Biomedical subjects

R W Hendler

Publications and source records attributed to R W Hendler.

At least 37 records · Page 2Linked to original sources

PubMed1994

Deconvolutions based on singular value decomposition and the pseudoinverse: a guide for beginners.

Singular value decomposition (SVD) is deeply rooted in the theory of linear algebra, and because of this is not readily understood by a large group of researchers who could profit from its application. In this paper, we discuss the subject on a level that should be understandable to scientists who are not well versed in linear algebra. However, because it is necessary that certain key concepts in linear algebra be appreciated in order to comprehend what is accomplished by SVD, we present the section, 'Bare basics of linear algebra'. This is followed by a discussion of the theory of SVD. Next we present step-by-step examples to illustrate how SVD is applied to deconvolute a titration involving a mixture of three pH indicators. One noiseless case is presented as well as two cases where either a fixed or varying noise level is present. Finally, we discuss additional deconvolutions of mixed spectra based on the use of the pseudoinverse.

Mathematical Computing↗

PubMed1994

Near infrared spectral changes of cytochrome aa3 during potentiometric titrations.

Singular value decomposition (SVD) was used to deconvolute the spectral changes occurring in the near infrared region during potentiometric titrations of cytochrome aa3. Overall oxidized minus reduced difference spectra revealed a broad absorbance feature centered near 830 nm with an apparent Em near 250 mV. However, SVD did not isolate any spectral species with an absorbance centered near 830 nm. It was found that the spectral changes occurring in the wavelength region from 650 to 950 nm were associated mainly with cytochromes a and a3. It was concluded that the absorbance at 830 nm should not be used as an independent measure of the concentration of CuA in cytochrome aa3.

Animals↗

PubMed1993

Multiwavelength analysis of the kinetics of reduction of cytochrome aa3 by cytochrome c.

Some new approaches to the kinetic study of the reduction of cytochrome aa3 by cytochrome c are presented. The primary innovations are the use of a spectrometer which can acquire multiwavelength data as fast as every 10 microseconds, and the application of a variety of analytical methods which can utilize simultaneously all of the time-resolved spectral data. These techniques include singular value decomposition (SVD), deconvolutions based on pure Gaussian models for absorption peaks, deconvolutions based on isolated absorption spectra for the pure components, and simulations of SVD-deduced and actual experimental difference spectra. The reduction characteristics of the anaerobic resting enzyme can be distinguished from those of pulsed forms. In the former case, only two electrons can be bound by cytochrome aa3, whereas in the latter case complete reduction of the enzyme is achieved.

Animals↗

PubMed1992

Redox interactions in cytochrome c oxidase: from the "neoclassical" toward "modern" models.

Because of recent experimental data on the redox characteristics of cytochrome c oxidase and renewed interest in the role of cooperativity in energy coupling, the question of redox cooperativity in cytochrome c oxidase is reexamined. Extensive redox cooperativity between more than two redox centers, some of which are spectrally invisible, may be expected for this electron transfer coupled proton pump. Such cooperativity, however, cannot be revealed by the traditional potentiometric experiments based on a difference in absorbance between two wavelengths. Multiwavelength analyses utilizing singular value decomposition and second derivatives of absorbance vs. wavelength have revealed a stronger cooperativity than consistent with the "neoclassical" model, which allowed only for weak negative cooperativity between two equipotential one-electron centers. A thermodynamic analysis of redox cooperativity is developed, which includes the possibilities of strong cooperative redox interactions, the involvement of invisible redox centers, conformational changes, and monomer/dimer equilibrations. The experimental observation of an oxidation of one of the cytochromes (a3) with a decrease in applied redox potential is shown to require both strong negative cooperativity and the participation of more than two one-electron centers. A number of "modern" models are developed using the analytical approaches described in this paper. By testing with experimental data, some of these models are falsified, whereas some are retained with suggestions for further testing.

Binding Sites↗

PubMed1991

Can ferricyanide oxidize carbon monoxide-liganded cytochrome a3?

