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The comparative analysis of primary and secondary structures, and hydropathy plots of hepatitis B virus (HBV) and hepatitis delta virus (HDV) proteins was carried out. Two short regions belonging to the HBV terminal protein were shown to be homologous to two regions; one encoded by HDV ORF5, and the other encoded by small ORF of the HDV antigenomic RNA strand. We propose a new protein containing both these regions may be synthesized in HDV infected cells. Stiking structural homology between the terminal protein of HBV and this predicted protein called HDAg' of HDV may indicate a possible functional similarity.'We hypothesize the HDAg' may interact with and inhibit the polymerase activity of HBV.

Vinculin is thought to be an important cytoskeletal protein in the linkage between actin cytoskeleton and integrin transmembrane receptors. We identified Vinculin (Vinc) gene in the X chromosome of D. melanogaster. Drosophila vinculin is highly homologous in its N- and C-terminal domains both to mammalian and nematode vinculins, and contains internal repeats and proline-rich region typical for vinculins. The X chromosome rearrangement In(1LR)pn2a was found to disrupt Vinc so that the coding sequence is interrupted by the (AAGAG)n satellite DNA. Northern analysis revealed that the Vinc transcript is completely absent in the In(1LR)pn2a homozygous flies. Surprisingly, these Vinc flies are viable and fertile. This finding highlights plasticity and adaptive capacity of cellular cytoskeletal and anchorage system.

Homeobox-containing sequences were isolated from a genomic library of zebrafish (Brachydanio rerio). A λ clone containing two homeobox cross-hybridizing regions was characterized. DNA sequencing of one of these regions (ZF-21) revealed that it contains a homeobox closely related to the Antennapedia class of Drosophila homeobox sequences. Moreover, the deduced amino acid sequence of the C-terminal end (81 residues including the homeobox) is identical to the corresponding part of the murine Hox-2.1 protein. Similar to Hox-2.1, a ZF-21 derived transcript of 2.3 kb is present in embryos at the somite forming stages.

The N-terminal amino acid sequences of two chloroform/methanol soluble globulins from barley and one form wheat are reported. They are homologous with N-terminal sequences previously reported for α-amylase and trypsin inhibitors from cereals and 2 S storage proteins from castor bean and rape. Three albumins were also purified from Aegilops squarrosa and Triticum monococcum. These had N-terminal amino acid sequences most closely related to the α-amylase and trypsin inhibitors. The relationships of this superfamily of seed proteins are discussed.

The sequences of three mitochondrial carriers involved in energy transfer, the ADP/ATP carrier, phosphate carrier and uncoupling carrier, are analyzed. Similarly to what has been previously reported for the ADP/ATP carrier and the uncoupling protein, now also the phosphate carrier is found to have a tripartite structure comprising three similar repeats of approx. 100 residues each. The three sequences show a fair overall homology with each other. More significant homologies are found by comparing the repeats within and between the carriers in a scheme where the sequences are spliced into repeats, which are arranged for maximum homology by allowing possible insertions or deletions. A striking conservation of critical residues, glycine, proline, of charged and of aromatic residues is found throughout all nine repeats. This is indicative of a similar structural principle in the repeats. Hydropathy profiles of the three proteins and a search for amphipathic α-spans reveal six membrane-spanning segments for each carrier, providing further support for the basic structural identity of the repeats. The proposed folding pattern of the carriers in the membrane is exemplified with the phosphate carrier. A possible tertiary arrangement of the repeats and the membranespanning helices is shown. The emergence of a mitochondrial carrier family by triplication and by divergent evolution from a common gene of about 100 residues is discussed.

Neural networks provide a basis for semiempirical studies of pattern matching between the primary and secondary structures of proteins. Networks of the perceptron class have been trained to classify the amino-acid residues into two categories for each of three types of secondary feature: α-helix or not, β-sheet or not, and random coil or not. The explicit prediction for the helices in rhodopsin is compared with both electron microscopy results and those of the Chou-Fasman method. A new measure of homology between proteins is provided by the network approach, which thereby leads to quantification of the differences between the primary structures of proteins.

The zebrafish genome was found to contain two sequences which cross-hybridize strongly with the engrailed gene of Drosophila. Several independent clones containing one of these cross-hybridizing sequences were isolated from a zebrafish genomic library. Characterization of this region (ZF-EN) by DNA sequencing showed that it shares about 70% sequence identity with the engrailed homeobox. More extensive homeobox homology (greater than 90%) was found relative to the murine En genes. The closest relationship exists between ZF-EN and En-2 where the C-terminal domains (104 amino acids) encoded by these genes are almost identical. We also observed that ZF-EN and En-2 are very similar with respect to their transcript sizes and temporal expression patterns.

By means of comparative analysis of primary and secondary structures, and hydropathy plots of hepadnavirus P proteins new functional domains were revealed additionally to the polymerase domain which had been found earlier in these proteins. The C-terminal part of P proteins was revealed to be significantly similar to ribonuclease H of E. coli. The ribonuclease H functional domain is known to be an integral entity of retrovirus reverse transcriptase as a rule. Availability of this domain indicates once more the putative reverse transcriptase properties of the P products. The proteins of hepadnaviruses were compared to terminal proteins of picornaviruses, adenoviruses and bacteriophages. The data obtained suggested that a conservative N-terminal region of P proteins functions as protein primer for DNA synthesis in hepadnaviruses.

Two forms of cytochrome b5, a soluble erythrocyte form and a membrane-bound liver form, were purified from pig and human, and structural differences between them were analyzed. Porcine and human erythrocyte cytochrome b5 consisted of 97 amino acid residues and contained the same catalytic domain structure (residue 1–96) as that of the corresponding liver cytochrome b5, but had one amino acid replacement at the C-terminus (residue 97). These results suggest that erythrocyte cytochrome b5 is not derived from the liver protein by proteolysis but a translational product from another distinct mRNA of cytochrome b5.

Evidence is presented, based on sequence comparison according to Hydrophobic Cluster Analysis, of a structural and evolutionary relationship between the human alpha/beta-interferon receptor and the human and mouse gamma-interferon receptor. These results predict that the human alpha/beta-interferon receptor extracellular part is organised in two homologous subdomains connected by a proline linker. They also predict that both subdomains present some homologies to the external domain of mouse and human gamma interferon receptor.