Research Articles
54. Pakhrin SC, Pokharel S, Aoki-Kinoshita KF, Beck MR, Dam TK, Caragea D, Kc DB. LMNglyPred: prediction of human N-linked glycosylation sites using embeddings from a pre-trained protein language model. Glycobiology. 2023 Apr 17:cwad033. doi: 10.1093/glycob/cwad033. Epub ahead of print. PMID: 37067908. https://academic.oup.com/glycob/advance-article-abstract/doi/10.1093/glycob/cwad033/7126679?redirectedFrom=fulltext&login=false
53. Abdullayev S, Kadav P, Bandyopadhyay P, Medrano FJ, Rabinovich GA, Dam TK, Romero A, Roy R. Selectively Modified Lactose and N-Acetyllactosamine Analogs at Three Key Positions to Afford Effective Galectin-3 Ligands. Int J Mol Sci. 2023 Feb 13;24(4):3718. doi: 10.3390/ijms24043718. PMID: 36835132; PMCID: PMC9962200.
52. Edwards JL, Kadav PD, Bandyopadhyay P, Dam TK. Revealing the Identity of Human Galectin-3 as a Glycosaminoglycan-Binding Protein. Methods Mol Biol. 2022;2442:137-150. doi: 10.1007/978-1-0716-2055-7_8. PMID: 35320524.
51. Kadav PD, Edwards JL, Krycia J, Bandyopadhyay P, Dam TK. Rapid Detection and Purification of Galectin-3 by the Capture and Release (CaRe) Method. Methods Mol Biol. 2022;2442:89-103. doi: 10.1007/978-1-0716-2055-7_5. PMID: 35320521.
50. Dam TK, Edwards JL, Kadav PD, Brewer CF. Mechanism of Mucin Recognition by Lectins: A Thermodynamic Study. Methods Mol Biol. 2022;2442:169-185. doi: 10.1007/978-1-0716-2055-7_10. PMID: 35320526.
49. Kadav, PD , Edwards, J.L., Bandyopadhyay, P., Brewer, C F, Dam, TK. Molecular and Mechanistic Basis of Lectin-Glycan Interactions. Comprehensive Glycoscience (Second Edition), Volume 3, 2021, Pages 346-404. https://www.sciencedirect.com/science/article/pii/B9780128194751000547#!
48. Welch CJ, Kadav PD, Edwards JL, Krycia J, Talaga ML, Bandyopadhyay P, Dam TK. A Rapid and Facile Purification Method for Glycan-Binding Proteins and Glycoproteins. Curr Protoc Protein Sci. 2020 Sep;101(1):e113. doi: 10.1002/cpps.113. PMID: 32882112. [Cover article] https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cpps.113
47. Welch CJ, Talaga ML, Kadav PD, Edwards JL, Bandyopadhyay P, Dam TK. A capture and release method based on noncovalent ligand cross-linking and facile filtration for purification of lectins and glycoproteins. J Biol Chem. 2020 Jan 3;295(1):223-236. doi: 10.1074/jbc.RA119.010625. Epub 2019 Dec 2. PMID: 31792056; PMCID: PMC6952606. https://www.jbc.org/article/S0021-9258(17)49562-7/fulltext
46. Talaga ML, Fan N, Fueri AL, Brown RK, Bandyopadhyay P, Dam TK. Multitasking Human Lectin Galectin-3 Interacts with Sulfated Glycosaminoglycans and Chondroitin Sulfate Proteoglycans. Biochemistry, 55, 4541-51, (2016). https://pubs.acs.org/doi/10.1021/acs.biochem.6b00504
45. Dam TK, Talaga ML, Fan N, Brewer CF. Measuring Multivalent Binding Interactions by Isothermal Titration Calorimetry. Methods Enzymol., 567, 71-95, (2016).
44. Fan N, Talaga ML, Brown RK, Fueri AL, Bandyopadhyay P, Dam TK. Glycan-Dependent Mutual and Reversible Sequestration of Two Thyroid Cancer Biomarkers. Thyroid, 25, 1339-46, (2015). https://www.liebertpub.com/doi/10.1089/thy.2015.0105?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub++0pubmed
43. Dam TK, Brewer CF. Probing lectin-mucin interactions by isothermal titration microcalorimetry. Methods Mol Biol. 2015;1207:75-90. doi: 10.1007/978-1-4939-1396-1_5.
