Structural Studies On Three-Fold Symmetric Plant Lectins

Lectins, multivalent carbohydrate-binding proteins of non-immune origin, have the unique ability to decode the information contained in complex carbohydrate structures of glycoproteins and glycolipids by stereo-specifically recognizing and binding to carbohydrates and carbohydrate linkages. The ubiquitous distribution of lectins in all forms of life and viruses along with their involvement in various biological processes such as cell-cell communication, host-pathogen interaction, cancer metastasis, embryogenesis, tissue development and mitogenic stimulation further emphasizes the importance of lectins in biological systems. Although not much is known about the endogenous roles of plant lectins, they constitute the most thoroughly studied class of lectins. On the basis of their subunit folds plant lectins have been divided in six major classes. They include jelly roll fold lectins (or legume lectins), hevein domain lectins (or cereal lectins), β-trefoil fold lectins, β-prism II fold lectins (or bulb lectins), β-prism I fold lectins and the most recently discovered lectin homologous to cyanovirin-N (http://www.cermav.cnrs.fr/lectines). Interestingly, of these, lectin subunits harbor an approximate three-fold symmetry in three cases and each subunit is believed to have evolved through successive gene duplication, fusion and divergent evolution. One of the major research activities in this laboratory involves structural studies on plant lectins. Decades of extensive studies in the laboratory have shed light on various structural and functional aspects of lectins such as variability in quaternary association, lectin-carbohydrate interactions, strategies for generating ligand specificity and multivalency. Furthermore, the β-prism I fold was first identified as a lectin fold in this laboratory through the X-ray analysis of the methyl-α-galactose complex of jacalin, one of the two lectins from the seeds of Artocarpus integrifolia. Subsequently, many other lectins with the same fold have been structurally characterized here and else where (http://www.cermav.cnrs.fr/lectines). They include mannose specific tetrameric artocarpin and dimeric banana lectin studied in this laboratory. Also investigated here is the structure of first dimeric β-prism II fold lectin, namely, garlic lectin. The subsequent work, carried out by the author, on the structure and dynamics of three-fold symmetric lectins form the subject matter of this thesis. Different web-servers available at NCBI and EXPASY web sites were used for sequence annotation studies. MRBAYES and MEGA were used for phylogenetic analysis. Molecular dynamics (MD) simulations were carried out using the simulation package GROMACS v.3.3.1. OPLS-AA/L and GLYCAM-06 force fields were used for proteins and carbohydrates respectively. Simulations were performed in explicit water system with TIP4P water model under NPT conditions with unit dielectric constant. The hanging drop method was used for crystallizing banana lectin and its complexes. Intensity data were collected on a MAR 345 image plate mounted on a Rigaku RU200 rotating-anode X-ray generator. The Oxford cryosystem was used when collecting data at low temperature. The data were processed using DENZO and SCALEPACK of HKL suite of programs. The structure factors from the processed data were calculated using TRUNCATE of CCP4 suite of programs. The molecular replacement program MOLREP was used for structure solution. Structure refinements were carried out using the CNS software package and REFMAC of CCP4. Model building was done using the molecular graphics program COOT. INSIGHT II, ALIGN, CONTACT, MUSTANG and SC of CCP4 were used for analysis of structural features. PROCHECK and web-server MOLPROBITY were used for the validation of the refined structures. The β-prism II fold lectins of known structure, all from monocots, invariably have three carbohydrate-binding sites in each subunit / domain. Until recently, β-prism I fold lectins of known structure were all from dicots and they exhibited one carbohydrate-binding site per subunit / domain. However, the recently determined structure of the β-prism I fold lectin from banana, a monocot, has two very similar carbohydrate-binding sites. This prompted a detailed analysis of all the sequences appropriate for the two lectin folds and which carry one or more relevant carbohydrate-binding motifs. The recent observation of a β-prism I fold lectin, griffithsin, with three binding sites in each domain further confirmed the need for such an analysis. The detailed sequence and phylogenetic analysis of all the β-prism I fold lectin or lectin-like sequences, available then, with particular attention to their carbohydrate-binding sites in them, in conjunction with the analysis of available three-dimensional structures demonstrate substantial diversity in the number of binding sites, unrelated to the taxonomical position of the plant source. However, the number of binding sites and the symmetry within the sequence exhibit reasonable correlation. The distribution of the two families of β-prism fold lectins among plants and the number of binding sites in them, appear to suggest that both of them arose through successive gene duplication, fusion and divergent evolution of the same primitive carbohydrate-binding motif involving a Greek key. Analysis with sequences in individual Greek keys as independent units lends further support to this conclusion. It would seem that the prepondence of three carbohydrate-binding sites per domain in monocot lectins, particularly those with the β-prism II fold, is related to the role of plant lectins in defence. Jacalin is the most thoroughly studied β-prism I fold lectin. A wealth of structural and thermodynamic data, mostly from this laboratory, led to a thorough characterization of carbohydrate-recognition in the case of jacalin. One aspect of jacalin that has not been investigated so far was its dynamics. The issue was addressed through reasonably long MD simulations, in explicit solvent system using all atom force field, of all the jacalin-carbohydrate complexes of known structure, models of unliganded molecules derived from the complexes and also models of relevant complexes where X-ray structures are not available. Results of the simulations and the available crystal structures involving jacalin permit delineation of the relatively rigid and flexible regions of the molecule and the dynamical variability of the hydrogen bonds involved in stabilizing the structure. Local flexibility appears to be related to solvent