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Halder S, Surolia A, Mukhopadhyay C. Dynamics simulation of soybean agglutinin (SBA) dimer reveals the impact of glycosylation on its enhanced structural stability. Carbohydr Res 2016; 428:8-17. [DOI: 10.1016/j.carres.2016.04.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 03/10/2016] [Accepted: 04/08/2016] [Indexed: 10/21/2022]
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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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Li Y, Li T, Li J, Liu D, Yang J, Yang J, Zhang F, Sun S. Molecular cloning, expression, and characterization of a Sophora alopecuroides lectin from Escherichia coli. Acta Biochim Biophys Sin (Shanghai) 2014; 46:749-56. [PMID: 25033829 DOI: 10.1093/abbs/gmu060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sophora alopecuroides lectin (SAL) has been isolated from the seeds and confirmed to have antifungal and antitumor activities, and presently the preparation of the natural lectin was cumbersome, time-consuming, and the yield was relatively low for further analysis. In this study, the signal peptide of lectin, the modification sites, and the secondary structure were analyzed, and the three-dimensional structures of SAL were modeled. The gene of SAL was amplified by the reverse transcription polymerase chain reaction, and cloned into the pET-30a vector and expressed in Escherichia coli BL21(DE3) by the induction of isopropyl-beta-d-thiogalactopyranoside. Totally, 400 mg of recombinant SAL (rSAL) was purified from 1 l of bacterial culture through Ni-NTA agarose column and the purity reached 95%. The recombinant protein was further confirmed by western blot using rSAL-specific antibody. The biological activity analysis results showed that rSAL exclusively bound to d-galactose and had universal hemagglutinating activities to human A, B, O, and AB, and rabbit and mouse erythrocytes. rSAL also inhibited the growth of fungi, the proliferation of cancer cells, and the HIV-I reverse transcriptase activity. In conclusion, this study indicates that rSAL can be produced in large quantities in the prokaryotic expression system and the recombinant protein still retains the various biological activities, which will make the large-scale production of SAL recombinant protein at dramatically reduced cost possible.
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Affiliation(s)
- Yang Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumuqi 830046, China
| | - Tingting Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumuqi 830046, China
| | - Jinyao Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumuqi 830046, China
| | - Dongliang Liu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumuqi 830046, China
| | - Jie Yang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumuqi 830046, China
| | - Jianhua Yang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumuqi 830046, China Texas Children's Cancer Center, Department of Pediatrics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fuchun Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumuqi 830046, China
| | - Surong Sun
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumuqi 830046, China
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Shetty KN, Latha VL, Rao RN, Nadimpalli SK, Suguna K. Affinity of a galactose-specific legume lectin from Dolichos lablab to adenine revealed by X-ray cystallography. IUBMB Life 2014; 65:633-44. [PMID: 23794513 DOI: 10.1002/iub.1177] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Accepted: 03/31/2013] [Indexed: 11/06/2022]
Abstract
Crystal structure analysis of a galactose-specific lectin from a leguminous food crop Dolichos lablab (Indian lablab beans) has been carried out to obtain insights into its quaternary association and lectin-carbohydrate interactions. The analysis led to the identification of adenine binding sites at the dimeric interfaces of the heterotetrameric lectin. Structural details of similar adenine binding were reported in only one legume lectin, Dolichos biflorus, before this study. Here, we present the structure of the galactose-binding D. lablab lectin at different pH values in the native form and in complex with galactose and adenine. This first structure report on this lectin also provides a high resolution atomic view of legume lectin-adenine interactions. The tetramer has two canonical and two DB58-like interfaces. The binding of adenine, a non-carbohydrate ligand, is found to occur at four hydrophobic sites at the core of the tetramer at the DB58-like dimeric interfaces and does not interfere with the carbohydrate-binding site. To support the crystallographic observations, the adenine binding was further quantified by carrying out isothermal calorimetric titration. By this method, we not only estimated the affinity of the lectin to adenine but also showed that adenine binds with negative cooperativity in solution.
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Affiliation(s)
- Kartika N Shetty
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
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Chandran T, Sharma A, Vijayan M. Generation of Ligand Specificity and Modes of Oligomerization in β-Prism I Fold Lectins. DYNAMICS OF PROTEINS AND NUCLEIC ACIDS 2013; 92:135-78. [DOI: 10.1016/b978-0-12-411636-8.00004-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Nascimento KS, Cunha AI, Nascimento KS, Cavada BS, Azevedo AM, Aires-Barros MR. An overview of lectins purification strategies. J Mol Recognit 2012; 25:527-41. [DOI: 10.1002/jmr.2200] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kelany S. Nascimento
- Institute for Biotechnology and Bioengineering (IBB), Centre for Biological and Chemical Engineering, Department of Bioengineering, Instituto Superior Técnico; Technical University of Lisbon; Av. Rovisco Pais; 1049-001; Lisbon; Portugal
| | - Ana I. Cunha
- Institute for Biotechnology and Bioengineering (IBB), Centre for Biological and Chemical Engineering, Department of Bioengineering, Instituto Superior Técnico; Technical University of Lisbon; Av. Rovisco Pais; 1049-001; Lisbon; Portugal
| | - Kyria S. Nascimento
- Biochemistry and Molecular Biology Department; Federal University of Ceará (UFC); CEP 60.455-970; Fortaleza; Ceará; Brazil
| | - Benildo S. Cavada
- Biochemistry and Molecular Biology Department; Federal University of Ceará (UFC); CEP 60.455-970; Fortaleza; Ceará; Brazil
| | - Ana M. Azevedo
- Institute for Biotechnology and Bioengineering (IBB), Centre for Biological and Chemical Engineering, Department of Bioengineering, Instituto Superior Técnico; Technical University of Lisbon; Av. Rovisco Pais; 1049-001; Lisbon; Portugal
| | - Maria Raquel Aires-Barros
- Institute for Biotechnology and Bioengineering (IBB), Centre for Biological and Chemical Engineering, Department of Bioengineering, Instituto Superior Técnico; Technical University of Lisbon; Av. Rovisco Pais; 1049-001; Lisbon; Portugal
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Ghosh G, Mandal DK. Differing structural characteristics of molten globule intermediate of peanut lectin in urea and guanidine-HCl. Int J Biol Macromol 2012; 51:188-95. [DOI: 10.1016/j.ijbiomac.2012.05.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 05/07/2012] [Accepted: 05/07/2012] [Indexed: 10/28/2022]
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Basu S, Bhattacharyya D, Banerjee R. Self-complementarity within proteins: bridging the gap between binding and folding. Biophys J 2012; 102:2605-14. [PMID: 22713576 DOI: 10.1016/j.bpj.2012.04.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 03/30/2012] [Accepted: 04/17/2012] [Indexed: 01/09/2023] Open
Abstract
Complementarity, in terms of both shape and electrostatic potential, has been quantitatively estimated at protein-protein interfaces and used extensively to predict the specific geometry of association between interacting proteins. In this work, we attempted to place both binding and folding on a common conceptual platform based on complementarity. To that end, we estimated (for the first time to our knowledge) electrostatic complementarity (Em) for residues buried within proteins. Em measures the correlation of surface electrostatic potential at protein interiors. The results show fairly uniform and significant values for all amino acids. Interestingly, hydrophobic side chains also attain appreciable complementarity primarily due to the trajectory of the main chain. Previous work from our laboratory characterized the surface (or shape) complementarity (Sm) of interior residues, and both of these measures have now been combined to derive two scoring functions to identify the native fold amid a set of decoys. These scoring functions are somewhat similar to functions that discriminate among multiple solutions in a protein-protein docking exercise. The performances of both of these functions on state-of-the-art databases were comparable if not better than most currently available scoring functions. Thus, analogously to interfacial residues of protein chains associated (docked) with specific geometry, amino acids found in the native interior have to satisfy fairly stringent constraints in terms of both Sm and Em. The functions were also found to be useful for correctly identifying the same fold for two sequences with low sequence identity. Finally, inspired by the Ramachandran plot, we developed a plot of Sm versus Em (referred to as the complementarity plot) that identifies residues with suboptimal packing and electrostatics which appear to be correlated to coordinate errors.
