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S Rüdiger

Publications and source records attributed to S Rüdiger.

At least 19 recordsLinked to original sources
PubMed2003

Dynamo effect in a driven helical flow.

The Roberts flow, a helical flow in the form of convectionlike rolls, is known to be capable of both kinematic and nonlinear dynamo action. We study the Roberts dynamo with particular attention being paid to the spatial structure of the generated magnetic field and its back-reaction on the flow. The dynamo bifurcation is decisively determined by the symmetry group of the problem, which is given by a subgroup of discrete transformations and a continuous translational invariance of the flow. In the bifurcation the continuous symmetry is broken while the discrete subgroup symmetry completely survives. Its actions help in understanding the spatial structures of the magnetic field and of the modified flow. In accordance with experimental observations, the magnetic field component perpendicular to the originally invariant direction is much stronger than the component in this direction. Furthermore, the magnetic field is largely concentrated in layers separating the convectionlike rolls of the flow and containing, in particular, its stagnation points, which are isolated for the modified flow while they are line filling for the original Roberts flow. The magnetic field is strongest near beta-type stagnation points, with a two-dimensional unstable and a one-dimensional stable manifold, and is weak near alpha-type stagnation points, with a two-dimensional stable and a one-dimensional unstable manifold. This contrasts with the usual picture that dynamo action is promoted at the alpha points and impeded at the beta points. Both the creation of isolated stagnation points and the concentration of strong fields at the beta points may be understood as a result of the way in which the Roberts dynamo saturates. It is also found that, while the original Roberts flow is regular, the modified flow is chaotic in the layers between the convectionlike rolls where the magnetic field is concentrated. This chaoticity, which results from the back-reaction of the magnetic field on the flow, appears to merely enhance magnetic diffusion rather than to strengthen the dynamo effect.

Journal Article↗
PubMed2003

Dynamics of Turing patterns under spatiotemporal forcing.

We study, both theoretically and experimentally, the dynamical response of Turing patterns to a spatiotemporal forcing in the form of a traveling-wave modulation of a control parameter. We show that from strictly spatial resonance, it is possible to induce new, generic dynamical behaviors, including temporally modulated traveling waves and localized traveling solitonlike solutions. The latter make contact with the soliton solutions of Coullet [Phys. Rev. Lett. 56, 724 (1986)]] and generalize them. The stability diagram for the different propagating modes in the Lengyel-Epstein model is determined numerically. Direct observations of the predicted solutions in experiments carried out with light modulations in the photosensitive chlorine dioxide-iodine-malonic acid reaction are also reported.

Journal Article↗
PubMed2001

Binding specificity of Escherichia coli trigger factor.

The ribosome-associated chaperone trigger factor (TF) assists the folding of newly synthesized cytosolic proteins in Escherichia coli. Here, we determined the substrate specificity of TF by examining its binding to 2842 membrane-coupled 13meric peptides. The binding motif of TF was identified as a stretch of eight amino acids, enriched in basic and aromatic residues and with a positive net charge. Fluorescence spectroscopy verified that TF exhibited a comparable substrate specificity for peptides in solution. The affinity to peptides in solution was low, indicating that TF requires ribosome association to create high local concentrations of nascent polypeptide substrates for productive interaction in vivo. Binding to membrane-coupled peptides occurred through the central peptidyl-prolyl-cis/trans isomerase (PPIase) domain of TF, however, independently of prolyl residues. Crosslinking experiments showed that a TF fragment containing the PPIase domain linked to the ribosome via the N-terminal domain is sufficient for interaction with nascent polypeptide substrates. Homology modeling of the PPIase domain revealed a conserved FKBP(FK506-binding protein)-like binding pocket composed of exposed aromatic residues embedded in a groove with negative surface charge. The features of this groove complement well the determined substrate specificity of TF. Moreover, a mutation (E178V) in this putative substrate binding groove known to enhance PPIase activity also enhanced TF's association with a prolyl-free model peptide in solution and with nascent polypeptides. This result suggests that both prolyl-independent binding of peptide substrates and peptidyl-prolyl isomerization involve the same binding site.

