Biomedical subjects

Irena Roterman

Publications and source records attributed to Irena Roterman.

23 records · Page 2Linked to original sources

PubMed2003

Local and long-range structural effects caused by the removal of the N-terminal polypeptide fragment from immunoglobulin L chain lambda.

The role of the N-terminal polypeptide fragment of the immunoglobulin l-chain in V domain packing stability, and the flexibility of the whole chain was approached by molecular dynamics simulation. The observations were supported by experimental analysis. The N-terminal polypeptide fragment appeared to be the low-stability packing element in the V domain. At moderately elevated temperature it may be replaced at its packing locus by Congo red and then removed by proteolysis. After removal of Congo red by adsorption to (diethylamino)ethyl (DEAE) cellulose, the stability of complete L chain and of L chain devoid of the N-terminal polypeptide fragment were compared. The results indicated that the N-terminal polypeptide fragment plays an essential role in the stability of the V domain. Its removal makes the domain accessible for ANS and Congo red dye binding without heating. The decreased domain stability was registered in particular as increased root mean square (RMS) fluctuation and higher susceptibility to proteolytic attack. The long-range effect was most clearly manifested at 340 K as independent V and C domain fluctuation in the l-chain devoid of the N-terminal polypeptide fragment. This is likely due to the lack of direct connections between the N- and C-termini of the V domain polypeptide. In a complete V domain the connection involves residues 8-12 and 106-110 in particular. Partial or complete disruption of this connection increases the freedom of V domain rotation, while its increased cohesion strengthens the coupling of the V and C domains, making the whole L chain less flexible.

Amino Acid Sequence↗

PubMed2003

Search for structural similarity in proteins.

MOTIVATION: The expanding protein sequence and structure databases await methods allowing rapid similarity search. Geometric parameters-dihedral angle between two sequential peptide bond planes (V) and radius of curvature (R) as they appear in pentapeptide fragments in polypeptide chains-are proposed for use in evaluating structural similarity in proteins (VeaR). The parabolic (empirical) function expressing the radius of curvature's dependence on the V-angle in model polypeptides is altered in real proteins in a form characteristic for a particular protein. This can be used as a criterion for judging similarity. RESULTS: A structural comparison of proteins representing a wide spectrum of structures was assessed versus sequence similarity analysis based on the genetic semihomology algorithm. The term 'consensus structure', analogous to 'consensus sequence', was introduced for the serpine family. AVAILABILITY: Semihom-sequence comparison freely available on request from J. Leluk. VeaR-structural comparison freely available on request from I. Roterman.

Algorithms↗

PubMed2003

The structural abnormality of myeloma immunoglobulins tested by Congo red binding.

BACKGROUND: Frequently observed structural deviations of myeloma-derived immunoglobulins affect polypeptide chain packing and domain stability, enhancing their tendency to aggregate, with all the clinical consequences. Congo red complexation with myeloma immunoglobulins is proposed in this work as a general test to disclose the instability of these proteins. The large ribbon-like supramolecular ligands of Congo red form complexes with proteins by adhesion to beta-conformation polypeptide chains, if allowed to make contact with their backbone interfaces. This can occur in the case of myeloma-derived immunoglobulins with deficient polypeptide chain packing. MATERIAL/METHODS: Specially adapted two-dimensional agarose electrophoresis of serum proteins, which allows the transient contact of Congo red and serum proteins during migration, was used to reveal the presence of protein components amenable to ligand penetration and binding. The combination of electrophoresis and Congo red binding to proteins permits the removal of loosely attached dye and evaluation of the effective complexation properties of the immunoglobulin fraction directly in the serum. RESULTS: Comparative studies of dye complexation with two L chains having different reactivities with Congo red confirmed that dye binding depended on protein instability in the conditions used. Myeloma proteins revealed different binding capabilities in the test used here. CONCLUSIONS: The complexes formed by the supramolecular dye Congo red with myeloma immunoglobulins differ in stability. Those of high stability indicate the abnormal protein structure thought to produce clinical symptoms. This work proposes an easy technique to differentiate the stability of complexes.

Amino Acid Sequence↗

PubMed2003

Protein distorsion-derived mechanism of signal discrimination in monocytes revealed using Congo red to stain activated cells.

The supramolecular dye Congo red was used to check whether monocyte activation may be mediated by a torsion-dependent mechanism preventing transduction of weak random signals in cell contacts in a way corresponding to the discrimination mechanism found in complement fixation by immune complexes. Tight cell-cell contacts generating torsional effects may be expected to produce alteration of receptor structure, making them accessible for binding of supramolecular dyes. In this study, Congo red was used to observe the binding accessibility of (1) monocytes (human) induced by contact with cancer cells (HCV29T, human), (2) monocytes (mouse) stimulated by interaction with heat-aggregated IgG and (3) monocytes (mouse) activated by rosetting in the presence of an SRBC-anti-SRBC system. Microscopic studies confirmed the activation of monocytes manifested by their clustering and Congo red binding, but only tightly clustered cells appeared to attach the dye on the surface. Usually not the whole cell surface is found to be engaged in dye complexation. Staining occurs predominantly on the interfaces of reacting cells, making probable the suggestion that cell adhesion receptors are involved in dye binding. The cells in the central areas of tight clusters undergo accelerated death. In the presence of Congo red they are easily recognized as intensely fluorescent. The characteristic localization of dead cells in the central area of clusters indicates that death is not random but results from cell activation. The role of Congo red in this process remains to be clarified. The staining characteristics of monocytes after application of Congo red probably discloses the initial step in signal transduction generated by torsional movements in receptor proteins.

Animals↗

PubMed2003

The structure and protein binding of amyloid-specific dye reagents.

The self-assembling tendency and protein complexation capability of dyes related to Congo red and also some dyes of different structure were compared to explain the mechanism of Congo red binding and the reason for its specific affinity for beta-structure. Complexation with proteins was measured directly and expressed as the number of dye molecules bound to heat-aggregated IgG and to two light chains with different structural stability. Binding of dyes to rabbit antibodies was measured indirectly as the enhancement effect of the dye on immune complex formation. Self-assembling was tested using dynamic light scattering to measure the size of the supramolecular assemblies. In general the results show that the supramolecular form of a dye is the main factor determining its complexation capability. Dyes that in their compact supramolecular organization are ribbon-shaped may adhere to polypeptides of beta-conformation due to the architectural compatibility in this unique structural form. The optimal fit in complexation seems to depend on two contradictory factors involving, on the one hand, the compactness of the non-covalently stabilized supramolecular ligand, and the dynamic character producing its plasticity on the other. As a result, the highest protein binding capability is shown by dyes with a moderate self-assembling tendency, while those arranging into either very rigid or very unstable supramolecular entities are less able to bind.

Amyloid↗