Skip to main content
SpringerLink
Log in

Pattern Recognition in Legume Lectins to Extrapolate Amino Acid Variability to Sugar Specificity

  • Conference paper
  • First Online:
Biochemical Roles of Eukaryotic Cell Surface Macromolecules

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 842))

Abstract

Biologic recognition is critical for cell growth, its differentiation and a number of other physiological processes. Lectin carbohydrate interactions mediate and regulate these cellular processes. Hence they have attracted a lot of attention recently. Amongst lectins, those from legumes are the most widely studied. Herein, we report our findings based on the influence of amino acid constitution in maintaining the structural integrity and sugar binding specificity of these lectins. We have implemented a pattern recognition system represented by heatmaps and clustergrams. Percentage identity and amino acid composition of 46 legume lectins were computed to distinguish between different sugar specific lectins and derive a consensus amongst them. A clear distinction was apparent between different monosaccharide binding groups based on their composition, sequence identities and the specific amino residues in their combining sites.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  • Audette GF, Vandonselaar M, Delbaere LT (2000) The 2.2 Ã… resolution structure of the O(H) blood-group-specific lectin I from Ulex europaeus. J Mol Biol 304(3):423–433

    Article  CAS  PubMed  Google Scholar 

  • Babino A, Tello D, Rojas A, Bay S, Osinaga E, Alzari PM (2003) The crystal structure of a plant lectin in complex with the Tn antigen. FEBS Lett 536(1–3):106–110

    Article  CAS  PubMed  Google Scholar 

  • Benevides RG, Ganne G, Simoes Rda C, Schubert V, Niemietz M, Unverzagt C, Chazalet V, Breton C, Varrot A, Cavada BS, Imberty A (2012) A lectin from Platypodium elegans with unusual specificity and affinity for asymmeteric complex N glycans. J Biol Chem 287(31):26352–26364

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28:235–242

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bezerra EH, Rocha BA, Nagano CS, Bezerra Gde A, Moura TR, Bezerra MJ, Benevides RG, Sampaio AH, Assreuy AM, Delatorre P, Cavada BS (2011) Structural analysis of ConBr reveals molecular correlation between the carbohydrate recognition domain and endothelial NO synthase activation. Biochem Biophys Res Commun 408(4):566–570

    Article  CAS  PubMed  Google Scholar 

  • Bourne Y, Roussel A, Frey M, Rougé P, Fontecilla-Camps JC, Cambillau C (1990) Three-dimensional structures of complexes of Lathyrus ochrus isolectin I with glucose and mannose: fine specificity of the monosaccharide-binding site. Proteins 8(4):365–376

    Article  CAS  PubMed  Google Scholar 

  • Buts L, Dao-Thi MH, Loris R, Wyns L, Etzler M, Hamelryck T (2001) Weak protein-protein interactions in lectins: the crystal structure of a vegetative lectin from the legume Dolichos biflorus. J Mol Biol 309(1):193–201

    Article  CAS  PubMed  Google Scholar 

  • Buts L, Garcia-Pino A, Wyns L, Loris R (2006) Structural basis of carbohydrate recognition by a Man(alpha1-2)Man-specific lectin from Bowringia milbraedii. Glycobiology 16(7):635–640

    Article  CAS  PubMed  Google Scholar 

  • da Silva LC, Correia MT (2014) Plant lectins and Toll-like receptors: implications for therapy of microbial infections. Front Microbiol 5:20

    PubMed  PubMed Central  Google Scholar 

  • de Oliveira TM, Delatorre P, da Rocha BA, de Souza EP, Nascimento KS, Bezerra GA, Moura TR, Benevides RG, Bezerra EH, Moreno FB, Freire VN, de Azevedo WF Jr, Cavada BS (2008) Crystal structure of Dioclea rostrata lectin: insights into understanding the pH-dependent dimer-tetramer equilibrium and the structural basis for carbohydrate recognition in Diocleinae lectins. J Struct Biol 164(2):177–182

    Article  CAS  PubMed  Google Scholar 

  • de Souza GA, Oliveira PS, Trapani S, Santos AC, Rosa JC, Laure HJ, Faça VM, Correia MT, Tavares GA, Oliva G, Coelho LC, Greene LJ (2003) Amino acid sequence and tertiary structure of Cratylia mollis seed lectin. Glycobiology 13(12):961–972