42. Talaga ML, Fan N, Fueri AL, Brown RK, Chabre YM, Bandyopadhyay P, Roy R, Dam TK. Significant other half of a glycoconjugate: contributions of scaffolds to lectin-glycoconjugate interactions. Biochemistry. 2014 Jul 15;53(27):4445-54. doi: 10.1021/bi5001307. Epub 2014 Jul 3. https://pubs.acs.org/doi/10.1021/bi5001307
41. Haugstad KE, Gerken TA, Stokke BT, Dam TK, Brewer CF, Sletmoen M. Enhanced self-association of mucins possessing the T and Tn carbohydrate cancer antigens at the single-molecule level. Biomacromolecules. 2012 May 14;13(5):1400-9. doi: 10.1021/bm300135h. Epub 2012 Apr 3. https://pubs.acs.org/doi/10.1021/bm300135h
40. Dam TK, Cavada BS, Nagano CS, Rocha BA, Benevides RG, Nascimento KS, de Sousa LA, Oscarson S, Brewer CF. Fine specificities of two lectins from Cymbosema roseum seeds: a lectin specific for high-mannose oligosaccharides and a lectin specific for blood group H type II trisaccharide. Glycobiology. 2011 Jul;21(7):925-33. doi: 10.1093/glycob/cwr025. Epub 2011 Mar 15. https://academic.oup.com/glycob/article/21/7/925/1989994?login=false
39. Dam, T. K. and Brewer, C. F., Maintenance of cell surface glycan density by lectin-glycan interactions: a homeostatic and innate immune regulatory mechanism. Glycobiology 20, 1061-1064 (2010). https://academic.oup.com/glycob/article/20/9/1061/1999363?login=false
39. Dam, T. K. and Brewer, C. F., Multivalent lectin-carbohydrate interactions energetics and mechanisms of binding. Adv. Carbohydrate Chem. Biochem. 63, 139-164 (2010).
38. Dam, T. K. and Brewer, C. F., Lectins as pattern recognition molecules: the effects of epitope density in innate immunity. Glycobiology 20, 270-279 (2010). https://academic.oup.com/glycob/article/20/3/270/1994162?login=false
37. André, S., Denis Giguère, D., Dam, T. K., Fred Brewer, C. F., Gabius, H-J. and Roy, R. Synthesis and screening of a small glycomimetic library for inhibitory activity on medically relevant galactoside-specific lectins in assays of increasing biorelevance. New J. Chem., 2010 DOI: 10.1039/c0nj00277a (2010).
36. Dam, T. K., Gerken, T. A. and Brewer, C. F. Thermodynamics of multivalent carbohydrate-lectin cross-linking interactions: importance of entropy in the bind and jump mechanism. Biochemistry, 48, 3822-3827 (2009). https://pubs.acs.org/doi/10.1021/bi9002919
35. Sletmoen, M., Dam, T. K., Gerken, T. A., Stokke, B. T. and Brewer, C. F. Single-molecule pair studies of the interactions of the a-GalNAc (Tn-antigen) form of porcine submaxillary mucin with soybean agglutinin. Biopolymers, 91, 719-728 (2009). https://onlinelibrary.wiley.com/doi/10.1002/bip.21213
34. Szabo, P., Dam, T. K., Smetana, K., Dvoránková, B., Kübler, D., Brewer, C. F. and Gabius, H.-J., Phosphorylated human lectin galectin-3: Analysis of ligand binding by histochemical monitoring of normal/malignant squamous epithelia and by isothermal titration calorimetry. Anat. Histol. Embryol., 38, 68-75 (2009). https://onlinelibrary.wiley.com/doi/10.1111/j.1439-0264.2008.00899.x
33. Dam, T. K. and Brewer, C. F., Thermodynamic approaches to the study of affinity of clustered carbohydrate epitopes in galectin-glycoconjugate interactions in Animal Lectins: A Functional View, (Vasta and Ahmed ed.), Taylor and Francis, pp. 31-46 (2009). https://www.taylorfrancis.com/books/mono/10.1201/9781420006971/animal-lectins-gerardo-vasta-phd-hafiz-ahmed-phd
