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Luo M, Ri S, Liu L, Ri S, Kim Y, Kim T, Ju K, Zhou W, Tong D, Shi W, Liu G. Identification, characterization, and agglutinating activity of a novel C-type lectin domain family 3 member B (CLEC3B) discovered in golden pompano, Trachinotus ovatus. FISH & SHELLFISH IMMUNOLOGY 2023; 140:108988. [PMID: 37541635 DOI: 10.1016/j.fsi.2023.108988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/06/2023] [Accepted: 08/02/2023] [Indexed: 08/06/2023]
Abstract
The lectins are a large family of carbohydrate-binding proteins that play important roles in the innate immune response of various organisms. Although C-type lectin domain family 3 member B (CLEC3B), an important member of C-type lectin, has been well documented in humans and several other higher vertebrates, little is currently known about this molecule in economically important marine fish species. In this study, through transcriptomic and BLAST screening, a novel CLEC3B gene was identified in the golden pompano (Trachinotus ovatus). The T. ovatus CLEC3B (ToCLEC3B) was subsequently characterized by bioinformatic analysis and compared with those reported in other species. In addition, the expression patterns of ToCLEC3B in different tissues under normal condition and at different times post pathogen challenge were assessed. Furthermore, the agglutinating activity of ToCLEC3B with and without Ca2+ against different bacteria and blood cells of donor species were verified using the recombinant T. ovatus CLEC3B (rToCLEC3B). Our results demonstrated that ToCLEC3B is a Ca2+-dependent galactose-binding lectin with a single copy of carbohydrate recognition domain (CRD). Similar to CLEC3B reported in other species, the CRD domain of ToCLEC3B consists of two α-helices, six β-sheets, and four loops, forming two Ca2+- and a galactose-binding sites. According to the phylogenetic analysis, the ToCLEC3B was highly similar (similarity at 95.00%) to that of its relative, the greater amberjack (Seriola dumerili). The expression of ToCLEC3B was detected in all tissues examined under normal condition and was significantly up-regulated by injection of pathogenic microbes. In addition, the rToCLEC3B exhibited strong agglutinating activity against different bacteria and blood cells of donor species in the presence of Ca2+. Our results indicate that ToCLEC3B is a constitutive and inducible acute-phase immune factor in the host's innate immune response of T. ovatus.
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Affiliation(s)
- Ming Luo
- Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences, Haikou, 571126, PR China
| | - Sanghyok Ri
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China; College of Life Science, Kim Hyong Jik University of Education, Pyongyang, 99903, Democratic People's Republic of Korea
| | - Longlong Liu
- Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences, Haikou, 571126, PR China
| | - Songnam Ri
- College of Life Science, Kim Hyong Jik University of Education, Pyongyang, 99903, Democratic People's Republic of Korea
| | - Yongchol Kim
- College of Life Science, Kim Hyong Jik University of Education, Pyongyang, 99903, Democratic People's Republic of Korea
| | - Tongchol Kim
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China; College of Life Science, Kim Hyong Jik University of Education, Pyongyang, 99903, Democratic People's Republic of Korea
| | - Kwangjin Ju
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China; College of Aquaculture, Wonsan Fisheries University, Wonsan, 999093, Democratic People's Republic of Korea
| | - Weishang Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Difei Tong
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Wei Shi
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Guangxu Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China.
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2
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Conroy DW, Xu Y, Shi H, Gonzalez Salguero N, Purusottam RN, Shannon MD, Al-Hashimi HM, Jaroniec CP. Probing Watson-Crick and Hoogsteen base pairing in duplex DNA using dynamic nuclear polarization solid-state NMR spectroscopy. Proc Natl Acad Sci U S A 2022; 119:e2200681119. [PMID: 35857870 PMCID: PMC9335254 DOI: 10.1073/pnas.2200681119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The majority of base pairs in double-stranded DNA exist in the canonical Watson-Crick geometry. However, they can also adopt alternate Hoogsteen conformations in various complexes of DNA with proteins and small molecules, which are key for biological function and mechanism. While detection of Hoogsteen base pairs in large DNA complexes and assemblies poses considerable challenges for traditional structural biology techniques, we show here that multidimensional dynamic nuclear polarization-enhanced solid-state NMR can serve as a unique spectroscopic tool for observing and distinguishing Watson-Crick and Hoogsteen base pairs in a broad range of DNA systems based on characteristic NMR chemical shifts and internuclear dipolar couplings. We illustrate this approach using a model 12-mer DNA duplex, free and in complex with the antibiotic echinomycin, which features two central adenine-thymine base pairs with Watson-Crick and Hoogsteen geometry, respectively, and subsequently extend it to the ∼200 kDa Widom 601 DNA nucleosome core particle.
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Affiliation(s)
- Daniel W. Conroy
- aDepartment of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Yu Xu
- bDepartment of Chemistry, Duke University, Durham, NC 27708
| | - Honglue Shi
- bDepartment of Chemistry, Duke University, Durham, NC 27708
| | | | - Rudra N. Purusottam
- aDepartment of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Matthew D. Shannon
- aDepartment of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Hashim M. Al-Hashimi
- bDepartment of Chemistry, Duke University, Durham, NC 27708
- cDepartment of Biochemistry, Duke University Medical Center, Durham, NC 27710
- dDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032
- 1To whom correspondence may be addressed. or
| | - Christopher P. Jaroniec
- aDepartment of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- 1To whom correspondence may be addressed. or
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Iram S, Rahman S, Ali S, Kim J. Tetranectin targeting by epigallocatechin gallate suppresses colon cancer cell proliferation. Int J Biol Macromol 2022; 209:211-219. [PMID: 35358581 DOI: 10.1016/j.ijbiomac.2022.03.160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 11/05/2022]
Abstract
Tetranectin is a serum protein that binds to plasminogen and enhances its proteolytic activation, which underlies the involvement of tetranectin in the development of several carcinomas including colon cancer. In the present study, structure-based in silico screening of natural products showed that epigallocatechin gallate with anticancer effects binds to tetranectin. Binding to epigallocatechin gallate to tetranectin was confirmed by intrinsic fluorescence quenching assays and isothermal titration calorimetry. Furthermore, epigallocatechin gallate efficiently inhibited the activity of tetranectin to enhance the activation of plasminogen. We also found that tetranectin enhanced the proliferation of CT-26 colon cancer cells. Epigallocatechin gallate showed its cytotoxic effect on CT-26 cells due to its binding to tetranectin and the consequent suppression of the cell proliferation. These results demonstrate that the anticancer effect of epigallocatechin gallate is mediated, at least in part, by inhibiting tetranectin as a binding target.