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Affiliation(s)
- Sankar Basu
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India
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Tan-Wilson A, Bandak B, Prabu-Jeyabalan M. The PA domain is crucial for determining optimum substrate length for soybean protease C1: structure and kinetics correlate with molecular function. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2012; 53:27-32. [PMID: 22285412 DOI: 10.1016/j.plaphy.2012.01.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2011] [Accepted: 01/03/2012] [Indexed: 05/31/2023]
Abstract
A subtilisin-like enzyme, soybean protease C1 (EC 3.4.21.25), initiates the degradation of the β-conglycinin storage proteins in early seedling growth. Previous kinetic studies revealed a nine-residue (P5-P4') length requirement for substrate peptides to attain optimum cleavage rates. This modeling study used the crystal structure of tomato subtilase (SBT3) as a starting model to explain the length requirement. The study also correlates structure to kinetic studies that elucidated the amino acid preferences of soybean protease C1 for P1, P1' and P4' locations of the cleavage sequence. The interactions of a number of protease C1 residues with P5, P4 and P4' residues of its substrate elucidated by this analysis can explain why the enzyme only hydrolyzes peptide bonds outside of soybean storage protein's core double β-barrel cupin domains. The findings further correlate with the literature-reported hypothesis for the subtilisin-specific protease-associated (PA) domain to play a critical role. Residues of the SBT3 PA domain also interact with the P2' residue on the substrate's carboxyl side of the scissile bond, while those on protease C1 interact with its substrate's P4' residue. This stands in contrast with the subtilisin BPN' that has no PA domain, and where the enzyme makes stronger interaction with residues on the amino side of the cleaved bond. The variable patterns of interactions between the substrate models and PA domains of tomato SBT3 and soybean protease C1 illustrate a crucial role for the PA domain in molecular recognition of their substrates.
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Affiliation(s)
- Anna Tan-Wilson
- Department of Biological Sciences, State University of New York at Binghamton, 4400 Vestal Parkway East, Binghamton, NY 13902, USA
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Arif SM, Vijayan M. Structural diversity based on variability in quaternary association. A case study involving eubacterial and related SSBs. Methods Mol Biol 2012; 922:23-35. [PMID: 22976175 DOI: 10.1007/978-1-62703-032-8_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Eubacterial and related single-stranded DNA-binding proteins (SSBs) exhibit considerable variability in their quaternary association in spite of their having the same tertiary fold. The variability involves differences in the orientation of dimers in the tetrameric molecule (or of two-domain subunits in the dimeric molecule) and that of monomers in each dimer. The presence of an additional strand in mycobacterial and related SSBs, which clamps the dimers together, is a major determinant of the mode of quaternary association in them. The variability in quaternary structure has implications to the stability of the protein and possibly to its mode of DNA binding.
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Affiliation(s)
- S M Arif
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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Sharma A, Vijayan M. Quaternary association in β-prism I fold plant lectins: Insights from X-ray crystallography, modelling and molecular dynamics. J Biosci 2011; 36:793-808. [DOI: 10.1007/s12038-011-9166-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Varejão N, Correia MTS, Foguel D. Characterization of the Unfolding Process of the Tetrameric and Dimeric Forms of Cratylia mollis Seed Lectin (CRAMOLL 1): Effects of Natural Fragmentation on Protein Stability. Biochemistry 2011; 50:7330-40. [DOI: 10.1021/bi200320x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nathalia Varejão
- Instituto
de Bioquímica Médica, Programa de Biologia Estrutural,
Centro Nacional de Ressonância Magnética Nuclear de
Macromoléculas, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, 21941-902, Rio
de Janeiro, RJ, Brazil
| | - Maria Tereza S. Correia
- Departamento de Bioquímica, Laboratório de Glicoproteínas, Universidade Federal de Pernambuco, 50670-420, Recife,
Pernambuco, PE, Brazil
| | - Debora Foguel
- Instituto
de Bioquímica Médica, Programa de Biologia Estrutural,
Centro Nacional de Ressonância Magnética Nuclear de
Macromoléculas, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, 21941-902, Rio
de Janeiro, RJ, Brazil
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Sen D, Mandal DK. Pea lectin unfolding reveals a unique molten globule fragment chain. Biochimie 2011; 93:409-17. [DOI: 10.1016/j.biochi.2010.10.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 10/19/2010] [Indexed: 10/18/2022]
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Molla AR, Maity SS, Ghosh S, Mandal DK. Organization and dynamics of tryptophan residues in tetrameric and monomeric soybean agglutinin: studies by steady-state and time-resolved fluorescence, phosphorescence and chemical modification. Biochimie 2009; 91:857-67. [PMID: 19383525 DOI: 10.1016/j.biochi.2009.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Accepted: 04/11/2009] [Indexed: 10/20/2022]
Abstract
We have investigated the organization and dynamics of tryptophan residues in tetrameric, monomeric and unfolded states of soybean agglutinin (SBA) by selective chemical modification, steady-state and time-resolved fluorescence, and phosphorescence. Oxidation with N-bromosuccinimide (NBS) modifies two tryptophans (Trp 60 and Trp 132) in tetramer, four (Trp 8, Trp 203 and previous two) in monomer, and all six (Trp 8, Trp 60, Trp 132, Trp 154, Trp 203 and Trp 226) in unfolded state. Utilizing wavelength-selective fluorescence approach, we have observed a red-edge excitation shift (REES) of 10 and 5 nm for tetramer and monomer, respectively. A more pronounced REES (21 nm) is observed after NBS oxidation. These results are supported by fluorescence anisotropy experiments. Acrylamide quenching shows the Stern-Volmer constant (K(SV)) for tetramer, monomer and unfolded SBA being 2.2, 5.0 and 14.6 M(-1), respectively. Time-resolved fluorescence studies exhibit biexponential decay with the mean lifetime increasing along tetramer (1.0 ns) to monomer (1.9 ns) to unfolded (3.6 ns). Phosphorescence studies at 77 K give more structured spectra, with two (0,0) bands at 408.6 (weak) and 413.2 nm for tetramer. However, a single (0,0) band appears at 411.8 and 407.2 nm for monomer and unfolded SBA, respectively. The exposure of hydrophobic surface in SBA monomer has been examined by 8-anilino-1-naphthalenesulfonate (ANS) binding, which shows approximately 20-fold increase in ANS fluorescence compared to that for tetramer. The mean lifetime of ANS also shows a large increase (12.0 ns) upon binding to monomer. These results may provide important insight into the role of tryptophans in the folding and association of SBA, and oligomeric proteins in general.
