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Sivaji N, Suguna K, Surolia A, Vijayan M. Structural and related studies on Mevo lectin from Methanococcus voltae A3: the first thorough characterization of an archeal lectin and its interactions. Glycobiology 2020; 31:315-328. [PMID: 32651948 DOI: 10.1093/glycob/cwaa063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 07/01/2020] [Indexed: 12/15/2022] Open
Abstract
Crystallographic and solution studies of Mevo lectin and its complexes, the first effort of its kind on an archeal lectin, reveal a structure similar to β-prism I fold lectins from plant and animal sources, but with a quaternary association involving a ring structure with seven-fold symmetry. Each subunit in the heptamer carries one sugar binding site on the first Greek key motif. The oligomeric interface is primarily made up of a parallel β-sheet involving a strand of Greek key I of one subunit and Greek key ΙΙΙ from a neighboring subunit. The crystal structures of the complexes of the lectin with mannose, αMan(1,2)αMan, αMan(1,3)αMan, a mannotriose and a mannopentose revealed a primary binding site similar to that found in other mannose specific β-prism I fold lectins. The complex with αMan(1,3)αMan provides an interesting case in which a few subunits have the reducing end at the primary binding site, while the majority have the nonreducing end at the primary binding site. The structures of complexes involving the trisaccharide and the pentasaccharide exhibit cross-linking among heptameric molecules. The observed arrangements may be relevant to the multivalency of the lectin. Phylogenetic analysis of amino acid sequences indicates that Mevo lectin is closer to β-prism I fold animal lectins than with those of plant origin. The results presented here reinforce the conclusion regarding the existence of lectins in all three domains of life. It would also appear that lectins evolved to the present form before the three domains diverged.
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Affiliation(s)
- Nukathoti Sivaji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Kaza Suguna
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Avadhesha Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Mamannamana Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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Chandran T, Sivaji N, Surolia A, Vijayan M. Ligand binding and retention in snake gourd seed lectin (SGSL). A crystallographic, thermodynamic and molecular dynamics study. Glycobiology 2018; 28:968-977. [PMID: 30099481 DOI: 10.1093/glycob/cwy072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 08/06/2018] [Indexed: 11/14/2022] Open
Abstract
Snake gourd seed lectin (SGSL) is a non-toxic homolog of type II ribosome-inactivating proteins (RIPs) which contain a catalytic domain and a lectin domain. Isothermal titration calorimetry (ITC) measurements of the interactions of the protein with LacNAc, Lac, Gal, Me-α-Gal were carried out and the crystal structures of the native protein and its complex with Lac were determined. The crystal structure of the Me-α-Gal complex has already been determined. While the crystal structure showed the presence of two-sugar-binding sites, one on each of the two domains of the lectin chain, ITC measurements indicated the presence of only one binding site. In order to resolve this anomaly, molecular dynamics (MD) simulations were carried out on the native protein and on its complexes with Me-α-Gal and Lac. Simulations were also performed on the protein after reducing the inter-chain disulfide bridge between the two chains. The crystal structures and the simulations confirmed the robustness of the protein structure, irrespective of the presence or absence of the disulfide bridge. The simulations indicated that although two sites can bind sugar, only the ligand at one site is retained in a dynamic situation. The studies thus bring out the subtle relationship between binding and retention of the ligand.
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Affiliation(s)
| | - Nukathoti Sivaji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Avadhesha Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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Sivaji N, Abhinav KV, Vijayan M. Crystallization and biochemical characterization of an archaeal lectin from Methanococcus voltae A3. Acta Crystallogr F Struct Biol Commun 2017; 73:300-304. [PMID: 28471363 PMCID: PMC5417321 DOI: 10.1107/s2053230x17006173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 04/24/2017] [Indexed: 12/13/2022] Open
Abstract
A lectin from Methanococcus voltae A3 has been cloned, expressed, purified and characterized. The lectin appears to be specific for complex sugars. The protein crystallized in a tetragonal space group, with around 16 subunits in the asymmetric unit. Sequence comparisons indicate the lectin to have a β-prism I fold, with poor homology to lectins of known three-dimensional structure.
