1
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Caulton SG, Lambert C, Tyson J, Radford P, Al-Bayati A, Greenwood S, Banks EJ, Clark C, Till R, Pires E, Sockett RE, Lovering AL. Bdellovibrio bacteriovorus uses chimeric fibre proteins to recognize and invade a broad range of bacterial hosts. Nat Microbiol 2024; 9:214-227. [PMID: 38177296 PMCID: PMC10769870 DOI: 10.1038/s41564-023-01552-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 11/07/2023] [Indexed: 01/06/2024]
Abstract
Predatory bacteria, like the model endoperiplasmic bacterium Bdellovibrio bacteriovorus, show several adaptations relevant to their requirements for locating, entering and killing other bacteria. The mechanisms underlying prey recognition and handling remain obscure. Here we use complementary genetic, microscopic and structural methods to address this deficit. During invasion, the B. bacteriovorus protein CpoB concentrates into a vesicular compartment that is deposited into the prey periplasm. Proteomic and structural analyses of vesicle contents reveal several fibre-like proteins, which we name the mosaic adhesive trimer (MAT) superfamily, and show localization on the predator surface before prey encounter. These dynamic proteins indicate a variety of binding capabilities, and we confirm that one MAT member shows specificity for surface glycans from a particular prey. Our study shows that the B. bacteriovorus MAT protein repertoire enables a broad means for the recognition and handling of diverse prey epitopes encountered during bacterial predation and invasion.
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Affiliation(s)
- Simon G Caulton
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Carey Lambert
- School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, UK
- Biodiscovery Institute, School of Life Sciences, Nottingham University, Nottingham, UK
| | - Jess Tyson
- School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, UK
| | - Paul Radford
- School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, UK
| | - Asmaa Al-Bayati
- School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, UK
- Northern Technical University, Kirkuk, Iraq
| | - Samuel Greenwood
- School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, UK
| | - Emma J Banks
- School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, UK
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Callum Clark
- School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, UK
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Rob Till
- School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, UK
| | - Elisabete Pires
- Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - R Elizabeth Sockett
- School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, UK.
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2
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Krishnan H, Gopinath SCB. A potent anticoagulant hybrid of snake venom derived FIX-binding protein and anti-factor IX RNA aptamer: Assessed by in-silico and electrochemical analyses. Int J Biol Macromol 2023; 247:125740. [PMID: 37423441 DOI: 10.1016/j.ijbiomac.2023.125740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Anticoagulant therapies are crucial in the management of surgical complications as well as the prophylaxis of thrombosis. Many studies are being conducted on the Habu snake-venom anticoagulant, FIX-binding protein (FIX-Bp), for its greater potency and strong affinity to FIX clotting factor. On the other hand, the capacity to promptly reverse such acute anticoagulation is equally important. Combining a reversible anticoagulant with FIX-Bp may be advantageous in maintaining the balance between adequate anticoagulation and repealing when necessary. In this study, authors integrated FIX-Bp and RNA aptamer-based anticoagulants into a single target, FIX clotting factor, in order to achieve a robust anticoagulant effect. An in-silico and electrochemical approach were used to investigate the combination of FIX-Bp and RNA aptamers as a bivalent anticoagulant and to verify the competing or predominant binding sites of each anticoagulant. The in-silico analysis discovered that both the venom- and aptamer-anticoagulant had a strong affinity for the FIX protein at the Gla-domain and EGF-1 domain by holding 9 conventional hydrogen bonds with the binding energy of -34.859 kcal/mol. The electrochemical technique verified that both anticoagulants had different binding sites. The impedance load upon RNA aptamer binding to FIX protein was 14 %, whereas the addition of FIX-Bp caused a significant impedance rise of 37 %. This indicates that the addition of aptamers prior to FIX-Bp is a promising strategy for the conception of a hybrid anticoagulant.
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Affiliation(s)
- Hemavathi Krishnan
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), 01000 Kangar, Perlis, Malaysia
| | - Subash C B Gopinath
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), 01000 Kangar, Perlis, Malaysia; Faculty of Chemical Engineering & Technology, Universiti Malaysia Perlis (UniMAP), 02600 Arau, Perlis, Malaysia; Micro System Technology, Centre of Excellence (CoE), Universiti Malaysia Perlis (UniMAP), Pauh Campus, 02600 Arau, Perlis, Malaysia; Department of Computer Science and Engineering, Faculty of Science and Information Technology, Daffodil International University, Daffodil Smart City, Birulia, Savar, Dhaka 1216, Bangladesh.
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3
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Puzari U, Goswami M, Rani K, Patra A, Mukherjee AK. Computational and in vitro analyses to identify the anticoagulant regions of Echicetin, a snake venom anticoagulant C-type lectin (snaclec): possibility to develop anticoagulant peptide therapeutics? J Biomol Struct Dyn 2023; 41:15569-15583. [PMID: 36994880 DOI: 10.1080/07391102.2023.2191138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/05/2023] [Indexed: 03/31/2023]
Abstract
Snake venom C-type lectins (Snaclecs) display anticoagulant and platelet-modulating activities; however, their interaction with the critical components of blood coagulation factors was unknown. Computational analysis revealed that Echicetin (Snaclec from Echis carinatus venom) interacted with heavy chain of thrombin, and heavy and light chains of factor Xa (FXa). Based on FXa and thrombin binding regions of Echicetin, the two synthetic peptides (1A and 1B) were designed. The in silico binding studies of the peptides with thrombin and FXa showed that peptide 1B interacted with both heavy and light chains of thrombin and, peptide 1A interacted with only heavy chain of thrombin. Similarly, peptide 1B interacted with both heavy and light chains of FXa; however, peptide 1A interacted only with heavy chain of FXa. Alanine screening predicted the hot-spots residues for peptide 1A (Aspartic acid6, Valine8, Valine9, and Tyrosine17 with FXa, and Isoleucine14, Lysine15 with thrombin) and peptide 1B (Valine16 with FXa). Spectrofluorometric interaction study showed a lower Kd value for peptide 1B binding with both FXa and thrombin than peptide 1A, indicating higher binding strength of the former peptide. The circular dichroism spectroscopy also established the interaction between thrombin and the custom peptides. The in vitro study demonstrated higher anticoagulant activity of peptide 1B than peptide 1A due to higher inhibition of thrombin and FXa. Inhibition of anticoagulant activity of the peptides by respective anti-peptide antibodies corroborates our hypothesis that peptides 1A and 1B represent the anticoagulant regions of Echicetin and may be developed as antithrombotic peptide drug prototypes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Upasana Puzari
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | - Mahasweta Goswami
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | - Komal Rani
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | - Aparup Patra
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, Assam, India
| | - Ashis K Mukherjee
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, Assam, India
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4
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Dohnálek J, Skálová T. C-type lectin-(like) fold - Protein-protein interaction patterns and utilization. Biotechnol Adv 2022; 58:107944. [PMID: 35301089 DOI: 10.1016/j.biotechadv.2022.107944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 11/02/2022]
Abstract
The C-type lectin-like fold (CTL fold) is a building block of many proteins, including saccharide-binding lectins, natural killer cell receptors, macrophage mannose receptor, selectins, collectins, snake venoms and others. Some are important players in innate immunity and are involved in the first-line response to virally infected cells or cancer cells, some play a role in antimicrobial defense, and some are potential targets for fight against problems connected with allergies, obesity, and autoimmunity. The structure of a CTL domain typically contains two α-helices, two small β-sheets and a long surface loop, with two or three disulfide bridges stabilizing the structure. This small domain is often involved in interactions with a target molecule, however, utilizing varied parts of the domain surface, with or without structural modifications. More than 500 three-dimensional structures of CTL fold-containing proteins are available in the Protein Data Bank, including a significant number of complexes with their key interacting partners (protein:protein complexes). The amount of available structural data enables a detailed analysis of the rules of interaction patterns utilized in activation, inhibition, attachment and other pathways or functionalities. Interpretation of known CTL receptor structures and all other CTL-containing proteins and complexes with described three-dimensional structures, complemented with sequence/structure/interaction correlation analysis offers a comprehensive view of the rules of interaction patterns of the CTL fold. The results are of value for prediction of interaction behavior of so far not understood CTL-containing proteins and development of new protein binders based on this fold, with applications in biomedicine or biotechnologies. It follows from the available structural data that almost the whole surface of the CTL fold is utilized in protein:protein interactions, with the heaviest frequency of utilization in the canonical interaction region. The individual categories of interactions differ in the interface buildup strategy. The strongest CTL binders rely on interfaces with large interaction area, presence of hydrophobic core, or high surface complementarity. The typical interaction surfaces of the fold are not conserved in amino acid sequence and can be utilized in design of new binders for biotechnological applications.