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Affiliation(s)
- Sana Iram
- Department of Medical Biotechnology and Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Safikur Rahman
- Department of Botany, Munshi Singh College, BR Ambedkar Bihar University, Muzaffarpur, Bihar 845401, India
| | - Shahid Ali
- Department of Medical Biotechnology and Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Jihoe Kim
- Department of Medical Biotechnology and Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Republic of Korea.
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4
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Multimerin-2 is a ligand for group 14 family C-type lectins CLEC14A, CD93 and CD248 spanning the endothelial pericyte interface. Oncogene 2017; 36:6097-6108. [PMID: 28671670 PMCID: PMC5671938 DOI: 10.1038/onc.2017.214] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 04/06/2017] [Accepted: 04/14/2017] [Indexed: 12/27/2022]
Abstract
The C-type lectin domain containing group 14 family members CLEC14A and CD93 are proteins expressed by endothelium and are implicated in tumour angiogenesis. CD248 (alternatively known as endosialin or tumour endothelial marker-1) is also a member of this family and is expressed by tumour-associated fibroblasts and pericytes. Multimerin-2 (MMRN2) is a unique endothelial specific extracellular matrix protein that has been implicated in angiogenesis and tumour progression. We show that the group 14 C-type lectins CLEC14A, CD93 and CD248 directly bind to MMRN2 and only thrombomodulin of the family does not. Binding to MMRN2 is dependent on a predicted long-loop region in the C-type lectin domain and is abrogated by mutation within the domain. CLEC14A and CD93 bind to the same non-glycosylated coiled-coil region of MMRN2, but the binding of CD248 occurs on a distinct non-competing region. CLEC14A and CD248 can bind MMRN2 simultaneously and this occurs at the interface between endothelium and pericytes in human pancreatic cancer. A recombinant peptide of MMRN2 spanning the CLEC14A and CD93 binding region blocks CLEC14A extracellular domain binding to the endothelial cell surface as well as increasing adherence of human umbilical vein endothelial cells to the active peptide. This MMRN2 peptide is anti-angiogenic in vitro and reduces tumour growth in mouse models. These findings identify novel protein interactions involving CLEC14A, CD93 and CD248 with MMRN2 as targetable components of vessel formation.
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5
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Aretz J, Wamhoff EC, Hanske J, Heymann D, Rademacher C. Computational and experimental prediction of human C-type lectin receptor druggability. Front Immunol 2014; 5:323. [PMID: 25071783 PMCID: PMC4090677 DOI: 10.3389/fimmu.2014.00323] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 06/26/2014] [Indexed: 01/21/2023] Open
Abstract
Mammalian C-type lectin receptors (CTLRS) are involved in many aspects of immune cell regulation such as pathogen recognition, clearance of apoptotic bodies, and lymphocyte homing. Despite a great interest in modulating CTLR recognition of carbohydrates, the number of specific molecular probes is limited. To this end, we predicted the druggability of a panel of 22 CTLRs using DoGSiteScorer. The computed druggability scores of most structures were low, characterizing this family as either challenging or even undruggable. To further explore these findings, we employed a fluorine-based nuclear magnetic resonance screening of fragment mixtures against DC-SIGN, a receptor of pharmacological interest. To our surprise, we found many fragment hits associated with the carbohydrate recognition site (hit rate = 13.5%). A surface plasmon resonance-based follow-up assay confirmed 18 of these fragments (47%) and equilibrium dissociation constants were determined. Encouraged by these findings we expanded our experimental druggability prediction to Langerin and MCL and found medium to high hit rates as well, being 15.7 and 10.0%, respectively. Our results highlight limitations of current in silico approaches to druggability assessment, in particular, with regard to carbohydrate-binding proteins. In sum, our data indicate that small molecule ligands for a larger panel of CTLRs can be developed.
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Affiliation(s)
- Jonas Aretz
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces , Potsdam , Germany ; Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin , Berlin , Germany
| | - Eike-Christian Wamhoff
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces , Potsdam , Germany ; Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin , Berlin , Germany
| | - Jonas Hanske
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces , Potsdam , Germany ; Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin , Berlin , Germany
| | - Dario Heymann
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces , Potsdam , Germany
| | - Christoph Rademacher
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces , Potsdam , Germany ; Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin , Berlin , Germany
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6
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Petrovskaya LE, Shingarova LN, Dolgikh DA, Kirpichnikov MP. Alternative scaffold proteins. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:581-91. [DOI: 10.1134/s1068162011050141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Byla P, Andersen MH, Holtet TL, Jacobsen H, Munch M, Gad HH, Thøgersen HC, Hartmann R. Selection of a novel and highly specific tumor necrosis factor alpha (TNFalpha) antagonist: insight from the crystal structure of the antagonist-TNFalpha complex. J Biol Chem 2010; 285:12096-100. [PMID: 20179326 DOI: 10.1074/jbc.m109.063305] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Inhibition of tumor necrosis factor alpha (TNFalpha) is a favorable way of treating several important diseases such as rheumatoid arthritis, Crohn disease, and psoriasis. Therefore, an extensive range of TNFalpha inhibitory proteins, most of them based upon an antibody scaffold, has been developed and used with variable success as therapeutics. We have developed a novel technology platform using C-type lectins as a vehicle for the creation of novel trimeric therapeutic proteins with increased avidity and unique properties as compared with current protein therapeutics. We chose human TNFalpha as a test target to validate this new technology because of the extensive experience available with protein-based TNFalpha antagonists. Here, we present a novel and highly specific TNFalpha antagonist developed using this technology. Furthermore, we have solved the three-dimensional structure of the antagonist-TNFalpha complex by x-ray crystallography, and this structure is presented here. The structure has given us a unique insight into how the selection procedure works at a molecular level. Surprisingly little change is observed in the C-type lectin-like domain structure outside of the randomized regions, whereas a substantial change is observed within the randomized loops. Thus, the overall integrity of the C-type lectin-like domain is maintained, whereas specificity and binding affinity are changed by the introduction of a number of specific contacts with TNFalpha.
