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Wong Ho Wan. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2003. / Includes bibliographical references (leaves 140-153). / Abstracts in English and Chinese. / Thesis Committee --- p.I / Statement --- p.II / Acknowledgements --- p.III / Abstract --- p.IV / 摘要 --- p.VI / List of Tables --- p.VIII / List of Figures --- p.IX / List of Abbreviations --- p.XI / Table of Contents --- p.XIII / Chapter 1 --- General introduction --- p.1 / Chapter 2 --- Literature reviews --- p.4 / Chapter 2.1 --- LRP and winged bean --- p.4 / Chapter 2.1.1 --- Nutritional values of crop plants --- p.4 / Chapter 2.1.2 --- Lysine-rich protein (LRP) --- p.7 / Chapter 2.1.2.1 --- Identification of lysine-rich protein (LRP) --- p.7 / Chapter 2.1.2.2 --- Cloning cDNA for WBLRP --- p.7 / Chapter 2.1.2.3 --- Transgenic Expression of LRP in other plants --- p.8 / Chapter 2.1.3 --- Unknowns remained --- p.8 / Chapter 2.2 --- Food allergy and gastro-immunity --- p.10 / Chapter 2.2.1 --- What is allergy? 一 A brief introduction --- p.10 / Chapter 2.2.2 --- Food allergy and its symptoms --- p.12 / Chapter 2.2.3 --- Gastrointestinal immunity --- p.13 / Chapter 2.2.4 --- Possible mechanism of food allergy --- p.16 / Chapter 2.2.5 --- Available tests and limitations --- p.18 / Chapter 2.2.6 --- Radioallergosorbent test (RAST) --- p.19 / Chapter 2.2.7 --- Digestibility test --- p.20 / Chapter 2.2.8 --- Betv-1 Allergen Family --- p.21 / Proteins --- p.23 / Chapter 2.3 --- Pathogenesis-related proteins --- p.23 / Chapter 2.3.1 --- Defense-related proteins and pathogenesis-related proteins (PRs) --- p.23 / Chapter 2.3.2 --- Class 10 PR proteins (PR-10s) --- p.25 / Chapter 2.3.3 --- The expression patterns of PR-10s --- p.27 / Chapter 2.3.3.1 --- Pathogens-induced and signal-induced expression --- p.27 / Chapter 2.3.3.2 --- Spatially- and developmentally-regulated expression --- p.28 / Chapter 2.3.3.3 --- Other induction patterns --- p.29 / Chapter 2.3.4 --- Functions ofPR-10s --- p.30 / Chapter 2.4 --- Development of hypotheses and experiments --- p.32 / Chapter 3 --- Materials and methods --- p.36 / Chapter 3.1 --- Introduction --- p.36 / Chapter 3.2 --- Materials --- p.38 / Chapter 3.2.1 --- Chemicals --- p.38 / Chapter 3.2.2 --- Apparatus and commercial kits --- p.39 / Chapter 3.2.3 --- Vectors and bacterial strains --- p.39 / Chapter 3.2.4 --- Plant and animal materials --- p.40 / Chapter 3.2.5 --- Computer software --- p.40 / Chapter 3.3 --- Purification of LRP --- p.41 / Chapter 3.3.1 --- Purification of LRP from winged bean --- p.41 / Chapter 3.3.1.1 --- Extraction of total protein --- p.41 / Chapter 3.3.1.2 --- Differential pI precipitation --- p.41 / Chapter 3.3.1.3 --- Determination of the pI point of LRP --- p.42 / Chapter 3.3.1.4 --- Native tricine-PAGE and gel elution --- p.42 / Chapter 3.3.2 --- Purification from E. coli --- p.45 / Chapter 3.3.2.1 --- Construction of pET vector expressing recombinant LRP (rLRP) --- p.45 / Chapter 3.3.2.2 --- Expression of rLRP --- p.50 / Chapter 3.3.2.3 --- Purification by gel electrophoresis and gel band elution --- p.50 / Chapter 3.4 --- Anti-serum production --- p.52 / Chapter 3.5 --- Allergy tests --- p.53 / Chapter 3.5.1 --- Pepsin digestion --- p.53 / Chapter 3.5.1.1 --- Determination of optimal concentration of pepsin --- p.53 / Chapter 3.5.1.2 --- Pepsin digestion of allergenic and non-allergenic model proteins --- p.55 / Chapter 3.5.1.3 --- Pepsin digestion of LRP and immunodetection --- p.55 / Chapter 3.5.2 --- Trypsin digestion --- p.56 / Chapter 3.5.2.1 --- Determination of optimal trypsin concentration --- p.56 / Chapter 3.5.2.2 --- Trypsin digestion of allergenic and non-allergenic model proteins --- p.57 / Chapter 3.5.2.3 --- Trypsin digestion of LRP and immuno-detection --- p.57 / Chapter 3.5.3 --- Pepsin and trypsin digestion --- p.58 / Chapter 3.5.3.1 --- Digestions of allergenic model proteins --- p.58 / Chapter 3.5.3.2 --- Digestion of LRP --- p.58 / Chapter 3.5.4 --- IgE binding tests --- p.58 / Chapter 3.6 --- Physiology studies --- p.59 / Chapter 3.6.1 --- Preparation for the studies --- p.59 / Chapter 3.6.1.1 --- Growing winged bean in the field --- p.59 / Chapter 3.6.1.2 --- Growing winged bean in sterile conditions --- p.60 / Chapter 3.6.1.3 --- Production ofLRP-cDNA probe --- p.60 / Chapter 3.6.2 --- Detecting the expression of LRP in winged bean --- p.61 / Chapter 3.6.2.1 --- RNA extraction --- p.61 / Chapter 3.6.2.2 --- RT-PCR and DNA sequencing --- p.62 / Chapter 3.6.2.3 --- RNA electrophoresis and northern blot analysis --- p.63 / Chapter 3.6.2.4 --- Protein extraction --- p.63 / Chapter 3.6.2.5 --- Western blot and immuno-detection --- p.63 / Chapter 3.6.3 --- Expression of LRP in germinating winged bean seeds --- p.64 / Chapter 3.6.3.1 --- Seed germination --- p.64 / Chapter 3.6.3.2 --- Detection of LRP in germinating seeds --- p.64 / Chapter 3.6.4 --- RNase activity test --- p.65 / Chapter 4 --- Results --- p.67 / Chapter 4.1 --- Purification of LRP --- p.67 / Chapter 4.1.1 --- Purification from winged bean --- p.67 / Chapter 4.1.1.1 --- Identification of pI point of LRP --- p.67 / Chapter 4.1.1.2 --- Native tricine PAGE and gel elution --- p.70 / Chapter 4.1.2 --- Purification from E. coli --- p.71 / Chapter 4.1.2.1 --- Construction of pET-LRP vector --- p.71 / Chapter 4.1.2.2 --- Expression of rLRP and gel purification --- p.74 / Chapter 4.2 --- Antiserum production --- p.76 / Chapter 4.3 --- Allergy tests --- p.81 / Chapter 4.3.1 --- Pepsin digestion --- p.81 / Chapter 4.3.2 --- Trypsin digestion --- p.89 / Chapter 4.3.3 --- Pepsin and trypsin digestion --- p.96 / Chapter 4.3.4 --- Human serum IgE binding test --- p.104 / Chapter 4.4 --- Physiological studies --- p.105 / Chapter 4.4.1 --- Samples preparation --- p.105 / Chapter 4.4.2 --- RT-PCR and DNA sequencing --- p.105 / Chapter 4.4.3 --- Expression profile of WBLRP in winged bean somatic organs --- p.108 / Chapter 4.4.4 --- Expression profile ofWBLRP in winged bean flower --- p.111 / Chapter 4.4.5 --- Expression profile ofWBLRP in winged bean maturing seeds --- p.114 / Chapter 4.4.6 --- Expression profile of WBLRP gene in winged bean germinating seeds --- p.117 / Chapter 4.4.7 --- Functional assay of LRP --- p.121 / Chapter 5 --- Discussion --- p.124 / Chapter 5.1 --- LRP purification and antibody production --- p.124 / Chapter 5.2 --- Allergy tests --- p.125 / Chapter 5.3 --- Expression of LRP in WB --- p.131 / Chapter 5.4 --- Functional assay of LRP --- p.134 / Chapter 5.5 --- Hypothesis Testing --- p.135 / Chapter 5.6 --- Future prospective， --- p.136 / Chapter 6 --- Conclusion --- p.138 / Chapter 7 --- References --- p.140

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The journey of structural studies on lectins, starting with ConA in the 70s, has crossed many milestones. Lectins, multivalent carbohydrate-binding proteins of non-immune origin, specifically bind diverse sugar structures. They have received considerable attention in recent times on account of the realization of the importance of protein-sugar interactions, especially at the cell surface, in biological recognition. They occur in plants, animals, fungi, bacteria and viruses. Plant lectins constitute about 40% of the lectins of known structure. They can be classified into five structural groups, each characterized by a specific fold. Among them, legume lectins constitute the most extensively investigated group. Basic Winged bean lectin (WBAI) is a glycosylated, homodimeric, legume lectin with Mr 58000. The structure of WBAI complexed with methyl-a-galactose, determined earlier in this laboratory, provided information about the oligomeric state and the carbohydrate specificity of the lectin in terms of lectin-monosaccharide interactions. The present work was initiated to understand the carbohydrate specificity of the lectin, especially at the oligosaccharide level, with special reference to its blood group specificity. The hanging drop method was used for crystallizing WBAI and its complexes. Intensity data were collected on Mar Research imaging plates mounted on Rigaku RU-200 or ULTRAX-18 X-ray generators. 