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Affiliation(s)
- Jan Dohnálek
- Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Průmyslová 595, 25250 Vestec, Czech Republic.
| | - Tereza Skálová
- Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Průmyslová 595, 25250 Vestec, Czech Republic
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5
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Jebali J, Zakraoui O, Aissaoui D, Abdelkafi-Koubaa Z, Srairi-Abid N, Marrakchi N, Essafi-Benkhadir K. Lebecetin, a snake venom C-type lectin protein, modulates LPS-induced inflammatory cytokine production in human THP-1-derived macrophages. Toxicon 2020; 187:144-150. [PMID: 32918926 DOI: 10.1016/j.toxicon.2020.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/11/2020] [Accepted: 09/07/2020] [Indexed: 10/25/2022]
Abstract
The excessive production of inflammatory mediators results in an overactive immune response leading to the worsening of various human diseases. Thus, there is a still need to identify molecules able to regulate the inflammatory response. Lebecetin, a C-type lectin protein isolated from Macrovipera lebetina snake venom, was previously characterized as a platelet aggregation inhibitor and antitumor active biomolecule. In the present work, we investigated its effect on the production of some cytokines linked to inflammatory response and the underlying mechanisms in lipopolysaccharide (LPS)-induced THP1 macrophages. Interestingly, we found that lebecetin reduced the levels of the pro-inflammatory cytokines TNF-α, IL-6, and IL-8 while it partially increased LPS-induced secretion of the immunomodulatory cytokine IL-10. Furthermore, this modulatory effect was accompanied by decreased activation of ERK1/2, p38, AKT kinases and NF-κB along with reduced expression of αvβ3 integrin. Thus, this study highlights the promising role of lebecetin as a natural biomolecule that could manage the inflammatory response involved in the development and progression of inflammatory diseases.
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Affiliation(s)
- Jed Jebali
- Institut Pasteur de Tunis, LR11IPT08/LR16IPT08 Laboratoire des Venins et Molécules Thérapeutiques, 1002, Tunis, Tunisia; Université de Tunis El Manar, 1068, Tunis, Tunisia.
| | - Ons Zakraoui
- Institut Pasteur de Tunis, LR11IPT04/LR16IPT04 Laboratoire d'Epidémiologie Moléculaire et de Pathologie Expérimentale Appliquée Aux Maladies Infectieuses, 1002, Tunis, Tunisia; Université de Tunis El Manar, 1068, Tunis, Tunisia
| | - Dorra Aissaoui
- Institut Pasteur de Tunis, LR11IPT08/LR16IPT08 Laboratoire des Venins et Molécules Thérapeutiques, 1002, Tunis, Tunisia; Université de Tunis El Manar, 1068, Tunis, Tunisia
| | - Zaineb Abdelkafi-Koubaa
- Institut Pasteur de Tunis, LR11IPT08/LR16IPT08 Laboratoire des Venins et Molécules Thérapeutiques, 1002, Tunis, Tunisia; Université de Tunis El Manar, 1068, Tunis, Tunisia
| | - Najet Srairi-Abid
- Institut Pasteur de Tunis, LR11IPT08/LR16IPT08 Laboratoire des Venins et Molécules Thérapeutiques, 1002, Tunis, Tunisia; Université de Tunis El Manar, 1068, Tunis, Tunisia
| | - Naziha Marrakchi
- Institut Pasteur de Tunis, LR11IPT08/LR16IPT08 Laboratoire des Venins et Molécules Thérapeutiques, 1002, Tunis, Tunisia; Université de Tunis El Manar, 1068, Tunis, Tunisia; Faculté de Médecine de Tunis, Tunis, Tunisia
| | - Khadija Essafi-Benkhadir
- Institut Pasteur de Tunis, LR11IPT04/LR16IPT04 Laboratoire d'Epidémiologie Moléculaire et de Pathologie Expérimentale Appliquée Aux Maladies Infectieuses, 1002, Tunis, Tunisia; Université de Tunis El Manar, 1068, Tunis, Tunisia.
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6
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Eble JA. Structurally Robust and Functionally Highly Versatile-C-Type Lectin (-Related) Proteins in Snake Venoms. Toxins (Basel) 2019; 11:toxins11030136. [PMID: 30823637 PMCID: PMC6468738 DOI: 10.3390/toxins11030136] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/19/2019] [Accepted: 02/20/2019] [Indexed: 12/31/2022] Open
Abstract
Snake venoms contain an astounding variety of different proteins. Among them are numerous C-type lectin family members, which are grouped into classical Ca2+- and sugar-binding lectins and the non-sugar-binding snake venom C-type lectin-related proteins (SV-CLRPs), also called snaclecs. Both groups share the robust C-type lectin domain (CTLD) fold but differ in a long loop, which either contributes to a sugar-binding site or is expanded into a loop-swapping heterodimerization domain between two CLRP subunits. Most C-type lectin (-related) proteins assemble in ordered supramolecular complexes with a high versatility of subunit numbers and geometric arrays. Similarly versatile is their ability to inhibit or block their target molecules as well as to agonistically stimulate or antagonistically blunt a cellular reaction triggered by their target receptor. By utilizing distinct interaction sites differentially, SV-CLRPs target a plethora of molecules, such as distinct coagulation factors and receptors of platelets and endothelial cells that are involved in hemostasis, thrombus formation, inflammation and hematogenous metastasis. Because of their robust structure and their high affinity towards their clinically relevant targets, SV-CLRPs are and will potentially be valuable prototypes to develop new diagnostic and therapeutic tools in medicine, provided that the molecular mechanisms underlying their versatility are disclosed.
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Affiliation(s)
- Johannes A Eble
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstr. 15, 48149 Münster, Germany.
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7
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Estevão-Costa MI, Sanz-Soler R, Johanningmeier B, Eble JA. Snake venom components in medicine: From the symbolic rod of Asclepius to tangible medical research and application. Int J Biochem Cell Biol 2018; 104:94-113. [PMID: 30261311 DOI: 10.1016/j.biocel.2018.09.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/03/2018] [Accepted: 09/19/2018] [Indexed: 12/21/2022]
Abstract
Both mythologically and logically, snakes have always fascinated man. Snakes have attracted both awe and fear not only because of the elegant movement of their limbless bodies, but also because of the potency of their deadly venoms. Practically, in 2017, the world health organization (WHO) listed snake envenomation as a high priority neglected disease, as snakes inflict up to 2.7 million poisonous bites, around 100.000 casualties, and about three times as many invalidities on man. The venoms of poisonous snakes are a cocktail of potent compounds which specifically and avidly target numerous essential molecules with high efficacy. The individual effects of all venom toxins integrate into lethal dysfunctions of almost any organ system. It is this efficacy and specificity of each venom component, which after analysis of its structure and activity may serve as a potential lead structure for chemical imitation. Such toxin mimetics may help in influencing a specific body function pharmaceutically for the sake of man's health. In this review article, we will give some examples of snake venom components which have spurred the development of novel pharmaceutical compounds. Moreover, we will provide examples where such snake toxin-derived mimetics are in clinical use, trials, or consideration for further pharmaceutical exploitation, especially in the fields of hemostasis, thrombosis, coagulation, and metastasis. Thus, it becomes clear why a snake captured its symbolic place at the Asclepius rod with good reason still nowadays.
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Affiliation(s)
- Maria-Inacia Estevão-Costa
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstr. 15, 48149, Münster, Germany
| | - Raquel Sanz-Soler
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstr. 15, 48149, Münster, Germany
| | - Benjamin Johanningmeier
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstr. 15, 48149, Münster, Germany
| | - Johannes A Eble
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstr. 15, 48149, Münster, Germany.
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8
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Mathiharan YK, Murthy M. Molecular dynamics studies on the domain swapped Salmonella typhimurium survival protein SurE: insights on the possible reasons for catalytic cooperativity. J Biomol Struct Dyn 2018; 36:2303-2311. [DOI: 10.1080/07391102.2017.1351400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - M.R.N. Murthy
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560 012, India
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9
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Dramatic and concerted conformational changes enable rhodocetin to block α2β1 integrin selectively. PLoS Biol 2017; 15:e2001492. [PMID: 28704364 PMCID: PMC5509089 DOI: 10.1371/journal.pbio.2001492] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 06/15/2017] [Indexed: 01/08/2023] Open
Abstract
The collagen binding integrin α2β1 plays a crucial role in hemostasis, fibrosis, and cancer progression amongst others. It is specifically inhibited by rhodocetin (RC), a C-type lectin-related protein (CLRP) found in Malayan pit viper (Calloselasma rhodostoma) venom. The structure of RC alone reveals a heterotetramer arranged as an αβ and γδ subunit in a cruciform shape. RC specifically binds to the collagen binding A-domain of the integrin α2 subunit, thereby blocking collagen-induced platelet aggregation. However, until now, the molecular basis for this interaction has remained unclear. Here, we present the molecular structure of the RCγδ-α2A complex solved to 3.0 Å resolution. Our findings show that RC undergoes a dramatic structural reorganization upon binding to α2β1 integrin. Besides the release of the nonbinding RCαβ tandem, the RCγ subunit interacts with loop 2 of the α2A domain as result of a dramatic conformational change. The RCδ subunit contacts the integrin α2A domain in the “closed” conformation through its helix C. Combined with epitope-mapped antibodies, conformationally locked α2A domain mutants, point mutations within the α2A loop 2, and chemical modifications of the purified toxin protein, this molecular structure of RCγδ-α2A complex explains the inhibitory mechanism and specificity of RC for α2β1 integrin. In animals, collagen-mediated platelet aggregation is an essential component of the blood’s clotting response following vascular injury. A small group of snake venom toxins belonging to the C-type lectin protein family exert their harmful effects by directly targeting this pathway. Rhodocetin (RC) is a heterotetrameric protein found in the venom of the Malayan pit viper (C. rhodostoma). RC specifically binds α2β1 integrin, the key protein required for collagen-mediated platelet aggregation. In this study, we describe the interaction between RC and α2β1 integrin at atomic resolution. This study reveals that RC undergoes a massive structural reorganization upon α2β1 integrin binding, such that RC’s αβ subunit is released from its γδ subunit and a γδ-α2β1 integrin complex is formed. The inhibitory nature of this complex can be readily explained as RC binding along the top surface of the α2β1 integrin and directly above the collagen binding site. As a result, access of collagen to its binding site is blocked, thereby preventing collagen-mediated platelet aggregation.