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Affiliation(s)
- Povilas Byla
- Centre for Structural Biology, Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
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8
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Gourdine JP, Cioci G, Miguet L, Unverzagt C, Silva DV, Varrot A, Gautier C, Smith-Ravin EJ, Imberty A. High affinity interaction between a bivalve C-type lectin and a biantennary complex-type N-glycan revealed by crystallography and microcalorimetry. J Biol Chem 2008; 283:30112-20. [PMID: 18687680 PMCID: PMC2662075 DOI: 10.1074/jbc.m804353200] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Revised: 07/21/2008] [Indexed: 01/02/2023] Open
Abstract
Codakine is an abundant 14-kDa mannose-binding C-type lectin isolated from the gills of the sea bivalve Codakia orbicularis. Binding studies using inhibition of hemagglutination indicated specificity for mannose and fucose monosaccharides. Further experiments using a glycan array demonstrated, however, a very fine specificity for N-linked biantennary complex-type glycans. An unusually high affinity was measured by titration microcalorimetry performed with a biantennary Asn-linked nonasaccharide. The crystal structure of the native lectin at 1.3A resolution revealed a new type of disulfide-bridged homodimer. Each monomer displays three intramolecular disulfide bridges and contains only one calcium ion located in the canonical binding site that is occupied by a glycerol molecule. The structure of the complex between Asn-linked nonasaccharide and codakine has been solved at 1.7A resolution. All residues could be located in the electron density map, except for the capping beta1-4-linked galactosides. The alpha1-6-linked mannose binds to calcium by coordinating the O3 and O4 hydroxyl groups. The GlcNAc moiety of the alpha1,6 arm engages in several hydrogen bonds with the protein, whereas the GlcNAc on the other antenna is stacked against Trp(108), forming an extended binding site. This is the first structural report for a bivalve lectin.
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Affiliation(s)
- Jean-Philippe Gourdine
- Département de Biologie, Université des Antilles et de la Guyane, Pointe-à-Pitre, F-97159 Guadeloupe, France
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9
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Recombinant production and characterization of the carbohydrate recognition domain from Atlantic salmon C-type lectin receptor C (SCLRC). Protein Expr Purif 2008; 59:38-46. [PMID: 18272393 DOI: 10.1016/j.pep.2008.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Revised: 01/08/2008] [Accepted: 01/09/2008] [Indexed: 11/20/2022]
Abstract
The Atlantic salmon C-type lectin receptor C (SCLRC) locus encodes a potential oligomeric type II receptor. C-type lectins recognize carbohydrates in a Ca(2+)-dependent manner through structurally conserved, yet functionally diverse, C-type lectin-like domains (CTLDs). Many conserved amino acids in animal CTLDs are present in SCLRC, with the notable exception of an asparagine crucially involved in Ca(2+)- and carbohydrate-binding, which is tyrosine in SCLRC. SCLRC also contains six cysteines that form three disulfide bonds. Although SCLRC was originally identified as an up-regulated transcript responding to Aeromonas salmonicida infection, the biological role of this protein is still unknown. To study the structure and ligand binding properties of SCLRC, we created a homology model of the 17kDa CTLD and produced it as an affinity-tagged protein in the periplasm of Escherichia coli by co-expression of proteins that facilitate disulfide bond formation. The recombinant form of SCLRC was characterized by a protease protection assay, a solid-phase carbohydrate-binding assay, and frontal affinity chromatography. On the basis of this characterization, we classify SCLRC as a C-type lectin that binds to mannose and its derivatives.
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10
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Gill DS, Damle NK. Biopharmaceutical drug discovery using novel protein scaffolds. Curr Opin Biotechnol 2006; 17:653-8. [PMID: 17055245 DOI: 10.1016/j.copbio.2006.10.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Revised: 08/25/2006] [Accepted: 10/09/2006] [Indexed: 11/26/2022]
Abstract
In recent years, biopharmaceutical drug products have become hugely successful. However, they are often complex molecules that are expensive to manufacture. Commercial needs for cost-effective therapies have therefore led to the development of novel protein scaffold technologies that are increasingly being used for biopharmaceutical drug discovery. Major new scaffolds include single-domain antibodies, small modular immunopharmaceuticals, tetranectins, AdNectins, A-domain proteins, lipocalins and ankyrin repeat proteins. These scaffolds offer low-cost alternatives to classical antibody therapeutic strategies and some have shown early clinical promise. Further progress in the field will permit the commercially successful development of sophisticated protein therapeutics against complex disease targets.
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Affiliation(s)
- Davinder S Gill
- Wyeth Research, Biological Technologies 87 CambridgePark Drive, Cambridge, Massachusetts 02140, USA.
