Current Protein and Peptide Science - Volume 1, Issue 2, 2000

Interest in synthetic immunogenic peptides is increasingly growing due to the continuous achievements in the understanding of the molecular basis of the immune response. Moreover, the use of peptide fragments to generate antibodies capable of recognizing and neutralizing viral particles could be a valuable alternative to conventional vaccines they are safe, they can be designed to induce defined immune responses and they can be synthesised in large quantities in high purity. However,their relatively low immunogenicity requires the development of effective adjuvants and or their incorporation into controlled release formulations. Several different strategies have been used for the induction and analysis of protective immune responses induced by short peptides against infectious diseases. In the present article we summarise the different approaches used to potentiate the immune response induced by a continuous epitope of hepatitis A virus co-linear link of T-cell epitopes in different orientations, incorporation into liposomes, and preparation of homogeneous and heterogeneous Multiple Antigenic Peptides.

DNA replication is the process underlying evolution and the propagation of living organisms. Since the discovery of DNA-dependent DNA polymerases more than 40 years ago, the mechanisms governing DNA replication have been extensively studied in bacteria and eukarya. During the last several years, these studies have been extended to the third domain of life, the archaea. Although archaea are prokaryotes, their replication machinery and the proteins participating in the initiation of DNA replication are more similar to those found in eukarya than bacteria. It appears, however, that replication in archaea is a simpler version of the eukaryotic one as fewer polypeptides participate in each phase of the replication process. The archaeal replication apparatus also has several unique features not found in eukaryotic organisms. Furthermore, like bacteria, members of this domain thrive under a broad range of environmental conditions including extreme temperature, high salt, pH, etc. Thus, the replication machinery had to adapt to these extreme conditions. This article summarizes our current understanding of the mechanisms governing DNA replication in archaea and highlights similarities and differences between archaeal replication and that of bacteria and eukarya.

In recent years, phage display of peptides and proteins has become a very popular method in oncology, immunology, protein engineering and ligand-receptor studies among others. Antibody fragments, as Fabs or single chain Fv, have been among the first proteins to be displayed on the surface of a filamentous bacteriophage with a procedure initially described in 1990 by McCafferty et al. (Nature, 348, 552-554). From that time, molecular biology techniques have allowed the creation of large repertoires of antibody fragments from antibody V genes, bypassing hybrydoma technology and even immunisation. A large number of phage antibody libraries, from which molecules of the desired functional properties can be rapidly selected, have been built and distributed in many laboratories world-wide. Antibody fragments recovered from phage libraries generally show moderate binding strength; with different systems of biopanning binders can be obtained with dissociation constant ranged between 10-5 to 10-8 M. Nevertheless, antibody fragments can be furtherly modified to improve affinity or avidity, respectively by mutating crucial residues of complementarity determining regions or by increasing the number of binding sites making dimeric, trimeric or multimeric molecules. Here, we summarise the latest progress in this field, with particular reference to applications of scFv in the diagnosis and therapy of solid tumours and in the molecular mimicry of viral antigens and membrane receptors. In fact, the production of artificial protein epitopes by phage antibodies is becoming a valid system to overcome problems caused by difficult cloning and low expression of particular recombinant proteins.

The structural class and subcellular location are the two important features of proteins that are closely related to their biological functions. With the rapid increase in new protein sequences entering into data banks, it is highly desirable to develop a fast and accurate method for predicting the attributes of these features for them. This can expedite the functionality determination of new proteins and the process of prioritizing genes and proteins identified by genomics efforts as potential molecular targets for drug design. Various prediction methods have been developed during the last two decades. This review is devoted to presenting a systematic introduction and comparison of the existing methods in respect to the prediction algorithm and classification scheme. The attention is focused on the state-of-the-art, which is featured by the covarient-discriminant algorithm developed very recently, as well as some new classification schemes for protein structural classes and subcellular locations. Particularly, addressed are also the physical chemistry foundation of the existing prediction methods, and the essence why the covariant-discriminant algorithm is so powerful.

The alpha beta-hydrolase fold family of enzymes is rapidly becoming one of the largest group of structurally related enzymes with diverse catalytic functions. Members in this family include acetylcholinesterase, dienelactone hydrolase, lipase, thioesterase, serine carboxypeptidase, proline iminopeptidase, proline oligopeptidase, haloalkane dehalogenase, haloperoxidase, epoxide hydrolase, hydroxynitrile lyase and others. The enzymes all have a Nucleophile-His-Acid catalytic triad evolved to efficiently operate on substrates with different chemical composition or physicochemical properties and in various biological contexts. For example, acetylcholine esterase catalyzes the cleavage of the neurotransmitter acetylcholine, at a rate close to the limits of diffusion of substrate to the active site of the enzyme. Dienelactone hydrolase uses substrate-assisted catalysis to degrade aromatic compounds. Lipases act adsorbed at the water lipid interface of their neutral water-insoluble ester substrates. Most lipases have their active site buried under secondary structure elements, a flap, which must change conformation to allow substrate to access the active site. Thioesterases are involved in a multitude of biochemical processes including bioluminiscence, fatty acid- and polyketide biosynthesis and metabolism. Serine carboxypeptidases recognize the negatively charged carboxylate terminus of their peptide substrates. Haloalkane dehalogenase is a detoxifying enzyme that converts halogenated aliphatics to the corresponding alcohols, while haloperoxidase catalyzes the halogenation of organic compounds. Hydroxynitrile lyase cleaves carbon-carbon bonds in cyanohydrins with concomitant hydrogen cyanide formation as a defense mechanism in plants. This paper gives an overview of catalytic activities reported for this family of enzymes by discussing selected examples. The current state of knowledge of the molecular basis for catalysis and substrate specificity is outlined. Relationships between active site anatomy, topology and conformational rearrangements in the protein molecule is discussed in the context of enzyme mechanism of action.