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Torsten Becker

Publications and source records attributed to Torsten Becker.

9 recordsLinked to original sources
PubMed2006

Influence of the membrane potential on the protonation of bacteriorhodopsin: insights from electrostatic calculations into the regulation of proton pumping.

Proton binding and release are elementary steps for the transfer of protons within proteins, which is a process that is crucial in biochemical catalysis and biological energy transduction. Local electric fields in proteins affect the proton binding energy compared to aqueous solution. In membrane proteins, also the membrane potential affects the local electrostatics and can thus be crucial for protein function. In this paper, we introduce a procedure to calculate the protonation probability of titratable sites of a membrane protein in the presence of a membrane potential. In the framework of continuum electrostatics, we use a modified Poisson-Boltzmann equation to include the influence of the membrane potential. Our method considers that in a transmembrane protein each titratable site is accessible for protons from only one side of the membrane depending on the hydrogen bond pattern of the protein. We show that the protonation of sites receiving their protons from different sides of the membrane is differently influenced by the membrane potential. In addition, the effect of the membrane potential is combined with the effect of the pH gradient resulting from proton pumping. Our method is applied to bacteriorhodopsin, a light-activated proton pump. We find that the proton pumping of this protein might be regulated by Asp115, a conserved residue for which no function has been identified yet. According to our calculations, the interaction of Asp115 with Asp85 leads to the protonation of the latter if the pH gradient or the membrane potential becomes too large. Since Asp85 is the primary proton acceptor in the photocycle, bacteriorhodopsin molecules in which Asp85 is protonated cannot pump protons. Furthermore, we estimate how the membrane potential affects the energetics of the individual proton-transfer reactions of the photocycle. Most reactions, except the initial proton transfer from the Schiff base to Asp85, are influenced. Our calculations give new insights into the mechanism with which bacteriorhodopsin senses the membrane potential and the pH gradient and how the proton pumping is regulated by these parameters.

Animals↗
PubMed2006

Stepped defibrillation waveform is substantially more efficient than the 50/50% tilt biphasic.

BACKGROUND: Even with biphasic waveforms, patients with high defibrillation thresholds (DFTs) still are seen; thus, improved defibrillation waveforms may be of clinical utility. The stepped waveform has three parts: the first portion is positive with two capacitors in parallel, the second is positive with the capacitors in series, and the last portion is negative, also with the capacitors in series. OBJECTIVES: The purpose of this study was to assess the clinical utility of improved defibrillation waveforms. METHODS: We measured the delivered energy DFT in 20 patients in a dual-site study using the stepped waveform and a 50/50% tilt biphasic truncated exponential as the control. All shocks were delivered using an arbitrary waveform defibrillator, which was programmed to mimic two 220-microF capacitors (110 microF in series and 440 microF in parallel). RESULTS: The peak voltage at DFT was reduced in 19 of the 20 patients. The median peak voltage was reduced by 32.0%, from 472 V to 321 V (P <.001). The median energy DFT was reduced by 33%, from 11.7 J to 7.8 J (P = .008). The mean voltage and energy were reduced by 25.3% and 20.2%, respectively. On average, the stepped waveform was able to defibrillate as well as the 50/50% tilt biphasic, with 33% more energy. The benefit was more pronounced in patients with either a lower ejection fraction or a superior vena cava coil. The benefit of the stepped waveform had an inverse quadratic correlation with the resistance (r(2) = 0.47), suggesting that the capacitance values chosen for the stepped waveform were close to optimal for a 35-Omega resistance. CONCLUSION: The stepped waveform reduced the DFT compared to the 50/50% tilt waveform in this preliminary study.

Arrhythmias, Cardiac↗
PubMed2006

Synthetic glycopeptides from the mucin family as potential tools in cancer immunotherapy.

Compared to glycoproteins of healthy cells, glycoproteins of tumor cells are often aberrantly glycosylated. Thus, glycopeptide fragments of surface glycoproteins of tumor cells are of interest as tumor-associated antigens for the distinction between normal and tumor cells. Cancer immunotherapy directed at selectively targeting these tumor-associated glycoprotein structure alterations--deficient glycosylation and, thus, exposure of peptide epitopes which are masked in normal cells--is considered a promising approach for the treatment of cancer. For this purpose, glycoproteins from the mucin family are of particular interest. Mucins belong to a class of heavily O-glycosylated, high-molecular weight glycoproteins present on the surface of many epithelial cells. The mucin core protein consists of numerous tandem repeats rich in serine, threonine and proline. In their tumor-associated forms, epithelial mucins carry cryptic saccharide structures such as T(N)-, T-, sialyl-T(N)- and sialyl-T antigens and more complex oligosaccharides (e.g. Lewis(y)). In contrast to glycoproteins isolated from natural sources, synthetic glycopeptides can be obtained in high purity and with exactly defined structure. In this review, methodologies for the synthesis of mucin-type glycopeptides containing complex tumor-associated antigen structures are described. Due to the low immunogenicity often exhibited by synthetic tumor-associated glycopeptide antigens, their conjugation to carrier proteins or suitable T-cell epitopes is essential for the development of anti-tumor vaccines. The results of immunological evaluations of synthetic (glyco)peptides and oligosaccharides are described. Some of these synthetic vaccines show promising activities inducing proliferation of T-cells and cytotoxic T-cell responses.

Animals↗
PubMed2005

Electrostatic potential at the retinal of three archaeal rhodopsins: implications for their different absorption spectra.