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10
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Eichberg S, Sanz L, Calvete JJ, Pla D. Constructing comprehensive venom proteome reference maps for integrative venomics. Expert Rev Proteomics 2016; 12:557-73. [PMID: 26400467 DOI: 10.1586/14789450.2015.1073590] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Understanding the molecular basis of complex adaptive traits, such as snake venom, demands qualitative and quantitative comparisons of the temporal and spatial patterns of venom variation. Here, we assessed the proof-of-concept that locus-resolved reference venom proteome maps can be achieved through efficient pre-MS venom proteome decomplexation, peptide-centric MS/MS analysis and species-specific database searching. METHODS Venom proteome components were fractionated and quantified by RP-HPLC, SDS-PAGE and 2DE prior to LC-MS/MS matching against a species-specific transcriptomic dataset. RESULTS Combination of RP-HPLC/SDS-PAGE and 2DE followed by LC-MS/MS showed the existence of ∼178-180 venom protein species generated from ∼48 unique transcripts. CONCLUSIONS Our results underscore that if sufficient pre-MS and MS efforts are applied, comprehensive venom maps can be achieved. And - equally important - dissociating the venom decomplexing steps from the protein identification process represents the key to achieving a quantitative and locus-resolved insight of the venom proteome.
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Affiliation(s)
- Susann Eichberg
- a 1 Beuth Hochschule für Technik Berlin, Luxemburger Straße 10, 13353 Berlin, Germany
| | - Libia Sanz
- b 2 Laboratorio de Venómica Estructural y Funcional, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Juan J Calvete
- b 2 Laboratorio de Venómica Estructural y Funcional, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Davinia Pla
- b 2 Laboratorio de Venómica Estructural y Funcional, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
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11
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Crystallographic studies on protein misfolding: Domain swapping and amyloid formation in the SH3 domain. Arch Biochem Biophys 2016; 602:116-126. [PMID: 26924596 DOI: 10.1016/j.abb.2016.02.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 12/18/2022]
Abstract
Oligomerization by 3D domain swapping is found in a variety of proteins of diverse size, fold and function. In the early 1960s this phenomenon was postulated for the oligomers of ribonuclease A, but it was not until the 1990s that X-ray diffraction provided the first experimental evidence of this special manner of oligomerization. Nowadays, structural information has allowed the identification of these swapped oligomers in over one hundred proteins. Although the functional relevance of this phenomenon is not clear, this alternative folding of protomers into intertwined oligomers has been related to amyloid formation. Studies on proteins that develop 3D domain swapping might provide some clues on the early stages of amyloid formation. The SH3 domain is a small modular domain that has been used as a model to study the basis of protein folding. Among SH3 domains, the c-Src-SH3 domain emerges as a helpful model to study 3D domain swapping and amyloid formation.
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12
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Mathiharan YK, Savithri HS, Murthy MRN. Insights into stabilizing interactions in the distorted domain-swapped dimer ofSalmonella typhimuriumsurvival protein. ACTA ACUST UNITED AC 2015; 71:1812-23. [DOI: 10.1107/s1399004715011992] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Accepted: 06/22/2015] [Indexed: 11/11/2022]
Abstract
The survival protein SurE fromSalmonella typhimurium(StSurE) is a dimeric protein that functions as a phosphatase. SurE dimers are formed by the swapping of a loop with a pair of β-strands and a C-terminal helix between two protomers. In a previous study, the Asp230 and His234 residues were mutated to Ala to abolish a hydrogen bond that was thought to be crucial for C-terminal helix swapping. These mutations led to functionally inactive and distorted dimers in which the two protomers were related by a rotation of 167°. New salt bridges involving Glu112 were observed in the dimeric interface of the H234A and D230A/H234A mutants. To explore the role of these salt bridges in the stability of the distorted structure, E112A, E112A/D230A, E112A/H234A, E112A/D230A/H234A, R179L/H180A/H234A and E112A/R179L/H180A/H234A mutants were constructed. X-ray crystal structures of the E112A, E112A/H234A and E112A/D230A mutants could be determined. The dimeric structures of the E112A and E112A/H234A mutants were similar to that of native SurE, while the E112A/D230A mutant had a residual rotation of 11° between theBchains upon superposition of theAchains of the mutant and native dimers. The native dimeric structure was nearly restored in the E112A/H234A mutant, suggesting that the new salt bridge observed in the H234A and D230A/H234A mutants was indeed responsible for the stability of their distorted structures. Catalytic activity was also restored in these mutants, implying that appropriate dimeric organization is necessary for the activity of SurE.
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13
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C-type lectin-like proteins from snake venoms. Toxicon 2012; 60:512-9. [DOI: 10.1016/j.toxicon.2012.03.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 02/28/2012] [Accepted: 03/01/2012] [Indexed: 11/21/2022]
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14
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Yamamoto-Suzuki Y, Sakurai Y, Fujimura Y, Matsumoto M, Hamako J, Kokubo T, Kitagawa H, Kawsar SMA, Fujii Y, Ozeki Y, Matsushita F, Matsui T. Identification and Recombinant Analysis of Botrocetin-2, a Snake Venom Cofactor for von Willebrand Factor-Induced Platelet Agglutination. Biochemistry 2012; 51:5329-38. [DOI: 10.1021/bi300442c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yukiyo Yamamoto-Suzuki
- Department
of Biology, Faculty of Medical Technology, Fujita Health University School of Health Sciences, Toyoake, Aichi
470-1192, Japan
| | - Yoshihiko Sakurai
- Department
of Pediatrics, Nara Medical University,
Kashihara, Nara 634-8522, Japan
| | - Yoshihiro Fujimura
- Department of Transfusion Medicine, Nara Medical University, Kashihara, Nara 634-8522, Japan
| | - Masanori Matsumoto
- Department of Transfusion Medicine, Nara Medical University, Kashihara, Nara 634-8522, Japan
| | - Jiharu Hamako
- Department of Physiology, Faculty of Medical Management and Information
Science, Fujita Health University School of Health Sciences, Toyoake, Aichi 470-1192, Japan
| | - Tetsuro Kokubo
- Division of Molecular and Cellular Biology, Science of Supramolecular
Biology, International Graduate School of Arts and Sciences, Yokohama City University, Yokohama, Kanagawa 230-0045,
Japan
| | - Hitoshi Kitagawa
- Department of Veterinary
Internal Medicine, Faculty of Applied Biological Sciences, Gifu University, Yanagido, Gifu 501-1193, Japan
| | - Sarkar M. A. Kawsar
- Laboratory of Carbohydrate and Protein
Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong-4331, Bangladesh
| | - Yuki Fujii
- Section of Functional Morphology,
Faculty of Pharmaceutical and Sciences, Nagasaki International University, Sasebo, Nagasaki, 859-3298, Japan
| | - Yasuhiro Ozeki
- Laboratory of Marine Biochemistry,
Department of Environmental Biosciences, International Graduate School
of Arts and Sciences, Yokohama City University, Yokohama, Kanagawa 236-0027, Japan
| | - Fumio Matsushita
- Department
of Biology, Faculty of Medical Technology, Fujita Health University School of Health Sciences, Toyoake, Aichi
470-1192, Japan
| | - Taei Matsui
- Department
of Biology, Faculty of Medical Technology, Fujita Health University School of Health Sciences, Toyoake, Aichi
470-1192, Japan
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15
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Shen D, Xu X, Wu H, Peng L, Zhang Y, Song J, Su Q. Metal ion binding to anticoagulation factor II from the venom of Agkistrodon acutus: stabilization of the structure and regulation of the binding affinity to activated coagulation factor X. J Biol Inorg Chem 2011; 16:523-37. [PMID: 21197556 DOI: 10.1007/s00775-010-0752-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2010] [Accepted: 12/14/2010] [Indexed: 11/26/2022]
Abstract
Anticoagulation factor II (ACF II) isolated from the venom of Agkistrodon acutus is an activated coagulation factor X (FXa)-binding protein with both anticoagulant and hypotensive activities. The thermodynamics of the binding of alkaline earth metal ions to ACF II and their effects on the stability of ACF II and the binding of ACF II to FXa were investigated by isothermal titration calorimetry, fluorescence, differential scanning calorimetry, and surface plasmon resonance. The binding of ACF II to FXa does not have an absolute requirement for Ca(2+). Mg(2+), Sr(2+), and Ba(2+) can induce the binding of ACF II to FXa. The radii of the cations bound in ACF II crucially affect the binding affinity of ACF II for cations and the structural stability of ACF II against guanidine hydrochloride and thermal denaturation, whereas the radii of cations bound in FXa markedly affect the binding affinity between ACF II and FXa. The binding affinities of ACF II for cations and the capacities of metal-induced stabilization of ACF II follow the same trend: Ca(2+) > Sr(2+) > Ba(2+). The metal-induced binding affinities of ACF II for FXa follow the trend Mg(2+) > Ca(2+) > Sr(2+) > Ba(2+). Although Mg(2+) shows significantly low binding affinity with ACF II, Mg(2+) is the most effective to induce the binding of ACF II with FXa. Our observations suggest that in blood the bindings of Ca(2+) in two sites of ACF II increase the structural stability of ACF II, but these bindings are not essential for the binding of ACF II with FXa, and that the binding of Mg(2+) and Ca(2+) to FXa may be essential for the recognition between FXa and ACF II. Like Ca(2+), the abundant Mg(2+) in blood also plays an important role in the anticoagulation of ACF II.