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 AMoRe was used for structure solution. Structure refinement was carried out using the CNS software package. Model building was done using the molecular graphics program O. INSIGHT II, ALIGN, CONTACT and PROCHECK of CCP4 were used for the analysis and validation of the refined structures. WBAI exhibits differential affinity for different monosaccharide derivatives of galactose. In order to elucidate the structural basis for this differential affinity, the crystal structures of the complexes of basic winged bean lectin with galactose, 2-methoxygalactose, N-acetylgalactosamine and methyl-a-N-acetylgalactosamine have been determined. Lectin-sugar interactions involve four hydrogen bonds and a stacking interaction in all of them. In addition, a N-H O hydrogen bond involving the hydroxyl group substituted at C2 exists in the galactose and 2-methoxygalactose complexes. The additional hydrophobic interaction, involving the methyl group, in the latter leads to the higher affinity of the methyl derivative. In the lectin - N- acetylgalactosamine complex the N-H O hydrogen bond is lost, but a compensatory hydrogen bond involving the oxygen atom of the acetamido group is formed. In addition, the CH3 moiety of the acetamido group is involved in hydrophobic interactions. Consequently, the 2-methyl and the acetamido derivatives of galactose have nearly the same affinity for the lectin. The methyl group, a-linked to the galactose, takes part in additional hydrophobic interactions. Therefore, methyl-a- N-acetylgalactosamine has higher affinity than N-acetylgalactosamine to the lectin. The structures of basic winged bean lectin-sugar complexes provide a framework for examining the relative affinity of galactose and galactosamine for the lectins that bind to them. The complexes also lead to a structural explanation for the blood group specificity of basic winged bean lectin, in terms of its monosaccharide specificity. The Tn-determinant (GalNAc-a-O-Ser/Thr) is a human specific tumor associated carbohydrate antigen. Having epithelial origin, it is expressed in many carcinogenic tumors including breast, prostate, lung and pancreatic cancers. The crystal structure of WBAI in complex with GalNAc-a-O-Ser (Tn-antigen) has been elucidated, in view of its relevance to diagnosis and prognosis of various human cancers. The Gal moiety occupies the primary binding site and makes interactions similar to those found in other Gal/GalNAc specific legume lectins. The nitrogen and oxygen atoms of the acetamido group of the sugar make two hydrogen bonds with the protein atoms whereas its methyl group is stabilized by hydrophobic interactions. A water bridge formed between the terminal oxygen atoms of the serine residue of the Tn-antigen and the side chain oxygen atom of Asn128 of the lectin increase the affinity of the lectin for Tn-antigen compared to that for GalNAc. A comparison with the available structures reveals that while the interactions of the glyconic part of the antigen are conserved, the mode of stabilization of the serine residue differs and depends on the nature of the protein residues in its vicinity. The structure provides a qualitative explanation for the thermodynamic parameters of the formation of the complex of the lectin with Tn-antigen. Modelling studies indicate the possibility of an additional hydrogen bond with the lectin when the antigen is part of a glycoprotein. WBAI binds A-blood group substance with higher affinity and B-blood group substance with lesser affinity. It does not bind the O substance. The crystal structures of the lectin, complexed with A -reactive and B - reactive di and tri saccharides, have been determined. In addition, the complexes of the lectin with fucosylated A- and B-trisaccharides and with a variant of the A-trisaccharide have been modelled. These structures and models provide valuable insights into the structural basis of blood group specificities. All the four carbohydrate binding loops of the lectin contribute to the primary combining site while the loop of variable length contributes to the secondary binding site. In a significant advance to the current understanding, the interactions at the secondary binding site also contribute substantially, albeit in a subtle manner, to determine the blood group specificity. Compared to the interactions of the B- trisaccharide with the lectin, the third sugar residue