Biomedical subjects

L Konieczny

Publications and source records attributed to L Konieczny.

At least 19 recordsLinked to original sources

PubMed2004

Limited conformational space for early-stage protein folding simulation.

MOTIVATION: The problem of early-stage protein folding is critical for protein structure prediction. The model presented introduces a common definition of protein structures which may be treated as the possible in silico early-stage form of the polypeptide chain. Limitation of the conformational space to the ellipse path on the Ramachandran map was tested as a possible sub-space to represent the early-stage structure for simulation of protein folding. The proposed conformational sub-space was developed on the basis of the backbone conformation, with side-chain interactions excluded. RESULTS: The ellipse-path-limited conformation of BPTI was created using the criterion of shortest distance between Phi, Psi angles in native form of protein and the Phi, Psi angles belonging to the ellipse. No knots were observed in the structure created according to ellipse-path conformational sub-space. The energy minimization procedure applied to ellipse-path derived conformation directed structural changes toward the native form of the protein with SS-bonds system introduced to the procedure. AVAILABILITY: Program 'Ellipse' to create the ellipse-path derived structure available on request: myroterm@cyf-kr.edu.pl

Algorithms↗

PubMed2004

Lysozyme folded in silico according to the limited conformational sub-space.

The conformational sub-space oriented on early-stage protein folding is applied to lysozyme folding. The part of the Ramachandran map distinguished on the basis of a geometrical model of the polypeptide chain limited to the mutual orientation of the peptide bond planes is shown to deliver the initial structure of the polypeptide for the energy minimization procedure in the ab initio model of protein folding prediction. Two forms of energy minimization and molecular dynamics simulation procedures were applied to the assumed early-stage protein folding of lysozyme. One of them included the disulphide bond system and the other excluded it. The post-energy-minimization and post-dynamics structures were compared using RMS-D and non-bonding contact maps to estimate the degree of approach to the native, target structure of the protein molecule obtained using the limited conformational sub-space for the early stage of folding.

Computer Simulation↗

PubMed2004

Intramolecular signaling in immunoglobulins -- new evidence emerging from the use of supramolecular protein ligands.

The postulated intramolecular signaling in immunoglobulins generated by antigen binding has been controversial for years. The high heterogeneity of immune complexes as signaling systems and the requirement of the immobilized antigen form for efficient triggering of effector activity is likely the reason for the lack of clarity. Here we present new evidence supporting the notion of intramolecular signaling, based on the use of supramolecular dyes that bind to signal-derived specific sites in immunoglobulins.

Antigen-Antibody Complex↗

PubMed2002

Egg yolk platelet proteins from Xenopus laevis are amyloidogenic.

The association of amphibian (Xenopus laevis) egg yolk platelet proteins, represented predominantly by lipovitellin, was studied as a model of the formation of amyloid deposits. Two kinds of molecular organization formed by this protein material - native and heat-denatured - were found to exhibit amyloid properties although they differ significantly in structural organization. The first consisted in protein molecules arranged in the natural, physiological, net-like platelet organization, with a tendency to orient uni-directionally. The second was obtained by the gradual removal of Congo red from lipovitellin denatured by heating in an excess of dye. This procedure produced the twisted fibrillar organization of molecules typical for amyloids, represented predominantly by end-to-end associated major polypeptide chains of lipovitellin. Both native and denatured structural forms bind Congo red and produce a green birefringence effect, confirming the near parallel alignment of the complexed Congo red molecules. However, a dye(1,4-bis(1-amino-4-sulfonaphtyl-2-azo)phenylene) closely related to Congo red but with a very weak self-assembling tendency appeared inactive when the spectral shift was studied in a cross-polarization system, indicating in this way that dye supramolecularity is an extra factor which may determine binding to amyloid proteins and specific spectral effects.

Amyloid↗

PubMed2001

Heat-induced formation of a specific binding site for self-assembled Congo Red in the V domain of immunoglobulin L chain lambda.

