carboxylates in aqueous solutions invariably results in an expansion of the solution due to the disappearance of two charges and is accompanied by little enthalpic change. The reactions occur with thermally activated, apparent bimolecular rates on the order of 10(10) M(-1)s(-1). In the case of aqueous solutions of poly-L-glutamic acid at pH around the pK(a) of the coil-to-helix transition, diffusional binding of a proton by carboxylates is followed by a sequential reaction with rate 1.06 (+/- 0.05) x 10(7)s(-1). This step is not thermally activated in the temperature range we have investigated and is likely related to local formation of hydrogen bonds near the protonation site. This structural event may constitute a rate-limiting step in helix propagation.

Fast events in protein folding: structural volume changes accompanying the early events in the N-->I transition of apomyoglobin induced by ultrafast pH jump.

Ultrafast, laser-induced pH jump with time-resolved photoacoustic detection has been used to investigate the early protonation steps leading to the formation of the compact acid intermediate (I) of apomyoglobin (ApoMb). When ApoMb is in its native state (N) at pH 7.0, rapid acidification induced by a laser pulse leads to two parallel protonation processes. One reaction can be attributed to the binding of protons to the imidazole rings of His24 and His119. Reaction with imidazole leads to an unusually large contraction of -82 +/- 3 ml/mol, an enthalpy change of 8 +/- 1 kcal/mol, and an apparent bimolecular rate constant of (0.77 +/- 0.03) x 10(10) M(-1) s(-1). Our experiments evidence a rate-limiting step for this process at high ApoMb concentrations, characterized by a value of (0. 60 +/- 0.07) x 10(6) s(-1). The second protonation reaction at pH 7. 0 can be attributed to neutralization of carboxylate groups and is accompanied by an apparent expansion of 3.4 +/- 0.2 ml/mol, occurring with an apparent bimolecular rate constant of (1.25 +/- 0.02) x 10(11) M(-1) s(-1), and a reaction enthalpy of about 2 kcal/mol. The activation energy for the processes associated with the protonation of His24 and His119 is 16.2 +/- 0.9 kcal/mol, whereas that for the neutralization of carboxylates is 9.2 +/- 0.9 kcal/mol. At pH 4.5 ApoMb is in a partially unfolded state (I) and rapid acidification experiments evidence only the process assigned to carboxylate protonation. The unusually large contraction and the high energetic barrier observed at pH 7.0 for the protonation of the His residues suggests that the formation of the compact acid intermediate involves a rate-limiting step after protonation.

An experimental methodology for measuring volume changes in proton transfer reactions in aqueous solutions.

A fast perturbation in proton concentration can be induced in aqueous solution using a pulsed ultraviolet laser and suitable photolabile compounds which, upon photoexcitation, irreversibly release protons. The volume change and the rate constant for the reaction of the photodetached protons with proton-accepting groups in solution can be monitored using time resolved photoacoustics. A typical proton concentration jump of 1 microM can be obtained with a 200-microJ laser pulse at 308 nm. Reaction dynamics from 20 ns to 5 micros can be easily followed. The methodology we establish represents a direct, time-resolved measurement of the reaction volume in proton transfer processes and an extension to the nanosecond-microsecond range of traditional relaxation techniques, such as stopped-flow. We report example applications to reactions involving simple molecules and polypeptides.

Photoacoustic analysis of proteins: volumetric signals and fluorescence quantum yields.

