Biomedical subjects

Dirk Linke

Publications and source records attributed to Dirk Linke.

7 recordsLinked to original sources

PubMed2006

Gene duplication of the eight-stranded beta-barrel OmpX produces a functional pore: a scenario for the evolution of transmembrane beta-barrels.

The repeating unit of outer membrane beta-barrels from Gram-negative bacteria is the beta-hairpin, and representatives of this protein family always have an even strand number between eight and 22. Two dominant structural forms have eight and 16 strands, respectively, suggesting gene duplication as a possible mechanism for their evolution. We duplicated the sequence of OmpX, an eight-stranded beta-barrel protein of known structure, and obtained a beta-barrel, designated Omp2X, which can fold in vitro and in vivo. Using single-channel conductance measurements and PEG exclusion assays, we found that Omp2X has a pore size similar to that of OmpC, a natural 16-stranded barrel. Fusions of the homologous proteins OmpX, OmpA and OmpW were able to fold in vitro in all combinations tested, revealing that the general propensity to form a beta-barrel is sufficient to evolve larger barrels by simple genetic events.

Amino Acid Sequence↗

PubMed2006

Analysis of Bartonella adhesin A expression reveals differences between various B. henselae strains.

Bartonella henselae causes cat scratch disease and the vasculoproliferative disorders bacillary angiomatosis and peliosis hepatis in humans. One of the best known pathogenicity factors of B. henselae is Bartonella adhesin A (BadA), which is modularly constructed, consisting of head, neck/stalk, and membrane anchor domains. BadA is important for the adhesion of B. henselae to extracellular-matrix proteins and endothelial cells (ECs). In this study, we analyzed different B. henselae strains for BadA expression, autoagglutination, fibronectin (Fn) binding, and adhesion to ECs. We found that the B. henselae strains Marseille, ATCC 49882, Freiburg 96BK3 (FR96BK3), FR96BK38, and G-5436 express BadA. Remarkably, BadA expression was lacking in a B. henselae ATCC 49882 variant, in strains ATCC 49793 and Berlin-1, and in the majority of bacteria of strain Berlin-2. Adherence of B. henselae to ECs and Fn reliably correlated with BadA expression. badA was present in all tested strains, although the length of the gene varied significantly due to length variations of the stalk region. Sequencing of the promoter, head, and membrane anchor regions revealed only minor differences that did not correlate with BadA expression, apart from strain Berlin-1, in which a 1-bp deletion led to a frameshift in the head region of BadA. Our data suggest that, apart from the identified genetic modifications (frameshift deletion and recombination), other so-far-unknown regulatory mechanisms influence BadA expression. Because of variations between and within different B. henselae isolates, BadA expression should be analyzed before performing infection experiments with B. henselae.

Adhesins, Bacterial↗

PubMed2006

Trimeric autotransporter adhesins: variable structure, common function.

Trimeric autotransporter adhesins (TAAs) are important virulence factors in gram-negative pathogens. Despite the variety of hosts ranging from plants to mammals and the specialized regulation of TAAs, their molecular organization follows surprisingly simple rules: they form trimeric surface structures with a head-stalk-anchor architecture. The head and stalk are composed of a small set of domains, building blocks that are frequently arranged repetitively. We propose that this repetitive arrangement facilitates recombination of domains to modulate the specificity of the common function: adhesion to the host.

Adhesins, Bacterial↗

PubMed2006

Expression, crystallization and preliminary X-ray crystallographic studies of the outer membrane protein OmpW from Escherichia coli.

OmpW is an eight-stranded 21 kDa molecular-weight beta-barrel protein from the outer membrane of Gram-negative bacteria. It is a major antigen in bacterial infections and has implications in antibiotic resistance and in the oxidative degradation of organic compounds. OmpW from Escherichia coli was cloned and the protein was expressed in inclusion bodies. A method for refolding and purification was developed which yields properly folded protein according to circular-dichroism measurements. The protein has been crystallized and crystals were obtained that diffracted to a resolution limit of 3.5 angstroms. The crystals belong to space group P422, with unit-cell parameters a = 122.5, c = 105.7 angstroms. A homology model of OmpW is presented based on known structures of eight-stranded beta-barrels, intended for use in molecular-replacement trials.

