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J Novotný

Publications and source records attributed to J Novotný.

At least 91 records · Page 5Linked to original sources
PubMed1988

Different structures in the amino-terminal domain of the ornithine transcarbamylase leader peptide are involved in mitochondrial import and carboxyl-terminal cleavage.

The cytoplasmic precursor of mitochondrial ornithine transcarbamylase (carbamoyl-phosphate:L-ornithine carbamoyltransferase, EC 2.1.3.2) contains an amino-terminal leader peptide of 32 amino acids. Secondary structure and helical-wheel analyses predict that the extreme amino-terminal domain (residues 1-15) forms an alpha-helix. To test this thesis, leucine residues at positions 2, 5, 8, and 9 were systematically replaced by either helix-breaking glycine residues or by helix-preserving alanine residues. Triple substitutions of glycine for leucine in positions 2, 5, and 9 or 5, 8, and 9 abolished the uptake of the rat precursor by intact mitochondria, whereas similar alanine substitutions had much less effect. Theoretical computations predicted that the decreased helical stability of the Gly-5,8,9 substitution could be significantly increased by replacing a serine in position with phenylalanine. The introduction of Phe-3, indeed, restored the mitochondrial uptake of the mutant precursor. These results lend strong support to the hypothesis that an alpha-helix is present at the leader's amino terminus during the import of the precursor by mitochondria. Although the precursors with the triply-substituted leaders were impaired with respect to import, they were still cleaved readily by a protease found in a mitochondrial matrix fraction. Substitution of glycine or alanine for all four leucine residues, however, rendered the leader uncleavable at the carboxyl-terminal cleavage site. These results suggest that the structure of the amino-terminal domain is important for recognition of the carboxyl-terminal cleavage sites by the matrix proteases.

Amino Acid Sequence↗
PubMed1987

Correlation among sites of limited proteolysis, enzyme accessibility and segmental mobility.

The relationship among accessibility to an enzyme, flexibility, and limited proteolysis was explored. Regions accessible to large probes, comparable in size to proteolytic enzymes, were computed in the crystallographic structures of thermolysin, trypsinogen and ribonuclease. Positions of these accessible regions were compared with sites of autolytic/proteolytic attacks, and with locations of flexible backbone segments. All the proteolytic sites were found to be exceptionally accessible. Most of them were also flexible, but at least one prominent site in trypsinogen appeared to be rigid. Thus, surface exposure seems to be more essential to proteolysis than flexibility.

Biological Availability↗
PubMed1987

Molecular structure of mammalian neuropeptide Y: analysis by molecular cloning and computer-aided comparison with crystal structure of avian homologue.

Identification and characterization of the cDNA encoding rat neuropeptide Y revealed the nucleotide sequence coding for a 98-amino acid precursor. The deduced amino acid sequence for rat neuropeptide Y is identical to the human peptide and is highly homologous to avian pancreatic polypeptide. The tertiary structure of avian pancreatic polypeptide has been previously derived from crystallographic data by Blundell and coworkers. The homology between neuropeptide Y and avian pancreatic polypeptide preserves all of the residues essential for the maintenance of the tertiary structure. Thus, it has been possible to compute a three-dimensional model of the mammalian neuropeptide, neuropeptide Y, based on the known structure of the avian homologue. This model suggest that neuropeptide preserves a compact tertiary structure characterized by extensive hydrophobic interactions between an N-terminal polyproline-II-like helix and a C-terminal alpha-helix. The model has been used to identify amino acids residing in key positions within this structure and, thereby, to direct future analysis of neuropeptide Y structure-function relationships.

Amino Acid Sequence↗
PubMed1986

Static accessibility model of protein antigenicity: the case of scorpion neurotoxin.