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Affiliation(s)
- Dengke Shen
- Department of Chemistry, University of Science and Technology of China, Hefei, People's Republic of China
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16
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Complex assemblies of factors IX and X regulate the initiation, maintenance, and shutdown of blood coagulation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 99:51-103. [PMID: 21238934 DOI: 10.1016/b978-0-12-385504-6.00002-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Blood hemostasis is accomplished by a complex network of (anti-)coagulatory and fibrinolytic processes. These physiological processes are implemented by the assembly of multiprotein complexes involving both humoral and cellular components. Coagulation factor X, and particularly, factor IX, exemplify the dramatic enhancement that is obtained by the synergistic interaction of cell surface, inorganic and protein cofactors, protease, and substrate. With a focus on structure-function relationship, we review the current knowledge of activity modulation principles in the coagulation proteases factors IX and X and indicate future challenges for hemostasis research. This chapter is organized by describing the principles of hierarchical activation of blood coagulation proteases, including endogenous and exogenous protease activators, cofactor binding, substrate specificities, and protein inhibitors. We conclude by outlining pharmaceutical opportunities for unmet needs in hemophilia and thrombosis.
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17
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Clemetson KJ. Snaclecs (snake C-type lectins) that inhibit or activate platelets by binding to receptors. Toxicon 2010; 56:1236-46. [DOI: 10.1016/j.toxicon.2010.03.011] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2010] [Accepted: 03/15/2010] [Indexed: 11/25/2022]
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18
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Xu XL, Zhou YS, Liu QL, Hou JG, Yang JL, Xie YS. Single-Molecular Imaging of Anticoagulation Factor I from Snake Venom by Atomic Force Microscopy. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.20020200919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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19
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Shen D, Xu X, Zhang L, Wu H, Peng L. Identification of a nitric oxide-dependent hypotensive effect of anticoagulation factor II from the venom of Agkistrodon acutus. Biochem Pharmacol 2010; 79:498-506. [DOI: 10.1016/j.bcp.2009.08.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Revised: 08/25/2009] [Accepted: 08/25/2009] [Indexed: 10/20/2022]
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20
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Arpijuntarangkoon J, Rojnuckarin P, Muanpasitporn C, Kaeothip S, Sangvanich P, Intragumtornchai T. Molecular cloning and sequence analysis of alboaggregin B. Platelets 2009; 18:266-72. [PMID: 17538847 DOI: 10.1080/09537100601078232] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Green pit viper (Trimeresurus albolabris) venom contains a variety of C-type lectin-like proteins (CLPs) causing platelet aggregation and consumptive thrombocytopenia in biting victims. Alboaggregin B (AL-B), a heterodimeric glycoprotein (Gp) Ib-binding protein, was purified from the venom, but there is no reported cDNA sequence and the platelet agglutination mechanism is poorly understood. The full-length AL-B beta clone was obtained from T. albolabris venom gland cDNA library. AL-B alpha was, later, derived using 3'-RACE based on the conserved sequence. In this study, purified AL-B dimer agglutinated human platelets with the EC(50) of 180 nM and was completely inhibited by anti GpIb antibody. MALDI ToF mass spectroscopy found no glycosylation. The peptide mass fingerprints were matched with deduced amino acid sequences of cloned genes. AL-B alpha and beta contained 156 and 146 amino acid, respectively, including 23-residue signal peptides. AL-B beta showed the conserved hydrophilic patches, putative sites for GpIb binding. Furthermore, there was another conserved motif (SRTY) exclusively in platelet-agglutinating AL-B, TSV-GPIb-BP and Mamushigin. We propose that these three CLPs may function as bivalent adhesive proteins linking two GpIb molecules on adjacent platelets.
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21
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Xu X, Zhang L, Shen D, Wu H, Peng L, Li J. Effect of metal ion substitutions in anticoagulation factor I from the venom of Agkistrodon acutus on the binding of activated coagulation factor X and on structural stability. J Biol Inorg Chem 2009; 14:559-71. [PMID: 19184130 DOI: 10.1007/s00775-009-0470-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Accepted: 01/11/2009] [Indexed: 11/29/2022]
Abstract
Anticoagulation factor I (ACF I) isolated from the venom of Agkistrodon acutus is an activated coagulation factor X (FXa)-binding protein that binds in a Ca(2+)-dependent fashion with marked anticoagulant activity. The thermodynamics of the binding of alkaline earth metal ions to ACF I and the effects of alkaline earth metal ions on the guanidine hydrochloride (GdnHCl)-induced unfolding of ACF I and the binding of ACF I to FXa were studied by isothermal titration calorimetry, fluorescence, circular dichroism, and surface plasmon resonance, respectively. The results indicate that the ionic radii of the cations occupying Ca(2+)-binding sites in ACF I crucially affect the binding affinity of ACF I for alkaline earth metal ions as well as the structural stability of ACF I against GdnHCl denaturation. Sr(2+) and Ba(2+), with ionic radii larger than the ionic radius of Ca(2+), can bind to Ca(2+)-free ACF I (apo-ACF I), while Mg(2+), with an ionic radius smaller than that of Ca(2+), shows significantly low affinity for the binding to apo-ACF I. All bindings of Ca(2+), Sr(2+), and Ba(2+) ions in two sites of ACF I are mainly enthalpy-driven and the entropy is unfavorable for them. Sr(2+)-stabilized ACF I exhibits slightly lower resistance to GdnHCl denaturation than Ca(2+)-ACF I, while Ba(2+)-stabilized ACF I exhibits much lower resistance to GdnHCl denaturation than Ca(2+)-ACF I. Mg(2+) and Sr(2+), with ionic radii close to that of Ca(2+), can bind to FXa and therefore also induce the binding of ACF I to FXa, whereas Ba(2+), with a much larger ionic radius than Ca(2+), cannot support the binding of ACF I with FXa. Our observations suggest that bindings of Ca(2+), Sr(2+), and Ba(2+) ions in two sites of ACF I increase the structural stability of ACF I, but these bindings are not essential for the binding of ACF I with FXa, and that the binding of Mg(2+), Ca(2+), and Sr(2+) ions to FXa may be essential for the recognition between FXa and ACF I.
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Affiliation(s)
- Xiaolong Xu
- Department of Chemistry, University of Science and Technology of China, Hefei, People's Republic of China.
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22
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Zingali RB. INTERACTION OF SNAKE-VENOM PROTEINS WITH BLOOD COAGULATION FACTORS: MECHANISMS OF ANTICOAGULANT ACTIVITY. TOXIN REV 2008. [DOI: 10.1080/15569540600567412] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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23
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Lu Q, Clemetson JM, Clemetson KJ. SNAKE VENOM C-TYPE LECTINS INTERACTING WITH PLATELET RECEPTORS. TOXIN REV 2008. [DOI: 10.1080/15569540600567438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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24
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Oliveira-Carvalho AL, Guimarães PR, Abreu PA, Dutra DL, Junqueira-de-Azevedo IL, Rodrigues CR, Ho PL, Castro HC, Zingali RB. Identification and characterization of a new member of snake venom thrombin inhibitors from Bothrops insularis using a proteomic approach. Toxicon 2008; 51:659-71. [DOI: 10.1016/j.toxicon.2007.11.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2007] [Revised: 11/28/2007] [Accepted: 11/29/2007] [Indexed: 10/22/2022]
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25
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Gopinath S, Shikamoto Y, Mizuno H, Kumar P. Snake-venom-derived Factor IX-binding protein specifically blocks the gamma-carboxyglutamic acid-rich-domain-mediated membrane binding of human Factors IX and X. Biochem J 2007; 405:351-7. [PMID: 17407444 PMCID: PMC1904519 DOI: 10.1042/bj20061737] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A potent anticoagulant protein, IX-bp (Factor IX binding protein), has been isolated from the venom of Trimeresurus flavoviridis (habu snake) and is known to bind specifically to the Gla (gamma-carboxyglutamic acid-rich) domain of Factor IX. To evaluate the molecular basis for its anticoagulation activity, we assessed its interactions with various clotting factors. We found that the anticoagulation activity is primarily due to binding to the Gla domains of Factors IX and X, thus preventing these factors from recognizing phosphatidylserine on the plasma membrane. The present study suggests that ligands that bind to the Gla domains of Factors IX and X may have the potential to become novel anticoagulants.
