Conformational and epitope mapping of herpes-simplex-virus type-1 thymidine kinase using synthetic peptide segments

Calcein permeability of liposomes mediated by type A botulinum neurotoxin and its light and heavy chains

The mode of botulinum neurotoxin action involves binding of its heavy chain for internalization into the presynaptic end of a nerve cell through endocytosis. The low-pH conditions of endosomes trigger translocation of the light chain across the endosomal membrane to the cytosol, where the light chain cleaves specific target proteins involved in the docking and fusion of synaptic vesicles for acetylcholine release. In an effort to model the interaction of botulinum neurotoxin and its subunit chains with lipid bilayer at low pH during the translocation process, we have examined type A botulinum neurotoxin-mediated calcein release from asolectin liposomes. At equimolar concentration (0.1 microM), the neurotoxin and its heavy and light chains evoked 23%, 58%, and 28% calcein release, respectively. Calcein release was observed only when the cis-side (the side to which neurotoxin samples were added) pH was lowered to 4. Calcein release activity of the heavy chain was mostly blocked (76%) by a polyclonal antibody raised against the neurotoxin. Additionally, two peptide-specific polyclonal antibodies derived from the N-terminal and C-terminal halves of the heavy chain were also able to block the calcein release activity by 15-20%. In summary, these results suggest that calcein release from liposomes is specifically mediated by the heavy chain, and the light chain also integrates into the membrane. Implications of these results for the molecular mode of neurotoxin light-chain translocation across the endosomal membrane are discussed.

Comparison of antibodies directed against receptor segments of NPY-receptors

The Y1-, Y2-, Y4- and Y5-receptor, which belong to the rhodopsin-like G-protein coupled, 7 transmembrane helix spanning receptors, bind the 36-mer neuromodulator NPY (neuropeptide Y) with nanomolar affinity. Synthetic fragments of the second (E2) and third (E3) extracellular loop were used to generate subtype selective anti-receptor antibodies against the Y-receptors. As investigated on intact receptors by ELISA and on solubilized receptors by SDS-PAGE and subsequent Western blotting, subtype selectivity was only partly achieved. Nevertheless, selectivity can be obtained by using several antisera in combination. These antibodies represent tools for molecular mass determination, receptor purification by affinity chromatography with antibody-columns and receptor localization studies.

A transferred NOE study of a tricyclic analog of acyclovir bound to thymidine kinase

A purine derivative with an acyclic sugar analog, 3,9-dihydro-3-[(2-hydroxyethoxy)methyl]-6-ethyl-9-oxo-5H-imidazo [1,2-a]purine, was studied in the free state and in complex with herpes simplex virus thymidine kinase (HSV1 TK). Transferred NOE experiments, combined with a full relaxation matrix analysis of the substrate's spin system, resulted in a set of distance constraints for all proton pairs. These constraints were used in structure determination procedures based on simulated annealing and molecular dynamics simulations to obtain a family of structures compatible with the experimental NMR data. The results indicate that, although in both states the chains have the syn orientation with respect to the aromatic rings, in the free state the substrate's acyclic moiety is relatively disordered, while in the bound state only one specific conformation is preferred. Fluctuations can only be seen in the case of the terminal hydroxyl group, for which no NOE was recorded and hence no constraints were available.

Secondary structure prediction of adenylate kinase by circular dichroism spectroscopy of synthetic peptides

The synthesis of 13 segments of porcine adenylate kinase (AK 1) consisting each of 15 residues and covering the whole sequence of AK 1 is reported. The peptides were obtained by multiple peptide synthesis applying Fmoc/tert. butyl strategy. For the conformational analysis by circular dichroism spectroscopy different mixtures of phosphate buffer (pH 7), trifluoroethanol and methanol were used. Ten peptides showed alpha-helical conformation in all solvents except of pure buffer. The conformation of these peptides correlated well with the secondary structure obtained by homology modelling and even more striking with the X-ray structure of adenylate kinase, which was published recently. In contrast, three peptides, which were suggested to adopt no helical conformation did not show any content of alpha-helicity in any of the solvents that we investigated. One peptide, which contains a beta-sheet according to the X-ray analysis revealed a high content of beta-conformation by CD in buffer and in mixtures with trifluoroethanol. The two other peptides revealed mainly random coil in all solvents which we investigated. Therefore, we conclude that synthetic peptides are suitable tools to investigate the secondary structure of protein segments and that this conformation is frequently preserved in the intact protein.

Analysis of antibody response to the measles virus using synthetic peptides of the fusion protein. Evidence of non-random pairing of T and B cell epitopes

The measles virus induces a life-long immune response associated with antibodies specific for the fusion protein. To map the linear immunodominant recognition sites of the fusion (F) protein of the measles virus, we have reacted a complete set of 108 overlapping pentadecapeptides with purified IgG obtained from donor sera with elevated anti-measles titers. The antibodies recognized about 20% of the peptides and generated a characteristic binding pattern, defining about 6 or 7 distinctive regions (31-75; 111-145; 151-165; 191-215; 271-320; 421-440; 481-530) which include the major hydrophobic segment (111-145) of the intersubunit region and the C-terminal Cys-cluster region. The binding sites were located in close proximity of the few experimentally defined T cell epitopes. This pairing of T and B cell epitopes was corroborated by computer-assisted T cell prediction. The significance of a non-random association of T and B cell epitopes for processing and presentation is discussed. It is speculated that in long-term immunity against measles (F protein), B cells of the same sIg specificity play an important role both as antigen presenting cells and as antibody producing cells. In contrast to human sera from late convalescent donors, mouse and rabbit MV antisera with high neutralizing titers as well as neutralizing MV-F specific monoclonal antibodies did not react with the peptides.