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Affiliation(s)
- Anisur R Molla
- Department of Chemistry & Biochemistry, Presidency College, 86/1 College Street, Kolkata 700 073, West Bengal, India
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Insights into the structural basis of the pH-dependent dimer-tetramer equilibrium through crystallographic analysis of recombinant Diocleinae lectins. Biochem J 2008; 409:417-28. [PMID: 17937659 DOI: 10.1042/bj20070942] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The structural ground underlying the pH-dependency of the dimer-tetramer transition of Diocleinae lectins was investigated by equilibrium sedimentation and X-ray crystal structure determination of wild-type and site-directed mutants of recombinant lectins. Synthetic genes coding for the full-length alpha-chains of the seed lectins of Dioclea guianensis (termed r-alphaDguia) and Dioclea grandiflora (termed r-alphaDGL) were designed and expressed in Escherichia coli. This pioneering approach, which will be described in detail in the present paper, yielded recombinant lectins displaying carbohydrate-binding activity, dimer-tetramer equilibria and crystal structures indistinguishable from their natural homologues. Conversion of the pH-stable tetrameric r-alphaDGL into a structure exhibiting pH-dependent dimer-tetramer transition was accomplished through mutations that abolished the interdimeric interactions at the central cavity of the tetrameric lectins. Both the central and the peripheral interacting regions bear structural information for formation of the canonical legume lectin tetramer. We hypothesize that the strength of the ionic contacts at these sites may be modulated by the pH, leading to dissociation of those lectin structures that are not locked into a pH-stable tetramer through interdimeric contacts networking the central cavity loops.
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Affiliation(s)
- M Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
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Multiplicity of carbohydrate-binding sites in β-prism fold lectins: occurrence and possible evolutionary implications. J Biosci 2007; 32:1089-110. [DOI: 10.1007/s12038-007-0111-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Sinha S, Surolia A. Attributes of glycosylation in the establishment of the unfolding pathway of soybean agglutinin. Biophys J 2007; 92:208-16. [PMID: 16980353 PMCID: PMC1697847 DOI: 10.1529/biophysj.106.092668] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2006] [Accepted: 08/29/2006] [Indexed: 11/18/2022] Open
Abstract
Soybean agglutinin (gSBA) is a tetrameric legume lectin, each of whose subunits are glycosylated. Earlier studies have shown that this protein shows exceptionally high stability in terms of free energy of unfolding when compared to other proteins from the same family. This article deals with the unfolding reactions of the nonglycosylated recombinant form of the protein rSBA and its comparison with the glycosylated counterpart gSBA. The nonglycosylated form features a lower stability when compared to the glycosylated form. Further, the unfolding pathways in the two are widely different. Although the glycosylated form undergoes a simple two-state unfolding, the nonglycosylated species unfolds via a compact monomeric intermediate that is not a molten globule. Representative isothermal and thermal denaturation profiles show that glycosylation accounts for a stabilization of approximately 9 kcal/mol of the tetramer, whereas the difference in T(m) between the two forms is 26 degrees C. Computational studies on the glycan-protein interactions at the noncanonical interface of the protein show that quite a number of hydrogen bond and hydrophobic interactions stabilize the glycoprotein tetramer.
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Affiliation(s)
- Sharmistha Sinha
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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Natchiar SK, Suguna K, Surolia A, Vijayan M. Peanut agglutinin, a lectin with an unusual quaternary structure and interesting ligand binding properties. CRYSTALLOGR REV 2007. [DOI: 10.1080/08893110701382087] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Levy ED, Pereira-Leal JB, Chothia C, Teichmann SA. 3D complex: a structural classification of protein complexes. PLoS Comput Biol 2006; 2:e155. [PMID: 17112313 PMCID: PMC1636673 DOI: 10.1371/journal.pcbi.0020155] [Citation(s) in RCA: 254] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2006] [Accepted: 10/05/2006] [Indexed: 11/18/2022] Open
Abstract
Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes. The millions of genes sequenced over the past decade correspond to a much smaller set of protein structural domains, or folds—probably only a few thousand. Since structural data is being accumulated at a fast pace, classifications of domains such as SCOP help significantly in understanding the sequence–structure relationship. More recently, classifications of interacting domain pairs address the relationship between sequence divergence and domain–domain interaction. One level of description that has yet to be investigated is the protein complex level, which is the physiologically relevant state for most proteins within the cell. Here, Levy and colleagues propose a classification scheme for protein complexes, which will allow a better understanding of their structural properties and evolution.
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Affiliation(s)
- Emmanuel D Levy
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom.