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Affiliation(s)
- Subash C. B. Gopinath
- *Functional Nucleic Acids Group, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba City 305-8566, Ibaraki, Japan
| | - Yasuo Shikamoto
- †Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba City 305-8566, Ibaraki, Japan
| | - Hiroshi Mizuno
- *Functional Nucleic Acids Group, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba City 305-8566, Ibaraki, Japan
- ‡VALWAY Technology Center, NEC Soft Co. Ltd, 1-18-7, Shinkiba, Koto-ku, Tokyo 136-8627, Japan
| | - Penmetcha K. R. Kumar
- *Functional Nucleic Acids Group, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba City 305-8566, Ibaraki, Japan
- To whom correspondence should be addressed (email )
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26
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Brown J, O'Callaghan CA, Marshall ASJ, Gilbert RJC, Siebold C, Gordon S, Brown GD, Jones EY. Structure of the fungal beta-glucan-binding immune receptor dectin-1: implications for function. Protein Sci 2007; 16:1042-52. [PMID: 17473009 PMCID: PMC2206667 DOI: 10.1110/ps.072791207] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Revised: 03/19/2007] [Accepted: 03/20/2007] [Indexed: 10/23/2022]
Abstract
The murine molecule dectin-1 (known as the beta-glucan receptor in humans) is an immune cell surface receptor implicated in the immunological defense against fungal pathogens. Sequence analysis has indicated that the dectin-1 extracellular domain is a C-type lectin-like domain, and functional studies have established that it binds fungal beta-glucans. We report several dectin-1 crystal structures, including a high-resolution structure and a 2.8 angstroms resolution structure in which a short soaked natural beta-glucan is trapped in the crystal lattice. In vitro characterization of dectin-1 in the presence of its natural ligand indicates higher-order complex formation between dectin-1 and beta-glucans. These combined structural and biophysical data considerably extend the current knowledge of dectin-1 structure and function, and suggest potential mechanisms of defense against fungal pathogens.
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Affiliation(s)
- James Brown
- CR-UK Receptor Structure Research Group, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
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27
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Hamako J, Suzuki Y, Hayashi N, Kimura M, Ozeki Y, Hashimoto K, Matsui T. Amino acid sequence and characterization of C-type lectin purified from the snake venom of Crotalus ruber. Comp Biochem Physiol B Biochem Mol Biol 2007; 146:299-306. [PMID: 17251046 DOI: 10.1016/j.cbpb.2006.11.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2006] [Revised: 10/12/2006] [Accepted: 11/09/2006] [Indexed: 11/24/2022]
Abstract
Galactoside-binding lectin was purified from the snake venom of Crotalus ruber by affinity chromatography on a lactose-agarose column, and the complete amino acid sequence was determined. The C. ruber venom lectin (CRL) showed a single band of 28 kDa by SDS-polyacrylamide electrophoresis under non-reducing conditions, but it showed a single band of 15 kDa under reducing conditions, indicating that CRL is a disulfide-linked homodimer of 15 kDa subunit. CRL specifically recognized beta-galactosides such as thiodigalactoside followed by N-acetylgalactosamine when examined with their inhibitory effects on CRL-induced hemagglutination. A CRL subunit was composed of 135 residues containing nine Cys residues and showed a high similarity to other C-type galactoside-binding lectins from snake venoms. C. atrox lectin (CAL) showed almost the same sequence except for eight amino acid residues. Neither CRL nor CAL induced platelet aggregation by itself or inhibited platelet aggregation mediated by von Willebrand factor or fibrinogen with agonists. CRL showed a similar oligomeric form and the sugar specificity as CAL, but it showed different divalent cation sensitivity such as Mn(2+) and Ni(2+). Homology modeling suggested that the amino acid substitution found in CRL does not affect sugar recognition of the lectin but might alter the conformation and influence the sugar binding pocket induced by the metal-ion binding.
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Affiliation(s)
- Jiharu Hamako
- Course of Medical Communication, Fujita Health University College Toyoake, Aichi 470-1192, Japan
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28
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Xu X, Chen J, Zhang L, Wang S, Shen D, Liu Q. Calcium Ion-Induced Stabilization and Refolding of Agkisacutacin from Agkistrodon Acutus Venom Studied by Fluorescent Spectroscopy. J Fluoresc 2007; 17:215-21. [PMID: 17279335 DOI: 10.1007/s10895-007-0160-x] [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] [Received: 11/24/2006] [Accepted: 01/17/2007] [Indexed: 10/23/2022]
Abstract
Agkisacutacin isolated from the venom of Agkistrodon acutus is a coagulation factor IX / coagulation factor X-binding protein with marked anticoagulant- and platelet-modulating activities. Ca(2+) ion-induced stabilization and refolding of Agkisacutacin have been studied by following fluorescent measurements. Ca(2+) ions not only increase the structural stability of agkisacutacin against GdnHCl denaturation, but also induce its refolding. The GdnHCl-induced unfolding of the apo-agkisacutacin and the purified agkisacutacin is a single-step process with no detectable intermediate state. Ca(2+) ions play an important role in the stabilization of the structure of agkisacutacin. Ca(2+)-stabilized agkisacutacin exhibits higher resistance to GdnHCl denaturation than the apo-agkisacutacin. It is possible to induce refolding of the unfolded apo-agkisacutacin merely by adding 1 mM Ca(2+) ions without changing the concentration of the denaturant. The kinetic result of Ca(2+)-induced refolding provides evidences for that agkisacutacin consists of at least two refolding phases and the first phase of Ca(2+)-induced refolding should involve the formation of the compact Ca(2+)-binding site regions, and subsequently, the protein undergoes further conformational rearrangements to form the native structure.
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Affiliation(s)
- Xiaolong Xu
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, PR China.
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29
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Abstract
Over the last several decades, research on snake venom toxins has provided not only new tools to decipher molecular details of various physiological processes, but also inspiration to design and develop a number of therapeutic agents. Blood circulation, particularly thrombosis and haemostasis, is one of the major targets of several snake venom proteins. Among them, anticoagulant proteins have contributed to our understanding of molecular mechanisms of blood coagulation and have provided potential new leads for the development of drugs to treat or to prevent unwanted clot formation. Some of these anticoagulants exhibit various enzymatic activities whereas others do not. They interfere in normal blood coagulation by different mechanisms. Although significant progress has been made in understanding the structure-function relationships and the mechanisms of some of these anticoagulants, there are still a number of questions to be answered as more new anticoagulants are being discovered. Such studies contribute to our fight against unwanted clot formation, which leads to death and debilitation in cardiac arrest and stroke in patients with cardiovascular and cerebrovascular diseases, arteriosclerosis and hypertension. This review describes the details of the structure, mechanism and structure-function relationships of anticoagulant proteins from snake venoms.
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Affiliation(s)
- R Manjunatha Kini
- Protein Science Laboratory, Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore.
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30
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Morita T. Structure-Function Relationships of C-Type Lectin-Related Proteins. PATHOPHYSIOLOGY OF HAEMOSTASIS AND THROMBOSIS 2006; 34:156-9. [PMID: 16707919 DOI: 10.1159/000092415] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The structural and functional studies of the first identified C-type lectin-like protein (CLP), blood coagulation factor IX/factor X-binding protein (IX/X-bp), have been instrumental in defining how new functionally heterodimeric CLPs are generated from monomeric carbohydrate recognition domain in C-type lectins by three-dimensional domain swapping. The crystal structures of gamma-carboxyglutamic acid domains of coagulation factors X and IX have recently been clarified in structural studies of complexes between the gamma-carboxyglutamic acid domain of factors X and X-bp (a venom CLP) and between the gamma-carboxyglutamic acid domain of factors IX and IX-bp (a venom CLP).
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Affiliation(s)
- Takashi Morita
- Department of Biochemistry, Meiji Pharmaceutical University, Noshio, Kiyose, Tokyo, Japan.