Bacterial Outer Membrane Proteins↗

PubMed2006

Purification of the YadA membrane anchor for secondary structure analysis and crystallization.

Non-fimbrial adhesins, such as Yersinia YadA, Moraxella UspA1 and A2, Haemophilus Hia and Hsf, or Bartonella BadA, represent an important class of molecules by which pathogenic proteobacteria adhere to their hosts. They form trimeric surface structures with a head-rod-anchor architecture. Whereas their head and rod domains may be of heterologous origin, their anchor domains are homologous and display the properties of autotransporters. Conflicting topology models exist for these membrane anchors. Here, we describe the expression and purification of the membrane anchor of YadA from Yersinia enterocolitica for structural biology experiments. We expressed YadA-M in the Escherichia coli outer membrane. After solubilization and purification, it is a trimer of extreme stability. Using protein FTIR and secondary structure analysis, we show that the anchor is a beta-barrel, but contains a helical part at its N-terminus. We have crystallized the protein under various conditions and present X-ray data to 3.8 A resolution.

Adhesins, Bacterial↗

PubMed2006

Bartonella quintana variably expressed outer membrane proteins mediate vascular endothelial growth factor secretion but not host cell adherence.

Bartonella quintana causes trench fever, endocarditis, and the vasculoproliferative disorders bacillary angiomatosis and peliosis hepatis in humans. Little is known about the interaction of this pathogen with host cells. We attempted to elucidate the interaction of B. quintana with human macrophages (THP-1) and epithelial cells (HeLa 229). Remarkably, only B. quintana strain JK-31 induced secretion of vascular endothelial growth factor (VEGF) from THP-1 and HeLa 229 cells upon infection similar to the secretion induced by B. henselae Marseille, whereas other strains (B. quintana 2-D70, B. quintana Toulouse, and B. quintana Munich) did not induce such secretion. Immunofluorescence testing and electron microscopy revealed that the B. quintana strains unable to induce VEGF secretion did not express the variable outer membrane proteins (Vomps) on their surfaces. Surprisingly, the increase in VEGF secretion mediated by B. quintana JK-31 was not paralleled by elevated host cell adherence rates compared with the rates for Vomp-negative B. quintana strains. Our results suggest that the Vomps play a leading role in the angiogenic reprogramming of host cells by B. quintana but not in the adherence to host cells.

Amino Acid Sequence↗

PubMed2004

Folding kinetics and structure of OEP16.

The chloroplast outer membrane contains different, specialized pores that are involved in highly specific traffic processes from the cytosol into the chloroplast and vice versa. One representative member of these channels is the outer envelope protein 16 (OEP16), a cation-selective high conductance channel with high selectivity for amino acids. Here we study the mechanism and kinetics of the folding of this membrane protein by fluorescence and circular dichroism spectroscopy, using deletion mutants of the two single tryptophanes Trp-77-->Phe-77 and Trp-100-->Phe-100. In addition, the wild-type spectra were deconvoluted, depicting the individual contributions from each of the two tryptophan residues. The results show that both tryptophan residues are located in a completely different environment. The Trp-77 is deeply buried in the hydrophobic part of the protein, whereas the Trp-100 is partially solvent exposed. These results were further confirmed by studies of fluorescence quenching with I(-). The kinetics of the protein folding are studied by stopped flow fluorescence and circular dichroism measurements. The folding process depends highly on the detergent concentration and can be divided into an ultrafast phase (k > 1000 s(-1)), a fast phase (200-800 s(-1)), and a slow phase (25-70 s(-1)). The slow phase is absent in the W100F mutant. Secondary structure analysis and comparision with closely related proteins led to a new model of the structure of OEP16, suggesting that the protein is, in contrast to most other outer membrane proteins studied so far, purely alpha-helical, consisting of four transmembrane helices. Trp-77 is located in helix II, whereas the Trp-100 is located in the loop between helices II and III, close to the interface to helix III. We suggest that the first, very fast process corresponds to the formation of the helices, whereas the insertion of the helices into the detergent micelle and the correct folding of the II-III loop may be the later, rate-limiting steps of the folding process.

Amino Acid Sequence↗