Evidence for the oxidation of CO-liganded cytochrome a3 by ferricyanide has been published recently. These observations conflict with the long-held belief that ferricyanide is thermodynamically incapable of oxidizing the CO complex. The present paper examines the facts on which the earlier idea was based. It is concluded that the earlier evidence did not establish that ferricyanide was incompetent as an oxidant for CO-liganded cytochrome a3.

Carbon Monoxide↗

PubMed1991

Potentiometric and spectral studies with the two-subunit cytochrome aa3 from Paracoccus denitrificans. Comparison with the 13-subunit beef heart enzyme.

Previous work from this laboratory has revealed a complex and interactive redox behavior for the active metal centers in beef heart cytochrome aa3. All of these centers are contained in two of the 13 subunits which make up the enzyme. The isolated cytochrome aa3 of Paracoccus denitrificans contains only two subunits. The purpose of the current investigation was to see if the complex redox behavior is dependent on the presence of the additional 11 peptides that are present in the mammalian enzyme. In this paper we report that the structurally simpler bacterial enzyme displays a redox behavior which is very similar to that seen with the mammalian enzyme. Therefore, the observed redox behavior does not depend on interactions involving the additional peptides.

Animals↗

PubMed1991

Comparison of energy-transducing capabilities of the two- and three-subunit cytochromes aa3 from Paracoccus denitrificans and the 13-subunit beef heart enzyme.

In the accompanying paper, we have shown that the two-subunit cytochrome aa3 isolated from Paracoccus denitrificans displays the same kind of complex and interactive redox behavior as the 13-subunit cytochrome aa3 from beef heart. Therefore, the redox characteristics are not dependent on the additional 11 subunits. In the current work, we have examined the energy-transducing capabilities of both the two- and three-subunit enzymes obtained from Paracoccus denitrificans in relation to that of the 13-unit mammalian enzyme. We have found that in all of the tested functions, which included the development of delta psi and delta pH, and the pumping of protons, that the two-subunit enzyme is at least as efficient as the structurally more complex mammalian enzyme. There is thus a correlation between the complex redox behavior and energy transducing capabilities of the two enzymes. There was also no difference in energy-transducing capabilities between the two- and three-subunit forms of the bacterial enzyme. It seems that only 2 subunits are required for an efficient energy-transducing cytochrome aa3. The most likely role of the additional subunits in the mammalian enzyme, therefore, seems to be in regulation.

Animals↗

PubMed1990

High voltage redox properties of cytochrome c oxidase.

In earlier studies evidence was obtained for the existence of both high and low redox potential forms of cytochrome a3 (Hendler et al. 1986. Biophys. J. 49:717-729; Hendler and Sidhu. 1988. Biophys. J. 54:121-133). The current paper describes additional experiments that support this conclusion and then reviews a large number of experimental observations that appear to be consistent with the view that cytochrome a3 displays at least (see Sidhu and Hendler. 1990. Biophys. J. 57:1125-1140) two different forms, which are distinguishable by their redox potentials, spectra, and reactivity with CO.

Biophysical Phenomena↗

PubMed1990

Characterization of two low Em forms of cytochrome a3 and their carbon monoxide complexes in mammalian cytochrome c oxidase.

Evidence is presented for the existence of two forms of low-potential cytochrome a3. One appears to be similar to the low-spin form reported by Nicholls, P., and V. Hildebrandt (1978 Biochem. J. 173:65-72) and Wrigglesworth, J. M., J. Elsden, A. Chapman, N. Van der Water, and M. F. Grahn (1988. Biochim. Biophys. Acta. 936:452-464). It has a reduced Soret peak near 428 nm and a prominent alpha peak near 602 nm. This form is seen when the enzyme is either supplemented with lipoprotein or incorporated into a liposomal membrane, preexposed to a voltage greater than 400 mV for at least 30 min, and titrated in the presence of approximately 1 mM K3Fe(CN)6. The other form has a reduced Soret peak near 446 nm, and no prominent alpha peak. The 428-nm form has an Em near 175 mV and forms a CO complex with an Em near 225 mV. The 446-nm form has an Em near 200 mV and forms a CO complex with an Em near 335 mV.