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31
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Hatakeyama T, Hozawa T, Hirotani I, Tsuda N, Kusunoki M, Shiba K. Characterization of a recombinant C-type lectin, rCEL-IV, expressed in Escherichia coli cells using a synthetic gene. Biochim Biophys Acta Gen Subj 2006; 1760:318-25. [PMID: 16503091 DOI: 10.1016/j.bbagen.2006.01.011] [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] [Received: 05/25/2005] [Revised: 01/15/2006] [Accepted: 01/18/2006] [Indexed: 11/28/2022]
Abstract
The body fluid of marine invertebrate Cucumaria echinata (Holothuroidea) contains four Ca2+-dependent galactose-specific lectins. One of these lectins, CEL-IV, is composed of a C-type carbohydrate-recognition domain homotetramer. CEL-IV exhibits higher specificity for alpha-galactosides than for beta-galactosides, while other C. echinata lectins show preferential binding of beta-galactosides. We constructed an artificial synthetic gene for recombinant CEL-IV (rCEL-IV) based on the amino acid sequence previously determined from the purified protein. rCEL-IV was expressed in Escherichia coli cells as inclusion bodies. After the refolding process, most of rCEL-IV spontaneously formed a homotetramer structure having interchain disulfide bonds. The secondary structure of rCEL-IV was similar to that of the native one, as judged by the comparison of the far UV-circular dichroism spectra of rCEL-IV and native CEL-IV (nCEL-IV). Carbohydrate-binding specificity of rCEL-IV was confirmed to be similar to that of nCEL-IV from the results of the binding-inhibition assay using liposomes composed of rabbit erythrocyte lipids. Crystals of rCEL-IV were obtained in a few days by the sitting drop vapor diffusion method. These results indicate that rCEL-IV achieved essentially correct three-dimensional structure, including the carbohydrate-binding sites, and it would be very useful for further study on the carbohydrate-recognition mechanism by mutational and X-ray crystallographic analyses.
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Affiliation(s)
- Tomomitsu Hatakeyama
- Department of Applied Chemistry, Faculty of Engineering, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
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32
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Xu XL, Chen JX, Zhang LY, Liu XH, Liu WQ, Liu QL. Effects of rare earth ions on the conformational stability of anticoagulation factor II fromAgkistrodon acutus venom probed by fluorescent spectroscopy. Biopolymers 2006; 82:167-75. [PMID: 16475157 DOI: 10.1002/bip.20476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Anticoagulation factor II (ACF II) isolated from the venom of Agkistrodon acutus is an activated coagulation factor X-binding protein in a Ca(2+)-dependent fashion with marked anticoagulant activity. The equilibrium unfolding of rare earth ions (RE(3+))-reconstituted ACF II in guanidine hydrochloride (GdnHCl) solution was studied by fluorescence. The GdnHCl-induced unfolding of RE(3+) (Nd(3+), Sm(3+), Eu(3+), Gd(3+))-reconstituted ACF II follows a three-state transition with a stable intermediate state. Substitutions of the RE(3+) ions for Ca(2+) in ACF II decrease the conformational stability of its native state but markedly increase the conformational stability of its intermediate state. The free energy change of RE(3+)-ACF II from the intermediate state to denatured state linearly increases with the increase of ionic potentials of bound metal ions (Ca(2+), Nd(3+), Sm(3+), Eu(3+), and Gd(3+)). The refolding of ACF II from the unfolded state to the intermediate state can be induced merely by adding 10 microM RE(3+) ions without changing the concentration of the denaturant. The kinetic results of the RE(3+)-induced refolding provide evidence indicating that the intermediate state of RE(3+)-ACF II consists of at least two refolding phases and that the refolding rate constant values of the faster phase decrease with the increase of the difference between the radii of Ca(2+) and RE(3+), but the refolding rate constant values of the slower phase are similar to each other. The results of this study indicate that the size of metal ion is the major factor responsible for the metal ion-induced conformational stabilization of the native ACF II, while the metal ionic potential plays a predominant role in stabilizing the conformation for the intermediate state.
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Affiliation(s)
- Xiao-Long Xu
- Department of Chemistry, University of Science and Technology of China, Hefei, People's Republic of China.
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33
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Zhong SR, Jin Y, Wu JB, Chen RQ, Jia YH, Wang WY, Xiong YL, Zhang Y. Characterization and molecular cloning of dabocetin, a potent antiplatelet C-type lectin-like protein from Daboia russellii siamensis venom. Toxicon 2005; 47:104-12. [PMID: 16330060 DOI: 10.1016/j.toxicon.2005.10.002] [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: 04/05/2005] [Revised: 09/28/2005] [Accepted: 10/08/2005] [Indexed: 11/25/2022]
Abstract
A novel C-type lectin-like protein, dabocetin, was purified from Daboia russellii siamensis venom. On SDS-polyacrylamide gel electrophoresis, it showed a single band with an apparent molecular weight of 28 kDa and two distinct bands with the apparent molecular weights of 15.0 kDa and 14.5 kDa under non-reducing and reducing conditions, respectively. cDNA clones containing the coding sequences for dabocetin alpha and beta subunits were isolated and sequenced. The deduced protein sequences of both subunits were confirmed by N-terminal amino acid sequencing and trypsin-digested peptide mass fingerprinting. Dabocetin did not induce platelet aggregation in platelet-rich plasma. It also had little effect on the platelet aggregation induced by ADP, TMVA or stejnulxin. Whereas, dabocetin inhibited ristocetin-induced platelet agglutination in platelet-rich plasma in a dose-dependent manner with an IC50 value of 0.35 microM. Flow cytometry analysis showed that dabocetin significantly inhibited mAb SZ2 binding to platelet membrane glycoprotein Ib alpha, indicating that platelet membrane glycoprotein Ib is involved in the inhibitory effect of dabocetin on ristocetin-induced platelet agglutination.
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Affiliation(s)
- Shu-Rong Zhong
- Department of Animal Toxinology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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Bazaa A, Marrakchi N, El Ayeb M, Sanz L, Calvete JJ. Snake venomics: Comparative analysis of the venom proteomes of the Tunisian snakesCerastes cerastes, Cerastes vipera andMacrovipera lebetina. Proteomics 2005; 5:4223-35. [PMID: 16206329 DOI: 10.1002/pmic.200402024] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The protein composition of the crude venoms of the three most important vipers of Tunisia was analyzed by RP-HPLC, N-terminal sequence analysis, MALDI-TOF mass determination, and in-gel tryptic digestion followed by PMF and CID-MS/MS of selected peptide ions in a quadrupole-linear IT instrument. Our results show that the venom proteomes of Cerastes cerastes, Cerastes vipera, and Macrovipera lebetina are composed of proteins belonging to a few protein families. However, each venom showed distinct degree of protein composition complexity. The three venoms shared a number of protein classes though the relative occurrence of these toxins was different in each snake species. On the other hand, the venoms of the Cerastes species and Macrovipera lebetina each contained unique components. The comparative proteomic analysis of Tunisian snake venoms provides a comprehensible catalogue of secreted proteins, which may contribute to a deeper understanding of the biological effects of the venoms, and may also serve as a starting point for studying structure-function correlations of individual toxins.
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Affiliation(s)
- Amine Bazaa
- Laboratoire des Venins et Toxines, Institut Pasteur de Tunis, Tunis-Belvedere, Tunisia
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35
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Suzuki N, Fujimoto Z, Morita T, Fukamizu A, Mizuno H. pH-Dependent Structural Changes at Ca2+-binding Sites of Coagulation Factor IX-binding Protein. J Mol Biol 2005; 353:80-7. [PMID: 16165155 DOI: 10.1016/j.jmb.2005.08.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2005] [Revised: 08/08/2005] [Accepted: 08/11/2005] [Indexed: 12/01/2022]
Abstract
Coagulation factor IX-binding protein, isolated from Trimeresurus flavoviridis (IX-bp), is a C-type lectin-like protein. It is an anticoagulant consisting of homologous subunits, A and B. Each subunit has a Ca(2+)-binding site with a unique affinity (K(d) values of 14muM and 130muM at pH 7.5). These binding characteristics are pH-dependent and, under acidic conditions, the Ca(2+) binding of the low-affinity site was reduced considerably. In order to identify which site has high affinity and to investigate the pH-dependent Ca(2+) release mechanism, we have determined the crystal structures of IX-bp at pH 6.5 and pH 4.6 (apo form), and compared the Ca(2+)-binding sites with each other and with those of the solved structures under alkaline conditions; pH 7.8 and pH 8.0 (complexed form). At pH 6.5, Glu43 in the Ca(2+)-binding site of subunit A displayed two conformations. One (minor) is that in the alkaline state, and the other (major) is that at pH 4.6. However, the corresponding Gln43 residue of subunit B is in only a single conformation, which is almost identical with that in the alkaline state. At pH 4.6, Glu43 of subunit A adopts a conformation similar to that of the major conformer observed at pH 6.5, while Gln43 of subunit B assumes a new conformation, and both Ca(2+) positions are occupied by water molecules. These results showed that Glu43 of subunit A is much more sensitive to protonation than Gln43 of subunit B, and the conformational change of Glu43 occurs around pH6.5, which may correspond to the step of Ca(2+) release.
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Affiliation(s)
- Nobuhiro Suzuki
- Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
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36
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Hu S, Li W, Chen L, Liu J. Expression of a recombinant anticoagulant C-type lectin-like protein ACFI in Pichia pastoris: heterodimerization of two subunits is required for its function. Toxicon 2005; 46:716-24. [PMID: 16199073 DOI: 10.1016/j.toxicon.2005.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2005] [Revised: 07/19/2005] [Accepted: 07/20/2005] [Indexed: 10/25/2022]
Abstract
ACFI is an anticoagulant C-type lectin-like protein (CLP) isolated from Agkistrodon acutus venom. To investigate the function of ACFI and its subunits, the cDNAs of two subunits were transformed and expressed in Pichia pastoris separately or together by a novel strategy using two vectors with different selectable markers. The results showed that recombinant homodimers were secreted when the subunits were expressed alone, while heterodimers (rACFI) were secreted when two subunits were co-expressed. The secreted proteins were purified from culture supernatants in one step by metal-chelating affinity chromatography with the yields of 1-4 mg/L. PAGE and ELISA showed that rACFI competed the binding of native ACFI for human factor X and IX with affinities of 1.6 and 30 nM, respectively. In addition, rACFI prolonged the activated partial thromboplastin time (APTT) in a concentration dependent manner as same as native ACFI. However, recombinant alpha or beta homodimers completely lost these activities, indicating the heterodimerization of two subunits is required for its function. It also suggests that P. pastoris is a promising system for structure-function studies of snake CLPs.