A series of proteins has been examined using time-resolved, pulsed-laser volumetric photoacoustic spectroscopy. Photoacoustic waveforms were collected to measure heat release for calculation of fluorescence quantum yields, and to explore the possibility of photoinduced nonthermal volume changes occurring in these protein samples. The proteins studied were the green fluorescent protein (GFP); intestinal fatty acid binding protein (IFABP), and adipocyte lipid-binding protein (ALBP), each labeled noncovalently with 1-anilinonaphthalene-8-sulfonate (1,8-ANS) and covalently with 6-acryloyl-2-(dimethylamino)naphthalene (acrylodan); and acrylodan-labeled IFABP and ALBP with added oleic acid. Of this group of proteins, only the ALBP labeled with 1,8-ANS showed significant nonthermal volume changes at the beta = 0 temperature (approximately 3.8 degrees C) for the buffer used (10 mM Tris-HCI, pH 7.5) (beta is the thermal cubic volumetric expansion coefficient). For all of the proteins except for acrylodan-labeled IFABP, the fluorescence quantum yields calculated assuming simple energy conservation were anomalously high, i.e., the apparent heat signals were lower than those predicted from independent fluorescence measurements. The consistent anomalies suggest that the low photoacoustic signals may be characteristic of fluorophores buried in proteins, and that photoacoustic signals derive in part from the microenvironment of the absorbing chromophore.

Paranodal structure in diabetic sensory polyneuropathy.

Observations have been made on the structure of the paranodal region at nodes of Ranvier in the sural nerve of patients with diabetic sensory polyneuropathy. The structure of the paranodes was examined with particular attention to the definition and assessment of axoglial dysjunction, which has been claimed to be a characteristic feature of both human and experimental diabetic neuropathy and which has been related to paranodal swelling. In the present series of cases it was not possible to confirm that axoglial dysjunction is a distinctive feature of diabetic polyneuropathy in fibres not undergoing active demyelination or wallerian-type degeneration, neither was excessive paranodal enlargement found.

How many phenotypes from one genotype? The case of Prion diseases.

The usual assumption, namely that the underlying biochemical reactions in an organism tend to a unique steady-state, is shown to be not always correct. There are certain pathway mechanisms (e.g. positive feedback) which allow the system to exists in two alternative stable steady states. This bistability implies that environmental perturbations can "switch" the system from either state to the other. Such a switch takes place at the metabolic level and hence a single genotype can display two different, alternative, phenotypes without involving any changes in gene expression. The infective transmission of Scrapie-type diseases is explained here by such a mechanism involving protein-only changes.

Ultrastructural localization of sympathetic axons in experimental rat sciatic nerve neuromas.

The ultrastructural localization of sympathetic axons was investigated in normal rat sciatic nerves and experimental sciatic nerve neuromas. The best ultrastructural localization of noradrenaline in the dense-cored vesicles of sympathetic axons was accomplished following pretreatment of rats with nialamide and 5-hydroxy dopamine, followed by fixation according to the modified chromaffin technique of Tranzer and Richards (1976). After such preparation, sympathetic axons containing 5-hydroxy dopamine-labelled dense-cored vesicles could be identified in normal sciatic nerve. Large accumulations of labelled dense-cored vesicles were also found in acute neuromas, up to 1 week after nerve section. Much smaller numbers of dense-cored vesicles could be identified in chronic neuromas from 2 to 3 weeks following nerve section. Sympathetic axons could also be identified following electron probe X-ray microanalysis of the tissue sections, using chromium detection as the marker for the noradrenaline-containing dense-cored vesicles. Unusual configurations of Schwann cell subunits, which enclosed myelinated fibres and sympathetic axon sprouts within the same basal lamina, were identified in the acute neuromas, 3-7 days after nerve section. Such configurations may be of relevance to the pathophysiological interaction which develops between sympathetic efferent and sensory fibres in peripheral nerve neuromas.

The pathology of charcot-marie-tooth disease and related disorders.

Approximately a quarter of a century ago, the disorders originally designated as Charcot-Marie-Tooth disease and Dejerine-Sottas disease were shown by combined clinical, electrophysiological and nerve biopsy studies to be genetically complex. In pathological terms they could be broadly classified into demyelinating neuropathies and axonopathies. Advances in the molecular genetics of these disorders, particularly for those with a demyelinating basis, have recently produced substantial new insights. The identification of mutations in genes for myelin proteins has provided the opportunity for investigating the precise mechanisms of these neuropathies, including the use of spontaneous and genetically engineered animal models.

A method for increasing the concentration of a specific internal metabolite in steady-state systems.