Moderate heating (40-50 degrees C) of immunoglobulins makes them accessible for binding with Congo Red and some related highly associated dyes. The binding is specific and involves supramolecular dye ligands presenting ribbon-like micellar bodies. The L chain lambda dimer, which upon heating disclosed the same binding requirement with respect to supramolecular dye ligands, was used in this work to identify the site of their attachment. Two clearly defined dye-protein (L lambda chain) complexes arise upon heating, here called complex I and complex II. The first is formed at low temperatures (up to 40-45 degrees C) and hence by a still native protein, while the formation of the second one is associated with domain melting above 55 degrees C. They contain 4 and 8 dye molecules bound per L chain monomer, respectively. Complex I also forms efficiently at high dye concentration even at ambient temperature. Complex I and its formation was the object of the present studies. Three structural events that could make the protein accessible to penetration by the large dye ligand were considered to occur in L chains upon heating: local polypeptide chain destabilization, VL-VL domain incoherence, and protein melting. Of these three possibilities, local low-energy structural alteration was found to correlate best with the formation of complex I. It was identified as decreased packing stability of the N-terminal polypeptide chain fragment, which as a result made the V domain accessible for dye penetration. The 19-amino acid N-terminal fragment becomes susceptible to proteolytic cleavage after being replaced by the dye at its packing locus. Its splitting from the dye-protein complex was proved by amino acid sequence analysis. The emptied packing locus, which becomes the site that holds the dye, is bordered by strands of amino acids numbered 74-80 and 105-110, as shown by model analysis. The character of the temperature-induced local polypeptide chain destabilization and its possible role in intramolecular antibody signaling is discussed.

Amino Acid Sequence↗

PubMed2001

Evidence that supramolecular Congo red is the sole ligation form of this dye for L chain lambda derived amyloid proteins.

The mechanism of Congo red binding to amyloid protein was studied in order to establish which of two structural dye versions present in water solutions--unimolecular and supramolecular--represent its actual ligation form. Immunoglobulin L chain lambda of amyloidogenic nature, expressed by Congo red binding and easy gel formation, was used as the model amyloid protein. Congo red was coassembled with rhodamine B, designed to be a marker of the Congo red micellar organisation in complexation with protein. The particular suitability of rhodamine B for this role results from significant difference in its binding affinity to Congo red and to protein. It associates readily with Congo red, becoming incorporated into its micellar organisation, but as homogenous dye it shows an almost complete inability to bind to protein. In view of these properties, Congo red was used as a vehicle to draw rhodamine B into complexation with protein, at the same time supplying evidence of its supramolecular ligation form. The results show that both soluble amyloid precursor L chain and the derived gel material attach rhodamine B coassembled with Congo red but not the homogenous rhodamine B. Despite its dynamic, supramolecular character, Congo red participates in complexation with amyloid proteins as an integral ligand unit.

Amyloid beta-Protein Precursor↗

PubMed2000

The conformational characteristics of Congo red, Evans blue and Trypan blue.

The structures of the closely related bis-azo dyes Evans blue, Trypan blue and Congo red, which appeared to have different self-assembly properties and correspondingly different abilities to form complexes with amyloids and some other proteins, were compared in this work. Ab initio and semi-empirical methods were used to find the optimal structures and partial charge distributions of the dyes. The optimal structures were searched using different widely used programs. The structures of Congo red and evans blue were found to be planar, except for the torsion on the central diphenyl bond connecting the two halves of the dye. Both symmetrical parts of the molecules appeared very close to planarity. However, Trypan blue exhibits non planarity on the di-azo bonds, as well as on the central bond between the symmetrical parts of the dye. In a consequence, the non planarity of this molecule is higher than in the case of its isomer, Evans blue and Congo red as well. The extra rotation around the azo bonds extorted by the close proximity of the sulfonic groups may be the direct cause of its poor self-assembling and complexation properties versus Evans blue.

Coloring Agents↗

PubMed2000

Case matching and relative clause attachment.

Two accounts of relative clause attachment will be discussed, the case-matching hypothesis proposed by Sauerland and Gibson (1998) and the attachment-binding dualism (Hemforth et al., in press a, b). While the case-matching hypothesis predicts that relative clauses are preferentially attached to NPs whose case matches that of the relative pronoun, attachment binding predicts that NPs are preferentially attached to the most salient host, that is NP1 in constructions with two NPs. We conducted two off-line studies, one sentence completion task and one magnitude estimation experiment using subject (nominative pronoun) and object (accusative pronoun) relative clauses that can be attached to either of the two nouns in a complex subject (NP1 = nominative, NP2 = genitive) or object NP (NP1 = accusative, NP2 = genitive). While attachment binding predicts an across-the-board NP1 preference, the case-matching hypothesis predicts an NP1 prefence only in the case of subject (object) NPs followed by subject (object) relative clauses. The results of both experiments provide evidence for attachment binding and against case matching.

Humans↗

PubMed2000

Locality and parsing complexity.

Two experiments, an off-line acceptability judgment study and an on-line self-paced reading experiment, were conducted to tackle the question of locality-based preferences in sentence processing. The material consisted of German verb-final sentences containing a relative clause that was either host adjacent or extraposed. While the off-line data seem to reflect locality based integration cost, the on-line data revealed a highly different picture. It is argued that, in the present constructions at least, locality is relevant for production rather than perception. In perception, heads can be anticipated through incremental integration of their arguments.

