Biomedical subjects

Ilia V Baskakov

Publications and source records attributed to Ilia V Baskakov.

22 records · Page 2Linked to original sources

PubMed2004

Synthesis, conformation, and immunogenicity of monosaccharide-centered multivalent HIV-1 gp41 peptides containing the sequence of DP178.

Several monosaccharide-centered multivalent HIV-1 gp41 peptides containing the sequence of DP178 were synthesized. Conformational studies showed that multivalent assembly enhanced the alpha-helical content of the peptide. Therefore, 2-, 3-, or 4-alpha-helix bundles of peptide DP178 could be obtained by assembling the peptide on a suitable bi-, tri-, or tetravalent template. Immunization studies indicated that while peptide DP178 alone was poorly immunogenic, the tetravalent peptide MVP-1 raised high titers of antibodies in mice that recognize not only peptide DP178 but also the native HIV-1 glycoprotein gp41, even in the absence of a carrier protein or adjuvant. The study suggests that carbohydrate-centered multivalent peptides provide not only a model for mimicking protein alpha-helix-bundle structure, but also an effective immunogen for raising high-titer antibodies against HIV-1 envelope glycoprotein gp41.

Amino Acid Sequence↗

PubMed2004

The peculiar nature of unfolding of the human prion protein.

Spontaneous conformational transition of the prion protein from an alpha-helical isoform to a beta-sheet-rich isoform underlies the pathogenesis of sporadic prion diseases. To study the rate-limiting steps of spontaneous conversion, the formation of amyloid fibrils by the recombinant human PrP C-terminal fragment spanning residues 90-231 (recPrP) was monitored in the presence of urea. The kinetics of spontaneous fibril formation displayed sigmoidal behavior involving a lag phase. The shortest lag phase was observed at partially denaturing conditions, close to the concentration of urea corresponding to the middle point of unfolding. This result indicates that unfolding intermediates may be important for the conversion. To test whether unfolding intermediates are formed, we employed size-exclusion chromatography and circular dichroism spectroscopy to monitor urea denaturation of recPrP. Both techniques showed a single sigmoidal transition with very similar thermodynamic parameters of denaturation and that the transition can be described by a simple equilibrium between folded and denatured states. Detailed analyses of data, however, revealed that the dimensions of both the native and denatured species gradually increases with urea. Expansion of the native species is also accompanied by an increase in efficiency of the energy transfer from a single Trp residue to 1-anilinonaphthalene-8-sulfonate dye as measured by fluorescence. These data illustrate that thermodynamic character of the native ensemble changes gradually with environmental conditions. Such behavior is consistent with the thermodynamically variable model, and may be linked to the ability of PrP to adopt distinct abnormal conformations under pathologic conditions.

Algorithms↗

PubMed2003

Autocatalytic conversion of recombinant prion proteins displays a species barrier.

The most unorthodox feature of the prion disease is the existence of an abnormal infectious isoform of the prion protein, PrP(Sc). According to the "protein-only" hypothesis, PrP(Sc) propagates its abnormal conformation in an autocatalytic manner using the normal isoform, PrP(C), as a substrate. Because autocatalytic conversion is considered a key element of prion replication, in this study I tested whether in vitro conversion of recombinant PrP into abnormal isoform displays specific features of an autocatalytic process. I found that recombinant human PrP formed two distinct beta-sheet rich isoforms, the beta-oligomer and the amyloid fibrils. The kinetics of the fibrils formation measured at different pH values were consistent with a model in which the beta-oligomer was not on the kinetic pathway to the fibrillar form. As judged by electron microscopy, an acidic pH favored to the long fibrils, whereas short fibrils morphologically similar to "prion rods" were formed at neutral pH. At neutral pH the conversion to the fibrils can be seeded with small aliquots of preformed fibrils. As small as 0.001% aliquot displayed seeding activity. The conversion of human PrP was seeded with high efficacy only with the preformed fibrils of human but not mouse PrP and vice versa. These studies illustrate that in vitro conversion of recombinant PrP displays specific features of an autocatalytic process and mimics the transmission barrier of prion propagation observed in vivo. I speculate that this model can be used as a rapid assay for assessing the intrinsic propensities of prion transmission between different species.

Amyloid↗

PubMed2002

Pathway complexity of prion protein assembly into amyloid.

In vivo under pathological conditions, the normal cellular form of the prion protein, PrP(C) (residues 23-231), misfolds to the pathogenic isoform PrP(Sc), a beta-rich aggregated pathogenic multimer. Proteinase K digestion of PrP(Sc) leads to a proteolytically resistant core, PrP 27-30 (residues 90-231), that can form amyloid fibrils. To study the kinetic pathways of amyloid formation in vitro, we used unglycosylated recombinant PrP corresponding to the proteinase K-resistant core of PrP(Sc) and found that it can adopt two non-native abnormal isoforms, a beta-oligomer and an amyloid fibril. Several lines of kinetic data suggest that the beta-oligomer is not on the pathway to amyloid formation. The preferences for forming either a beta-oligomer or amyloid can be dictated by experimental conditions, with acidic pH similar to that seen in endocytic vesicles favoring the beta-oligomer and neutral pH favoring amyloid. Although both abnormal isoforms have high beta-sheet content and bind 1-anilinonaphthalene-8-sulfonate, they are dissimilar structurally. Multiple pathways of misfolding and the formation of distinct beta-sheet-rich abnormal isoforms may explain the difficulties in refolding PrP(Sc) in vitro, the need for a PrP(Sc) template, and the significant variation in disease presentation and neuropathology.

Amyloid↗