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Del Sol FG, Cavada BS, Calvete JJ. 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 2006; 158:1-9. [PMID: 17251039 DOI: 10.1016/j.jsb.2006.08.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Revised: 08/17/2006] [Accepted: 08/25/2006] [Indexed: 11/26/2022]
Abstract
Structural determinants underlaying the pH-dependent dimer-tetramer transition of Diocleinae lectins were investigated from the structures of Cratylia floribunda seed lectin crystallized in conditions where it exist as a dimer (pH 4.6) or as a tetramer (pH 8.5). The acidic (aCFL) and the basic (bCFL) tetramers superimpose with overall r.m.s.d. of 0.53 A, though interdimer contacts are drastically reduced in aCFL, and the r.m.s.d. for the superposition of the 117-120 loops of aCFL vs. the bCFL tetramer is 1.29 A. Our data support the view that His51 plays a role in determining the conformation of the central cavity loops and that interdimer contacts involving ordered loop residues stabilize the canonical, pH-dependent tetramer. In the bCFL tetramer, hydrogen bonds between Asn118 and Thr120 of monomers A and D and residues Ser66, Ser108, Ser110, and Thr49 of the opposite monomer stabilize the canonical, pH-dependent tetrameric lectin structure. In CFL, Asn131 makes intradimer contacts with Asn122 and Ala123. In comparison, His131 in Dioclea grandiflora lectin establishes a network of interdimer interactions bridging the four central loops of the pH-independent tetramer. Our data provide new insights into the participation of specific amino acid residues in the mechanism of the quaternary association of Diocleinae lectins.
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Dev S, K ND, Sinha S, Surolia A. Thermodynamic analysis of three state denaturation of Peanut Agglutinin. IUBMB Life 2006; 58:549-55. [PMID: 17002983 DOI: 10.1080/15216540600902228] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Peanut Agglutinin (PNA) is a homotetrameric protein with a very unusual open quaternary structure. During denaturation, it first dissociates into a molten globule like state, which subsequently undergoes complete denaturation. Urea denaturation of PNA at neutral pH has been studied by intrinsic fluorescence spectroscopy and has been fitted to a three state model, A4 <=> 4I <=> 4U, to get all the relevant thermodynamic parameters. Urea denaturation leads to continuous red shift of wavelength maxima. The molten globule like state is formed in a short range of urea concentration. Refolding of the denatured PNA has been attempted by intrinsic fluorescence study. Refolding by instantaneous dilution shows the occurrence of the formation of an intermediate at a relatively rapid rate, within few seconds. The transition from PNA tetramer to molten globule like state is found to have a DeltaG value of approximately 33 kcal/mole while it is approximately 8 kcal/mole for the transition from molten globule like state to a completely denatured state. This in turn indicates that the tetramerization in PNA contributes significantly to the stability of the oligomer.
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Affiliation(s)
- Sagarika Dev
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
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24
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Dev S, Khan RH, Surolia A. 2,2,2-Trifluoroethanol-Induced structural change of peanut agglutinin at different pH: A comparative account. IUBMB Life 2006; 58:473-9. [PMID: 16916785 DOI: 10.1080/15216540600818150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Peanut Agglutinin (PNA) is a legume lectin with a unique open quarternary structure. It is a homotetrameric protein, the monomeric subunit of which is made up of 3 beta sheets. The structural change in this protein has been induced by 2,2,2-trifluoroethanol (TFE) at two different pH. At neutral pH, PNA exists as a homotetramer, while at pH 2.5, it is known to dissociate to a dimer. The effect of TFE has been studied at both the pH by intrinsic tryptophan fluorescence, far and near UV Circular Dichroism, ANS binding and dynamic light scattering. At low pH, 15% TFE is found to induce a molten globule like state that shows maximum ANS binding. Increasing concentration of TFE increases alpha helical content and the compactness of the protein. The compact PNA at higher concentration of TFE is structurally different from the native structure. The effect of TFE at neutral pH on PNA is somewhat different from that observed at low pH. TFE does not induce molten globule like state at this pH. The detailed study of the structural change of PNA by TFE has been presented.
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Affiliation(s)
- Sagarika Dev
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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25
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Kim WK, Henschel A, Winter C, Schroeder M. The many faces of protein-protein interactions: A compendium of interface geometry. PLoS Comput Biol 2006; 2:e124. [PMID: 17009862 PMCID: PMC1584320 DOI: 10.1371/journal.pcbi.0020124] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2006] [Accepted: 07/31/2006] [Indexed: 11/18/2022] Open
Abstract
A systematic classification of protein-protein interfaces is a valuable resource for understanding the principles of molecular recognition and for modelling protein complexes. Here, we present a classification of domain interfaces according to their geometry. Our new algorithm uses a hybrid approach of both sequential and structural features. The accuracy is evaluated on a hand-curated dataset of 416 interfaces. Our hybrid procedure achieves 83% precision and 95% recall, which improves the earlier sequence-based method by 5% on both terms. We classify virtually all domain interfaces of known structure, which results in nearly 6,000 distinct types of interfaces. In 40% of the cases, the interacting domain families associate in multiple orientations, suggesting that all the possible binding orientations need to be explored for modelling multidomain proteins and protein complexes. In general, hub proteins are shown to use distinct surface regions (multiple faces) for interactions with different partners. Our classification provides a convenient framework to query genuine gene fusion, which conserves binding orientation in both fused and separate forms. The result suggests that the binding orientations are not conserved in at least one-third of the gene fusion cases detected by a conventional sequence similarity search. We show that any evolutionary analysis on interfaces can be skewed by multiple binding orientations and multiple interaction partners. The taxonomic distribution of interface types suggests that ancient interfaces common to the three major kingdoms of life are enriched by symmetric homodimers. The classification results are online at http://www.scoppi.org.
