Identification of common structural features of binding sites in galactose-specific proteins

A novel C-type lectin from abalone, Haliotis discus discus, agglutinates Vibrio alginolyticus

Owing to its specific binding to carbohydrates, lectins play important roles in pathogen recognition and clearance in invertebrate animals. In this study, a novel C-type lectin (designated CLHd) gene was isolated from abalone, Haliotis discus discus, cDNA library. The complete cDNA sequence of the CLHd gene is 508 base pairs in length, and encodes 151 amino acids. CLHd shares a highly conserved carbohydrate recognition domain with C-type lectins from mollusk and fish. The mRNA expressions of CLHd in healthy and bacterial-challenged abalones were examined using semi-quantitative reverse transcriptase polymerase chain reaction (RT-PCR). CLHd mRNA transcription was up-regulated by Vibrio alginolyticus challenge and reached the maximum expression at 24h after the bacterial injection. To understand its biological activity, the recombinant CLHd gene was constructed and expressed in Escherichia coli. The recombinant CLHd specifically agglutinated V. alginolyticus at a concentration of 50microg/ml in a calcium-dependant way. Both the gene expression analysis and recombinant protein activity assay suggest that CLHd is an important immune gene involved in the recognition and elimination of pathogens in abalones.

Recombinant perlucin nucleates the growth of calcium carbonate crystals: molecular cloning and characterization of perlucin from disk abalone, Haliotis discus discus

Perlucin is well known as an important functional protein regulating pearl formation and shell biomineralization. In this study, we cloned the perlucin gene from the abalone Haliotis discus discus cDNA library. The full-length cDNA of the abalone H. discus discus perlucin gene consisted of 1038 bp nucleotides, encoding a putative signal peptide of 22 amino acids and a mature protein of 129 amino acids, which shared 55% identity with the homologous protein in greenlip abalone. The mature protein coding sequence was inserted into pMal-c2X expression vector and it expressed the recombinant protein in E. coli (Rosetta-gammi DE3). The maltose binding protein (MBP) fusion perlucin successfully promoted calcium carbonate precipitation and directed calcite crystal morphological modification. The successful expression of active recombinant perlucin suggested that recombinant perlucin gene transfer has the capability by color modification to improve the pearl's value. In the view of molecular structure, perlucin was a typical C-type lectin, which contained one highly conserved carbohydrate recognition domain. Reverse transcription polymerase chain reaction (RT-PCR) results showed that perlucin gene was expressed not only in the mantle, but also in the gill and digestive tract. Further characterization of perlucin in abalone non-self recognition and disease resistance is promising and anticipated.

Glycolipid transfer proteins

Glycolipid transfer proteins (GLTPs) are small (24 kDa), soluble, ubiquitous proteins characterized by their ability to accelerate the intermembrane transfer of glycolipids in vitro. GLTP specificity encompasses both sphingoid- and glycerol-based glycolipids, but with a strict requirement that the initial sugar residue be beta-linked to the hydrophobic lipid backbone. The 3D architecture of GLTP reveals liganded structures with unique lipid-binding modes. The biochemical properties of GLTP action at the membrane surface have been studied rather comprehensively, but the biological role of GLTP remains enigmatic. What is clear is that GLTP differs distinctly from other known glycolipid-binding proteins, such as nonspecific lipid transfer proteins, lysosomal sphingolipid activator proteins, lectins, lung surfactant proteins as well as other lipid-binding/transfer proteins. Based on the unique conformational architecture that targets GLTP to membranes and enables glycolipid binding, GLTP is now considered the prototypical and founding member of a new protein superfamily in eukaryotes.

Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network

Background

Protein-Carbohydrate interactions are crucial in many biological processes with implications to drug targeting and gene expression. Nature of protein-carbohydrate interactions may be studied at individual residue level by analyzing local sequence and structure environments in binding regions in comparison to non-binding regions, which provide an inherent control for such analyses. With an ultimate aim of predicting binding sites from sequence and structure, overall statistics of binding regions needs to be compiled. Sequence-based predictions of binding sites have been successfully applied to DNA-binding proteins in our earlier works. We aim to apply similar analysis to carbohydrate binding proteins. However, due to a relatively much smaller region of proteins taking part in such interactions, the methodology and results are significantly different. A comparison of protein-carbohydrate complexes has also been made with other protein-ligand complexes.

Results

We have compiled statistics of amino acid compositions in binding versus non-binding regions- general as well as in each different secondary structure conformation. Binding propensities of each of the 20 residue types and their structure features such as solvent accessibility, packing density and secondary structure have been calculated to assess their predisposition to carbohydrate interactions. Finally, evolutionary profiles of amino acid sequences have been used to predict binding sites using a neural network. Another set of neural networks was trained using information from single sequences and the prediction performance from the evolutionary profiles and single sequences were compared. Best of the neural network based prediction could achieve an 87% sensitivity of prediction at 23% specificity for all carbohydrate-binding sites, using evolutionary information. Single sequences gave 68% sensitivity and 55% specificity for the same data set. Sensitivity and specificity for a limited galactose binding data set were obtained as 63% and 79% respectively for evolutionary information and 62% and 68% sensitivity and specificity for single sequences. Propensity and other sequence and structural features of carbohydrate binding sites have also been compared with our similar extensive studies on DNA-binding proteins and also with protein-ligand complexes.

