Biomedical subjects

Peter Krüger

Publications and source records attributed to Peter Krüger.

13 recordsLinked to original sources

PubMed2006

Berezinskii-Kosterlitz-Thouless crossover in a trapped atomic gas.

Any state of matter is classified according to its order, and the type of order that a physical system can possess is profoundly affected by its dimensionality. Conventional long-range order, as in a ferromagnet or a crystal, is common in three-dimensional systems at low temperature. However, in two-dimensional systems with a continuous symmetry, true long-range order is destroyed by thermal fluctuations at any finite temperature. Consequently, for the case of identical bosons, a uniform two-dimensional fluid cannot undergo Bose-Einstein condensation, in contrast to the three-dimensional case. However, the two-dimensional system can form a 'quasi-condensate' and become superfluid below a finite critical temperature. The Berezinskii-Kosterlitz-Thouless (BKT) theory associates this phase transition with the emergence of a topological order, resulting from the pairing of vortices with opposite circulation. Above the critical temperature, proliferation of unbound vortices is expected. Here we report the observation of a BKT-type crossover in a trapped quantum degenerate gas of rubidium atoms. Using a matter wave heterodyning technique, we observe both the long-wavelength fluctuations of the quasi-condensate phase and the free vortices. At low temperatures, the gas is quasi-coherent on the length scale set by the system size. As the temperature is increased, the loss of long-range coherence coincides with the onset of proliferation of free vortices. Our results provide direct experimental evidence for the microscopic mechanism underlying the BKT theory, and raise new questions regarding coherence and superfluidity in mesoscopic systems.

Letter↗

PubMed2005

Bose-Einstein condensates: microscopic magnetic-field imaging.

Today's magnetic-field sensors are not capable of making measurements with both high spatial resolution and good field sensitivity. For example, magnetic force microscopy allows the investigation of magnetic structures with a spatial resolution in the nanometre range, but with low sensitivity, whereas SQUIDs and atomic magnetometers enable extremely sensitive magnetic-field measurements to be made, but at low resolution. Here we use one-dimensional Bose-Einstein condensates in a microscopic field-imaging technique that combines high spatial resolution (within 3 micrometres) with high field sensitivity (300 picotesla).

Journal Article↗

PubMed2004

Theory of Ca L2,3-edge XAS using a novel multichannel multiple-scattering method.

A new method for calculating X-ray absorption spectroscopy (XAS) at the L2,3 edges of Ca and transition metals is presented. It is based on the multichannel multiple-scattering theory by Natoli et al. [Phys. Rev. B, (1990), 42, 1944-1968] combined with the eigen-channel R-matrix formalism. Atomic multiplet-like effects, owing to the Coulomb interaction of photoelectrons and the 2p hole, are taken into account through a configuration interaction ansatz for the final-state wavefunction. The various multiplet states lead to a set of channels for the photoelectron wavefunction, which is calculated in multiple-scattering theory. The method is applied to Ca, an important element for biological applications of XAS. An L3:L2 branching ratio of 3:4 is found, in good agreement with experiment but in contrast to the statistical value 2:1 obtained in all one-electron approaches. By using a linear mixture between statically screened (approximately 90%) and unscreened (approximately 10%) core-hole potential, the line shape, too, agrees well with the experimental one.

Calcium↗

PubMed2004

Fast initial decay of molecular excitations at insulator surfaces.

We investigate the initial decay of electron-hole excitations in a molecular layer after adsorption on an insulator substrate surface. This is done within ab initio many-body perturbation theory by calculating the time propagation of excited two-particle states. For a CO monolayer adsorbed on the MgO(001) surface we find very fast decay processes with lifetimes that are about 5 times shorter than the transfer of single charge carriers. This is due to a strong coupling of the molecular excitations to charge-transfer-exciton states between the adlayer and the substrate.

Journal Article↗

PubMed2004

Protein simulations: the absorption spectrum of barnase point mutants.