An approach is described by which it is possible to increase the concentration of any internal metabolite without affecting the concentrations of other metabolites and fluxes in the organism. This approach requires the manipulation of only a limited number of enzyme activities. The method shows which enzymes to manipulate and the extent of the manipulation required to achieve a given increase in a chosen metabolite. A case study involving tryptophan overproduction in Saccharomyces cerevisae is given as a practical example of how this method could be used.

Flux control coefficients determined by inhibitor titration: the design and analysis of experiments to minimize errors.

This paper is a study into the effects of experimental error on the estimated values of flux control coefficients obtained using specific inhibitors. Two possible techniques for analysing the experimental data are compared: a simple extrapolation method (the so-called graph method) and a non-linear function fitting method. For these techniques, the sources of systematic errors are identified and the effects of systematic and random errors are quantified, using both statistical analysis and numerical computation. It is shown that the graph method is very sensitive to random errors and, under all conditions studied, that the fitting method, even under conditions where the assumptions underlying the fitted function do not hold, outperformed the graph method. Possible ways of designing experiments to minimize the effects of experimental errors are analysed and discussed.

Dorsal root ganglion proteins in Friedreich's ataxia.

The polypeptide composition of dorsal root ganglia from 8 human controls, 6 Friedreich's ataxia (FA) patients and 1 patient with diabetic neuropathy was studied by sodium dodecyl sulphate (SDS)-polyacrylamide gel electrophoresis (PAGE). Silver-stained gels demonstrated a decrease in a 40-kDa protein in FA patients. This protein appeared to be present in normal amounts in the diabetic ganglion, suggesting that this 40-kDa protein deficiency was not simply a reflection of reduced neuronal numbers but may be specific for FA.

Responses of metabolic systems to large changes in enzyme activities and effectors. 1. The linear treatment of unbranched chains.

This first paper in a series investigates the problem of predicting and analysing the effects of large changes in enzyme activities or external nutrients/effectors on metabolic fluxes. We introduce the concept of a deviation index, D, which gives a measure of the relative change in a metabolic variable (e.g. flux) due to a large (non-infinitesimal) relative change in a parameter (e.g. enzyme). Using simplifying kinetic assumptions we have found, for an unbranched metabolic chain, a direct relationship between deviation indices and flux control coefficients. This relationship provides a method to estimate flux control coefficients using a single large change in enzyme activity. We also provide a method of predicting the effects of, for example, DNA manipulation or other techniques for enzyme activity/concentration changes on metabolic fluxes. Up-modulations of single enzymes rarely produce significant changes in fluxes. We show that combined changes of activity of a group of enzymes will produce a more than 'additive' response. We provide a method of predicting the effects of these combined changes, given either the flux control coefficients of the group of enzymes or the effects on the flux of changing the enzymes individually. A similar analysis is carried out for large changes in external nutrients or effectors. These amplification factors, f, give experimentally accessible estimates of the expected changes in metabolic variables. We provide three 'case studies' to illustrate our results.

Responses of metabolic systems to large changes in enzyme activities and effectors. 2. The linear treatment of branched pathways and metabolite concentrations. Assessment of the general non-linear case.

We extend the analysis of unbranched chains (preceding paper) to large parameter changes in branched systems using linear kinetic assumptions. More complex relationships between flux control coefficients and deviation indices are established. In particular, the deviation index in such systems depends on more than one control coefficient as well as on the magnitude of the enzyme change. Non-additivity of the indices is the general rule. Combined changes of groups of enzymes, whether co-ordinate or not, have also been formulated. Control coefficients can be estimated from a small number of independent large-change experiments. Alternatively, the amplification factors can be calculated given the knowledge of the control coefficients. A 'case study' using published data is presented. The movement of intermediate metabolites as a consequence of large parameter changes can be dealt with in a similar manner. Experimental methods for showing the admissibility of assuming the simplifying assumptions used are summarised. Some simulation studies show possible limits of the application of the approach and some aspects of the general, non-linear, case are discussed. It is concluded that, although metabolic systems are in principle non-linear, many behave, in practice, as quasi-linear systems. The relationships established between deviation indices and control coefficients therefore provide a practical way of predicting the effects of large-scale changes in parameters for many metabolic systems.