Scorpion neurotoxins are a family of homologous, 64 to 65 residue containing proteins with four invariant disulfide bridges. Previous experimental work established four antigenic epitopes in the Androctonus australis neurotoxin and localized them in the amino acid sequence. Using crystallographic coordinates of the Centruroides sculpturatus neurotoxin and computing its large sphere (radius 1 nm or 10 A) accessibility profiles, we identified six antigenic sites clustered into four surface regions. Three of four computed sites coincided with the epitopes identified and localized experimentally in the A. australis neurotoxin, while two of the computed sites partially overlapped the fourth epitope. To investigate the relationship between antigenicity and segmental flexibility, 8-ps molecular dynamics simulations were performed on the C. sculpturatus structure, average backbone temperature factors computed from the simulation, and results compared with the X-ray-derived B values. Most of the neurotoxin structure and, in particular, three of the four antigenic sites were found inflexible, as judged by the computed and/or crystallographic temperature factors. The remaining epitope was associated with only marginal above-average maxima of backbone B values, corresponding to root mean square atomic displacements of 0.5 A (50 pm). We conclude that neurotoxin antigenicity is determined by an exceptional surface exposure of relatively short loop segments and that segmental flexibility is not an essential component of antigenicity.

Animals↗
PubMed1986

Location of antigenic epitopes on antibody molecules.

Using X-ray crystallographic co-ordinates of immunoglobulins, surface regions accessible to a large spherical probe, comparable in size to an antibody domain, were computed. Locations of these exposed regions were compared with those of experimentally determined antigenic sites, i.e. idiotypic, allotypic and isotypic serological markers. In all cases, an excellent agreement was found. The most prominent computed epitopes correspond to convex parts of antibody surface made by reverse turn segments of the polypeptide chain. The computed epitopes occur in homologous positions in all the immunoglobulin domains, and most of the beta-sheet surfaces on the domains are poorly antigenic. The CH2 domain (Fc fragment) has many more antigenic sites than the Fab fragments (antigen-binding fragments). Variable domain epitopes (idiotypes) involve both hypervariable and framework residues, and only about 25% of the hypervariable residues are strongly antigenic. The results indicate that, in a vertebrate body, each antibody molecule may be recognized, and its concentration regulated, by at least 40 complementary anti-immunoglobulin antibodies; therefore, a possibility of an "immune network" with much higher connectivity than is generally assumed should be seriously contemplated.

Animals↗
PubMed1986

Antigenic determinants in proteins coincide with surface regions accessible to large probes (antibody domains).

We evaluated surface areas on proteins that would be accessible to contacts with large (1-nm radius) spherical probes. Such spheres are comparable in size to antibody domains that contain antigen-combining sites. We found that all the reported antigenic sites correspond to segments particularly accessible to a large sphere. The antigenic sites were also evident as the most prominently exposed regions (hills and ridges) in contour maps of the solvent-accessible (small-probe) surface. In myoglobin and cytochrome c, virtually all of the van der Waals surface is accessible to the large probe and therefore potentially antigenic; in myohemerythrin, distinct large-probe-inaccessible, and nonantigenic, surface regions are apparent. The correlation between large-sphere-accessibility and antigenicity in myoglobin, lysozyme, and cytochrome c appears to be better than that reported to exist between antigenicity and segmental flexibility; that is, surface regions that are rigid often constitute antigenic epitopes, whereas some of the flexible parts of the molecules do not appear antigenic. We propose that the primary reason why certain polypeptide-chain segments are antigenic is their exceptional surface exposure, making them readily available for contacts with antigen-combining sites. Exposure of these segments frequently results in high mobility and, in consequence, to the reported correlation between antigenicity and segmental flexibility.

Cytochrome c Group↗
PubMed1986

Coding sequence of the precursor of the beta subunit of rat propionyl-CoA carboxylase.