The near-UV absorption spectra of barnase double-point mutants are calculated using a combination of molecular dynamics and ab initio techniques. The atoms of the fluorescent probes are placed in a cloud of point charges, generated by molecular dynamics simulations. Ab initio calculations (CASPT2) are performed on these systems. Three molecular dynamics packages are compared-Amber5.0, CHARMM-c27b1, and GROMOS96-using indole as the fluorescent probe. It was found that calculated absorption spectra reproduce experimental values very well, provided detailed charge cloud descriptions are included. These calculations further sustain the hypothesis that different tryptophan rotamers can be present in proteins. Molecular dynamics calculations of the double-point mutants also point to the structural effect of counter ions.

Bacillus↗

PubMed2004

Simulation of the activation of alpha-chymotrypsin: analysis of the pathway and role of the propeptide.

Alpha-chymotrypsin undergoes a reversible conformational change from an inactive chymotrypsinogen-like structure at high pH to an active conformation at neutral pH. In order to gain insight into this process on a structural level, we applied molecular dynamics and targeted molecular dynamics simulations in aqueous environment on the activation and inactivation processes of three different types of chymotrypsin. These are the wild-type bovine chymotrypsin containing the propeptide and the bovine and rat chymotrypsin lacking the propeptide. From these simulations, the importance of the propeptide and of the sequence differences between the rat and bovine variants from the viewpoint of activation could be evaluated and compared with previous fluorescence stopped flow results. The obtained results show the unambiguous influence of the propeptide on the explored conformational space, whereas the sequence differences between bovine and rat chymotrypsin play a minor role. The main features of activation are present in both the wild type and the variant lacking the propeptide, despite the fact that different parts of the conformational space were explored. The comparison of all trajectories shows that particular amino acid residues, such as 17, 18, 19, 187, 217, 218, and 223, undergo large dihedral transitions during the activation process, suggesting a role as hinge residues during the conformational change.

Amino Acid Sequence↗

PubMed2004

MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.

MAPMAN is a user-driven tool that displays large data sets onto diagrams of metabolic pathways or other processes. SCAVENGER modules assign the measured parameters to hierarchical categories (formed 'BINs', 'subBINs'). A first build of TRANSCRIPTSCAVENGER groups genes on the Arabidopsis Affymetrix 22K array into >200 hierarchical categories, providing a breakdown of central metabolism (for several pathways, down to the single enzyme level), and an overview of secondary metabolism and cellular processes. METABOLITESCAVENGER groups hundreds of metabolites into pathways or groups of structurally related compounds. An IMAGEANNOTATOR module uses these groupings to organise and display experimental data sets onto diagrams of the users' choice. A modular structure allows users to edit existing categories, add new categories and develop SCAVENGER modules for other sorts of data. MAPMAN is used to analyse two sets of 22K Affymetrix arrays that investigate the response of Arabidopsis rosettes to low sugar: one investigates the response to a 6-h extension of the night, and the other compares wild-type Columbia-0 (Col-0) and the starchless pgm mutant (plastid phosphoglucomutase) at the end of the night. There were qualitatively similar responses in both treatments. Many genes involved in photosynthesis, nutrient acquisition, amino acid, nucleotide, lipid and cell wall synthesis, cell wall modification, and RNA and protein synthesis were repressed. Many genes assigned to amino acid, nucleotide, lipid and cell wall breakdown were induced. Changed expression of genes for trehalose metabolism point to a role for trehalose-6-phosphate (Tre6P) as a starvation signal. Widespread changes in the expression of genes encoding receptor kinases, transcription factors, components of signalling pathways, proteins involved in post-translational modification and turnover, and proteins involved in the synthesis and sensing of cytokinins, abscisic acid (ABA) and ethylene revealing large-scale rewiring of the regulatory network is an early response to sugar depletion.

Abscisic Acid↗

PubMed2003

Image states and excitons at insulator surfaces with negative electron affinity.