32. Dam, T. K., Torres, M., Brewer, C. F. and Casadevall, A., Isothermal titration calorimetry reveals differential binding thermodynamics of variable region-identical antibodies differing in constant region for a univalent ligand. J. Biol. Chem. 283, 31366-31370 (2008). https://www.jbc.org/article/S0021-9258(20)56876-2/fulltext
31. Dam, T. K., and Brewer, C. F., Effects of clustered epitopes in multivalent ligand-receptor interactions. Biochemistry, 47, 8470-8476 (2008). https://pubs.acs.org/doi/10.1021/bi801208b
30. Kübler, D., Hung, C. W., Dam, T. K., Kopitz, J., André, S., Kaltner, H., Lohr, M., Manning, J. C., He, L., Wang, H., Middelberg, A., Brewer, C. F., Reed, J., Lehmann, W. D. and Gabius, H. J. Phosphorylated human galectin-3: facile large-scale preparation of active lectin and detection of structural changes by CD spectroscopy. Biochim. Biophys. Acta. 1780, 716-722 (2008). https://www.sciencedirect.com/science/article/abs/pii/S0304416508000329?via%3Dihub
29. Dam, T. K., Gerken, T. A., Cavada, B. S., Nascimento, K. S., Moura, T. R., and Brewer, C. F., Binding studies of a-GalNAc specific lectins to the a-GalNAc (Tn-antigen) form of porcine submaxillary mucin and its smaller fragments. J. Biol. Chem. 282, 28256-28263 (2007). https://www.jbc.org/article/S0021-9258(20)58722-X/fulltext
28. Dam, T. K. and Brewer, C. F. Fundamentals of lectin-carbohydrate interactions, in Comprehensive Glycoscience, (Kamerling, J. P., ed.), Elsevier Ltd., Vol. 3, pp. 397-452 (2007). https://www.sciencedirect.com/referencework/9780444519672/comprehensive-glycoscience
27. Dam, T. K. and Brewer, C. F. Applications of isothermal titration calorimetry to lectin-
carbohydrate interactions, in Lectins: Analytical Technologies, (Nilsson, C., ed.),
Elsevier B.V., pp. 75-101 (2007). https://www.elsevier.com/books/lectins-analytical-technologies/nilsson/978-0-444-53077-6
26. Dam, T. K., Gabius, H.-J., André, S., Kaltner, H., Lensch, M., and Brewer, C. F. Galectins bind to the multivalent glycoprotein asialofetuin with enhanced affinities and a gradient of decreasing binding constants. Biochemistry, 44, 12564-12571 (2005). https://pubs.acs.org/doi/10.1021/bi051144z
25. Dam, T. K., Oscarson, S., Roy, R., Das, S. K., Page, D., Macaluso, F. and Brewer, C. F. Thermodynamic, kinetic and electron microscopy studies of concanavalin A and Dioclea grandiflora lectin cross-linked with synthetic divalent carbohydrates. J. Biol. Chem. 280, 8640-8646 (2005). https://www.jbc.org/article/S0021-9258(19)62869-3/fulltext
24. Dam, T. K. and Brewer, C. F. Multivalent protein-carbohydrate interactions: isothermal titration microcalorimetry studies. Methods in Enzymology (Energetics of Biological Macromolecules, Part D; J. M. Holt, M. L. Johnson & G.K. Ackers, ed.), 379, 107-128 (2004). https://www.sciencedirect.com/science/article/abs/pii/S0076687904790060?via%3Dihub
23. Zheng, R., Dam, T. K., Brewer, C.F. and Blanchard, J. S. Active site residues in Mycobacterium tuberculosis pantothenate synthetase required in the formation and stabilization of the adenylate intermediate. Biochemistry 43, 7171-7178 (2004). https://pubs.acs.org/doi/10.1021/bi049676n
22. Dam, T. K. and Brewer C. F. Carbohydrate-lectin cross-linking interactions: structural, thermodynamic, and biological studies. Methods in Enzymology (Recognition of Carbohydrates in Biological Systems; Y.C. Lee & R. T. Lee, ed.), 362, 455-486 (2003). https://www.sciencedirect.com/science/article/abs/pii/S0076687903010310?via%3Dihub