Amino Acid Sequence↗
PubMed2001

Its substrate specificity characterizes the DnaJ co-chaperone as a scanning factor for the DnaK chaperone.

The evolutionarily conserved DnaJ proteins are essential components of Hsp70 chaperone systems. The DnaJ homologue of Escherichia coli associates with chaperone substrates and mediates their ATP hydrolysis-dependent locking into the binding cavity of its Hsp70 partner, DnaK. To determine the substrate specificity of DnaJ proteins, we screened 1633 peptides derived from 14 protein sequences for binding to E.coli DnaJ. The binding motif of DnaJ consists of a hydrophobic core of approximately eight residues enriched for aromatic and large aliphatic hydrophobic residues and arginine. The hydrophobicity of this motif explains why DnaJ itself can prevent protein aggregation. Although this motif shows differences from DnaK's binding motif, DnaJ and DnaK share the majority of binding peptides. In contrast to DnaK, DnaJ binds peptides consisting of L- and D-amino acids, and therefore is not restricted by backbone contacts. These features allow DnaJ to scan hydrophobic protein surfaces and initiate the functional cycle of the DnaK system by associating with hydrophobic exposed patches and subsequent targeting of DnaK to these or to hydrophobic patches in spatial neighbourhood.

Amino Acid Motifs↗
PubMed2001

Tuning of chaperone activity of Hsp70 proteins by modulation of nucleotide exchange.

The Hsp70 chaperone activity in protein folding is regulated by ATP-controlled cycles of substrate binding and release. Nucleotide exchange plays a key role in these cycles by triggering substrate release. Structural searches of Hsp70 homologs revealed three structural elements within the ATPase domain: two salt bridges and an exposed loop. Mutational analysis showed that these elements control the dissociation of nucleotides, the interaction with exchange factors and chaperone activity. Sequence variations in the three elements classify the Hsp70 family members into three subfamilies, DnaK proteins, HscA proteins and Hsc70 proteins. These subfamilies show strong differences in nucleotide dissociation and interaction with the exchange factors GrpE and Bag-1.

Adenosine Diphosphate↗
PubMed2001

Functional dissection of trigger factor and DnaK: interactions with nascent polypeptides and thermally denatured proteins.

In Escherichia coli, the ribosome-associated Trigger Factor (TF) cooperates with the DnaK system in the folding of newly synthesized cytosolic polypeptides. Here we investigated the functional relationship of TF and DnaK by comparing various functional properties of both chaperones. First, we analyzed the ability of TF and DnaK to associate with nascent polypeptides and full-length proteins released from the ribosome. Toward this end, we established an E. coli based transcription/translation system containing physiological ratios of TF, DnaK and ribosomes. In this system, TF can be crosslinked to nascent polypeptides of sigma32. No TF crosslink was found to full-length sigma32, which is known to be a DnaK substrate. In contrast, DnaK crosslinked to both nascent and full-length sigma32. DnaK crosslinks critically depended on the type of chemical crosslinker. Crosslinks represent specific substrate-chaperone interactions since they relied on the association of the nascent polypeptides with the substrate binding pocket of DnaK. While DnaK is known to be the major chaperone to prevent protein aggregation under heat shock conditions, we found that TF did not prevent aggregation of thermally unfolded proteins in vitro and was not able to complement the heat-sensitive phenotype of a deltadnaK52 mutant in vivo. These data indicate that TF and DnaK show strong differences in their ability to prevent aggregation of denatured proteins and to associate with native like substrates, but share the ability to associate with nascent polypeptides.

Bacterial Outer Membrane Proteins↗
PubMed2000

Modulation of substrate specificity of the DnaK chaperone by alteration of a hydrophobic arch.