We discuss electronic excitation processes at two ionic insulator surfaces, LiF(001)-(1x1) and MgO(001)-(1x1), within ab initio many-body perturbation theory. Because of the negative electron affinity of the surfaces, the lowest unoccupied electronic states are image states located in the vacuum outside the surface. Excitations of electrons from the surface layer into these image states are much lower in energy than the bulk excitons. They are responsible for characteristic surface features in the electron energy-loss spectra of LiF(001) and MgO(001).

Journal Article↗

PubMed2003

Circular dichroism spectra of beta-peptides: sensitivity to molecular structure and effects of motional averaging.

Circular dichroism spectra of two beta-peptides, i.e. peptides composed of beta-amino acids, calculated using ensembles of configurations obtained by molecular dynamics simulation are presented. The calculations were based on 200 ns simulations of a beta-heptapeptide in methanol at 298 K and 340 K and a 50 ns simulation of a beta-hexapeptide in methanol at 340 K. In the simulations the peptides sampled both folded (helical) and unfolded structures. Trajectory structures with common backbone conformations were identified and grouped into clusters. The CD spectra were calculated for individual structures, based on peptide-group dipole transition moments obtained from semi-empirical molecular orbital theory and using the so-called matrix method. The single-structure spectra were then averaged over entire trajectories and over clusters of structures. Although certain features of the experimental CD spectra of the beta-peptides are reproduced by the trajectory-average spectra, there exist clear differences between the two sets of spectra in both wavelength and peak intensities. The analysis of individual contributions to the average spectra shows that, in general, the interpretation of a CD signal in terms of a single structure is not possible. Moreover, there is a large variation in the CD spectra calculated for a set of individual structures that belong to the same cluster, even when a structurally tight clustering criterion is used. This indicates that the CD spectra of these peptides are very sensitive to small local structural differences.

Circular Dichroism↗

PubMed2003

Anomalous x-ray reflectivity characterization of ion distribution at biomimetic membranes.

Anomalous x-ray reflectivity measurements provides detailed information on ion binding to biomembrane surfaces. Using a monochromatic beam tuned to various x-ray energies at the Argonne National Laboratory Advanced Photon Source and utilizing a newly commissioned x-ray liquid surfaces reflectometer, measurements at and away from ion absorption edges allow determination of the distribution of these ions as they accumulate near lipid membranes. As a model, the interaction of Ba2+ ions with DMPA- (1,2-dimyristoyl-sn-glycero-3-phosphatidic acid) monolayers at the aqueous surface is studied. We find an unexpectedly large concentration of barium at the interface, approximately 1.5 per DMPA-, forming a Stern layer of bound ions and a cloud of less densely bound ions near the lipid headgroups. This result can be understood only if one assumes that bound cations are partially speciated, e.g., as BaOH+.

Biomimetic Materials↗

PubMed2003

Deacylated pulmonary surfactant protein SP-C transforms from alpha-helical to amyloid fibril structure via a pH-dependent mechanism: an infrared structural investigation.

Bovine pulmonary surfactant protein C (SP-C) is a hydrophobic, alpha-helical membrane-associated lipoprotein in which cysteines C4 and C5 are acylated with palmitoyl chains. Recently, it has been found that the alpha-helix form of SP-C is metastable, and under certain circumstances may transform from an alpha-helix to a beta-strand conformation that resembles amyloid fibrils. This transformation is accelerated when the protein is in its deacylated form (dSP-C). We have used infrared spectroscopy to study the structure of dSP-C in solution and at membrane interfaces. Our results show that dSP-C transforms from an alpha-helical to a beta-type amyloid fibril structure via a pH-dependent mechanism. In solution at low pH, dSP-C is alpha-helical in nature, but converts to an amyloid fibril structure composed of short beta-strands or beta-hairpins at neutral pH. The alpha-helix structure of dSP-C is fully recoverable from the amyloid beta-structure when the pH is once again lowered. Attenuated total reflectance infrared spectroscopy of lipid-protein monomolecular films showed that the fibril beta-form of dSP-C is not surface-associated at the air-water interface. In addition, the lipid-associated alpha-helix form of dSP-C is only retained at the surface at low surface pressures and dissociates from the membrane at higher surface pressures. In situ polarization modulation infrared spectroscopy of protein and lipid-protein monolayers at the air-water interface confirmed that the residual dSP-C helix conformation observed in the attenuated total reflectance infrared spectra of transferred films is randomly or isotropically oriented before exclusion from the membrane interface. This work identifies pH as one of the mechanistic causes of amyloid fibril formation for dSP-C, and a possible contributor to the pathogenesis of pulmonary alveolar proteinosis.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2003