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11
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Hey T, Fiedler E, Rudolph R, Fiedler M. Artificial, non-antibody binding proteins for pharmaceutical and industrial applications. Trends Biotechnol 2006; 23:514-22. [PMID: 16054718 DOI: 10.1016/j.tibtech.2005.07.007] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2005] [Revised: 05/18/2005] [Accepted: 07/14/2005] [Indexed: 12/01/2022]
Abstract
Using combinatorial chemistry to generate novel binding molecules based on protein frameworks ('scaffolds') is a concept that has been strongly promoted during the past five years in both academia and industry. Non-antibody recognition proteins derive from different structural families and mimic the binding principle of immunoglobulins to varying degrees. In addition to the specific binding of a pre-defined target, these proteins provide favourable characteristics such as robustness, ease of modification and cost-efficient production. The broad spectrum of potential applications, including research tools, separomics, diagnostics and therapy, has led to the commercial exploitation of this technology by various small- and medium-sized companies. It is predicted that scaffold-based affinity reagents will broaden and complement applications that are presently covered by natural or recombinant antibodies. Here, we provide an overview on current approaches in the biotech industry, considering both scientific and commercial aspects.
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Affiliation(s)
- Thomas Hey
- Scil Proteins GmbH, Heinrich-Damerow-Str.1, 06120 Halle/Saale, Germany
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12
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Lundell A, Olin AI, Mörgelin M, al-Karadaghi S, Aspberg A, Logan DT. Structural basis for interactions between tenascins and lectican C-type lectin domains: evidence for a crosslinking role for tenascins. Structure 2005; 12:1495-506. [PMID: 15296743 DOI: 10.1016/j.str.2004.05.021] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2004] [Revised: 05/19/2004] [Accepted: 05/29/2004] [Indexed: 10/26/2022]
Abstract
The C-terminal G3 domains of lecticans mediate crosslinking to diverse extracellular matrix (ECM) proteins during ECM assembly, through their C-type lectin (CLD) subdomains. The structure of the rat aggrecan CLD in a Ca(2+)-dependent complex with fibronectin type III repeats 3-5 of rat tenascin-R provides detailed support for such crosslinking. The CLD loops bind Ca2+ like other CLDs, but no carbohydrate binding is observed or possible. This is thus the first example of a direct Ca(2+)-dependent protein-protein interaction of a CLD. Surprisingly, tenascin-R does not coordinate the Ca2+ ions directly. Electron microscopy confirms that full-length tenascin-R and tenascin-C crosslink hyaluronan-aggrecan complexes. The results are significant for the binding of all lectican CLDs to tenascin-R and tenascin-C. Comparison of the protein interaction surface with that of P-selectin in complex with the PGSL-1 peptide suggests that direct protein-protein interactions of Ca(2+)-binding CLDs may be more widespread than previously appreciated.
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Affiliation(s)
- Anna Lundell
- Department of Molecular Biophysics, Lund University, Box 124, S-221 00 Lund, Sweden
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13
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Zhao E, Liu HL, Tsai CH, Tsai HK, Chan CH, Kao CY. Cysteine separations profiles on protein sequences infer disulfide connectivity. Bioinformatics 2004; 21:1415-20. [PMID: 15585533 DOI: 10.1093/bioinformatics/bti179] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Disulfide bonds play an important role in protein folding. A precise prediction of disulfide connectivity can strongly reduce the conformational search space and increase the accuracy in protein structure prediction. Conventional disulfide connectivity predictions use sequence information, and prediction accuracy is limited. Here, by using an alternative scheme with global information for disulfide connectivity prediction, higher performance is obtained with respect to other approaches. RESULT Cysteine separation profiles have been used to predict the disulfide connectivity of proteins. The separations among oxidized cysteine residues on a protein sequence have been encoded into vectors named cysteine separation profiles (CSPs). Through comparisons of their CSPs, the disulfide connectivity of a test protein is inferred from a non-redundant template set. For non-redundant proteins in SwissProt 39 (SP39) sharing less than 30% sequence identity, the prediction accuracy of a fourfold cross-validation is 49%. The prediction accuracy of disulfide connectivity for proteins in SwissProt 43 (SP43) is even higher (53%). The relationship between the similarity of CSPs and the prediction accuracy is also discussed. The method proposed in this work is relatively simple and can generate higher accuracies compared to conventional methods. It may be also combined with other algorithms for further improvements in protein structure prediction. AVAILABILITY The program and datasets are available from the authors upon request. CONTACT cykao@csie.ntu.edu.tw.
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Affiliation(s)
- East Zhao
- Bioinformatics Laboratory, Department of Computer Science and Information Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, Taiwan 106
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14
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Guimarães-Gomes V, Oliveira-Carvalho AL, Junqueira-de-Azevedo IDLM, S Dutra DL, Pujol-Luz M, Castro HC, Ho PL, Zingali RB. Cloning, characterization, and structural analysis of a C-type lectin from Bothrops insularis (BiL) venom. Arch Biochem Biophys 2004; 432:1-11. [PMID: 15519291 DOI: 10.1016/j.abb.2004.08.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2004] [Revised: 08/16/2004] [Indexed: 10/26/2022]
Abstract
Lectins are carbohydrate-binding molecules that mediate a variety of biological processes. In this work, we identify and characterize a lectin from Bothrops insularis venom, with respect to its biochemical properties and theoretical structure. Initially, from a venom gland cDNA library, we cloned and sequenced a cDNA encoding a protein with high identity to snake venom lectins. A lectin molecule was purified to homogeneity from the venom by affinity column and gel filtration. This protein named BiL displayed hemagglutinating activity that was inhibited by galactose, lactose, and EDTA. Mass spectrometry analysis and sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that BiL is a disulfide-linked dimeric protein consisting of monomers with 16,206 m/z. The amino acid sequence, deduced from its cDNA sequence, was confirmed by Edman sequencing and by peptide mass fingerprint analysis. BiL shows similarity to other C-type lectin family members. Modeling studies provide insights into BiL dimeric structure and its structural determinants for carbohydrate and calcium binding.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Bothrops/metabolism
- Calcium/metabolism
- Carbohydrates/chemistry
- Chromatography, Gel
- Cloning, Molecular
- Crotalid Venoms/chemistry
- Crotalid Venoms/genetics
- DNA, Complementary/metabolism
- Dimerization
- Disulfides/chemistry
- Edetic Acid/pharmacology
- Electrophoresis, Polyacrylamide Gel
- Galactose/chemistry
- Gene Library
- Lectins/chemistry
- Lectins, C-Type/chemistry
- Lectins, C-Type/genetics
- Mass Spectrometry
- Methylation
- Models, Molecular
- Molecular Sequence Data
- Peptides/chemistry
- Polysaccharides/chemistry
- Protein Binding
- Protein Structure, Tertiary
- Sepharose/chemistry
- Sequence Homology, Amino Acid
- Software
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Time Factors
- Toxins, Biological/chemistry
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Affiliation(s)
- Viviane Guimarães-Gomes
- Rede Proteômica do Rio de Janeiro and Laboratório de Hemostase e Venenos (LabHemoVen), Departamento de Bioquímica Médica-ICB, Universidade Federal do Rio de Janeiro, CEP 21941-590, Rio de Janeiro/RJ, Brazil
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15
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Abstract
Originally discovered in 1994 by Folkman and coworkers, angiostatin was identified through its antitumor effects in mice and later shown to be a potent inhibitor of angiogenesis. An internal fragment of plasminogen, angiostatin consists of kringle domains that are known to be lysine-binding. The crystal structure of angiostatin was the first multikringle domain-containing structure to be published. This review will focus on what is known about the structure of angiostatin and its implications in function from the current literature.