21. Patil AR, Misquith S, Dam T. K., Sharma V, Kapoor M and Surolia A. Exploring enzyme amplification to characterize specificities of protein-carbohydrate recognition. Methods in Enzymology (Recognition of Carbohydrates in Biological Systems; Y.C. Lee & R. T. Lee, ed.); 362, 567-583 (2003). https://www.sciencedirect.com/science/article/abs/pii/S0076687903010383?via%3Dihub
20. Dam, T. K., Roy, R., Page, D. and Brewer, C. F. Negative cooperativity associated with binding of multivalent carbohydrates to lectins. Thermodynamic analysis of the “Multivalency Effect”. Biochemistry 41, 1351-1358 (2002). https://pubs.acs.org/doi/10.1021/bi015830j
19. Dam, T. K., Roy, R., Page, D. and Brewer, C. F. Thermodynamic binding parameters of individual epitopes of multivalent carbohydrates to concanavalin A as determined by “reverse” isothermal titration microcalorimetry. Biochemistry 41, 1359-1363 (2002). https://pubs.acs.org/doi/10.1021/bi015829k
18. Hegde, S. S., Dam, T. K., Brewer C. F. and Blanchard, J. S. (2002), Thermodynamics of aminoglycoside and acyl-coenzyme A binding to the Salmonella enterica AAC(6’)-Iy aminoglycoside N-acetyltransferase. Biochemistry 41, 7519-7527 (2002). https://pubs.acs.org/doi/10.1021/bi020190l
17. Dam, T. K. and Brewer, C. F. Thermodynamic studies of lectin-carbohydrate interactions by isothermal titration calorimetry. Chem. Rev. 102, 387-429 (2002). https://pubs.acs.org/doi/10.1021/cr000401x
16. Bachhawat, K., Kapoor, M., Dam, T.K. and Surolia, A. The reversible two states unfolding of a monocot mannose-binding lectin from garlic bulbs reveals the dominant role of the dimeric interface in its stabilization. Biochemistry 40, 7291-7300 (2001). https://pubs.acs.org/doi/10.1021/bi0027783
15. Cunto-Amesty, G., Dam, T.K., Lou, P., Monzavi-Karbassi, B., Brewer, C. F. Van Cott, T. C. and Kieber-Emmons, T., Directing the immune response to carbohydrate antigens. J. Biol. Chem. 276, 30490-30498 (2001). https://www.jbc.org/article/S0021-9258(20)89764-6/fulltext
14. Dam, T. K., Roy, R., Das, S. K., Oscarson, S. and Brewer, C. F. Binding of multivalent carbohydrates to concanavalin A and Dioclea grandiflora lectin.
Thermodynamic analysis of the “Multivalency Effect”. J. Biol. Chem. 275, 14223-14230 (2000). https://www.jbc.org/article/S0021-9258(19)80590-2/fulltext
13. Dam, T. K., Cavada, B. S., Grangeiro, T. B., Santos, C. F., Ceccatto V. M., de Sousa, F. A. M., Oscarson, S. and Brewer, C. F. Thermodynamic binding studies of lectins from the Diocleinae subtribe to deoxy analogs of the core trimannoside of asparagine-linked oligosaccharides. J. Biol. Chem. 275, 16119-16126 (2000). https://www.jbc.org/article/S0021-9258(19)80405-2/fulltext
12. Roy, R., Das, S. K., Santoyo-Gonzalez, F., Hernandez-Mateo, F., Dam, T. K., and Brewer, C. F. Synthesis of sugar-rods with phytohemagglutinin cross-linking properties by using the palladium-catalyzed sonogashira reaction. Chem. Eur. J. 6, 1757-1762 (2000). https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/(SICI)1521-3765(20000515)6:10%3C1757::AID-CHEM1757%3E3.0.CO;2-5
11. Lee, H. C., Goroncy, A. K., Peisach, J., Cavada, B. S., Grangeiro, T. B., Ramos, M. V., Sampaio A. H., Dam, T. K., and Brewer, C. F. Demonstration of a conserved histidine and two water ligands at the Mn2+ site in Diocleinae lectins by pulsed EPR spectroscopy. Biochemistry 39, 2340-2346 (2000). https://pubs.acs.org/doi/10.1021/bi992102b
