Molecular diversity of proteins in biological offense and defense systems

Allosteric regulation of the carbohydrate-binding ability of a novel conger eel galectin by D-mannoside

Conger eel has two galectins, termed congerins I and II (Con I and II), that function in mucus as biodefense molecules. Con I and II have acquired a novel protein fold via domain swapping and a new ligand-binding site by accelerated evolution, which enables recognition of some marine bacteria. In this study, we identified a new congerin isotype, congerin P (Con-P), from the peritoneal cells of conger eel. Although Con-P displayed obvious homology with galectins, we observed substitution of 7 out of 8 amino acid residues in the carbohydrate recognition domain that are conserved in all other known galectins. To understand the structure-function relationships of this unique galectin, recombinant Con-P was successfully expressed in Escherichia coli by using a Con II-tagged fusion protein system and subsequently characterized. In the presence of D-mannose, Con-P displayed 30-fold greater hemagglutinating activity than Con I; however, no activity was observed without mannose, indicating that D-mannoside can act as a modulator of Con-P. Frontal affinity chromatography analysis showed that activated Con-P, allosterically induced by mannose, displayed affinity for oligomannose-type sugars as well as N-acetyllactosamine-type β-galactosides. Thus, Con-P represents a new member of the galectin family with unique properties.

Diversified carbohydrate-binding lectins from marine resources

Marine bioresources produce a great variety of specific and potent bioactive molecules including natural organic compounds such as fatty acids, polysaccharides, polyether, peptides, proteins, and enzymes. Lectins are also one of the promising candidates for useful therapeutic agents because they can recognize the specific carbohydrate structures such as proteoglycans, glycoproteins, and glycolipids, resulting in the regulation of various cells via glycoconjugates and their physiological and pathological phenomenon through the host-pathogen interactions and cell-cell communications. Here, we review the multiple lectins from marine resources including fishes and sea invertebrate in terms of their structure-activity relationships and molecular evolution. Especially, we focus on the unique structural properties and molecular evolution of C-type lectins, galectin, F-type lectin, and rhamnose-binding lectin families.

On the information expressed in enzyme structure: more lessons from ribonuclease A

Brownian computations were directed at Ribonuclease A (RNase A) and variants in folded states so as to quantify information of the statistical type at the atom/covalent bond level. This advanced the research reported in this journal last year on the information properties of enzyme primary structure. Brownian computation data are illustrated for a sixteen-member library. The results identify signature traits that distinguish the folded wild type (WT) molecule from variants. The distinctions are explainable in terms of correlated information and dispersion energy. The Brownian tools used for this study can be directed at other protein families (e.g., kinases, isomerases, etc.) in rapid screening, QSAR, and design applications.

Positively selected sites of scorpion depressant toxins: possible roles in toxin functional divergence

Scorpion depressant toxins represent a distinct pharmacological group of sodium channel neurotoxins, identified by their preferential ability in induction of depressant and flaccid paralysis of insects. However, recent observations that some members in this group exhibit anti-mammal activity raise an interesting evolutionary question of whether it is a consequence of adaptive evolution to the early radiation of mammals on earth. By employing the maximum likelihood method, we provided convincing statistical evidence in favor of positive selection driving the evolution of the depressant toxins, and found that two of three positively selected sites are located on the functional surface of the toxins. A complex model of the scorpion depressant toxin LqhIT2 binding to insect sodium channel alpha-subunit (DmNav1) was constructed by structural bioinformatics approaches which highlights a possible direct interaction between these two sites and insect sodium channels. Our work presented here thus suggests that accelerated substitutions in these site residues could offer an evolutionary advantage for these toxins to adapt different channels from diverse origins.

Reconstruction of a probable ancestral form of conger eel galectins revealed their rapid adaptive evolution process for specific carbohydrate recognition

Recently, many cases of rapid adaptive evolution, which is characterized by the higher substitution rates of nonsynonymous substitutions to synonymous ones, have been identified in the various genes of venomous and biodefense proteins, including the conger eel galectins, congerins I and II (ConI and ConII). To understand the evolutionary process of congerins, we prepared a probable ancestral form, Con-anc, corresponding to the putative amino acid sequence at the divergence of ConI and ConII in phylogenetic tree with 76% and 61% sequence identities to the current proteins, respectively. Con-anc and ConII had comparable thermostability and similar carbohydrate specificities in general, whereas ConI was more thermostable and showed different carbohydrate specificities. Con-anc showed decreased specificity to oligosaccharides with alpha 2,3-sialyl galactose moieties. These suggest that ConI and ConII have evolved via accelerated evolution under significant selective pressure to increase the thermostability and to acquire the activity to bind to alpha2,3-sialyl galactose present in pathogenic bacteria, respectively. Furthermore, comparative mutagenesis analyses of Con-anc and congerins revealed the structural basis for specific recognition of ConII to alpha2,3-sialyl galactose moiety, and strong binding ability of ConI to oligosaccharides including lacto-N-biosyl (Galbeta1-3GlcNAc) or lacto-N-neobiosyl (Galbeta1-4GlcNAc) residues, respectively. Thus, protein engineering using a probable ancestral form presented here is a powerful approach not only to determine the evolutionary process but also to investigate the structure-activity relationships of proteins.