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Affiliation(s)
- J H Geiger
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA.
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16
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Ebner S, Sharon N, Ben-Tal N. Evolutionary analysis reveals collective properties and specificity in the C-type lectin and lectin-like domain superfamily. Proteins 2003; 53:44-55. [PMID: 12945048 DOI: 10.1002/prot.10440] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Members of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily share a common fold and are involved in a variety of functions, such as generalized defense mechanisms against foreign agents, discrimination between healthy and pathogen-infected cells, and endocytosis and blood coagulation. In this work we used ConSurf, a computer program recently developed in our lab, to perform an evolutionary analysis of this superfamily in order to further identify characteristics of all or part of its members. Given a set of homologous proteins in the form of multiple sequence alignment (MSA) and an inferred phylogenetic tree, ConSurf calculates the conservation score in every alignment position, taking into account the relationships between the sequences and the physicochemical similarity between the amino acids. The scores are then color-coded onto the three-dimensional structure of one of the homologous proteins. We provide here and at http://ashtoret.tau.ac.il/ approximately sharon a detailed analysis of the conservation pattern obtained for the entire superfamily and for two subgroups of proteins: (a) 21 CTLs and (b) 11 heterodimeric CTLD toxins. We show that, in general, proteins of the superfamily have one face that is constructed mostly of conserved residues and another that is not, and we suggest that the former face is involved in binding to other proteins or domains. In the CTLs examined we detected a region of highly conserved residues, corresponding to the known calcium- and carbohydrate-binding site of the family, which is not conserved throughout the entire superfamily, and in the CTLD toxins we found a patch of highly conserved residues, corresponding to the known dimerization region of these proteins. Our analysis also detected patches of conserved residues with yet unknown function(s).
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Affiliation(s)
- Sharon Ebner
- Department of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978, Israel
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17
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Natarajan K, Dimasi N, Wang J, Mariuzza RA, Margulies DH. Structure and function of natural killer cell receptors: multiple molecular solutions to self, nonself discrimination. Annu Rev Immunol 2002; 20:853-85. [PMID: 11861620 DOI: 10.1146/annurev.immunol.20.100301.064812] [Citation(s) in RCA: 235] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In contrast to T cell receptors, signal transducing cell surface membrane molecules involved in the regulation of responses by cells of the innate immune system employ structures that are encoded in the genome rather than generated by somatic recombination and that recognize either classical MHC-I molecules or their structural relatives (such as MICA, RAE-1, or H-60). Considerable progress has recently been made in our understanding of molecular recognition by such molecules based on the determination of their three-dimensional structure, either in isolation or in complex with their MHC-I ligands. Those best studied are the receptors that are expressed on natural killer (NK) cells, but others are found on populations of T cells and other hematopoietic cells. These molecules fall into two major structural classes, those of the immunoglobulin superfamily (KIRs and LIRs) and of the C-type lectin-like family (Ly49, NKG2D, and CD94/NKG2). Here we summarize, in a functional context, the structures of the murine and human molecules that have recently been determined, with emphasis on how they bind different regions of their MHC-I ligands, and how this allows the discrimination of tumor or virus-infected cells from normal cells of the host.
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MESH Headings
- Alleles
- Amino Acid Sequence
- Animals
- Antigens, CD/chemistry
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Antigens, Ly
- Histocompatibility Antigens Class I/chemistry
- Histocompatibility Antigens Class I/metabolism
- Humans
- Killer Cells, Natural/immunology
- Lectins, C-Type
- Leukocyte Immunoglobulin-like Receptor B1
- Macromolecular Substances
- Membrane Glycoproteins/chemistry
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/metabolism
- Mice
- Models, Molecular
- Molecular Sequence Data
- Molecular Structure
- NK Cell Lectin-Like Receptor Subfamily D
- Receptors, Immunologic/chemistry
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Receptors, KIR
- Receptors, KIR2DL1
- Receptors, NK Cell Lectin-Like
- Self Tolerance
- Sequence Homology, Amino Acid
- Signal Transduction
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Affiliation(s)
- Kannan Natarajan
- Molecular Biology Section, Laboratory of Immunology, NIAID, NIH, Bethesda, Maryland 20892-1892, USA.