accessibility. Hydrogen bonds involving side chains and water bridges involving buried water molecules appear to be important in the stabilization of loop structures. The lectin-carbohydrate interactions observed in crystal structures, the average parameters pertaining to them derived from simulations, energetic contribution of the stacking residue estimated from quantum mechanical calculations and the scatter of the locations of carbohydrate and carbohydrate-binding residues, are consistent with the known thermodynamic parameters of jacalin-carbohydrate interactions. The simulations, along with X-ray results, provide a fuller picture of carbohydrate binding by jacalin than provided by crystallographic analysis alone. The simulations confirm that in the unliganded structures water molecules tend to occupy the positions occupied by carbohydrate oxygens in the lectin-carbohydrate complexes. Population distributions in simulations of the free lectin, the ligands and the complexes indicate a combination of conformational selection and induced fit. Mannose-specific β-prism I fold lectins, like lectins belonging to other plant families, exhibit interesting variability in their quaternary association. Mannose specific artocarpin and MornigaM are tetrameric, heltuba is octameric in the crystal structure and banana lectin and calsepa are dimeric. The modes of the dimerization in the last two are however, entirely different. This variability was explored through modelling and molecular dynamics simulations based on the known three-dimensional structures. This study, which combines computational approaches and results of X-ray analyses, provides valuable insights into the origin of the variability in quaternary association. MD simulations on individual subunits and the oligomers provide insights into the changes in the structure brought about in the protomers on oligomerization, including swapping of the N-terminal stretch in one instance. The regions which undergo changes also tend to exhibit dynamic flexibility during MD simulations. The internal symmetries of individual oligomers are substantially retained during the calculations. Simulations were also carried out on models using all possible oligomers employing the four different protomers. The unique dimerization pattern observed in calsepa could be traced to unique substitutions in a peptide stretch involved in dimerization. The impossibility of a specific mode of oligomerization involving a particular protomer is often expressed in terms of unacceptable steric contacts or dissociation of the oligomer during simulations. The calculations also lead to a rationale for the observation of a heltuba tetramer in solution although the lectin exists as an octamer in the crystal, in addition to providing insights into relations among evolution, oligomerization and ligand binding. The known crystal structures of banana lectin in its native and ligand bound forms revealed interesting features including the presence of two functional carbohydrate-binding sites per subunit. However, some confusion remained on the role of glycosidic linkage in carbohydrate-binding. The three crystal structures reported in this thesis provide information on details of the interactions of mannose and mannosylα-1,3-mannose with banana lectin and evidence for the binding of glucosyl-α-1,2glucose to the lectin. The known structures involving the lectin include a complex with glucosyl-β-1,3-glucose. Modelling studies on the three disaccharide complexes with the reducing end and the non-reducing end at the primary binding site are also presented here. The results of the X-ray and modelling studies show that the disaccharides with an α-1,3 linkage prefers to have the non-reducing end at the primary binding site while the reducing end is preferred at the site when the linkage is β-1,3 in mannose/glucose specific β-prism I fold lectins. In the corresponding galactose-specific lectins, however, α-1,3 linked disaccharides cannot bind the lectin with the non-reducing end at the primary binding site on account of steric clashes with an aromatic residue which occurs only when the lectin is galactose-specific. MD simulations based on the known structures involving banana lectin enrich the information on lectin-carbohydrate interactions obtained from crystal structures. They demonstrate that conformational selection as well as induced fit operate when carbohydrates bind to banana lectin. Snake gourd seed lectin (SGSL) isolated from Trichosanthes anguina is a glycosylated, galactose-specific, non-toxic lectin similar to type II ribosome inactivating proteins (RIPs) with a molecular weight of ~53kDa. It was established through preliminary X-ray studies that chain A with molecular weight of ~23kDa adopts the same fold as that of type I RIPs and the toxic chain of type II RIPs. Chain B with molecular weight ~32kDa has two β-trefoil fold domains and is responsible for the lectin activity of the protein. The two chains are connected with a disulphide bond. The sequence of the protein could not be determined using conventional methods despite extensive effort. It was derived from X-ray data at 2.4 Å resolution, which was used for structure analysis. The non-toxicity of SGSL appears to result from a combination of changes in the catalytic site in chain A and sugar-binding site in chain B. Detailed analysis of the sequences of type II RIPs of known structure and their homologues with unknown structure, provide valuable insights into the evolution of this class of proteins. It also indicates some variability in carbohydrate-binding sites, which appears to contribute to different levels of toxicity exhibited by lectins from various sources. In addition to the work on plant lectins, the author was also involved in studies on the crystal structures of the adipic acid complexes of L- and DL-Lysine. This investigation is presented in an appendix. A part of the work presented in the thesis has been reported in the following publications. Sharma, A., Thamotharan, S., Roy, S., & Vijayan, M. (2006). X-ray studies of crystalline complexes involving amino acids and peptides. XLIII. Adipic acid complexes of L- and DL-lysine. Acta Cryst, C62, o148-o152. Sharma, A., Chandran, D., Singh, D.D., & Vijayan, M. (2007). Multiplicity of carbohydrate-binding sites in beta-prism fold lectins: occurrence and possible evolutionary implications. J Biosci, 32, 1089-1110. Sharma, A., Sekar, K., & Vijayan, M. (2009). Structure, dynamics, and interactions of jacalin. Insights from molecular dynamics simulations examined in conjunction with results of X-ray studies. Proteins, 77, 760-777