Animals↗

PubMed1989

Interactions between a new class of eukaryotic antimicrobial agents and isolated rat liver mitochondria.

Members of a newly discovered class of eukaryotic antimicrobial peptides are shown to release respiratory control in isolated rat-liver mitochondria. They also dissipate the membrane potential and inhibit respiration. The uncoupling activity of the peptides decreases with time probably due to the presence of proteases in the mitochondrial preparation. Quinine and Mg2+ reduce the activity of the peptides. The nature of the dependence of the respiratory rate on the concentration of added peptides suggests that they are active in a multimeric form, consistent with the formation of a channel across the inner mitochondrial membrane. The channel allows passage of sucrose.

Animals↗

PubMed1989

Magainin 2 amide and analogues. Antimicrobial activity, membrane depolarization and susceptibility to proteolysis.

We compared the abilities of synthetic magainin 2 amide and its analogues to inhibit the growth of Escherichia coli and to cause membrane depolarization in E. coli cells and cytochrome oxidase liposomes. The analogue, magainin A, was about 40-times more active than magainin 2 amide in inhibiting the growth of E. coli and had a much more sustained effect on the membrane potential. In the liposomal system, however, there was only approx. 20% difference between these two peptides in the reduction of membrane potential and uncoupling of respiration. Studies with pronase digestion suggested that the difference in potency may be due to differential susceptibility to proteolysis in the presence of membranes.

Amides↗

PubMed1989

Magainins and the disruption of membrane-linked free-energy transduction.

Magainins, a family of positively charged peptides, are partly if not wholly responsible for antimicrobial activity in skin extracts of Xenopus laevis. We report here that members of the magainin family--i.e., the 21-amino acid peptide PGLa and the 23-amino acid peptide magainin 2 amide (PGSa)--dissipate the electric potential across various energy-transducing membranes and thus uncouple respiration from other free-energy-requiring processes. We propose that this is a likely mechanism for the antimicrobial effects of these compounds.

Animals↗

PubMed1988

A new high potential redox transition for cytochrome aa3.

Using cyano-complexes of iron, tungsten, and molybdenum and a platinum working electrode, we have been able to attain and hold voltages in the range of 400 to 900 mV (vs. standard hydrogen electrode) in an aqueous medium. With this system we have obtained additional information in support of an earlier conclusion that cytochrome a3 has a high Em transition (i.e. greater than 460 mV) in addition to its Em in the 180-200 mV range (Hendler, R. W., K. V. S. Reddy, R. I. Shrager, and W. S. Caughey. 1986. Biophys. J. 49:717-729; Reddy, K. V. S., and R. W. Hendler. 1986. Biophys. J. 49:693-703). The proposed new transition has an Em near 770 mV and an n value greater than 1. The reduced form of the high-potential species of cytochrome a3 does not bind CO, in contrast to the reduced form of the low-potential species which does. A possible reaction scheme for cytochrome aa3 which incorporates the new information is presented.

Animals↗

PubMed1988

Direct measurement of the initial and early ratios of proton extrusion to oxygen uptake accompanying cytochrome c oxidation by rat liver mitoplasts.

We have recently described new methods that enable the sharp initiation of a respiratory pulse by photolysis of the CO complex of cytochrome oxidase in a stirred suspension of mitochondria, succinate, O2, and CO (Setty, O. H., R. I. Shrager, B. Bunow, B. Reynafarje, A. L. Lehninger, and R. W. Hendler. 1986. Biophys. J. 50:391-404). Data are collected directly into a microcomputer at 10-ms intervals from fast responding O2 and pH electrodes. These procedures eliminate delays and uncertainties due to mixing times, recorder response, and recovery of the O2 electrode from responding to the injection of O2. Correction procedures were also described for the inherent electrode delays. These procedures revealed an initial burst in medium acidification and a lag in O2 uptake that led to H+/O rates of 20-30 during the first 50 ms and relaxed to "normal" levels by 300 ms. Subsequent changes in [H+] and [O2] followed time courses that appeared to be, but were not strictly, first order. We describe here similar studies in which cytochrome c served as electron donor to site III of rat liver mitoplasts. A qualitatively similar but quantitatively smaller burst in medium acidification and H+/O ratio was seen in these studies. Implications of the previous (Setty et al., 1986) and current studies on defining "mechanistic" H+/O ratios are discussed.