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18
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Abad MC, Arni RK, Grella DK, Castellino FJ, Tulinsky A, Geiger JH. The X-ray crystallographic structure of the angiogenesis inhibitor angiostatin. J Mol Biol 2002; 318:1009-17. [PMID: 12054798 DOI: 10.1016/s0022-2836(02)00211-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Angiogenesis inhibitors have gained much public attention recently as anti-cancer agents and several are currently in clinical trials, including angiostatin (Phase I, Thomas Jefferson University Hospital, Philadelphia, PA). We report here the bowl-shaped structure of angiostatin kringles 1-3, the first multi-kringle structure to be determined. All three kringle lysine-binding sites contain a bound bicine molecule of crystallization while the former of kringle 2 and kringle 3 are cofacial. Moreover, the separation of the kringle 2 and kringle 3 lysiner binding sites is sufficient to accommodate the alpha-helix of the 30 residue peptide VEK-30 found in the kringle 2/VEK-30 complex. Together the three kringles produce a central cavity suggestive of a unique domain where they may function in concert.
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Affiliation(s)
- Marta C Abad
- Department of Chemistry, Michigan State University, East Lansing 48824, USA
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19
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Xu X, Gilpin B, Iba K, Maier A, Engvall E, Albrechtsen R, Wewer UM. Tetranectin in slow intra- and extrafusal chicken muscle fibers. J Muscle Res Cell Motil 2002; 22:121-32. [PMID: 11519735 DOI: 10.1023/a:1010377325382] [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: 11/12/2022]
Abstract
Tetranectin is a C-type lectin that occurs in the mammalian musculoskeletal system. In the present report we describe the first studies on an avian tetranectin. A full-length chicken tetranectin cDNA was isolated. Comparison of the deduced amino acid sequence of chicken tetranectin with mouse and human tetranectin showed an identity of 67 and 68%, respectively. Northern blot analysis demonstrated broad expression of chicken tetranectin mRNA, which was first detected on embryonic day 4. Tetranectin protein was detected in chicken serum and egg yolk. Since muscle is one of few tissues in which tetranectin protein is retained, we examined the distribution of tetranectin in various muscle types in chicken. Myofibers strongly positive for tetranectin were observed in several muscles including m. tibialis ant. and m. sartorius (from embryonic day 10 to adult). Using antibodies to fast and slow myosin heavy chains (MHC) and double immunostaining techniques, we found that tetranectin was restricted to slow (type I) muscle fibers. Similarly only slow intrafusal fibers accumulated tetranectin. The pattern of immunostaining in chickens differs markedly from that seen in mouse muscles, indicating that tetranectin performs a role in muscle that is not associated with a hitherto recognized muscle type or function.
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MESH Headings
- Adaptation, Physiological/physiology
- Amino Acid Sequence/genetics
- Animals
- Blood Proteins/genetics
- Blood Proteins/metabolism
- Caenorhabditis elegans Proteins/genetics
- Caenorhabditis elegans Proteins/metabolism
- Cattle
- Cell Differentiation/genetics
- Chick Embryo
- Chickens/anatomy & histology
- Chickens/growth & development
- Chickens/metabolism
- DNA, Complementary/metabolism
- Drosophila Proteins/genetics
- Drosophila Proteins/metabolism
- Gene Expression Regulation, Developmental/physiology
- Humans
- Immunohistochemistry
- Lectins/genetics
- Lectins/metabolism
- Lectins, C-Type
- Mice
- Molecular Sequence Data
- Muscle Contraction/physiology
- Muscle Fibers, Fast-Twitch/cytology
- Muscle Fibers, Fast-Twitch/metabolism
- Muscle Fibers, Slow-Twitch/cytology
- Muscle Fibers, Slow-Twitch/metabolism
- Muscle Spindles/cytology
- Muscle Spindles/growth & development
- Muscle Spindles/metabolism
- Muscle, Skeletal/embryology
- Muscle, Skeletal/growth & development
- Muscle, Skeletal/metabolism
- Myosin Heavy Chains/metabolism
- Phylogeny
- RNA, Messenger/metabolism
- Sequence Homology, Nucleic Acid
- Stem Cells/cytology
- Stem Cells/metabolism
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Affiliation(s)
- X Xu
- Institute of Molecular Pathology, University of Copenhagen, Denmark
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20
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Grégoire C, Marco S, Thimonier J, Duplan L, Laurine E, Chauvin JP, Michel B, Peyrot V, Verdier JM. Three-dimensional structure of the lithostathine protofibril, a protein involved in Alzheimer's disease. EMBO J 2001; 20:3313-21. [PMID: 11432819 PMCID: PMC125531 DOI: 10.1093/emboj/20.13.3313] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Neurodegenerative diseases are characterized by the presence of filamentous aggregates of proteins. We previously established that lithostathine is a protein overexpressed in the pre-clinical stages of Alzheimer's disease. Furthermore, it is present in the pathognomonic lesions associated with Alzheimer's disease. After self-proteolysis, the N-terminally truncated form of lithostathine leads to the formation of fibrillar aggregates. Here we observed using atomic force microscopy that these aggregates consisted of a network of protofibrils, each of which had a twisted appearance. Electron microscopy and image analysis showed that this twisted protofibril has a quadruple helical structure. Three-dimensional X-ray structural data and the results of biochemical experiments showed that when forming a protofibril, lithostathine was first assembled via lateral hydrophobic interactions into a tetramer. Each tetramer then linked up with another tetramer as the result of longitudinal electrostatic interactions. All these results were used to build a structural model for the lithostathine protofibril called the quadruple-helical filament (QHF-litho). In conclusion, lithostathine strongly resembles the prion protein in its dramatic proteolysis and amyloid proteins in its ability to form fibrils.