Humans↗

PubMed1999

Supramolecularity creates nonstandard protein ligands.

Congo red and a group of structurally related dyes long used to stain amyloid proteins are known to associate in water solutions. The self-association of some dyes belonging to this group appears particularly strong. In water solutions their molecules are arranged in ribbon-like micellar forms with liquid crystalline properties. These compounds have recently been found to form complexes with some native proteins in a non-standard way. Gaps formed by the local distribution of beta-sheets in proteins probably represent the receptor sites for these dye ligands. They may result from higher structural instability in unfolding conditions, but also may appear as long range cooperative fluctuations generated by ligand binding. Immunoglobulins G were chosen as model binding proteins to check the mechanism of binding of these dyes. The sites of structural changes generated by antigen binding in antibodies, believed to act as a signal propagated to distant parts of the molecule, were assumed to be suitable sites for the complexation of liquid-crystalline dyes. This assumption was confirmed by proving that antibodies engaged in immune complexation really do bind these dyes; as expected, this binding affects their function by significantly enhancing antigen binding and simultaneously inhibiting C1q attachment. Binding of these supramolecular dyes by some other native proteins including serpins and their natural complexes was also shown. The strict dependence of the ligation properties on strong self-assembling and the particular arrangement of dye molecules indicate that supramolecularity is the feature that creates non-standard protein ligands, with potential uses in medicine and experimental science.

Animals↗

PubMed1998

Supramolecular ligands: monomer structure and protein ligation capability.

The aim of this work was to define the chemical structure of compounds self-assembling in water solutions, which appear to interact with proteins as single ligands with their supramolecular nature preserved. For this purpose the ligation to proteins of bis azo dyes, represented by Congo red and its derivatives with designed structural alterations, were tested. The three parameters which characterize the reactivity of supramolecular material were determined in the same conditions for all studied dyes. These were: A) stability of the assembly products; B) binding to heat-denatured protein (human IgG); and C) binding to native protein (rabbit antibodies in the immune complex) measured by the enhancement of hemagglutination. The structural differences between the Congo red derivatives concerned the symmetry of the molecule and the structure of its non-polar component, which occupies the central part of the dye molecule and is thought to be crucial for self-assembly. Other dyes were also studied for the same purpose: Evans blue and Trypan blue, bis-ANS and ANS, as well as a group of compounds with a structural design unlike that of bis azo dyes. Compounds with rigid elongated symmetric molecules with a large non-polar middle fragment are expected to form a ribbon-like supramolecular organization in assembling. They appeared to have ligation properties related to their self-assembling tendency. The compounds with different structures, not corresponding to bis azo dyes, did not reveal ligation capability, at least in respect to native protein. The conditions of binding to denatured proteins seem less restrictive than the conditions of binding to native molecules. The molten hydrophobic protein interior becomes a new binding area allowing for complexation of even non-assembled molecules.

Congo Red↗

PubMed1998

Concentrations and decay rates of ozone in indoor air in dependence on building and surface materials.

The decay of ozone in indoor air was measured in a closed chamber after contact with different building materials and residential surfaces. The tested materials were: vinyl wall paper, woodchip paper, plywood, latex paint, fitted carpet, and plaster. In the summer of 1996, the entry of ozone from ambient air into indoor air during ventilation and the ozone decay in indoor air, after windows had been closed again, were studied. Measurements were done in a residential house on the outskirts of Berlin. The following results were gained: the chamber measurements showed a decay of ozone after contact with most of the materials put inside the chamber. Higher decay rates have been obtained for wall papers, plywood, fitted carpet and plaster. As described in the literature, ozone is able to react with olefines inside the materials and is able to form formaldehyde and other components. This formation of formaldehyde could also be confirmed in our investigations. Thus, in most cases, the formaldehyde concentrations were lower than the German guideline value of 0.1 ppm. The formation of formaldehyde could be prevented when a special wall paper that was coated with activated carbon was used. In the house, a complete ozone diffusion into indoor air took place during ventilation within 30 min. After closing the windows, the ozone concentrations decreased to the basic level before ventilation within 60-90 min.

Air Pollution, Indoor↗

PubMed1997

Effect of self association of bis-ANS and bis-azo dyes on protein binding.