Conclusion

Carbohydrates typically show a preference to bind aromatic residues and most prominently tryptophan. Higher exposed surface area of binding sites indicates a role of hydrophobic interactions. Neural networks give a moderate success of prediction, which is expected to improve when structures of more protein-carbohydrate complexes become available in future.

The liganding of glycolipid transfer protein is controlled by glycolipid acyl structure

Glycosphingolipids (GSLs) play major roles in cellular growth and development. Mammalian glycolipid transfer proteins (GLTPs) are potential regulators of cell processes mediated by GSLs and display a unique architecture among lipid binding/transfer proteins. The GLTP fold represents a novel membrane targeting/interaction domain among peripheral proteins. Here we report crystal structures of human GLTP bound to GSLs of diverse acyl chain length, unsaturation, and sugar composition. Structural comparisons show a highly conserved anchoring of galactosyl- and lactosyl-amide headgroups by the GLTP recognition center. By contrast, acyl chain chemical structure and occupancy of the hydrophobic tunnel dictate partitioning between sphingosine-in and newly-observed sphingosine-out ligand-binding modes. The structural insights, combined with computed interaction propensity distributions, suggest a concerted sequence of events mediated by GLTP conformational changes during GSL transfer to and/or from membranes, as well as during GSL presentation and/or transfer to other proteins.

Structures of glycosphingolipids bound to glycolipid transfer proteins reveal a sphingosine-in or -out binding depending on their acyl chain structure; these conformational changes suggest a mechanism for glycosphingolipid transfer.

Prediction of glycolipid-binding domains from the amino acid sequence of lipid raft-associated proteins: application to HpaA, a protein involved in the adhesion of Helicobacter pylori to gastrointestinal cells

Protein-glycolipid interactions mediate the attachment of various pathogens to the host cell surface as well as the association of numerous cellular proteins with lipid rafts. Thus, it is of primary importance to identify the protein domains involved in glycolipid recognition. Using structure similarity searches, we could identify a common glycolipid-binding domain in the three-dimensional structure of several proteins known to interact with lipid rafts. Yet the three-dimensional structure of most raft-targeted proteins is still unknown. In the present study, we have identified a glycolipid-binding domain in the amino acid sequence of a bacterial adhesin (Helicobacter pylori adhesin A, HpaA). The prediction was based on the major properties of the glycolipid-binding domains previously characterized by structural searches. A short (15-mer) synthetic peptide corresponding to this putative glycolipid-binding domain was synthesized, and we studied its interaction with glycolipid monolayers at the air-water interface. The synthetic HpaA peptide recognized LacCer but not Gb3. This glycolipid specificity was in line with that of the whole bacterium. Molecular modeling studies gave some insights into this high selectivity of interaction. It also suggested that Phe147 in HpaA played a key role in LacCer recognition, through sugar-aromatic CH-pi stacking interactions with the hydrophobic side of the galactose ring of LacCer. Correspondingly, the replacement of Phe147 with Ala strongly affected LacCer recognition, whereas substitution with Trp did not. Our method could be used to identify glycolipid-binding domains in microbial and cellular proteins interacting with lipid shells, rafts, and other specialized membrane microdomains.

Modelling of carbohydrate-aromatic interactions: ab initio energetics and force field performance

Aromatic amino acid residues are often present in carbohydrate-binding sites of proteins. These binding sites are characterized by a placement of a carbohydrate moiety in a stacking orientation to an aromatic ring. This arrangement is an example of CH/pi interactions. Ab initio interaction energies for 20 carbohydrate-aromatic complexes taken from 6 selected ultra-high resolution X-ray structures of glycosidases and carbohydrate-binding proteins were calculated. All interaction energies of a pyranose moiety with a side chain of an aromatic residue were calculated as attractive with interaction energy ranging from -2.8 to -12.3 kcal/mol as calculated at the MP2/6-311+G(d) level. Strong attractive interactions were observed for a wide range of orientations of carbohydrate and aromatic ring as present in selected X-ray structures. The most attractive interaction was associated with apparent combination of CH/pi interactions and classical H-bonds. The failure of Hartree-Fock method (interaction energies from +1.0 to -6.9 kcal/mol) can be explained by a dispersion nature of a majority of the studied complexes. We also present a comparison of interaction energies calculated at the MP2 level with those calculated using molecular mechanics force fields (OPLS, GROMOS, CSFF/CHARMM, CHEAT/CHARMM, Glycam/AMBER, MM2 and MM3). For a majority of force fields there was a strong correlation with MP2 values. RMSD between MP2 and force field values were 1.0 for CSFF/CHARMM, 1.2 for Glycam/AMBER, 1.2 for GROMOS, 1.3 for MM3, 1.4 for MM2, 1.5 for OPLS and to 2.3 for CHEAT/CHARMM (in kcal/mol). These results show that molecular mechanics approximates interaction energies very well and support an application of molecular mechanics methods in the area of glycochemistry and glycobiology.