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Affiliation(s)
- Siyi Hu
- Life Science School, University of Science & Technology of China, Hefei 230027, Anhui, People's Republic of China
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37
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Abstract
Snake venoms are complex mixtures of biologically active proteins and peptides. Many of them affect hemostasis by activating or inhibiting coagulant factors or platelets, or by disrupting endothelium. Based on sequence, these snake venom components have been classified into various families, such as serine proteases, metalloproteinases, C-type lectins, disintegrins and phospholipases. The various members of a particular family act selectively on different blood coagulation factors, blood cells or tissues. For almost every factor involved in coagulation or fibrinolysis there is a venom protein that can activate or inactivate it. Venom proteins affect platelet function by binding or degrading vWF or platelet receptors, activating protease-activated receptors or modulating ADP release and thromboxane A2 formation. Some venom enzymes cleave key basement membrane components and directly affect capillary blood vessels to cause hemorrhaging. L-Amino acid oxidases activate platelets via H2O2 production.
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Affiliation(s)
- Q Lu
- Theodor Kocher Institute, University of Berne, Berne, Switzerland
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Lu Q, Navdaev A, Clemetson JM, Clemetson KJ. Snake venom C-type lectins interacting with platelet receptors. Structure–function relationships and effects on haemostasis. Toxicon 2005; 45:1089-98. [PMID: 15876445 DOI: 10.1016/j.toxicon.2005.02.022] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2004] [Indexed: 11/16/2022]
Abstract
Snake venoms contain components that affect the prey either by neurotoxic or haemorrhagic effects. The latter category affect haemostasis either by inhibiting or activating platelets or coagulation factors. They fall into several types based upon structure and mode of action. A major class is the snake C-type lectins or C-type lectin-like family which shows a typical folding like that in classic C-type lectins such as the selectins and mannose-binding proteins. Those in snake venoms are mostly based on a heterodimeric structure with two subunits alpha and beta, which are often oligomerized to form larger molecules. Simple heterodimeric members of this family have been shown to inhibit platelet functions by binding to GPIb but others activate platelets via the same receptor. Some that act via GPIb do so by inducing von Willebrand factor to bind to it. Another series of snake C-type lectins activate platelets by binding to GPVI while yet another series uses the integrin alpha(2)beta(1) to affect platelet function. The structure of more and more of these C-type lectins have now been, and are being, determined, often together with their ligands, casting light on binding sites and mechanisms. In addition, it is relatively easy to model the structure of the C-type lectins if the primary structure is known. These studies have shown that these proteins are quite a complex group, often with more than one platelet receptor as ligand and although superficially some appear to act as inhibitors, in fact most function by inducing thrombocytopenia by various routes. The relationship between structure and function in this group of venom proteins will be discussed.
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Affiliation(s)
- Qiumin Lu
- Theodor Kocher Institute, University of Berne, Freiestrasse 1, CH-3012, Berne, Switzerland
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39
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Morita T. Structures and functions of snake venom CLPs (C-type lectin-like proteins) with anticoagulant-, procoagulant-, and platelet-modulating activities. Toxicon 2005; 45:1099-114. [PMID: 15922777 DOI: 10.1016/j.toxicon.2005.02.021] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
C-type lectin-like proteins (CLPs) have a variety of biological activities, including anticoagulant- and platelet-modulating activities but have no lectin activity. CLPs are made up of heterodimers or oligomers of heterodimers, while C-type lectins from snake venom are composed exclusively of homodimers or homooligomers. In the last decade, numerous CLPs, such as blood coagulation factor IX/X-binding protein and botrocetin, have been isolated from various snake venoms, sequenced, and characterized. In addition, RVV-X (factor X activator) and carinactivase-1 (prothrombin activator) are metalloproteases composed of two C-type lectin-like domains that recognize the Gla domain of factor X and prothrombin, respectively. The basic structures of these CLPs include two homologous subunits: subunit alpha (A chain) of 14-15 kDa and subunit beta (B chain) of 13-14 kDa. CLPs occur in a variety of oligomeric forms, including alphabeta, (alphabeta)(2), and (alphabeta)(4). The basic homologous dimer (alphabeta) of these CLPs is formed by three-dimensional (3D) domain swapping. The CLPs constitute a new protein family and are useful tools for elucidating the mechanisms involved in clotting and platelet activation as well as the structure-function relationships of both blood clotting factors and platelet glycoproteins.
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Affiliation(s)
- Takashi Morita
- Department of Biochemistry, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose, Tokyo 204-8588, Japan.
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40
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Ogawa T, Chijiwa T, Oda-Ueda N, Ohno M. Molecular diversity and accelerated evolution of C-type lectin-like proteins from snake venom. Toxicon 2005; 45:1-14. [PMID: 15581677 DOI: 10.1016/j.toxicon.2004.07.028] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2004] [Accepted: 07/26/2004] [Indexed: 11/24/2022]
Abstract
A number of C-type lectin-like proteins that affect thrombosis and hemostasis by inhibiting or activating specific platelet membrane receptors or blood coagulation factors have been isolated from the venom of various snake species and characterized and more than 80 have been sequenced. Recent data on the primary sequences and 3D structures of C-type lectins and C-type lectin-like proteins from snake venoms have enabled us to analyze their molecular evolution. Statistical analysis of their cDNA sequences shows that C-type lectin-like proteins, with some exceptions, have evolved in an accelerated manner to acquire their diverse functions. Phylogenetic analysis shows that the A and B chains of C-type lectin-like proteins are clearly separated from C-type lectins and that the A and B chains are further divided into a group of platelet receptor-binding proteins and a group of coagulation factor-binding proteins. Elucidation of the tertiary structures of several C-type lectin-like proteins led to the discovery of a unique domain-swapping interaction between heterodimeric subunits, which creates a concave surface for ligand binding.
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Affiliation(s)
- Tomohisa Ogawa
- Department of Biomolecular Science, Graduate School of Life Sciences, Tohoku University, Sendai 981-8555, Japan.
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41
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Suzuki N, Shikamoto Y, Fujimoto Z, Morita T, Mizuno H. Crystallization and preliminary X-ray analysis of coagulation factor IX-binding protein from habu snake venom at pH 6.5 and 4.6. Acta Crystallogr Sect F Struct Biol Cryst Commun 2004; 61:147-9. [PMID: 16508118 PMCID: PMC1952379 DOI: 10.1107/s1744309104032439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2004] [Accepted: 12/08/2004] [Indexed: 05/06/2023]
Abstract
Coagulation factor IX-binding protein isolated from Trimeresurus flavoviridis (IX-bp) is a C-type lectin-like protein. It is an anticoagulant protein consisting of homologous subunits A and B. The subunits both contain a Ca2+-binding site with differing affinity (Kd values of 14 and 130 microM at pH 7.5). These binding characteristics are pH-dependent; under acidic conditions, the affinity of the low-affinity site was reduced considerably. In order to identify which site has high affinity and also to investigate the Ca2+-releasing mechanism, IX-bp was crystallized at pH 6.5 and 4.6. The crystals at pH 6.5 and 4.6 diffracted to 1.72 and 2.29 A resolution, respectively; the former crystals belong to the monoclinic space group P2(1), with unit-cell parameters a = 60.7, b = 63.5, c = 66.9 A, beta = 117.0 degrees, while the latter belong to the monoclinic space group C2, with a = 134.1, b = 37.8, c = 55.8 A, beta = 110.4 degrees.
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Affiliation(s)
- Nobuhiro Suzuki
- Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Department of Biochemisty, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Yasuo Shikamoto
- Department of Biochemisty, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Zui Fujimoto
- Department of Biochemisty, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Takashi Morita
- Department of Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588, Japan
| | - Hiroshi Mizuno
- Department of Biochemisty, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
- Correspondence e-mail:
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42
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Paaventhan P, Kong C, Joseph JS, Chung MCM, Kolatkar PR. Structure of rhodocetin reveals noncovalently bound heterodimer interface. Protein Sci 2004; 14:169-75. [PMID: 15576563 PMCID: PMC2253329 DOI: 10.1110/ps.04945605] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Rhodocetin is a unique heterodimer consisting of alpha- and beta-subunits of 133 and 129 residues, respectively. The molecule, purified from the crude venom of the Malayan pit viper, Calloselasma rhodostoma, functions as an inhibitor of collagen-induced aggregation. Rhodocetin has been shown to have activity only when present as a dimer. The dimer is formed without an intersubunit disulfide bridge, unlike all the other Ca(2+)-dependent lectin-like proteins. We report here the 1.9 A resolution structure of rhodocetin, which reveals the compensatory interactions that occur in the absence of the disulfide bridge to preserve activity.