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Affiliation(s)
- N. Sivaji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - K. V. Abhinav
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - M. Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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Abhinav KV, Sharma K, Surolia A, Vijayan M. Distortion of the ligand molecule as a strategy for modulating binding affinity: Further studies involving complexes of jacalin with β-substituted disaccharides. IUBMB Life 2017; 69:72-78. [DOI: 10.1002/iub.1593] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 12/09/2016] [Indexed: 11/11/2022]
Affiliation(s)
- K. V. Abhinav
- Molecular Biophysics Unit; , Indian Institute of Science; Bangalore India
| | - Kaushal Sharma
- Molecular Biophysics Unit; , Indian Institute of Science; Bangalore India
| | - A. Surolia
- Molecular Biophysics Unit; , Indian Institute of Science; Bangalore India
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Abhinav KV, Sharma K, Surolia A, Vijayan M. Effect of linkage on the location of reducing and nonreducing sugars bound to jacalin. IUBMB Life 2016; 68:971-979. [PMID: 27808459 DOI: 10.1002/iub.1572] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/23/2016] [Indexed: 11/08/2022]
Abstract
The crystal structures of jacalin complexed with Gal α-(1,4) Gal and Gal α-(1,3) Gal β-(1,4) Gal have been determined with the primary objective of exploring the effect of linkage on the location of reducing and non-reducing sugars in the extended binding site of the lectin, an issue which has not been studied thoroughly. Contrary to the earlier surmise based on simple steric considerations, the two structures demonstrate that α-linked sugars can bind to jacalin with nonreducing sugar at the primary binding site. This is made possible substantially on account of the hitherto underestimated plasticity of a non-polar region of the extended binding site. Modeling studies involving conformational search and energy minimization, along with available crystallographic and thermodynamic data, indicate a strong preference for complexation with Gal β-(1,3) Gal with the reducing Gal at the primary site, followed by that with Gal α-(1,3) Gal, with the reducing or non-reducing Gal located at the primary binding site. This observation is in consonance with the facility of jacalin to bind mucin type O-glycans containing T-antigen core. © 2016 IUBMB Life, 68(12):971-979, 2016.
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Affiliation(s)
- K V Abhinav
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Kaushal Sharma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Avadhesha Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Mamannamana Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
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Chandran T, Sharma A, Vijayan M. Structural studies on a non-toxic homologue of type II RIPs from bitter gourd: Molecular basis of non-toxicity, conformational selection and glycan structure. J Biosci 2016; 40:929-41. [PMID: 26648038 DOI: 10.1007/s12038-015-9573-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The structures of nine independent crystals of bitter gourd seed lectin (BGSL), a non-toxic homologue of type II RIPs, and its sugar complexes have been determined. The four-chain, two-fold symmetric, protein is made up of two identical two-chain modules, each consisting of a catalytic chain and a lectin chain, connected by a disulphide bridge. The lectin chain is made up of two domains. Each domain carries a carbohydrate binding site in type II RIPs of known structure. BGSL has a sugar binding site only on one domain, thus impairing its interaction at the cell surface. The adenine binding site in the catalytic chain is defective. Thus, defects in sugar binding as well as adenine binding appear to contribute to the non-toxicity of the lectin. The plasticity of the molecule is mainly caused by the presence of two possible well defined conformations of a surface loop in the lectin chain. One of them is chosen in the sugar complexes, in a case of conformational selection, as the chosen conformation facilitates an additional interaction with the sugar, involving an arginyl residue in the loop. The N-glycosylation of the lectin involves a plant-specific glycan while that in toxic type II RIPs of known structure involves a glycan which is animal as well as plant specific.
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Abhinav KV, Samuel E, Vijayan M. Archeal lectins: An identification through a genomic search. Proteins 2015; 84:21-30. [DOI: 10.1002/prot.24949] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/13/2015] [Accepted: 10/19/2015] [Indexed: 11/09/2022]
Affiliation(s)
- K. V. Abhinav
- Molecular Biophysics Unit, Indian Institute of Science; Bangalore 560 012 India
| | - Ebenezer Samuel
- Molecular Biophysics Unit, Indian Institute of Science; Bangalore 560 012 India
| | - M. Vijayan
- Molecular Biophysics Unit, Indian Institute of Science; Bangalore 560 012 India
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Abhinav KV, Sharma K, Swaminathan CP, Surolia A, Vijayan M. Jacalin-carbohydrate interactions: distortion of the ligand molecule as a determinant of affinity. ACTA ACUST UNITED AC 2015; 71:324-31. [PMID: 25664742 DOI: 10.1107/s139900471402553x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 11/21/2014] [Indexed: 11/10/2022]
Abstract
Jacalin is among the most thoroughly studied lectins. Its carbohydrate-binding site has also been well characterized. It has been postulated that the lower affinity of β-galactosides for jacalin compared with α-galactosides is caused by steric interactions of the substituents in the former with the protein. This issue has been explored energetically and structurally using different appropriate carbohydrate complexes of jacalin. It turns out that the earlier postulation is not correct. The interactions of the substituent with the binding site remain essentially the same irrespective of the anomeric nature of the substitution. This is achieved through a distortion of the sugar ring in β-galactosides. The difference in energy, and therefore in affinity, is caused by a distortion of the sugar ring in β-galactosides. The elucidation of this unprecedented distortion of the ligand as a strategy for modulating affinity is of general interest. The crystal structures also provide a rationale for the relative affinities of the different carbohydrate ligands for jacalin.
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Affiliation(s)
- K V Abhinav
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Kaushal Sharma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - C P Swaminathan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - A Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - M Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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