    Article  PubMed  Google Scholar 

  • Debraya H, Rougé P (1984) The fine sugar specificity of the Lathyrus ochrus seed lectin and isolectins. FEBS Lett 176(1):120–124

    Article  Google Scholar 

  • Del Sol FG, Cavada BS, Calvete JJ (2007) Crystal structures of Cratylia floribunda seed lectin at acidic and basic pHs. Insights into the structural basis of the pH-dependent dimer-tetramer transition. J Struct Biol 158(1):1–9

    Article  CAS  PubMed  Google Scholar 

  • Delbaere LT, Vandonselaar M, Prasad L, Quail JW, Wilson KS, Dauter Z (1993) Structures of the lectin IV of Griffonia simplicifolia and its complex with the Lewis b human blood group determinant at 2.0 Ã… resolution. J Mol Biol 230(3):950–965

    Article  CAS  PubMed  Google Scholar 

  • Duin RPW, Pekalska E (2007) The science of pattern recognition; achievements and perspectives. In: Duch W, Mandziuk J (eds) Challenges for computational intelligence, studies in computational intelligence, vol 63. Springer, Heidelberg, pp 221–259

    Chapter  Google Scholar 

  • Edelman GM, Cunningham BA, Reeke GN Jr, Becker JW, Waxdal MJ, Wang JL (1972) The covalent and three dimensional structure of concanavalin A. Proc Natl Acad Sci 69:2580–2584

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Etzler ME, Surolia A, Cummings RD (2009) L-type lectins (Chap. 29). In: Varki A, Cummings RD, Esko JD et al (eds) Essentials of glycobiology, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor

    Google Scholar 

  • Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server. In: Walker JM (ed) The proteomics protocols handbook. Humana, Totowa, pp 571–607

    Chapter  Google Scholar 

  • Geethanandan K, Abhilash J, Bharath SR, Sadasivan C, Haridas M (2011) X-ray structure of a galactose-specific lectin from Spatholobous parviflorous. Int J Biol Macromol 49(5): 992–998

    Article  CAS  PubMed  Google Scholar 

  • Hamelryck TW, Dao-Thi MH, Poortmans F, Chrispeels MJ, Wyns L, Loris R (1996a) The crystallographic structure of phytohemagglutinin-L. J Biol Chem 271(34):20479–20485

    Article  CAS  PubMed  Google Scholar 

  • Hamelryck TW, Poortmans F, Goossens A, Angenon G, Van Montagu M, Wyns L, Loris R (1996b) Crystal structure of arcelin-5, a lectin-like defense protein from Phaseolus vulgaris. J Biol Chem 271(51):32796–32802

    Article  CAS  PubMed  Google Scholar 

  • Hamelryck TW, Loris R, Bouckaert J, Dao-Thi MH, Strecker G, Imberty A, Fernandez E, Wyns L, Etzler ME (1999) Carbohydrate binding, quaternary structure and a novel hydrophobic binding site in two legume lectin oligomers from Dolichos biflorus. J Mol Biol 286(4):1161–1177

    Article  CAS  PubMed  Google Scholar 

  • Imberty A, Gautier C, Lescar J, Pérez S, Wyns L, Loris R (2000) An unusual carbohydrate binding site revealed by the structures of two Maackia amurensis lectins complexed with sialic acid-containing oligosaccharides. J Biol Chem 275(23):17541–17548

    Article  CAS  PubMed  Google Scholar 

  • Kolberg J, Michaelsen TE, Sletten K (1980) Subunit structure and N terminal sequences of the Lathyrus odoratus lectin. FEBS Lett 117:281–283

    Article  CAS  PubMed  Google Scholar 

  • Kundhavai Natchiar S, Arockia Jeyaprakash A, Ramya TN, Thomas CJ, Suguna K, Surolia A, Vijayan M (2004) Structural plasticity of peanut lectin: an X-ray analysis involving variation in pH, ligand binding and crystal structure. Acta Crystallogr D Biol Crystallogr 60(2):211–219

    Article  CAS  PubMed  Google Scholar 

  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) ClustalW and ClustalX version 2. Bioinformatics 23(21):2947–2948

    Article  CAS  PubMed  Google Scholar 

  • Liener IE, Sharon N, Goldstein IJ (1986) The lectins: properties, functions, and applications in biology and medicine. Academic Press, Orlando