Hsp70 chaperones assist protein folding by reversible interaction with extended hydrophobic segments of substrate polypeptides. We investigated the contribution of three structural elements of the substrate- binding cavity of the Escherichia coli homologue, DnaK, to substrate specificity by investigating mutant DnaK proteins for binding to cellulose-bound peptides. Deletion of the C-terminal subdomain (Delta539-638) and blockage of the access to the hydrophobic pocket in the substrate-binding cavity (V436F) did not change the specificity, although the latter exchange reduced the affinity to all peptides investigated. Mutations (A429W, M404A/A429W) that affect the formation of a hydrophobic arch spanning over the bound substrate disfavored DnaK binding, especially to peptides with short stretches of consecutive hydrophobic residues flanked by acidic residues, while binding to most other peptides remained unchanged. The arch thus contributes to the substrate specificity of DnaK. This finding is of particular interest, since of all the residues of the substrate-binding cavity that contact bound substrate, only the arch-forming residues show significant variation within the Hsp70 family.

Amino Acid Sequence↗
PubMed2000

Perfluorocarbons useful tools for medicine.

Perfluorocarbons (PFCs) combine rather unique chemical and physical properties together with physiological inertness. Due to this, they have become useful tools in medicine. Whereas the majority of applications benefit from their excellent oxygen solubility, there are several applications making use of other PFC properties. The great importance of PFC ultra-purity is especially emphasized.

Animals↗
PubMed2000

Multistep mechanism of substrate binding determines chaperone activity of Hsp70.

The 70 kDa heat shock proteins (the Hsp70 family) assist refolding of their substrates through ATP-controlled binding. We have analyzed mutants of DnaK, an Hsp70 homolog, altered in key residues of its substrate binding domain. Substrate binding occurs by a dynamic mechanism involving: a hydrophobic pocket for a single residue that is crucial for affinity, a two-layered closing device involving independent action of an alpha-helical lid and an arch, and a superimposed allosteric mechanism of ATP-controlled opening of the substrate binding cavity that operates largely through a beta-structured subdomain. Correlative evidence from mutational analysis suggests that the ADP and ATP states of DnaK differ in the frequency of the conformational changes in the alpha-helical lid and beta-domain that cause opening of the substrate binding cavity. The affinity for substrates, as defined by this mechanism, determines the efficiency of DnaJ-mediated and ATP hydrolysis mediated locking-in of substrates and chaperone activity of DnaK.

Adenosine Diphosphate↗
PubMed2000

Incomplete inhibition of platelet aggregation and glycoprotein IIb-IIIa receptor blockade by abciximab: importance of internal pool of glycoprotein IIb-IIIa receptors.

Resting platelets contain a substantial internal pool of GPIIb-IIIa complexes that is exposed on the surface of activated platelets. Whether the exposure of internal GPIIb-IIIa complexes on the activated platelet surface affects therapy with GPIIb-IIIa antagonists is poorly understood. We addressed this issue in thirteen patients who underwent elective coronary stenting and received abciximab. Platelet aggregation, surface expression of GPIIb-IIIa and P-selectin, receptor blockade of GPIIb-IIIa, and platelet release in response to ADP and thrombin-receptor activating peptide (TRAP) were determined ex vivo by Lumi-aggregometry and flow cytometry before, during and after abciximab administration. We found that inhibition of aggregation and GPIIb-IIIa blockade of ADP-stimulated platelets was almost complete during abciximab administration. In contrast, when TRAP was used to stimulate platelets ex vivo aggregation was only partially inhibited, most likely due to release of internal pool of unblocked GPIIb-IIIa complexes. Using electron microscopy we found that 7E3-occupied GPIIb-IIIa complexes are internalized into the surface connected system (SCS) and the alpha-granules of washed platelets which was associated with a reduced degranulation of the alpha-granula membrane protein P-selectin. We conclude, that despite internalization of abciximab into the internal pool of GPIIb-IIIa, upon strong platelet activation with thrombin a significant amount of unblocked internal GPIIb-IIIa can be exposed on the platelet surface and mediate platelet aggregation. Incomplete blockade of the internal GPIIb-IIIa pool may limit clinical efficacy of abciximab.