Animals↗

PubMed1987

Problems in the experimental determination of substrate-specific H+/O ratios during respiration.

Krab et al. (1984) have recently tried to resolve the long-standing controversy as to whether the mechanistic H+/O coupling ratio for electrons passing through sites II and III of the mammalian electron transport chain to O2 is 6 or 8. Using a mathematical model they concluded that the higher number reported by Costa et al. (1984) was an overestimate because of the unaccounted for delayed response of the O2 electrode. Responding to criticisms of Lehninger et al. (1985), they have recently used (Krab and Wikström, 1986) an improved mathematical model which shows that the higher number found by Costa et al. was probably due to an inadequate accounting for the effects of the proton leak process which accompanies the translocation process. The impression is left that the situation is now resolved in favor of the lower number. We agree that the procedures of Costa et al. do not properly account for the leak process, and provide further evidence in this paper of the magnitude of the problem. However, we disagree that the number 6.0, favored by Wikström et al., rests on any more solid experimental support. We provide evidence here for this conclusion and raise the question as to whether or not any unique, fixed, integral number exists for the H+/O ratio accompanying the oxidation of a particular substrate.

Animals↗

PubMed1986

Direct measurement of the initial proton extrusion to oxygen uptake ratio accompanying succinate oxidation by rat liver mitochondria.

The problem of obtaining very early ratios for the H+/O stoichiometry accompanying succinate oxidation by rat liver mitochondria was attacked using new techniques for direct measurement rather than extrapolations based on data obtained after mixing and the recovery of the electrode from initial injection of O2. Respiration was quickly initiated in a thoroughly mixed O2-containing suspension of mitochondria under a CO atmosphere by photolysis of the CO-cytochrome c oxidase complex-. Fast responding O2 and pH electrodes were used to collect data every 10 ms. The response time for each electrode was experimentally measured in each experiment and suitable corrections for electrode relaxations were made. With uncorrected data obtained after 0.8 s, the extrapolation back to zero time on the basis of single-exponential curve fitting confirmed values close to 8.0 as previously reported (Costa et al., 1984). The data directly obtained, however, indicate an initial burst in H+/O ratio that peaked to values of approximately 20 to 30 prior to 50 ms and which was no longer evident after 0.3 s. Newer information and considerations that place all extrapolation methods in question are discussed.

Animals↗

PubMed1986

Processing and analysis of potentiometric data.

Potentiometric titration curves have traditionally been collected as the difference in absorbance at two wavelengths, and analyzed by plotting voltage vs. log (oxidized/reduced). The collection method, designed to monitor changes in local peak height, is effective for that purpose only when spectral backgrounds do not change slope as voltage changes, and the analysis method is valid only for a single isolated component (one whose midpoint potential is far from that of anything else in the mixture). Yet these methods are commonly used where such restrictions do not pertain, e.g. the study of cytochromes in mitonchondria. In this paper, we present more appropriate methods of collection and analysis, and suggest that, even with the best available methods, any conclusion should be confirmed in several ways. Experimental results are presented in accompanying papers.

Electron Transport↗

PubMed1986

Complete analysis of the cytochrome components of beef heart mitochondria in terms of spectra and redox properties. The c1-cytochromes.

Using newer techniques for conducting and analyzing potentiometric titrations, we have studied the thermodynamic and spectral properties of cytochrome c1 in beef heart mitochondria. We find two species of cytochrome c1, both with n = 2 values for the number of electrons involved in their oxidation or reduction. One has an Em approximately 210 mV and a spectral peak near 555 nm and the other has an Em approximately 255 mV and a spectral peak nearer 553 nm. These Em values are pH-independent in the range of pH 6 to 8. The Em and n values of these two components are indistinguishable from those of two species of cytochrome aa3 (i.e. spectral feature of 605 nm).

Animals↗