    Google Scholar 

  • Loris R, Van Overberge D, Dao-Thi MH, Poortmans F, Maene N, Wyns L (1994) Structural analysis of two crystal forms of lentil lectin at 1.8 Ã… resolution. Proteins 20(4):330–346

    Article  CAS  PubMed  Google Scholar 

  • Loris R, Hamelryck T, Bouckaert J, Wyns L (1998) Legume lectin structure. Biochim Biophys Acta 1383:9–36

    Article  CAS  PubMed  Google Scholar 

  • Loris R, De Greve H, Dao-Thi MH, Messens J, Imberty A, Wyns L (2000) Structural basis of carbohydrate recognition by lectin II from Ulex europaeus, a protein with a promiscuous carbohydrate-binding site. J Mol Biol 301(4):987–1002

    Article  CAS  PubMed  Google Scholar 

  • Loris R, Van Walle I, De Greve H, Beeckmans S, Deboeck F, Wyns L, Bouckaert J (2004) Structural basis of oligomannose recognition by the Pterocarpus angolensis seed lectin. J Mol Biol 335(5):1227–1240

    Article  CAS  PubMed  Google Scholar 

  • MacQueen JB (1967) Some methods for classification and analysis of multivariate observations. In: Proceedings of 5th Berkeley symposium on mathematical statistics and probability, vol 1, University of California Press, Berkeley, pp 281–297

    Google Scholar 

  • Manoj N, Suguna K (2001) Signature of quaternary structure in the sequences of legume lectins. Protein Eng 14(10):735–745

    Article  CAS  PubMed  Google Scholar 

  • Manoj N, Srinivas VR, Suguna K (1999) Structure of basic winged-bean lectin and a comparison with its saccharide-bound form. Acta Crystallogr D Biol Crystallogr 55(4):794–800

    Article  CAS  PubMed  Google Scholar 

  • Manoj N, Srinivas VR, Surolia A, Vijayan M, Suguna K (2000) Carbohydrate specificity and salt-bridge mediated conformational change in acidic winged bean agglutinin. J Mol Biol 302(5):1129–1137

    Article  CAS  PubMed  Google Scholar 

  • MATLAB v7.5, MathWorks (2007) Bioinformatics toolbox: user’s guide (R2007b)

    Google Scholar 

  • Moreira GM, Conceição FR, McBride AJ, Pinto Lda S (2013) Structure predictions of two Bauhinia variegata lectins reveal patterns of C-terminal properties in single chain legume lectins. PLoS One 8(11)

    Google Scholar 

  • Moreno FB, Bezerra GA, Oliveira TM, de Souza EP, da Rocha BA, Benevides RG, Delatorre P, de Azevedo WF, Jr CBS (2007) Structural analysis of Canavalia maritima and Canavalia gladiata lectins complexed with different dimannosides: new insights into the understanding of the structure-biological activity relationship in legume lectins. J Struct Biol 160(2):168–176

    Article  CAS  PubMed  Google Scholar 

  • Moreno FB, de Oliveira TM, Martil DE, Viçoti MM, Bezerra GA, Abrego JR, Cavada BS, Filgueira de Azevedo W Jr (2008) Identification of a new quaternary association for legume lectins. J Struct Biol 161(2):133–143

    Article  CAS  PubMed  Google Scholar 

  • Mourey L, Pédelacq JD, Birck C, Fabre C, Rougé P, Samama JP (1998) Crystal structure of the arcelin-1 dimer from Phaseolus vulgaris at 1.9 Ã… resolution. J Biol Chem 273(21):12914–12922

    Article  CAS  PubMed  Google Scholar 

  • Mueller-Dieckmann C, Panjikar S, Tucker PA, Weiss MS (2005) On the routine use of soft X-rays in macromolecular crystallography. Part III The optimal data-collection wavelength. Acta Crystallogr D Biol Crystallogr 61(9):1263–1272

    Article  CAS  PubMed  Google Scholar 

  • Nagano CS, Calvete JJ, Barettino D, Pérez A, Cavada BS, Sanz L (2008) Insights into the structural basis of the pH-dependent dimer-tetramer equilibrium through crystallographic analysis of recombinant Diocleinae lectins. Biochem J 409(2):417–428

    Article  CAS  PubMed  Google Scholar 

  • Nóbrega RB, Rocha BA, Gadelha CA, Santi-Gadelha T, Pires AF, Assreuy AM, Nascimento KS, Nagano CS, Sampaio AH, Cavada BS, Delatorre P (2012) Structure of Dioclea virgata lectin: Relations between carbohydrate binding site and nitric oxide production. Biochimie 94(3):900–906