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Affiliation(s)
- Catherine Grégoire
- UMR CNRS 6032, Faculté de Pharmacie, Marseille, Laboratoire des Protéines Complexes, Université de Tours, UPRES EA 32-90, Faculté de Médecine, Marseille, Laboratoire de Génétique et de Physiologie du Développement, IBDM, Marseille and Unité de Neurogériatrie, Hôpital Sainte-Marguerite, Marseille, France Corresponding author e-mail:
| | - Sergio Marco
- UMR CNRS 6032, Faculté de Pharmacie, Marseille, Laboratoire des Protéines Complexes, Université de Tours, UPRES EA 32-90, Faculté de Médecine, Marseille, Laboratoire de Génétique et de Physiologie du Développement, IBDM, Marseille and Unité de Neurogériatrie, Hôpital Sainte-Marguerite, Marseille, France Corresponding author e-mail:
| | - Jean Thimonier
- UMR CNRS 6032, Faculté de Pharmacie, Marseille, Laboratoire des Protéines Complexes, Université de Tours, UPRES EA 32-90, Faculté de Médecine, Marseille, Laboratoire de Génétique et de Physiologie du Développement, IBDM, Marseille and Unité de Neurogériatrie, Hôpital Sainte-Marguerite, Marseille, France Corresponding author e-mail:
| | - Laure Duplan
- UMR CNRS 6032, Faculté de Pharmacie, Marseille, Laboratoire des Protéines Complexes, Université de Tours, UPRES EA 32-90, Faculté de Médecine, Marseille, Laboratoire de Génétique et de Physiologie du Développement, IBDM, Marseille and Unité de Neurogériatrie, Hôpital Sainte-Marguerite, Marseille, France Corresponding author e-mail:
| | - Emmanuelle Laurine
- UMR CNRS 6032, Faculté de Pharmacie, Marseille, Laboratoire des Protéines Complexes, Université de Tours, UPRES EA 32-90, Faculté de Médecine, Marseille, Laboratoire de Génétique et de Physiologie du Développement, IBDM, Marseille and Unité de Neurogériatrie, Hôpital Sainte-Marguerite, Marseille, France Corresponding author e-mail:
| | - Jean-Paul Chauvin
- UMR CNRS 6032, Faculté de Pharmacie, Marseille, Laboratoire des Protéines Complexes, Université de Tours, UPRES EA 32-90, Faculté de Médecine, Marseille, Laboratoire de Génétique et de Physiologie du Développement, IBDM, Marseille and Unité de Neurogériatrie, Hôpital Sainte-Marguerite, Marseille, France Corresponding author e-mail:
| | - Bernard Michel
- UMR CNRS 6032, Faculté de Pharmacie, Marseille, Laboratoire des Protéines Complexes, Université de Tours, UPRES EA 32-90, Faculté de Médecine, Marseille, Laboratoire de Génétique et de Physiologie du Développement, IBDM, Marseille and Unité de Neurogériatrie, Hôpital Sainte-Marguerite, Marseille, France Corresponding author e-mail:
| | - Vincent Peyrot
- UMR CNRS 6032, Faculté de Pharmacie, Marseille, Laboratoire des Protéines Complexes, Université de Tours, UPRES EA 32-90, Faculté de Médecine, Marseille, Laboratoire de Génétique et de Physiologie du Développement, IBDM, Marseille and Unité de Neurogériatrie, Hôpital Sainte-Marguerite, Marseille, France Corresponding author e-mail:
| | - Jean-Michel Verdier
- UMR CNRS 6032, Faculté de Pharmacie, Marseille, Laboratoire des Protéines Complexes, Université de Tours, UPRES EA 32-90, Faculté de Médecine, Marseille, Laboratoire de Génétique et de Physiologie du Développement, IBDM, Marseille and Unité de Neurogériatrie, Hôpital Sainte-Marguerite, Marseille, France Corresponding author e-mail:
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21
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Zeng R, Xu Q, Shao XX, Wang KY, Xia QC. Determination of the disulfide bond pattern of a novel C-type lectin from snake venom by mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2001; 15:2213-2220. [PMID: 11746888 DOI: 10.1002/rcm.500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The disulfide bond pattern of Trimeresurus stejnegeri lectin (TSL), a new member of the C-type lectin family, was determined by mass spectrometry. Four intrachain disulfide bonds of TSL, Cys(3)-Cys(14), Cys(31)-Cys(131), Cys(38)-Cys(133) and Cys(106)-Cys(123), and two interchain linkages, Cys(2)-Cys(2) and Cys(86)-Cys(86), were determined. Three strategies were used in this work. One intrachain (Cys(106)-Cys(123)) and one interchain (Cys(86)-Cys(86)) disulfide linkages were detected by standard MS methods. The disulfide bonds Cys(2)-Cys(2) and Cys(3)-Cys(14) were analyzed using a modified partial reduction procedure and MS/MS. The last two disulfide bonds were characterized by a MS/MS/MS technique. The strategies developed in this work could be applied more generally to detection of disulfide bond patterns.
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Affiliation(s)
- R Zeng
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, People's Republic of China
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22
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Graversen JH, Jacobsen C, Sigurskjold BW, Lorentsen RH, Moestrup SK, Thogersen HC, Etzerodt M. Mutational analysis of affinity and selectivity of kringle-tetranectin interaction. Grafting novel kringle affinity ontp the trtranectin lectin scaffold. J Biol Chem 2000; 275:37390-6. [PMID: 10964919 DOI: 10.1074/jbc.m004873200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
C-type lectin-like domains are found in many proteins, where they mediate binding to a wide diversity of compounds, including carbohydrates, lipids, and proteins. The binding of a C-type lectin-like domain to a ligand is often influenced by calcium. Recently, we have identified a site in the C-type lectin-like domain of tetranectin, involving Lys-148, Glu-150, and Asp-165, which mediates calcium-sensitive binding to plasminogen kringle 4. Here, we investigate the effect of conservative substitutions of these and a neighboring amino acid residue. Substitution of Thr-149 in tetranectin with a tyrosine residue considerably increases the affinity for plasminogen kringle 4, and, in addition, confers affinity for plasminogen kringle 2. As shown by isothermal titration calorimetry analysis, this new interaction is stronger than the binding of wild-type tetranectin to plasminogen kringle 4. This study provides further insight into molecular determinants of importance for binding selectivity and affinity of C-type lectin kringle interactions.