A correlation was found between the ability of dyes (ANS, bis-ANS, Congo red, Evans blue) to form self-associated supramolecular structures in water and their tendency to form complexes with proteins. The self-association ability of dyes was measured as the resistance of a molecular sieve to their penetration. Quantitative evaluation of dye-protein interaction involved measuring the effect of dye on antibodies that agglutinate sheep red blood cells. Enhancement of agglutination by dye was assumed to represent its protein complexation ability. The results confirm that, relative to monomers, self-associated ligands also have altered protein binding properties.

Anilino Naphthalenesulfonates↗

PubMed1997

The use of congo red as a lyotropic liquid crystal to carry stains in a model immunotargeting system--microscopic studies.

The lyotropic liquid crystal dye-Congo Red was used as a carrier in a model immunotargeting system constructed from sheep red blood cells (SRBC) representing the antigen target and rabbit IgG anti-SRBC as the specific driving immunoglobulin. Rhodamine B and Hemin stains were chosen as example chemicals carried to the target. The carried stains were introduced to the micellar organization of Congo Red by intercalation. Preserving its supramolecular organization, Congo Red binds spontaneously and selectively to antibodies that have altered structure extorted by interaction with the antigen in the immune complex. The functionality of the studied immunotargeting model was verified by fluorescence and electron microscopy. The results indicate that the supramolecular nature of protein ligands offers new ligation capabilities possibly useful for carrying stains or drugs in immune-oriented systems.

Animals↗

PubMed1996

Congo red-stabilized intermediates in the lambda light chain transition from native to molten state.

Disruption of tertiary interaction makes a protein accessible to penetration by different small molecular compounds. Their interaction may stabilize the altered protein conformation. Congo red is proposed here as a stabilizer of the molten globule state and also of highly reversible intermediates in the transition from native to molten state. Human immunoglobulin lambda light chain (dimer) was used. Two protein-Congo red complexes were found after heating lambda chain in the presence of Congo red. They differed in the amount of attached dye molecules. The binding of dye was interpreted as a two-step dye penetration process involving the peripheral parts of the protein in the first step (at lower temperatures). It was concluded that the liquid crystal properties of Congo red enable it to form specific complexes with proteins, which have become accessible to penetration by ligands after global or local disruption of tertiary interaction. This dye may thus be used as a stabilizer of unfolding intermediates in the step preceding the molten globule state.

Anilino Naphthalenesulfonates↗

PubMed1996

Indoor air pollution by different heating systems: coal burning, open fireplace and central heating.

Investigations of indoor air pollution by different heating systems in private homes are described. Sixteen homes, 7 with coal burning, 1 with open fireplace (wood burning) and 8 with central heating have been investigated. We measured the concentrations of carbon monoxide, carbon dioxide and sedimented dust in indoor air, of total suspended particulates, heavy metals and of polycyclic aromatic hydrocarbons in indoor and outdoor air. Measurements were taken during winter (heating period) and during summer (non-heating period). Generally, we found higher indoor air pollution in homes with coal burning and open fireplace than in homes with central heating. Especially, the concentrations of carbon monoxide, sedimented dust and of some heavy metals were higher. In one case, we found also high indoor air pollution in a home with central heating. This apartment is on the ground floor of a block of flats, and the central heating system in the basement showed a malfunctioning of the exhaust system.

Air Pollutants↗

PubMed1995

Geometrical analysis of structural changes in immunoglobulin domains' transition from native to molten state.

Molecular dynamics simulation (300, 320, 340 K) performed on the Fab (Kol) fragment of immunoglobulin G revealed that the structural changes associated with relaxation of peptides after their release from the stabilized by the tertiary interaction native conformation may be considered characteristic of the transition from native to molten state. The configuration of peptide chains at temperatures close to melting, liberated from the constraints associated with tertiary packing, was found to deviate toward helical rather than extended forms. The direction of the shift is diagonal on the phi-psi map. The torsional angles tend to concentrate in the Cea7 region, and some leak to the alphaR area. The geometrical parameters designed to describe the configuration of the peptide chain in Fab fragment also confirmed that during melting the peptides generally moved toward helical form.

Crystallography, X-Ray↗

PubMed1995

The detection of specific acute phase serum protein complexes and immune complexes by congo red binding.

The study concerns the problem of selective binding of Congo Red dye to serum proteins. The dye-binding structural motifs were assumed to appear in proteins as the result of local disruptions of tertiary interaction associated with biological activities. Functional structures of serum proteinase inhibitors and haptoglobins induced by interaction of these proteins with their natural substrates were found to bind Congo Red. Soluble immune complexes formed by bivalent hapten-bridged anti-TNP rabbit antibodies also appeared able to interact with the dye. The possible use of these effects for diagnostic analysis was suggested.

Acute-Phase Proteins↗