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Affiliation(s)
- Wan Kyu Kim
- Bioinformatics Group, Biotechnological Centre, Technische Universität Dresden, Dresden, Germany
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Andreas Henschel
- Bioinformatics Group, Biotechnological Centre, Technische Universität Dresden, Dresden, Germany
| | - Christof Winter
- Bioinformatics Group, Biotechnological Centre, Technische Universität Dresden, Dresden, Germany
| | - Michael Schroeder
- Bioinformatics Group, Biotechnological Centre, Technische Universität Dresden, Dresden, Germany
- * To whom correspondence should be addressed. E-mail:
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26
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Abstract
Considering the limited success of the most sophisticated docking methods available and the amount of computation required for systematic docking, cataloging all the known interfaces may be an alternative basis for the prediction of protein tertiary and quaternary structures. We classify domain interfaces according to the geometry of domain-domain association. By applying a simple and efficient method called "interface tag clustering," more than 4,000 distinct types of domain interfaces are collected from Protein Quaternary Structure Server and Protein Data Bank. Given a pair of interacting domains, we define "face" as the set of interacting residues in each single domain and the pair of interacting faces as an "interface." We investigate how the geometry of interfaces relates to a network of interacting protein families, such as how many different binding orientations are possible between two families or whether a family uses distinct surfaces or the same surface when the family has diverse interaction partners from various families. We show there are, on average, 1.2-1.9 different types of interfaces between interacting domains and a significant number of family pairs associate in multiple orientations. In general, a family tends to use distinct faces for each partner when the family has diverse interaction partners. Each face is highly specific to its interaction partner and the binding orientation. The relative positions of interface residues are generally well conserved within the same type of interface even between remote homologs. The classification result is available at http://www.biotec.tu-dresden.de/~wkim/supplement.
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Affiliation(s)
- Wan Kyu Kim
- Biotechnological Centre, TU Dresden, Germany
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27
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Ali MH, Imperiali B. Protein oligomerization: how and why. Bioorg Med Chem 2005; 13:5013-20. [PMID: 15993087 DOI: 10.1016/j.bmc.2005.05.037] [Citation(s) in RCA: 258] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2005] [Accepted: 05/25/2005] [Indexed: 11/16/2022]
Abstract
A large fraction of cellular proteins are oligomeric. Protein oligomerization may often be an advantageous feature from the perspective of protein evolution and has probably evolved by a variety of mechanisms. The study of protein oligomerization may provide insights into the early protein environment and the evolution of modern proteins. Oligomeric mini-proteins, short peptides with discrete protein-like structures, may serve as valuable models for understanding features of protein oligomerization.
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Affiliation(s)
- Mayssam H Ali
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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28
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Gallego del Sol F, Nagano C, Cavada BS, Calvete JJ. The first crystal structure of a Mimosoideae lectin reveals a novel quaternary arrangement of a widespread domain. J Mol Biol 2005; 353:574-83. [PMID: 16185708 DOI: 10.1016/j.jmb.2005.08.055] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2005] [Revised: 08/22/2005] [Accepted: 08/23/2005] [Indexed: 11/16/2022]
Abstract
The crystal structures of the apo and mannose-bound Parkia platycephala seed lectin represent the first structure of a Mimosoideae lectin and a novel circular arrangement of beta-prism domains, and highlight the adaptability of the beta-prism fold as a building block in the evolution of plant lectins. The P.platycephala lectin is a dimer both in solution and in the crystals. Mannose binding to each of the three homologous carbohydrate-recognition domains of the lectin occurs through different modes, and restrains the flexibility of surface-exposed loops and residues involved in carbohydrate recognition. The planar array of carbohydrate-binding sites on the rim of the toroid-shaped structure of the P.platycephala lectin dimer immediately suggests a mechanism to promote multivalent interactions leading to cross-linking of carbohydrate ligands as part of the host strategy against phytopredators and pathogens. The cyclic structure of the P.platycephala lectin points to the convergent evolution of a structural principle for the construction of lectins involved in host defense or in attacking other organisms.
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29
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Chatterjee A, Mandal DK. Quaternary association and reactivation of dimeric concanavalin A. Int J Biol Macromol 2005; 35:103-9. [PMID: 15769522 DOI: 10.1016/j.ijbiomac.2005.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2004] [Revised: 01/04/2005] [Accepted: 01/04/2005] [Indexed: 11/26/2022]
Abstract
The reconstitution of dimeric concanavalin A (ConA) in terms of quaternary association and reactivation, after denaturation in urea, has been investigated using intrinsic fluorescence, 8-anilino-1-naphthalenesulfonate (ANS) binding, far-UV circular dichroism (CD), and an activity assay developed through a combination of affinity binding and the o-phthalaldehyde (OPA) procedure of protein estimation. The equilibrium denaturation of dimeric ConA in urea exhibits a biphasic unfolding pathway involving an intermediate with hydrophobic exposure, and the overall free energy of stabilization for the dimeric protein is obtained as 16.3 kcal mol(-1). The time course of reassociation and regain of activity during reconstitution reveals that the reactivation of ConA runs almost parallel to the process of subunit association. The reactivation reaction follows second-order kinetics, with a rate constant (k) of 2.6 x 10(2) M(-1) s(-1). These results may provide insight into the relationship between quaternary association and function of legume lectins.
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Affiliation(s)
- Anindya Chatterjee
- Department of Chemistry, Presidency College, 86/1 College Street, Kolkata 700073, India
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30
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Sinha S, Mitra N, Kumar G, Bajaj K, Surolia A. Unfolding studies on soybean agglutinin and concanavalin a tetramers: a comparative account. Biophys J 2005; 88:1300-10. [PMID: 15542553 PMCID: PMC1305132 DOI: 10.1529/biophysj.104.051052] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2004] [Accepted: 11/03/2004] [Indexed: 11/18/2022] Open
Abstract
The unfolding pathway of two very similar tetrameric legume lectins soybean agglutinin (SBA) and Concanavalin A (ConA) were determined using GdnCl-induced denaturation. Both proteins displayed a reversible two-state unfolding mechanism. The analysis of isothermal denaturation data provided values for conformational stability of the two proteins. It was found that the DeltaG of unfolding of SBA was much higher than ConA at all the temperatures at which the experiments were done. ConA had a T(g) 18 degrees C less than SBA. The higher conformational stability of SBA in comparison to ConA is largely due to substantial differences in their degrees of subunit interactions. Ionic interactions at the interface of the two proteins especially at the noncanonical interface seem to play a significant role in the observed stability differences between these two proteins. Furthermore, SBA is a glycoprotein with a GlcNac2Man9 chain attached to Asn-75 of each subunit. The sugar chain in SBA lies at the noncanonical interface of the protein, and it is found to interact with the amino acid residues in the adjacent noncanonical interface. These interactions further stabilize SBA with respect to ConA, which is not glycosylated.