of the A -reactive trisaccharide forms an additional hydrogen bond with a lysine residue in the variable loop. In the former, the formation of such a hydrogen bond is prevented by a shift in the orientation of the third sugar resulting from an internal hydrogen bond in it. The formation of this bond is also facilitated by an interaction dependent change in the rotamer conformation of the lysyl residue of the variable loop. Thus, the difference in the interactions at the secondary site is generated by coordinated movements in the ligand as well as the protein. A comparison of the crystal structure and the model of the complex involving the variant of the A-trisaccharide results in the delineation of the relative contributions of the interactions at the primary and the secondary sites in determining blood group specificity. At the disaccharide level, WBAI exhibits higher affinity for á1-3 linked Gal/GalNAc containing oligosaccharides, compared to that of other á linked oligosaccharides. With an objective of understanding the preferential binding of WBAI for á 1-3 linked Gal/GalNAc containing oligosaccharides, crystal structure of the complexes of the lectin with Galá1-4Gal, Galá1-4GalâEt and Galá1-6Gal have been determined. The reducing sugar of the disaccharides with linkages other than á1-3 binds to the lectin through a water bridge whereas the same sugar moiety with á 1-3 linkage makes direct interactions with the loop L4 of the protein. The modelling study on the complex of the lectin with Galá1-2Gal further upholds this observation. Different structures involving WBAI, reported earlier and presented here, were used to investigate the plasticity of the lectin. The front curved â-sheet, which nestles the metal binding region and on which the carbohydrate binding loops are perched, is relatively rigid. On the contrary, the flat back â-sheet, involved in the quaternary association in legume lectins, is flexible. This flexibility is probably necessary to account for the variation in quaternary structure. With the results presented in this thesis, 14 crystal structures of WBAI, in the free form and in complex with different sugars, have been reported, all from this laboratory. It is now, perhaps, appropriate to examine the new information and insights gained from these investigations, on the structure and function of the lectin. Earlier X-ray studies of WBAI contributed substantially in establishing that legume lectins are a family of proteins in which small alterations in essentially the same tertiary structure lead to large alterations in quaternary association. Structural studies on WBAI, particularly those reported here, also contributed to the elucidation of the nuances of carbohydrate recognition by lectins. A comparative study of the available structures also revealed the flexible and rigid regions of the protein. The study of the influence of covalently linked sugars on the structure of Erythrina corallodendron lectin (ECorL), a homolog of WBAI, is the content of appendix of the thesis. The three-dimensional structure of the recombinant form of Erythrina Corallodendron lectin(rECorL) complexed with lactose, has been elucidated by X-ray crystallography. Comparison of this non-glycosylated structure with that of the native glycosylated lectin reveals that the tertiary and quaternary structures are identical in the two forms, with local changes observed at one of the glycosylation sites(Asn17). These changes take place in such a way that hydrogen bonds with the neighbouring protein molecules in rECorL compensate those made by the glycan with the protein in ECorl. contrary to an earlier report, this study demonstrates that the glycan attached to the lectin does not influence the oligomeric state of the lectin. Identical interactions between the lectin and the non-covalently bound lactose in the two forms indicate, in line with earlier reports, that glycosylation does not affect the carbohydrate specificity of the lectin. The present study, the first of its kind involving a glycosylated protein with a well defined glycan and the corresponding deglycosylated form, provides insights into the structural aspects of protein glycosylation.