Analysis of photoacoustic waveforms using the nonlinear least squares method.

Pulsed-laser photoacoustics is a technique which measures photoinduced enthalpic and volumetric changes on the nano- and microsecond timescales. Analysis of photoacoustic data generally requires deconvolution for a sum of exponentials, a procedure which has been developed extensively in the field of time-resolved fluorescence decay. Initial efforts to adapt an iterative nonlinear least squares computer program, utilizing the Marquardt algorithm, from the fluorescence field to photoacoustics indicated that significant modifications were needed. The major problem arises from the wide range of transient decay times which must be addressed by the photoacoustic technique. We describe an alternative approach to numerical convolution with exponential decays, developed to overcome the problems. Instead of using an approximation method (Simpson's rule) for evaluating the convolution integral, we construct a continuous instrumental response function by quadratic fitting of the discrete data and evaluate the convolution integral directly, without approximations. The success and limitations of this quadratic-fit convolution program are then demonstrated using simulated data. Finally, the program is applied to the analysis of experimental data to compare the resolution capabilities of two commercially available transducers. The advantages of a broadband, heavily damped transducer are shown for a standard organic photochemical system, the quenching of the triplet state of benzophenone by 2,5-dimethyl-2,4-hexadiene.

A fluorescence study of changes in noradrenergic sympathetic fibres in experimental peripheral nerve neuromas.

Experimental neuromas were produced in rats by sciatic nerve section and avulsion of the distal stumps. At intervals varying from 3 days to 8 weeks after nerve section, the developing neuromas were resected and processed for noradrenaline (NA) fluorescence microscopy by the sucrose-phosphate-glyoxylic acid (SPG) method. From serial longitudinal sections through the neuromas and the nerve proximally, counts of noradrenergic sympathetic axons were made, together with qualitative observations of axon sprouting and NA content. By 3 days after nerve section there was a massive sprouting of sympathetic axons, with increased NA content, particularly towards the distal tip of the neuroma. Axon counts remained high 1 week following section then fell to below normal levels at 2 weeks, returning towards normal 8 weeks after nerve section. These results are discussed in relation to the known pathophysiological interaction between sympathetic efferent and sensory afferent fibres, which develops in neuromas following nerve section.

Covalent modification and metabolic control analysis. Modification to the theorems and their application to metabolic systems containing covalently modifiable enzymes.

A study of the sensitivity properties of metabolic systems containing covalently modifiable enzymes and cascades has been carried out with the aid of metabolic control analysis. We have considered how the theorems of metabolic control analysis must be modified to take into account covalently modifiable enzymes, and have used these results to investigate the effects of increasing the total amount of modifiable enzyme. The sensitivity of system variables to an effector acting through a covalent-modification cycle has also been investigated.

Metabolic control analysis. Sensitivity of control coefficients to elasticities.

This paper illustrates a method to calculate the sensitivities of control coefficients to the elasticities which determine their values and it is shown that these sensitivities are systemic properties. We show, both theoretically and with a practical example, how they can be used to investigate: (a) the relative importance of a particular elasticity in the determination of the value of a control coefficient; (b) the effect of experimental error on the values of the control coefficients and (c) the construction of confidence limits around the values of the control coefficients.

The matrix method of metabolic control analysis: its validity for complex pathway structures.

The sensitivities of the variables of a metabolic system (such as fluxes and concentrations) to variations in enzyme concentration are expressed in metabolic control analysis as control coefficients. The matrix method is a system of writing matrix equations that generate expressions for the control coefficients in terms of the characteristics of the components (principally the enzymes). Previously, the matrix method has been considered in terms of simple pathway structures; here we justify its applicability to complex pathways, such as those with multiple branches. It is shown that this requires modification of the branch point relationship to take account of changes of flux along the limbs of the branch and of stoichiometric factors. The method of deriving the flux control coefficients with respect to different fluxes in the system is extended to cope with these circumstances.