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Affiliation(s)
- J H Graversen
- Laboratory of Gene Expression, Department of Molecular and Structural Biology and the Department of Medical Biochemistry, University of Aarhus, DK-8000 Aarhus C, Denmark
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23
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Zhou X, Alber F, Folkers G, Gonnet GH, Chelvanayagam G. An analysis of the helix-to-strand transition between peptides with identical sequence. Proteins 2000; 41:248-56. [PMID: 10966577 DOI: 10.1002/1097-0134(20001101)41:2<248::aid-prot90>3.0.co;2-j] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An analysis of peptide segments with identical sequence but that differ significantly in structure was performed over non-redundant databases of protein structures. We focus on those peptides, which fold into an alpha-helix in one protein but a beta-strand in another. While the study shows that many such structurally ambivalent peptides contain amino acids with a strong helical preference collocated with amino acids with a strong strand preference, the results overwhelmingly indicate that the peptide's environment ultimately dictates its structure. Furthermore, the first naturally occurring structurally ambivalent nonapeptide from evolutionary unrelated proteins is described, highlighting the intrinsic plasticity of peptide sequences. We even find seven proteins that show structural ambivalence under different conditions. Finally, a computer algorithm has been implemented to identify regions in a given sequence where secondary structure prediction programs are likely to make serious mispredictions.
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Affiliation(s)
- X Zhou
- Department of Computer Science, Eidgenössische Technische Hochshule, Zürich, Switzerland
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24
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Feinberg H, Park-Snyder S, Kolatkar AR, Heise CT, Taylor ME, Weis WI. Structure of a C-type carbohydrate recognition domain from the macrophage mannose receptor. J Biol Chem 2000; 275:21539-48. [PMID: 10779515 DOI: 10.1074/jbc.m002366200] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mannose receptor of macrophages and liver endothelium mediates clearance of pathogenic organisms and potentially harmful glycoconjugates. The extracellular portion of the receptor includes eight C-type carbohydrate recognition domains (CRDs), of which one, CRD-4, shows detectable binding to monosaccharide ligands. We have determined the crystal structure of CRD-4. Although the basic C-type lectin fold is preserved, a loop extends away from the core of the domain to form a domain-swapped dimer in the crystal. Of the two Ca(2+) sites, only the principal site known to mediate carbohydrate binding in other C-type lectins is occupied. This site is altered in a way that makes sugar binding impossible in the mode observed in other C-type lectins. The structure is likely to represent an endosomal form of the domain formed when Ca(2+) is lost from the auxiliary calcium site. The structure suggests a mechanism for endosomal ligand release in which the auxiliary calcium site serves as a pH sensor. Acid pH-induced removal of this Ca(2+) results in conformational rearrangements of the receptor, rendering it unable to bind carbohydrate ligands.
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Affiliation(s)
- H Feinberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA
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25
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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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26
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Poget SF, Legge GB, Proctor MR, Butler PJ, Bycroft M, Williams RL. The structure of a tunicate C-type lectin from Polyandrocarpa misakiensis complexed with D -galactose. J Mol Biol 1999; 290:867-79. [PMID: 10398588 DOI: 10.1006/jmbi.1999.2910] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
C-type lectins are calcium-dependent carbohydrate-recognising proteins. Isothermal titration calorimetry of the C-type Polyandrocarpa lectin (TC14) from the tunicate Polyandrocarpa misakiensis revealed the presence of a single calcium atom per monomer with a dissociation constant of 2.6 microM, and confirmed the specificity of TC14 for D -galactose and related monosaccharides. We have determined the 2.2 A X-ray crystal structure of Polyandrocarpa lectin complexed with D -galactose. Analytical ultracentrifugation revealed that TC14 behaves as a dimer in solution. This is reflected by the presence of two molecules in the asymmetric unit with the dimeric interface formed by antiparallel pairing of the two N-terminal beta-strands and hydrophobic interactions. TC14 adopts a typical C-type lectin fold with differences in structure from other C-type lectins mainly in the diverse loop regions and in the second alpha-helix, which is involved in the formation of the dimeric interface. The D -galactose is bound through coordination of the 3 and 4-hydroxyl oxygen atoms with a bound calcium atom. Additional hydrogen bonds are formed directly between serine, aspartate and glutamate side-chains of the protein and the sugar 3 and 4-hydroxyl groups. Comparison of the galactose binding by TC14 with the mannose binding by rat mannose-binding protein reveals how monosaccharide specificity is achieved in this lectin. A tryptophan side-chain close to the binding site and the distribution of hydrogen-bond acceptors and donors around the 3 and 4-hydroxyl groups of the sugar are essential determinants of specificity. These elements are, however, arranged in a very different way than in an engineered galactose-specific mutant of MBPA. Possible biological functions can more easily be understood from the fact that TC14 is a dimer under physiological conditions.
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Affiliation(s)
- S F Poget
- Cambridge Centre for Protein Engineering, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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27
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Graversen JH, Lorentsen RH, Jacobsen C, Moestrup SK, Sigurskjold BW, Thogersen HC, Etzerodt M. The plasminogen binding site of the C-type lectin tetranectin is located in the carbohydrate recognition domain, and binding is sensitive to both calcium and lysine. J Biol Chem 1998; 273:29241-6. [PMID: 9786936 DOI: 10.1074/jbc.273.44.29241] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tetranectin, a homotrimeric protein belonging to the family of C-type lectins and structurally highly related to corresponding regions of the mannose-binding proteins, is known specifically to bind the plasminogen kringle 4 protein domain, an interaction sensitive to lysine. Surface plasmon resonance and isothermal calorimetry binding analyses using single-residue and deletion mutant tetranectin derivatives produced in Escherichia coli showed that the kringle 4 binding site resides in the carbohydrate recognition domain and includes residues of the putative carbohydrate binding site. Furthermore, the binding analysis revealed that the interaction is sensitive to calcium in addition to lysine.
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Affiliation(s)
- J H Graversen
- Laboratory of Gene Expression, Department of Molecular and Structural Biology, University of Aarhus, DK-8000 Aarhus C, Denmark
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