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Affiliation(s)
- Sharmistha Sinha
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
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31
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Kulkarni KA, Srivastava A, Mitra N, Sharon N, Surolia A, Vijayan M, Suguna K. Effect of glycosylation on the structure of Erythrina corallodendron lectin. Proteins 2004; 56:821-7. [PMID: 15281133 DOI: 10.1002/prot.20168] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The three-dimensional structure of the recombinant form of Erythrina corallodendron lectin, complexed with lactose, has been elucidated by X-ray crystallography at 2.55 A resolution. 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 neighboring 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.
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Affiliation(s)
- K A Kulkarni
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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32
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Vogel C, Bashton M, Kerrison ND, Chothia C, Teichmann SA. Structure, function and evolution of multidomain proteins. Curr Opin Struct Biol 2004; 14:208-16. [PMID: 15093836 DOI: 10.1016/j.sbi.2004.03.011] [Citation(s) in RCA: 285] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Proteins are composed of evolutionary units called domains; the majority of proteins consist of at least two domains. These domains and nature of their interactions determine the function of the protein. The roles that combinations of domains play in the formation of the protein repertoire have been found by analysis of domain assignments to genome sequences. Additional findings on the geometry of domains have been gained from examination of three-dimensional protein structures. Future work will require a domain-centric functional classification scheme and efforts to determine structures of domain combinations.
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Affiliation(s)
- Christine Vogel
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
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33
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Bourne Y, Roig-Zamboni V, Barre A, Peumans WJ, Astoul CH, Van Damme EJM, Rougé P. The crystal structure of the Calystegia sepium agglutinin reveals a novel quaternary arrangement of lectin subunits with a beta-prism fold. J Biol Chem 2003; 279:527-33. [PMID: 14561768 DOI: 10.1074/jbc.m308218200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The high number of quaternary structures observed for lectins highlights the important role of these oligomeric assemblies during carbohydrate recognition events. Although a large diversity in the mode of association of lectin subunits is frequently observed, the oligomeric assemblies of plant lectins display small variations within a single family. The crystal structure of the mannose-binding jacalin-related lectin from Calystegia sepium (Calsepa) has been determined at 1.37-A resolution. Calsepa exhibits the same beta-prism fold as identified previously for other members of the family, but the shape and the hydrophobic character of its carbohydrate-binding site is unlike that of other members, consistent with surface plasmon resonance analysis showing a preference for methylated sugars. Calsepa reveals a novel dimeric assembly markedly dissimilar to those described earlier for Heltuba and jacalin but mimics the canonical 12-stranded beta-sandwich dimer found in legume lectins. The present structure exemplifies the adaptability of the beta-prism building block in the evolution of plant lectins and highlights the biological role of these quaternary structures for carbohydrate recognition.
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Affiliation(s)
- Yves Bourne
- AFMB-CNRS, CNRS UMR6098, F13402 Marseille Cedex 20, France.
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34
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Kapoor M, Srinivas H, Kandiah E, Gemma E, Ellgaard L, Oscarson S, Helenius A, Surolia A. Interactions of substrate with calreticulin, an endoplasmic reticulum chaperone. J Biol Chem 2003; 278:6194-200. [PMID: 12464625 DOI: 10.1074/jbc.m209132200] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Calreticulin is a molecular chaperone found in the endoplasmic reticulum in eukaryotes, and its interaction with N-glycosylated polypeptides is mediated by the glycan Glc(1)Man(7-9)GlcNAc(2) present on the target glycoproteins. Here, we report the thermodynamic parameters of its interaction with di-, tri-, and tetrasaccharide, which are truncated versions of the glucosylated arm of Glc(1)Man(7-9)GlcNAc(2), determined by the quantitative technique of isothermal titration calorimetry. This method provides a direct estimate of the binding constants (K(b)) and changes in enthalpy of binding (Delta H(b) degrees ) as well as the stoichiometry of the reaction. Unlike past speculations, these studies demonstrate unambiguously that calreticulin has only one site per molecule for binding its complementary glucosylated ligands. Although the binding of glucose by itself is not detectable, a binding constant of 4.19 x 10(4) m(-1) at 279 K is obtained when glucose occurs in alpha-1,3 linkage to Man alpha Me as in Glc alpha 1-3Man alpha Me. The binding constant increases by 25-fold from di- to trisaccharide and doubles from tri- to tetrasaccharide, demonstrating that the entire Glc alpha 1-3Man alpha 1-2Man alpha 1-2Man alpha Me structure of the oligosaccharide is recognized by calreticulin. The thermodynamic parameters thus obtained were supported by modeling studies, which showed that increased number of hydrogen bonds and van der Waals interactions occur as the size of the oligosaccharide is increased. Also, several novel findings about the recognition of saccharide ligands by calreticulin vis á vis legume lectins, which have the same fold as this chaperone, are discussed.
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Affiliation(s)
- Mili Kapoor
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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35
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Lescar J, Loris R, Mitchell E, Gautier C, Chazalet V, Cox V, Wyns L, Pérez S, Breton C, Imberty A. Isolectins I-A and I-B of Griffonia (Bandeiraea) simplicifolia. Crystal structure of metal-free GS I-B(4) and molecular basis for metal binding and monosaccharide specificity. J Biol Chem 2002; 277:6608-14. [PMID: 11714720 DOI: 10.1074/jbc.m109867200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Seeds from the African legume shrub Griffonia simplicifolia contain several lectins. Among them the tetrameric lectin GS I-B(4) has strict specificity for terminal alpha Gal residues, whereas the closely related lectin GS I-A(4) can also bind to alpha GalNAc. These two lectins are commonly used as markers in histology or for research in xenotransplantation. To elucidate the basis for the fine difference in specificity, the amino acid sequences of both lectins have been determined and show 89% identity. The crystal structure of GS I-B(4), determined at 2.5-A resolution, reveals a new quaternary structure that has never been observed in other legume lectins. An unexpected loss of both Ca(2+) and Mn(2+) ions, which are necessary for carbohydrate binding in legume lectins, may be related to a particular amino acid sequence Pro-Glu-Pro in the metal binding loop. Comparison with demetallized concanavalin A reveals a different process for the loss of metal ions and for the subsequent loss of carbohydrate binding activity. The GS I-A x alpha GalNAc and GS I-B x alpha Gal complexes were constructed using homology modeling and docking approaches. The unusual presence of an aromatic amino acid at position 47 (Tyr in I-A and Trp in I-B) explains the strong preference for alpha-anomeric sugars in both isolectins. Alteration at one amino acid position, Ala(106) in I-A versus Glu(106) in I-B, is the basis for the observed specificities toward alpha GalNAc and alpha Gal.