    Article  CAS  Google Scholar 

  • Olsen LR, Dessen A, Gupta D, Sabesan S, Sacchettini JC, Brewer CF (1997) X-ray crystallographic studies of unique cross-linked lattices between four isomeric biantennary oligosaccharides and soybean agglutinin. Biochemistry 36(49):15073–15080

    Article  CAS  PubMed  Google Scholar 

  • Rabijns A, Verboven C, Rougé P, Barre A, Van Damme EJ, Peumans WJ, De Ranter CJ (2001) Structure of a legume lectin from the bark of Robinia pseudoacacia and its complex with N-acetylgalactosamine. Proteins 44(4):470–478

    Article  CAS  PubMed  Google Scholar 

  • Rangel TB, Rocha BA, Bezerra GA, Assreuy AM, Pires Ade F, do Nascimento AS, Bezerra MJ, do Nascimento KS, Nagano CS, Sampaio AH, Gruber K, Delatorre P, Fernandes PM, Cavada BS (2012) Crystal structure of a pro-inflammatory lectin from the seeds of Dioclea wilsonii Standl. Biochimie 94(2):525–532

    Article  CAS  PubMed  Google Scholar 

  • Rao VSR, Lam K, Qasba PK (1998) Architecture of the sugar binding sites in carbohydrate binding proteins—a computer modeling study. Int J Biol Macromol 23(4):295–307

    Article  CAS  PubMed  Google Scholar 

  • Reeke GN Jr, Becker JW (1986) Three-dimensional structure of favin: saccharide binding-cyclic permutation in leguminous lectins. Science 234(4780):1108–1111

    Article  CAS  PubMed  Google Scholar 

  • Rocha BA, Delatorre P, Oliveira TM, Benevides RG, Pires AF, Sousa AA, Souza LA, Assreuy AM, Debray H, de Azevedo WF, Jr SAH, Cavada BS (2011) Structural basis for both pro- and anti-inflammatory response induced by mannose-specific legume lectin from Cymbosema roseum. Biochimie 93(5):806–816

    Article  CAS  PubMed  Google Scholar 

  • Rocha BA, Souza Teixeira C, da Silva HC, de Moura TR, Pereira-Júnior FN, do Nascimento KS, Nagano CS, Sampaio AH, Delatorre P, Cavada BS (2012) Crystal structure of the lectin of Camptosema pedicellatum: implications of a conservative substitution at the hydrophobic subsite. J Biochem 152(1):87–98

    Article  CAS  PubMed  Google Scholar 

  • Sanders DA, Moothoo DN, Raftery J, Howard AJ, Helliwell JR, Naismith JH (2001) The 1.2 Ã… resolution structure of the Con A-dimannose complex. J Mol Biol 310(4):875–884

    Article  CAS  PubMed  Google Scholar 

  • Shaanan B, Elgavish S (1998) Structures of the Erythrina corallodendron lectin and of its complexes with mono- and disaccharides. J Mol Biol 277(4):917–932

    Article  PubMed  Google Scholar 

  • Sharma V, Surolia A (1997) Analyses of carbohydrate recognition by legume lectins: size of the combining site loops and their primary specificity. J Mol Biol 267:433–445

    Article  CAS  PubMed  Google Scholar 

  • Sharma V, Srinivas VR, Adhikari P, Vijayan M, Surolia A (1998) Molecular basis of recognition by Gal/GalNAc specific legume lectins: influence of Glu 129 on the specificity of peanut agglutinin (PNA) towards C2-substituents of galactose. Glycobiology 8(10):1007–1012

    Article  CAS  PubMed  Google Scholar 

  • Sharon N, Lis H (1990) Legume lectins: a large family of homologous proteins. FASEB J 4:3198–3208

    Article  CAS  PubMed  Google Scholar 

  • Sharon N, Lis H (1995) Lectins-proteins with a sweet tooth: functions in cell recognition. Essays Biochem 30:59–75

    CAS  PubMed  Google Scholar 

  • Sharon N, Lis H (2002) How proteins bind carbohydrates: lessons from legume lectins. J Agric Food Chem 50:6586–6591

    Article  CAS  PubMed  Google Scholar 

  • Sharon N, Lis H (2004) History of lectins: from hemagglutinins to biological recognition molecules. Glycobiology 14(11):53–62