A cDNA encoding the cytoplasmic precursor of the beta subunit of the mitochondrial enzyme propionyl-CoA carboxylase (EC 6.4.1.3) was cloned and sequenced. The DNA sequence of 2070 nucleotides is almost identical in size to the major hybridizing mRNA from rat liver (2000 +/- 50 nucleotides), suggesting that the cloned DNA represents nearly all of the mRNA sequence. A polypeptide expressed in vitro from an mRNA transcript of this cDNA is indistinguishable in size from the beta subunit precursor (58,500 Da). An open reading frame of 1623 nucleotides, flanked by stop codons, encodes a polypeptide of 541 amino acids; the predicted amino acid sequence was confirmed as that of the beta subunit of propionyl-CoA carboxylase by matching it to the amino acid sequences of five peptides derived from pure mature rat enzyme. Although the exact length of the cleavable, NH2-terminal leader peptide has not been determined because the NH2-terminal residue of the mature subunit is blocked, the leader is most likely 40-42 amino acids in length and is highly positively charged. Computer-aided analysis of secondary structure suggests that the leader peptide consists of two alpha-helical segments, with the two most NH2-terminal arginine residues occupying opposite sites of the first helix; this helix has no apparent hydrophobic moment.

Amino Acid Sequence↗
PubMed1986

Secondary, tertiary, and quaternary structure of T-cell-specific immunoglobulin-like polypeptide chains.

To explore the possibility that the difference in antigen recognition between B and T cells derives from a structural difference in their respective antigen-specific receptors (immunoglobulins on B cells and immunoglobulin-like molecules on T cells), we compared the extracellular segments of the T-cell receptor alpha, beta, and gamma polypeptide chains and the N-terminal segment of the T-cell T8 (Lyt-2) antigen chain with the corresponding regions of immunoglobulins whose three-dimensional structures are known. The results indicate that the four T-cell polypeptide chains are organized into immunoglobulin-like domains consisting of multistranded antiparallel beta-sheet bilayers. Invariant amino acid side chains that are conserved in diverse immunoglobulins, including those that mediate domain-domain interactions and form a constant scaffold for antibody binding sites, are also conserved in the chains encoded by the T-cell receptor genes and in the N-terminal domain of T8 (Lyt-2). It appears that the binding sites of the antigen-specific T-cell alpha beta-chain receptors and of antibodies are very similar in their overall dimensions and geometry: a T-cell alpha beta receptor molecule probably has an antigen-specific binding site that is fundamentally no different than the conventional binding site of an antibody.

Amino Acid Sequence↗
PubMed1986

Study of the antigenic determinants of human renin.

The primary structure of human renin, recently established from the complementary DNA sequence of its messenger RNA, shows a strong homology to other aspartyl proteases. This homology has permitted the construction of a model of the three-dimensional structure of renin based on the crystallographically determined structures of three aspartyl proteases: penicillopepsin, endothiapepsin, and rhizopuspepsin. Using an algorithm in which a spherical probe approximating the size of the antibody-binding domain (1-nm radius) was allowed to contact the surface of the renin model, we predicted 12 to 15 peptides to be immunogenic epitopes. We synthesized peptides corresponding to three different regions of the model: Cys-Gly-Ser-Asp-Pro-Gln-His-Tyr-Glu-Gly-amide (C-180-188), Tyr-Leu-Leu-Cys-Glu-Asp-Gly-Cys-Leu-Ala-Leu-amide (Y-215-224; disulfide bond between cysteines) and Tyr-Gly-Ser-Ser-Thr-Leu-Leu-Cys-Glu-Asp-Gly-Cys-Leu-Ala-Leu-amide (Y-211-224; disulfide bond between cysteines), and Cys-Tyr-Ser-Ser-Lys-Lys-Leu-Cys-Gly (C-290-296-G; disulfide bond between cysteines). All four peptides were tested for their binding to 11 polyclonal and 7 monoclonal antibodies raised against pure human renin, in both a solution assay and an enzyme-linked immunosorbent assay. Peptides Y-215-224 and Y-211-224 bound to all 11 polyclonal antibodies in the solution assay, and peptide Y211-224 bound to eight of them in the enzyme-linked immunosorbent assay. Therefore, region 211-224 can be identified as a major epitope of the human renin molecule.(ABSTRACT TRUNCATED AT 250 WORDS)

Antibodies↗