The color tuning mechanism of the rhodopsin protein family has been in the focus of research for decades. However, the structural basis of the tuning mechanism in general and of the absorption shift between rhodopsins in particular remains under discussion. It is clear that a major determinant for spectral shifts between different rhodopsins are electrostatic interactions between the chromophore retinal and the protein. Based on the Poisson-Boltzmann equation, we computed and compared the electrostatic potential at the retinal of three archaeal rhodopsins: bacteriorhodopsin (BR), halorhodopsin (HR), and sensory rhodopsin II (SRII) for which high-resolution structures are available. These proteins are an excellent test case for understanding the spectral tuning of retinal. The absorption maxima of BR and HR are very similar, whereas the spectrum of SRII is considerably blue shifted--despite the structural similarity between these three proteins. In agreement with their absorption maxima, we find that the electrostatic potential is similar in BR and HR, whereas significant differences are seen for SRII. The decomposition of the electrostatic potential into contributions of individual residues, allowed us to identify seven residues that are responsible for the differences in electrostatic potential between the proteins. Three of these residues are located in the retinal binding pocket and have in fact been shown to account for part of the absorption shift between BR and SRII by mutational studies. One residue is located close to the beta-ionone ring of retinal and the remaining three residues are more than 8 A away from the retinal. These residues have not been discussed before, because they are, partly because of their location, no obvious candidates for the spectral shift among BR, HR, and SRII. However, their contribution to the differences in electrostatic potential is evident. The counterion of the Schiff base, which is frequently discussed to be involved in the spectral tuning, does not contribute to the dissimilarities between the electrostatic potentials.

Amino Acid Sequence↗
PubMed2004

Direct determination of vibrational density of states change on ligand binding to a protein.

The change in the vibrational density of states of a protein (dihydrofolate reductase) on binding a ligand (methotrexate) is determined using inelastic neutron scattering. The vibrations of the complex soften significantly relative to the unbound protein. The resulting free-energy change, which is directly determined by the density of states change, is found to contribute significantly to the binding equilibrium.

Deuterium Oxide↗
PubMed2004

Neutron frequency windows and the protein dynamical transition.

Proteins undergo an apparent dynamical transition on temperature variation that has been correlated with the onset of function. The transition in the mean-square displacement, , that is observed using a spectrometer or computer simulation, depends on the relationship between the timescales of the relaxation processes activated and the timescale accessible to the instrument or simulation. Models are described of two extreme situations---an "equilibrium" model, in which the long-time dynamics changes with temperature and all motions are resolved by the instrument used; and a "frequency window" model, in which there is no change in the long-time dynamics but as the temperature increases, the relaxation frequencies move into the instrumental range. Here we demonstrate that the latter, frequency-window model can describe the temperature and timescale dependences of both the intermediate neutron scattering function and derived from molecular dynamics simulations of a small protein in a cryosolution. The frequency-window model also describes the energy-resolution and temperature-dependences of obtained from experimental neutron scattering on glutamate dehydrogenase in the same solvent. Although equilibrium effects should also contribute to dynamical transitions in proteins, the present results suggests that frequency-window effects can play a role in the simulations and experiments examined. Finally, misquotations of previous findings are discussed in the context of solvent activation of protein dynamics and the possible relationship of this to activity.

Biophysics↗
PubMed2003

Energy resolution and dynamical heterogeneity effects on elastic incoherent neutron scattering from molecular systems.

Incoherent neutron scattering is widely used to probe picosecond-nanosecond time scale dynamics of molecular systems. In systems of spatially confined atoms the relatively high intensity of elastic incoherent neutron scattering is often used to obtain a first estimate of the dynamics present. For many complex systems, however, experimental elastic scattering is difficult to interpret unambiguously using analytical dynamical models that go beyond the determination of an average mean-square displacement. To circumvent this problem a description of the scattering is derived here that encompasses a variety of analytical models in a common framework. The framework describes the time-converged part of the dynamic structure factor [the elastic incoherent scattering function (EISF)] and lends itself to practical use by explicitly incorporating effects due to the finite energy resolution of the instrument used. The dependence of the elastic scattering on wave vector is examined, and it is shown how heterogeneity in the distribution of mean-square displacements can be related to deviations of the scattering from Gaussian behavior. In this case, a correction to fourth order in the scattering vector can be used to extract the variance of the distribution of mean-square displacements. The formalism is used in a discussion of measurements on dynamics accompanying the glass transition in molecular systems. By fitting to experimental data obtained on a protein solution the present methodology is used to show how the existence of a temperature-dependent relaxation frequency can lead to a transition in the measured mean-square displacement in the absence of an EISF change.

Journal Article↗
PubMed2003

[Non-contact mapping of the left atrium using a multi electrode mapping array].

In contrast to the sequential mapping systems such as the conventional and the electroanatomic mapping, the non-contact mapping provides simultaneous mapping. The non-contact-mapping system detects far-field endocardial potentials from a multielectrode-array catheter and reconstructs over 3,000 unipolar virtual electrograms. Based on the virtual electrograms, the system produces an instantaneous three-dimensional (3-D) isopotential map. High-density mapping of the endocardial activation sequence allows immediate and simultaneous identification of a propagation vector along the line and the identification of an arrhythmogenic focus on a single beat. The methods and results of different ablation strategies for atrial fibrillation using the non-contact-mapping system are reported.

Atrial Fibrillation↗