MD simulation of protein-ligand interaction: formation and dissociation of an insulin-phenol complex.

Complexes of proteins with small ligands are of utmost importance in biochemistry, and therefore equilibria, formation, and decay have been investigated extensively by means of biochemical and biophysical methods. Theoretical studies of the molecular dynamics of such systems in solution are restricted to 10 ns, i.e., to fast processes. Only recently new theoretical methods have been developed not to observe the process in real time, but to explore its pathway(s) through the energy landscape. From the profiles of free energy, equilibrium and kinetic quantities can be determined using transition-state theory. This study is dedicated to the pharmacologically relevant insulin-phenol complex. The distance of the center of mass chosen as a reaction coordinate allows a reasonable description over most of the pathway. The analysis is facilitated by analytical expressions we recently derived for distance-type reaction coordinates. Only the sudden onset of rotations at the very release of the ligand cannot be parameterized by a distance. They obviously require a particular treatment. Like a preliminary study on a peptide, the present case emphasizes the contribution of internal friction inside a protein, which can be computed from simulation data. The calculated equilibrium constant and the friction-corrected rates agree well with experimental data.

Binding Sites↗

PubMed2002

Effect of hydrophobic surfactant protein SP-C on binary phospholipid monolayers. Molecular machinery at the air/water interface.

Fluorescent and modified dark-field microscopies were used to investigate the phase behavior of physiologically relevant lipid/protein monomolecular films containing surfactant protein C(SP-C). Synthetic human SP-C(1-34) was labeled at its N-terminus using the fluorescent probe 6-(((4(4,4-difluoro-5-(2-thienyl)-4-bora-3a,4a-diaza-s-indacene-3-yl)phenoxy)acetyl)amino)hexanoic acid (BODIPY/TR-X). Using dual fluorescent labeling (lipid and protein) in the monolayers, we have correlated (at physiologically small concentrations of the protein) the lipid phase separation and protein distribution in situ. A comparison of the lipid and protein dye fluorescent micrographs indicates that SP-C(1-34) is preferentially associated with the disordered lipid phase. Three concepts arise from our results. (1) The presence of SP-C alone does not result in the complete dissolution of condensed phase domains in a fashion that we have previously reported for the entire hydrophobic surfactant protein (SP-B/C) fraction (Biophys. J. 77 (1999) 903). Rather, the use of relatively high amounts ( approximately 10 wt.%) of the labeled SP-C protein is needed to reproduce the fluorescence monolayer morphology previously observed for small concentrations ( approximately 1 wt.%) of the natural SP-B/C mixture. (2) Scattered light, dark-field microscopy performed using grazing angle laser illumination reveals the presence of surface-associated, three-dimensional (3D) structures of micrometer-sized dimensions when the labeled BODIPY/TR-X:SP-C(1-34) protein is included in the monolayer, as previously observed with the naturally isolated SP-B/C mixture. The 3D structures are associated exclusively with the presence of the SP-C protein in disordered monolayer phases. (3) To explain these results, we have derived a molecular model accounting for the structure and physico-chemical properties of the SP-C protein in terms of its energetics. The molecular events involved in the SP-C-mediated production of the 3D surface particles are explained using the analogy of a simple molecular machine, namely a loaded spring. This interpretation is supported by an energetic analysis that suggests the major factor contributing to the formation of the 3D particles is the energy liberated by re-expansion of the surrounding phospholipid film into the area vacated by the SP-C protein as it re-orients away from the surface.

Air↗