Lectins are multivalent carbohydrate binding proteins that specifically recognise diverse sugar structures and mediate a variety of biological processes, such as cell-cell and host-pathogen interactions, serum glycoprotein turnover and innate immune responses. Lectins have received considerable attention in recent years on account of their properties which have led to their wide use in research and biomedical applications. Seeds of leguminous plants are rich sources of lectins, but they are also found in all classes and families of organisms. Legume lectins have similar tertiary structures, but exhibit a large variety of quaternary structures. The carbohydrate binding site in them is made up of four loops, the first three of which are highly conserved in all legume lectins. The fourth loop, which is variable, is implicated in conferring specificity. Legume lectins which share the same monosaccharide specificity often exhibit markedly different oligosaccharide specificities. The introductory chapter gives a broad overview of lectins from a structural point of view. The rest of the thesis is primarily concerned with structural studies on lectins from seeds of the winged bean (Psophocarpus tetragonolobus). Winged bean seeds contain a basic lectin (WBAI) (pi > 9.5) and an acidic lectin (WBAII) (pi -5.5). Both these lectins are N-glycosylated homodimers with about 240 amino acid residues per monomer. They show a high affinity for methyl-a-D-galactose at the monosaccharide level but have entirely different affinities for oligosaccharides. WBAI agglutinates human type A and B erythrocytes but not O type, while WBAII binds specifically to the terminally monofucosylated H-antigenic (responsible for O blood group reactivity) determinants on the cell surface. In this context, the current study seeks to characterise the carbohydrate binding site of a saccharide-free form of WBAI and determine the structural basis of carbohydrate recognition in WBAII. The study also aims to identify the factors responsible for the differences in carbohydrate specificities between WBAI and WBAII. Diffraction data from a saccharide-free crystal form of WBAI and two crystal forms (Form I and II) of WBAII complexed with methyl-a-D-galactose were collected on a MAR imaging plate system mounted on a Rigaku RU200 rotating anode X-ray generator. The data were processed using the MAR-XDS and DENZO/SCALEPACK suites of programs. The structures were solved by the molecular replacement method using AMoRe. The model used in the case of WBAI and Form I of WBAII was the structure of WBAI in complex with methyl-a-D-galactose (PDB coderlWBL), while the structure of Form II of WBAH was solved using a partially refined model of Form I. The refinements and model building were performed using the programs X-PLOR/CNS and O respectively. A comparison of the structures of the saccharide-free and bound forms of WBAI revealed three water molecules occupying the carbohydrate binding site, which mimic the hydrogen bonded interactions made by the saccharide in the structure of the complex. Also a shift of -0.6 A in the variable loop, towards the saccharide in the structure of the complex was observed. Significant differences in the conformation of a loop involved in crystal packing interactions were also observed. An analysis of protein hydration demonstrates, among other things, the role of water molecules in stabilising the structure of the loops around the carbohydrate binding site. The crystal structures of the two forms of WBAH were solved at 3.0 A and 3.3. A resolution. The structure of the complex revealed the role of the length of the variable loop in generating the difference in oligosaccharide specificity between WBAI and WB All. The difference in the pi values between the two lectins is caused by substitutions occurring in loops and edges of sheets. A distinct structural difference between WBAH and all the other legume lectins of known structure is in the new disposition of the 34-45 loop with an r.m.s deviation of -6.0A in Coc positions compared to its position in other lectins. This change in conformation is caused by the formation of salt bridges by amino acid residues unique to WB All in the 34-45 loop and its neighbourhood. Thermodynamic studies on the binding of H-antigenic determinant to WBAII showed a predominance of entropic contribution suggesting a hydrophobically driven binding, not yet observed in lectin-sugar interactions. An analysis involving the docking of H-type II trisaccharide (Fuca(l-2)Galf}(l-4)GlcNAc) into the carbohydrate binding site and a comparison with the binding sites of other legume lectins revealed the role of a Tyr in the variable loop and an Asn in the second loop that are unique to WBAII in generating this unique binding property. Earlier work on peanut lectin and WBAI demonstrated that the modes of dimerisation of legume lectins are governed by features intrinsic to the protein. A phylogenetic analysis of the sequences of all legume lectins whose structures are available has been performed to examine the relationship among the various classes of oligomers and classes of sugar specificity. The information thus obtained showed that groups of legume lectins that share a common mode of dimerisation cluster together. A sequence alignment based on structures revealed amino acid residues unique to each of these clusters that may be important in determining the modes of observed dimerisation. While pursuing structural studies on WBAI and WBAII, the author has also been involved in an ongoing small molecule project in the laboratory, which involves preparation and X-ray structure determination of the complexes of carboxylic acids with amino acids and peptides. The work carried out in the project is described in the appendix.