10. Chandra, N. R., Ramachandraiah, G., Bachhawat, K., Dam, T. K., Surolia, A. and Vijayan, M. Crystal structure of a dimeric mannose-specific agglutinin from garlic: quaternary association and carbohydrate specificity. J. Mol. Biol. 285, 1157-1168 (1999). https://www.sciencedirect.com/science/article/abs/pii/S0022283698923531?via%3Dihub
9. Dam, T. K., Oscarson, S. and Brewer, C. F. Thermodynamics of binding of the core trimannoside of asparagine-linked carbohydrates and deoxy analogs to Dioclea grandiflora lectin. J. Biol. Chem. 273, 32812-32817 (1998). https://www.jbc.org/article/S0021-9258(19)58950-5/fulltext
8. Dam, T. K., Oscarson, S., Sacchettini, J. C. and Brewer, C. F. Differential solvation of “core” trimannoside complexes of the Dioclea grandiflora lectin and concanavalin A detected by primary solvent isotope effects in isothermal titration microcalorimetry. J. Biol. Chem. 273, 32826-32832 (1998). https://www.jbc.org/article/S0021-9258(19)58952-9/fulltext
7. Dam, T. K., Cavada, B. S., Grangeiro, T. B., Santos, C. F., de Sousa, F. A. M., Oscarson, S. and Brewer, C. F. Diocleinae lectins are a group of proteins with conserved binding sites for the core trimannoside of asparagine-linked oligosaccharide and differential specificities for complex carbohydrates. J. Biol. Chem. 273, 12082-12088 (1998). https://www.jbc.org/article/S0021-9258(19)84232-1/fulltext
6. Dam, T. K., Bachhawat, K., Rani, P. G. and Surolia, A. Garlic (Allium sativum) lectins bind to high mannose oligosaccharide chains. J. Biol. Chem. 273, 5528-5535 (1998). https://www.jbc.org/article/S0021-9258(18)67805-6/fulltext
5. Gupta, D., Dam, T. K., Oscarson, S. and Brewer, C. F. Thermodynamics of lectin- carbohydrate interactions. Binding of the core trimannoside of asparagine-linked carbohydrates and deoxy analogs to concanavalin A. J. Biol. Chem. 272, 6388-6392 (1997). https://www.jbc.org/article/S0021-9258(18)41155-6/fulltext
4. Chandra, N. R., Dam, T.K., Surolia, A. and Vijayan, M. Crystallization and preliminary crystallographic studies on the mannose specific lectin from garlic. Acta Cryst. D53, 787-788 (1997). https://pubmed.ncbi.nlm.nih.gov/15299871/
3. Dam, T. K.*, Bandyopadhyay, P., Sarkar, M., Ghosal, J., Bhattacharya, A. and Choudhury, A. Purification and partial characterization of a heparin-binding lectin from the marine clam Anadara granosa. Biochem Biophys. Res. Commun. 203, 36-45 (1994). https://www.sciencedirect.com/science/article/abs/pii/S0006291X84721450?via%3Dihub
2. Dam, T. K., Sarkar, M., Ghosal, J. and Choudhury, A. Purification and partial characterization of a N-glycolylneuraminic acid specific lectin from the clam Anadara granosa (L). Biochem. Biophys. Res. Commun. 196, 422-429 (1993). https://www.sciencedirect.com/science/article/abs/pii/S0006291X83722667?via%3Dihub
1.Dam, T. K., Sarkar, M., Ghosal, J. and Choudhury, A. A Novel galactosyl binding lectin from the plasma of the blood clam, Anadara granosa (L) and a study of its combining site. Mol. Cell. Biochem. 117, 1-9 (1992). https://pubmed.ncbi.nlm.nih.gov/1480160/
Publication of a Teaching Tool
Dam, T. K. and Bandyopadhyay, P. Continuous and Rapid Testing (CaRT): A Simple Tool for Assessment and Communication. The Teaching Professor, December 1, 2016
Book Review
Book Review: Brewer, C. F. and Dam, T. K. Reviewed the book entitled “Essentials of Glycobiology” Edited by Varki et al., (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.). The review was published in Carbohydrate Research. 325, 233-234 (2000).