Abciximab↗
PubMed1999

Identification of thermolabile Escherichia coli proteins: prevention and reversion of aggregation by DnaK and ClpB.

UNLABELLED: We systematically analyzed the capability of the major cytosolic chaperones of Escherichia coli to cope with protein misfolding and aggregation during heat stress in vivo and in cell extracts. Under physiological heat stress conditions, only the DnaK system efficiently prevented the aggregation of thermolabile proteins, a surprisingly high number of 150-200 species, corresponding to 15-25% of detected proteins. Identification of thermolabile DnaK substrates by mass spectrometry revealed that they comprise 80% of the large (>/=90 kDa) but only 18% of the small (</=30 kDa) cytosolic proteins and include essential proteins. The DnaK system in addition acts with ClpB to form a bi-chaperone system that quantitatively solubilizes aggregates of most of these proteins. Efficient solubilization also occurred in an in vivo order-of-addition experiment in which aggregates were formed prior to induction of synthesis of the bi-chaperone system. Our data indicate that large-sized proteins are most vulnerable to thermal unfolding and aggregation, and that the DnaK system has central, dual protective roles for these proteins by preventing their aggregation and, cooperatively with ClpB, mediating their disaggregation. KEYWORDS: chaperones/heat-shock response/Hsp70/protein denaturation/thermotolerance

Bacterial Proteins↗
PubMed1999

Substrate specificity of the SecB chaperone.

The bacterial chaperone SecB assists translocation of proteins across the inner membrane. The mechanism by which it differentiates between secretory and cytosolic proteins is poorly understood. To identify its binding motif, we screened 2688 peptides covering sequences of 23 proteins for SecB binding. The motif is approximately 9 residues long and is enriched in aromatic and basic residues, whereas acidic residues are disfavored. Its identification allows the prediction of binding regions within protein sequences with up to 87% accuracy. SecB-binding regions occur statistically every 20-30 residues. The occurrence and affinity of binding regions are similar in SecB-dependent and -independent secretory proteins and in cytosolic proteins, and SecB lacks specificity toward signal sequences. SecB cannot thus differentiate between secretory and non-secretory proteins via its binding specificity. This conclusion is supported by the finding that SecB binds denatured luciferase, thereby allowing subsequent refolding by the DnaK system. SecB may rather be a general chaperone whose involvement in translocation is mediated by interactions of SecB and signal sequences of SecB-bound preproteins with the translocation apparatus.

Amino Acids↗
PubMed1999

Distribution of binding sequences for the mitochondrial import receptors Tom20, Tom22, and Tom70 in a presequence-carrying preprotein and a non-cleavable preprotein.

Preproteins destined for mitochondria either are synthesized with amino-terminal signal sequences, termed presequences, or possess internal targeting information within the protein. The preprotein translocase of the outer mitochondrial membrane (designated Tom) contains specific import receptors. The cytosolic domains of three import receptors, Tom20, Tom22, and Tom70, have been shown to interact with preproteins. Little is known about the internal targeting information in preproteins and the distribution of binding sequences for the three import receptors. We have studied the binding of the purified cytosolic domains of Tom20, Tom22, and Tom70 to cellulose-bound peptide scans derived from a presequence-carrying cleavable preprotein, cytochrome c oxidase subunit IV, and a non-cleavable preprotein with internal targeting information, the phosphate carrier. All three receptor domains are able to bind efficiently to linear 13-mer peptides, yet with different specificity. Tom20 preferentially binds to presequence segments of subunit IV. Tom22 binds to segments corresponding to the carboxyl-terminal part of the presequence and the amino-terminal part of the mature protein. Tom70 does not bind efficiently to any region of subunit IV. In contrast, Tom70 and Tom20 bind to multiple segments within the phosphate carrier, yet the amino-terminal region is excluded. Both charged and uncharged peptides derived from the phosphate carrier show specific binding properties for Tom70 and Tom20, indicating that charge is not a critical determinant of internal targeting sequences. This feature contrasts with the crucial role of positively charged amino acids in presequences. Our results demonstrate that linear peptide segments of preproteins can serve as binding sites for all three receptors with differential specificity and imply different mechanisms for translocation of cleavable and non-cleavable preproteins.