Identification of important residues within the putative nucleoside binding site of HSV-1 thymidine kinase by random sequence selection: analysis of selected mutants in vitro

Random sequence mutagenesis in conjunction with genetic complementation was used to map the function of amino acid residues within the putative nucleoside binding site of the herpes simplex virus type 1 (HSV-1) thymidine kinase (TK). Six codons of the putative nucleoside binding site of the HSV-1 tk were substituted by a duplex of extended oligonucleotides containing 20% random sequences. Approximately 260 mutants were screened for the ability to genetically complement a TK-deficient Escherichia coli. Of those screened, 32% conferred TK activity. Approximately 60% of the TK positive clones contained single amino acid changes, 23% contained double changes, and 13.4% encoded the wild-type TK amino acid sequence. A small percentage of clones, 2.4% and 1.2%, contained triple or quadruple alterations, respectively. Three residues (D162, H163, and R164) appeared to be highly conserved especially with regard to the type of residues able to substitute. Secondary screening results indicated that several of the mutants had higher affinities for acyclovir and/or 3'-azido-3'-deoxythymidine than thymidine in complementation assays. In addition, a number of clones were unable to form colonies on selection medium at elevated temperatures (42 degrees C). Eight selected mutants were subcloned into an in vitro transcription vector and the derived transcripts used to program a rabbit reticulocyte lysate cell-free translation system. Biologically active translation products were then analyzed in vitro for thymidine kinase activity, for thermal stability, and for the ability to phosphorylate selected nucleoside analogues. Two of the eight mutants had an elevated thymidine kinase activity, two were significantly thermolabile, and three exhibited enhanced efficiency in phosphorylation of nucleoside analogues.

Analysis of the neutralizing antibody response to the measles virus using synthetic peptides of the haemagglutinin protein

Infection or immunization with measles virus induces a protective immune reaction including neutralizing antibodies against the haemagglutinin and fusion protein. The reactivity of the polyclonal IgG response of sera obtained from late convalescent donors was studied, using overlapping 15mer peptides covering the complete sequence of the measles virus haemagglutinin. Most sera reacted with a similar set of peptides generating a characteristic binding pattern. The reactive peptides correspond to a region mediating cell hemolysis (aa310-325), to regions which serve as targets to neutralizing antibodies and to a putative transmembrane region (aa35-58). The latter region contains also a human T-cell epitope providing evidence of a non-random association of T- and B-cell epitopes. We also immunized different strains of mice and rabbits with measles virus. In contrast to the human sera, animal sera with strong neutralizing activities did not react with any of the H-protein peptides. The mostly weak reactivities with the linear sequences contrast with the strong neutralizing activities of the human or animal antibodies, suggesting that these primarily recognize the fusion protein or conformational epitopes of the haemagglutinin protein.

Epitope mapping: synthetic approaches to the understanding of molecular recognition in the immune system

Progress in the field of immunochemistry is rapidly increasing due to very efficient methods of epitope mapping. Experimental results on the allele-specific sequence motifs of MHC-binding peptides allow the exact forecast of T-cell epitopes and, in combination with B-cell prediction methods and synthetic adjuvant systems, fully synthetic vaccines may be constructed. Methods of multiple peptide synthesis are of particular use for such constructs and for the fine mapping of monoclonal antibodies or sera of patients. Peptide libraries, containing hundred thousands of different oligopeptides are made available for novel screening procedures. These techniques and their applications in various fields are summarized and discussed with respect to efficiency and productivity.

Modelling by homology of the HSV1-TK sequence embedded structural alignment

Modelling by homology is an approach to the rational design of new drugs based on the construction of ligand protein interaction complexes. Because in most cases the 3D-structure of the target protein is not known from biophysical data, this approach yields a theoretical procedure which establishes at least parts of the protein by comparison with isofunctional proteins, assuming that much of the structural information is embedded in the amino acid sequence. This approach should be of considerable importance for proteins with divergent primary structures but with a high degree of isofunctionality, the latter demanding a similar active site folding pattern. This study is a pattern recognition approach based on additive secondary structure prediction and surface probabilities from residue variabilities. The comparison of the additive properties yields a sequence alignment of the viral thymidine kinases with the adenylate kinases having a closely related functionality. X-ray structures of adenylate kinases can then be used as templates to derive a 3D-structure prediction of the thymidine kinase active site.

Structural biology and diabetes mellitus: molecular pathogenesis and rational drug design

Emerging concepts in the aetiology and pathogenesis of Type 1 (insulin-dependent) diabetes mellitus may offer new opportunities for treatment and cure. Here we describe recent advances in structural molecular biology and molecular design relevant to rational drug discovery. Such approaches focus on the three-dimensional structures of macromolecules and their interactions. In the coming decade such techniques may be applied to a wide variety of diabetes-related targets.

Viral thymidine kinases and their relatives

Thymidine kinases were described for cellular life long before it was shown that they could also be encoded by viruses, but the viral thymidine kinase genes were the first to be sequenced. These enzymes have been extraordinarily useful to the researcher, serving first to help label DNA, then to get thymidine analogs incorporated into DNA for therapeutic and other purposes and more recently to move genes from one genome to another. Knowledge of the nucleotide and amino acid sequences of these enzymes has allowed some deductions about their possible three-dimensional structure, as well as the location on the polypeptide of various functions; it has also allowed their classification into two main groups: the herpesviral thymidine/eukaryotic deoxycytidine kinases and the poxviral and cellular thymidine kinases; the relationships of the mitochondrial enzyme are still not clear.