Purification, characterization and cDNA cloning of a novel lipopolysaccharide-binding lectin from the shrimp Penaeus monodon

In invertebrates, C-type lectin plays an important role in innate immunity by mediating the recognition of pathogens to host cells and clearing microinvaders. A few C-type lectins have been identified from shrimps, but none of their gene or protein sequences is known to date. In this paper, a C-type lectin (named PmLec) specific for bacterial lipopolysaccharide was purified from the serum of the shrimp Penaeus monodon. The binding of PmLec to lipopolysaccharide was mainly mediated through the O-antigen. PmLec had a strong hemagglutinating and bacterial-agglutinating activity as well as an opsonic effect that enhances hemocyte phagocytosis. The PmLec cDNA sequence was obtained from the cDNA library of P. monodon by polymerase chain reaction with the degenerated primer designed according to the amino-terminal residue sequence of purified PmLec. A 546-bp open reading frame was found to encode a putative protein comprising 182 amino acids and containing a preceding signal peptide of 17 amino acids. A C-type lectin domain existed in PmLec, but no glycosylation site was found. The recombinant PmLec protein expressed in Escherichia coli also showed the same agglutinating activity and opsonic effect as that of the native protein. This is the first report of a lectin cDNA from the shrimp. PmLec functions as a pattern-recognition protein and an opsonin in the shrimp, and it provides a clue to elucidate the role of lectin in the innate immunity of aquatic invertebrates at the molecular level.

Insights into the Role of the Aromatic Residue in Galactose-Binding Sites: MP2/6-311G++** Study on Galactose− and Glucose−Aromatic Residue Analogue Complexes

The presence of an aromatic residue (Trp, Phe, Tyr) facing the nonpolar face of galactose is a common feature of galactose-specific lectins. The interactions such as those between the C-H groups of galactose and the pi-electron cloud of aromatic residues have been characterized as weak hydrogen bonds between soft acids and soft bases, largely governed by dispersive and charge transfer interactions. An analysis of the binding sites of several galactose-specific lectins revealed that the spatial position-orientation of galactose relative to the binding site aromatic residue varies substantially. The effect of variations in position-orientations of galactose on the interaction energies of galactose-aromatic residue complexes has not been determined so far. In view of this, MP2/6-311G++** calculations were performed on galactose- and glucose-aromatic residue analogue complexes in eight position-orientations. The results show that the strength of the C-H...pi interactions in galactose-aromatic residue complexes is comparable to that of a hydrogen bond. Rather than the type of aromatic residue, the position-orientation of the saccharide appears to be more critical in determining the strength of their interactions. Earlier studies have found the binding site aromatic residue to be critical, but its role was not clear. This study shows that the aromatic residue is important for discriminating galactose from glucose, in addition to its contribution to binding energy.

Energetics of galactose- and glucose-aromatic amino acid interactions: implications for binding in galactose-specific proteins

An aromatic amino acid is present in the binding site of a number of sugar binding proteins. The interaction of the saccharide with the aromatic residue is determined by their relative position as well as orientation. The position-orientation of the saccharide relative to the aromatic residue was found to vary in different sugar-binding proteins. In the present study, interaction energies of the complexes of galactose (Gal) and of glucose (Glc) with aromatic residue analogs have been calculated by ab initio density functional (U-B3LYP/ 6-31G**) theory. The position-orientations of the saccharide with respect to the aromatic residue observed in various Gal-, Glc-, and mannose-protein complexes were chosen for the interaction energy calculations. The results of these calculations show that galactose can interact with the aromatic residue with similar interaction energies in a number of position-orientations. The interaction energy of Gal-aromatic residue analog complex in position-orientations observed for the bound saccharide in Glc/Man-protein complexes is comparable to the Glc-aromatic residue analog complex in the same position-orientation. In contrast, there is a large variation in interaction energies of complexes of Glc- and of Gal- with the aromatic residue analog in position-orientations observed in Gal-protein complexes. Furthermore, the conformation wherein the O6 atom is away from the aromatic residue is preferred for the exocyclic -CH2OH group in Gal-aromatic residue analog complexes. The implications of these results for saccharide binding in Gal-specific proteins and the possible role of the aromatic amino acid to ensure proper positioning and orientation of galactose in the binding site have been discussed.

A role for insect galectins in parasite survival

Insect galectins are associated with embryonic development or immunity against pathogens. Here, we show that they can be exploited by parasites for survival in their insect hosts. PpGalec, a tandem repeat galectin expressed in the midgut of the sandfly Phlebotomus papatasi, is used by Leishmania major as a receptor for mediating specific binding to the insect midgut, an event crucial for parasite survival, and accounts for species-specific vector competence for the most widely distributed form of cutaneous leishmaniasis in the Old World. In addition, these studies demonstrate the feasibility of using midgut receptors for parasite ligands as target antigens for transmission-blocking vaccines.