Amino Acid Sequence↗
PubMed1999

Root resorption and signs of repair in Papillon-Lefèvre syndrome. A case study.

The aim of this investigation was to describe some tooth-related histological features of prepubertal periodontitis. Teeth extracted during treatment of two Papillon-Lefevre syndrome patients were processed by means of the sawing and grinding technique. Light microscopy examination revealed little or no cementum in the coronal parts of the roots. Resorptions of various depths (0.02 to 1.5 mm) and to various extents (affecting up to 1/3 of the root surface) were observed in the 5 investigated teeth. Some resorptive defects on 1 of the examined incisors showed signs of spontaneous repair. Extrinsic fibers were inserted into the new cellular intrinsic fiber cementum which had formed directly on the bottom of the defect. Intact acellular extrinsic fiber cementum was found where fibers were still attached. Here, the characteristic of pristine cementum, a hyaline layer of peripheral dentin, could be identified. If resorption was not present, the cementum did not show any signs of hypoplasia. Thus, histological features of prepubertal periodontitis in the current material were (i) areas of extensive resorption, (ii) signs of spontaneous repair, and (iii) healthy cementum.

Child↗
PubMed1999

Combined systemic and local antimicrobial therapy of periodontal disease in Papillon-Lefèvre syndrome. A report of 4 cases.

4 patients, 2 pairs of siblings, suffering from Papillon-Lefèvre syndrome were treated for periodontal disease. Following extraction of hopeless teeth, the children received scaling and adjunctive systemic antibiotics (metronidazole and amoxicillin for 7 to 10 days). In addition, they performed supragingival pulsated jet irrigation with 0.06% chlorhexidine digluconate 1 x daily. In 2 siblings, A. actinomycetemcomitans was suppressed subgingivally below detectable levels, pocket probing depths were reduced to 4 mm or less, and plaque and bleeding indices were low. No further disease progression was seen over a 3-year-period. Another female patient also showed clinical improvement and suppression of subgingival A. actinomycetemcomitans and B. forsythus up to the 9-month-follow-up, while her sister showed further attachment loss over the course of 4 years. The present case reports indicated that in some patients suffering from Papillon-Lefèvre syndrome periodontal disease may be arrested by means of (i) oral hygiene instruction, (ii) extraction of severely diseased teeth, (iii) scaling, (iv) systemic antibiotics and (v) long-term antimicrobial irrigation.

Aggregatibacter actinomycetemcomitans↗
PubMed1997

Substrate specificity of the DnaK chaperone determined by screening cellulose-bound peptide libraries.

Hsp70 chaperones assist protein folding by ATP-dependent association with linear peptide segments of a large variety of folding intermediates. The molecular basis for this ability to differentiate between native and non-native conformers was investigated for the DnaK homolog of Escherichia coli. We identified binding sites and the recognition motif in substrates by screening 4360 cellulose-bound peptides scanning the sequences of 37 biologically relevant proteins. DnaK binding sites in protein sequences occurred statistically every 36 residues. In the folded proteins these sites are mostly buried and in the majority found in beta-sheet elements. The binding motif consists of a hydrophobic core of four to five residues enriched particularly in Leu, but also in Ile, Val, Phe and Tyr, and two flanking regions enriched in basic residues. Acidic residues are excluded from the core and disfavored in flanking regions. The energetic contribution of all 20 amino acids for DnaK binding was determined. On the basis of these data an algorithm was established that predicts DnaK binding sites in protein sequences with high accuracy.

Algorithms↗