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Affiliation(s)
- Julien Lescar
- Centre de Recherches sur les Macromolécules Végétales, CNRS, Université Joseph Fourier, BP 53, F-38041 Grenoble cedex 09, France
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36
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Chandra NR, Prabu MM, Suguna K, Vijayan M. Structural similarity and functional diversity in proteins containing the legume lectin fold. PROTEIN ENGINEERING 2001; 14:857-66. [PMID: 11742104 DOI: 10.1093/protein/14.11.857] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Knowledge of structural relationships in proteins is increasingly proving very useful for in silico characterizations and is also being exploited as a prelude to almost every investigation in functional and structural genomics. A thorough understanding of the crucial features of a fold becomes necessary to realize the full potential of such relationships. To illustrate this, structures containing the legume lectin-like fold were chosen for a detailed analysis since they exhibit a total lack of sequence similarity among themselves and also belong to diverse functional families. A comparative analysis of 15 different families containing this fold was therefore carried out, which led to the determination of the minimal structural principles or the determining region of the fold. A critical evaluation of the structural features, such as the curvature of the front sheet, the presence of the hydrophobic cores and the binding site loops, suggests that none of them are crucial for either the formation or the stability of the fold, but are required to generate diversity and specificity to particular carbohydrates. In contrast, the presence of the three sheets in a particular geometry and also their topological connectivities seem to be important. The fold has been shown to tolerate different types of protein-protein associations, most of them exhibiting different types of quaternary associations and some even existing as complexes with other folds. The function of every family in this study is discussed with respect to its fold, leading to the suggestion that this fold can be linked to carbohydrate recognition in general.
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Affiliation(s)
- N R Chandra
- Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India
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37
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Srinivas VR, Reddy GB, Ahmad N, Swaminathan CP, Mitra N, Surolia A. Legume lectin family, the 'natural mutants of the quaternary state', provide insights into the relationship between protein stability and oligomerization. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1527:102-11. [PMID: 11479026 DOI: 10.1016/s0304-4165(01)00153-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Legume lectins family of proteins, despite having the same 'jelly roll' tertiary structural fold at monomeric level, exhibit considerable variation in their quaternary structure arising out of small changes in their sequence. Nevertheless, their folding behavior and stability correlates very well with their patterns of assembly into dimers and tetramers. A conservation of their fold during evolution, its wide distribution in many protein families together with the availability of structural information on them make them interesting as proteins to explore the effect of inter- versus intra-subunit interactions in the stability of multimeric proteins. Additionally, as 'natural mutants' of quaternary association, proteins of legume lectin family provide interesting paradigms for studies addressing the effect of subunit oligomerization on the stability, folding and function as well as the evolution of multimeric structures.
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Affiliation(s)
- V R Srinivas
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012
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38
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Wah DA, Romero A, Gallego del Sol F, Cavada BS, Ramos MV, Grangeiro TB, Sampaio AH, Calvete JJ. Crystal structure of native and Cd/Cd-substituted Dioclea guianensis seed lectin. A novel manganese-binding site and structural basis of dimer-tetramer association. J Mol Biol 2001; 310:885-94. [PMID: 11453695 DOI: 10.1006/jmbi.2001.4814] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Diocleinae legume lectins are a group of oligomeric proteins whose subunits display a high degree of primary structure and tertiary fold conservation but exhibit considerable diversity in their oligomerisation modes. To elucidate the structural determinants underlaying Diocleinae lectin oligomerisation, we have determined the crystal structures of native and cadmium-substituted Dioclea guianensis (Dguia) seed lectin. These structures have been solved by molecular replacement using concanavalin (ConA) coordinates as the starting model, and refined against data to 2.0 A resolution. In the native (Mn/Ca-Dguia) crystal form (P4(3)2(1)2), the asymmetric unit contains two monomers arranged into a canonical legume lectin dimer, and the tetramer is formed with a symmetry-related dimer. In the Cd/Cd-substituted form (I4(1)22), the asymmetric unit is occupied by a monomer. In both crystal forms, the tetrameric association is achieved by the corresponding symmetry operators. Like other legume lectins, native D. guianensis lectin contains manganese and calcium ions bound in the vicinity of the saccharide-combining site. The architecture of these metal-binding sites (S1 and S2) changed only slightly in the cadmium/cadmium-substituted form. A highly ordered calcium (native lectin) or cadmium (Cd/Cd-substituted lectin) ion is coordinated at the interface between dimers that are not tetrameric partners in a similar manner as the previously identified Cd(2+) in site S3 of a Cd/Ca-ConA. An additional Mn(2+) coordination site (called S5), whose presence has not been reported in crystal structures of any other homologous lectin, is present in both, the Mn/Ca and the Cd/Cd-substituted D. guianensis lectin forms. On the other hand, comparison of the primary and quaternary crystal structures of seed lectins from D. guianensis and Dioclea grandiflora (1DGL) indicates that the loop comprising residues 117-123 is ordered to make interdimer contacts in the D. grandiflora lectin structure, while this loop is disordered in the D. guianensis lectin structure. A single amino acid difference at position 131 (histidine in D. grandiflora and asparagine in D. guianensis) drastically reduces interdimer contacts, accounting for the disordered loop. Further, this amino acid change yields a conformation that may explain why a pH-dependent dimer-tetramer equilibrium exists for the D. guianensis lectin but not for the D. grandiflora lectin.
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Affiliation(s)
- D A Wah
- Centro de Investigaciones Biológicas, C.S.I.C., Madrid, Spain
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39
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Buts L, Dao-Thi MH, Loris R, Wyns L, Etzler M, Hamelryck T. Weak protein-protein interactions in lectins: the crystal structure of a vegetative lectin from the legume Dolichos biflorus. J Mol Biol 2001; 309:193-201. [PMID: 11491289 DOI: 10.1006/jmbi.2001.4639] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The legume lectins are widely used as a model system for studying protein-carbohydrate and protein-protein interactions. They exhibit a fascinating quaternary structure variation, which becomes important when they interact with multivalent glycoconjugates, for instance those on cell surfaces. Recently, it has become clear that certain lectins form weakly associated oligomers. This phenomenon may play a role in the regulation of receptor crosslinking and subsequent signal transduction. The crystal structure of DB58, a dimeric lectin from the legume Dolichos biflorus reveals a separate dimer of a previously unobserved type, in addition to a tetramer consisting of two such dimers. This tetramer resembles that formed by DBL, the seed lectin from the same plant. A single amino acid substitution in DB58 affects the conformation and flexibility of a loop in the canonical dimer interface. This disrupts the formation of a stable DBL-like tetramer in solution, but does not prohibit its formation in suitable conditions, which greatly increases the possibilities for the cross-linking of multivalent ligands. The non-canonical DB58 dimer has a buried symmetrical alpha helix, which can be present in the crystal in either of two antiparallel orientations. Two existing structures and datasets for lectins with similar quaternary structures were reconsidered. A central alpha helix could be observed in the soybean lectin, but not in the leucoagglutinating lectin from Phaseolus vulgaris. The relative position and orientation of the carbohydrate-binding sites in the DB58 dimer may affect its ability to crosslink mulitivalent ligands, compared to the other legume lectin dimers.