    Article  CAS  Google Scholar 

  • Shetty KN, Latha VL, Rao RN, Nadimpalli SK, Suguna K (2013) Affinity of a galactose-specific legume lectin from Dolichos lablab to adenine revealed by X-ray crystallography. IUBMB Life 65(7):633–644

    Article  CAS  PubMed  Google Scholar 

  • Srinivas VR, Reddy GB, Ahmad N, Swaminathan CP, Mitra N, Surolia A (2001) Legume lectin family, the ‘natural mutants of the quaternary state’, provide insights into the relationship between protein stability and oligomerization. Biochim Biophys Acta 1527:102–111

    Article  CAS  PubMed  Google Scholar 

  • Suddath FL, Prasthofer T, Phillips SR, Engler JA (1989) Design, expression, and crystallization of recombinant lectin from the garden pea (Pisum sativum). J Biol Chem 264(12):6793–6796

    PubMed  Google Scholar 

  • Sundberg EJ, Trastoy B, Bonsor DA, Perez-Ojeda ME, Jimeno ML, Garcia-Fernandez JM, Chiara JL (2012) Synthesis and biophysical study of disassembling nano hybrid bioconjugates with a cubic octasilsesquioxane core. Adv Funct Mater 22:3191–3201

    Article  CAS  Google Scholar 

  • Svensson C, Teneberg S, Nilsson CL, Kjellberg A, Schwarz FP, Sharon N, Krengel U (2002) High-resolution crystal structures of Erythrina cristagalli lectin in complex with lactose and 2′-alpha-L-fucosyllactose and correlation with thermodynamic binding data. J Mol Biol 321(1):69–83

    Article  CAS  PubMed  Google Scholar 

  • Swamy MJ, Sastry MVK, Surolia A (1985) Prediction and comparison of the secondary structure of legume lectins. J Biosci 9(3–4):203–212

    Article  CAS  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tempel W, Tschampel S, Woods RJ (2002) The xenograft antigen bound to Griffonia simplicifolia lectin 1-B(4). X-ray crystal structure of the complex and molecular dynamics characterization of the binding site. J Biol Chem 277(8):6615–6621

    Article  CAS  PubMed  Google Scholar 

  • Thomas CJ, Surolia A (2000) Mode of molecular recognition of l-fucose by fucose-binding legume lectins. Biochem Biophys Res Commun 268:262–267

    Article  CAS  PubMed  Google Scholar 

  • Weisstein E (1995) K-Means clustering algorithm. From MathWorld—A Wolfram Web Resource. http://mathworld.wolfram.com/K-MeansClusteringAlgorithm.html

  • Xu D, Zhang Y (2013) Toward optimal fragment generations for ab initio protein structure assembly. Proteins 81(2):229–239

    Article  CAS  PubMed  Google Scholar 

  • Young NM, Oomen RP (1992) Analysis of sequence variation among legume lectins. J Mol Biol 228:924–934

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y (2012) http://zhanglab.ccmb.med.umich.edu/PSSpred

Download references

Acknowledgements

This work has been funded by Council of Scientific and Industrial Research (CSIR), India. A.S. is a Bhatnagar fellow, N.G.J. thanks Department of Science and Technology (DST), Govt of India for INSPIRE Fellowship. M.A.S. is a D.S. Kothari fellow supported by University Grants Commission (UGC), India.

Author information

Authors and Affiliations

  1. Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560 012, India

    Nisha Jayaprakash Grandhi, Ashalatha Sreshty Mamidi & Avadhesha Surolia

Authors
  1. Nisha Jayaprakash Grandhi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ashalatha Sreshty Mamidi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Avadhesha Surolia
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Avadhesha Surolia .

Editor information

Editors and Affiliations

  1. Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India

    Abhijit Chakrabarti

  2. Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India

    Avadhesha Surolia

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer International Publishing Switzerland

About this paper

Cite this paper

Grandhi, N.J., Mamidi, A.S., Surolia, A. (2015). Pattern Recognition in Legume Lectins to Extrapolate Amino Acid Variability to Sugar Specificity. In: Chakrabarti, A., Surolia, A. (eds) Biochemical Roles of Eukaryotic Cell Surface Macromolecules. Advances in Experimental Medicine and Biology, vol 842. Springer, Cham. https://doi.org/10.1007/978-3-319-11280-0_13

Download citation

Publish with us

Policies and ethics

Search

Navigation