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Affiliation(s)
- L Buts
- ULTR-Ultrastructure Department, Vrije Universiteit Brussel, Sint-Genesius-Rode Belgium.
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Ravishankar R, Thomas CJ, Suguna K, Surolia A, Vijayan M. Crystal structures of the peanut lectin-lactose complex at acidic pH: retention of unusual quaternary structure, empty and carbohydrate bound combining sites, molecular mimicry and crystal packing directed by interactions at the combining site. Proteins 2001; 43:260-70. [PMID: 11288176 DOI: 10.1002/prot.1037] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The crystal structures of a monoclinic and a triclinic form of the peanut lectin-lactose complex, grown at pH 4.6, have been determined. They contain two and one crystallographically independent tetramers, respectively. The unusual "open" quaternary structure of the lectin, observed in the orthorhombic complex grown in neutral pH, is retained at the acidic pH. The sugar molecule is bound to three of the eight subunits in the monoclinic crystals, whereas the combining sites in four are empty. The lectin-sugar interactions are almost the same at neutral and acidic pH. A comparison of the sugar-bound and free subunits indicates that the geometry of the combining site is relatively unaffected by ligand binding. The combining site of the eighth subunit in the monoclinic crystals is bound to a peptide stretch in a loop from a neighboring molecule. The same interaction exists in two subunits of the triclinic crystals, whereas density corresponding to sugar exists in the combining sites of the other two subunits. Solution studies show that oligopeptides with sequences corresponding to that in the loop bind to the lectin at acidic pH, but only with reduced affinity at neutral pH. The reverse is the case with the binding of lactose to the lectin. A comparison of the neutral and acidic pH crystal structures indicates that the molecular packing in the latter is directed to a substantial extent by the increased affinity of the peptide loop to the combining site at acidic pH.
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Affiliation(s)
- R Ravishankar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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41
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Abstract
The Erythrina corallodendron lectin (EcorL) crystallizes in monoclinic and hexagonal crystal forms. Comparison of the newly determined hexagonal form (PDB code 1fyu) with the monoclinic form shows that the dimeric structure of EcorL reflects the inherent biological structure of the protein and is not an artifact of the crystal packing. To further understand the factors determining the dimerization modes of legume lectins, EcorL, concanavalin A (ConA), and Griffonia simplicifolia (GS4) were taken as representatives of the three unique dimers found in the family. Six virtual homodimers were generated. The hydropathy, amino acid composition, and solvation energy were calculated for all nine homodimers. Each of the three native dimers has a distinct chemical composition. EcorL has a dominant hydrophobic component, and ConA has a strong polar component, but in GS4 the three components contribute equally to the interface. This distribution pattern at the interface is unique to the native dimers and distinct from the partition observed in the virtual dimers. Amino acid composition of other members of the family that dimerize like EcorL or ConA maintain the same pattern of amino acids distribution observed in EcorL and ConA. However, lectins that dimerize like GS4 do not show a particularly distinct distribution. In all cases, the calculated solvation energy of the native dimer was lower than that of the virtual dimers, suggesting that the observed mode of dimerization is the most stable organization for the given sequence and tertiary structure. The dimerization type cannot be predicted by sequence analysis.
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Affiliation(s)
- S Elgavish
- Department of Biological Chemistry, The Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
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Sharon N, Lis H. The Structural Basis for Carbohydrate Recognition By Lectins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2001; 491:1-16. [PMID: 14533786 DOI: 10.1007/978-1-4615-1267-7_1] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
1. Different carbohydrate-specific proteins, such as lectins, may combine with the same monosaccharide or oligosaccharide by different H-bonding and hydrophobic side chains. 2. Homologous proteins with distinct specificities may bind different monosaccharides (e.g., for glucose and galactose that differ in the configuration of a single hydroxyl) by the same set of invariant residues that are identically positioned in their tertiary structures. 3. The energetics of protein-carbohydrate interactions cannot be derived from structural information. 4. Nature solves in a variety of different ways the problem of constructing combining sites for carbohydrates, just as it provides diverse solutions for other functions of proteins.
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Affiliation(s)
- N Sharon
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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Abstract
Lectins - carbohydrate-binding proteins involved in a variety of recognition processes - exhibit considerable structural diversity. Three new lectin folds and further elaborations of known folds have been described recently. Large variability in quaternary association resulting from small alterations in essentially the same tertiary structure is a property exhibited specially by legume lectins. The strategies used by lectins to generate carbohydrate specificity include the extensive use of water bridges, post-translational modification and oligomerization. Recent results pertaining to influenza and foot-and-mouth viruses further elaborate the role of lectins in infection.
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Affiliation(s)
- M Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560 012, India.
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Bouckaert J, Hamelryck T, Wyns L, Loris R. Novel structures of plant lectins and their complexes with carbohydrates. Curr Opin Struct Biol 1999; 9:572-7. [PMID: 10508764 DOI: 10.1016/s0959-440x(99)00007-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Several novel structures of legume lectins have led to a thorough understanding of monosaccharide and oligosaccharide specificity, to the determination of novel and surprising quaternary structures and, most importantly, to the structural identification of the binding site for adenine and plant hormones. This deepening of our understanding of the structure/function relationships among the legume lectins is paralleled by advances in two other plant lectin families - the monocot lectins and the jacalin family. As the number of available crystal structures increases, more parallels between plant and animal lectins become apparent.
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Affiliation(s)
- J Bouckaert
- Laboratorium voor Ultrastruktuur, Vlaams Interuniversitair Instituut voor Biotechnologie, Vrije Universiteit Brussel, Paardenstraat 65, B-1640, Sint-Genesius-Rode, Belgium
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