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43
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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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44
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Ogawa T, Shirai T, Shionyu-Mitsuyama C, Yamane T, Kamiya H, Muramoto K. The speciation of conger eel galectins by rapid adaptive evolution. Glycoconj J 2004; 19:451-8. [PMID: 14758068 DOI: 10.1023/b:glyc.0000014074.38755.1d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Many cases of accelerated evolution driven by positive Darwinian selection are identified in the genes of venomous and reproductive proteins. This evolutional phenomenon might have important consequences in their gene-products' functions, such as multiple specific toxins for quick immobilization of the prey and the establishment of barriers to fertilization that might lead to speciation, and in the molecular evolution of novel genes. Recently, we analyzed the molecular evolution of two galectins isolated from the skin mucus of conger eel (Conger myriaster), named congerins I and II, by cDNA cloning and X-ray structural analysis, and we found that they have evolved in the rapid adaptive manner to emergence of a new structure including strand-swapping and a unique new ligand-binding site. In this review article we summarize and discuss the molecular evolution, especially the rapid adaptive evolution, and the structure-function relationships of conger eel galectins.
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Affiliation(s)
- Tomohisa Ogawa
- Department of Biomolecular Science, Graduate School of Life Sciences, Tohoku University, Sendai 981-8555, Japan.
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45
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Siigur E, Aaspõllu A, Trummal K, Tõnismägi K, Tammiste I, Kalkkinen N, Siigur J. Factor X activator from Vipera lebetina venom is synthesized from different genes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2004; 1702:41-51. [PMID: 15450849 DOI: 10.1016/j.bbapap.2004.07.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Revised: 07/27/2004] [Accepted: 07/29/2004] [Indexed: 10/26/2022]
Abstract
Vipera lebetina venom contains specific coagulant Factor X activator (VLFXA) that cleaves the Arg52-Ile53 bond in the heavy chain of human factor X. VLFXA is a glycoprotein that is composed of a heavy chain (HC) and two light chains (LC) linked by disulfide bonds. The complete amino acid sequences of the three chains of the factor X activator from V. lebetina snake venom are deduced from the nucleotide sequences of cDNAs encoding these chains. The full-length cDNA (2347 bp) sequence of the HC encodes an open reading frame (ORF) of 612 amino acids that includes signal peptide, propeptide and mature metalloproteinase with disintegrin-like and cysteine-rich domains. The light chain LC1 contains 123 and LC2 135 amino acid residues. Both light chains belong to the class of C-type lectin-like proteins. The N-termini of VLFXA chains and inner sequences of peptide fragments detected by liquid chromatography-electrospray ionization tandem mass spectrometry (LC MS/MS) from protein sequence are 100% identical to the sequences deduced from the cDNA. The molecular masses of tryptic fragments of VLFXA chains analyzed by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) also confirm the protein sequences deduced from the cDNAs. These are the first cloned factor X activator heavy and light chains. We demonstrate that the heavy and light chains are synthesized from different genes.
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Affiliation(s)
- Ene Siigur
- National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, Tallinn 12618, Estonia
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46
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Sugawara H, Kusunoki M, Kurisu G, Fujimoto T, Aoyagi H, Hatakeyama T. Characteristic Recognition of N-Acetylgalactosamine by an Invertebrate C-type Lectin, CEL-I, Revealed by X-ray Crystallographic Analysis. J Biol Chem 2004; 279:45219-25. [PMID: 15319425 DOI: 10.1074/jbc.m408840200] [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] [Indexed: 11/06/2022] Open
Abstract
CEL-I is a C-type lectin, purified from the sea cucumber Cucumaria echinata, that shows a high specificity for N-acetylgalactosamine (GalNAc). We determined the crystal structures of CEL-I and its complex with GalNAc at 2.0 and 1.7 A resolution, respectively. CEL-I forms a disulfide-linked homodimer and contains two intramolecular disulfide bonds, although it lacks one intramolecular disulfide bond that is widely conserved among various C-type carbohydrate recognition domains (CRDs). Although the sequence similarity of CEL-I with other C-type CRDs is low, the overall folding of CEL-I was quite similar to those of other C-type CRDs. The structure of the complex with GalNAc revealed that the basic recognition mode of GalNAc was very similar to that for the GalNAc-binding mutant of the mannose-binding protein. However, the acetamido group of GalNAc appeared to be recognized more strongly by the combination of hydrogen bonds to Arg115 and van der Waals interaction with Gln70. Mutational analyses, in which Gln70 and/or Arg115 were replaced by alanine, confirmed that these residues contributed to GalNAc recognition in a cooperative manner.
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Affiliation(s)
- Hajime Sugawara
- Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
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47
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Kassab BH, de Carvalho DD, Oliveira MA, Baptista GR, Pereira GAG, Novello JC. Cloning, expression, and structural analysis of recombinant BJcuL, a c-type lectin from the Bothrops jararacussu snake venom. Protein Expr Purif 2004; 35:344-52. [PMID: 15135412 DOI: 10.1016/j.pep.2004.02.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2003] [Revised: 02/17/2004] [Indexed: 12/01/2022]
Abstract
The lactose-binding lectin from Bothrops jararacussu venom (BJcuL) is a homodimer belonging to group VII of the c-type animal lectins. BJcuL has also been shown to serve as an interesting tool for combating tumor progression by inhibiting cancer and endothelial cell growth. However, detailed structural studies of BJcuL and its biological mechanisms of cytotoxicity are yet to be reported, perhaps because of the non-availability of recombinant proteins in necessary quantities. Intending to increase the present information about structural and consequently the understating of biological studies, the cDNA coding for BJcuL from a venom gland has been cloned and sequenced. The mature protein-coding region was amplified by PCR with specific oligonucleotides, and subcloned into the pET-15b vector to express the recombinant BJcuL in Escherichia coli BL21 (DE3). The deduced amino acid sequence exhibits a high degree of sequence identity with c-type lectins (CTLs) and c-type lectin-like domains (CTLDs). An insoluble and inactive 18.5-kDa protein was overexpressed after 1.0mM IPTG induction. The recombinant BJcuL was recovered and denatured in a buffer with 6M urea and purified on a nickel-affinity column. Protein refolding was carried out on this column, during procedure purification, followed by dialysis against CTBS and then by gel filtration for separation of the active dimmer. The refolding process of rBJcuL and the analysis of its structure were confirmed by biological assay, circular dichroism, and MALDI-TOF.
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Affiliation(s)
- Bayki H Kassab
- Departamento de Bioquímica, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), CP 6109, Campinas-SP 13083-970, Brazil.
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48
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Morita T. Use of Snake Venom Inhibitors in Studies of the Function and Tertiary Structure of Coagulation Factors. Int J Hematol 2004; 79:123-9. [PMID: 15005338 DOI: 10.1532/ijh97.03172] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
C-type lectin-like proteins (CLPs) of snake venom have a variety of biological properties, acting for example as anticoagulants, procoagulants, and agonists/antagonists of platelet activation. The structural and functional studies of the first identified venom CLP, factors IX/X-binding protein (IX/X-bp), have contributed to our understanding of the roles of magnesium ions in the blood coagulation cascade reaction. The crystal structures of gamma-carboxyglutamic acid (Gla) domains of cpagulation factors X and IX have recently been clarified in structural studies of complexes between the Gla domain of factor X and X-bp (a venom CLP) and between the Gla domain of factor IX and IX-bp (a venom CLP).
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Affiliation(s)
- Takashi Morita
- Department of Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo, Japan.
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Jasti J, Paramasivam M, Srinivasan A, Singh TP. Crystal Structure of Echicetin from Echis carinatus (Indian Saw-scaled Viper) at 2.4Å Resolution. J Mol Biol 2004; 335:167-76. [PMID: 14659748 DOI: 10.1016/j.jmb.2003.10.048] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Echicetin is a heterodimeric protein from the venom of the Indian saw-scaled viper, Echis carinatus. It binds to platelet glycoprotein Ib (GPIb) and thus inhibits platelet aggregation. It has two subunits, alpha and beta, consisting of 131 and 123 amino acid residues, respectively. The two chains are linked with a disulphide bond. The level of amino acid sequence homology between two subunits is 50%. The protein was purified from the venom of E.carinatus and crystallized using ammonium sulphate as a precipitant. The crystal structure has been determined at 2.4A resolution and refined to an R-factor of 0.187. Overall dimensions of the heterodimer are approximately 80Ax35Ax35A. The backbone folds of the two subunits are similar. The central portions of the polypeptide chains of alpha and beta-subunits move into each other to form a tight dimeric association. The remaining portions of the chains of both subunits fold in a manner similar to those observed in the carbohydrate-binding domains of C-type lectins. In echicetin, the Ca(2+)-binding sites are not present, despite being topologically equivalent to other similar Ca(2+)-binding proteins of the superfamily. The residues Ser41, Glu43 and Glu47 in the calcium-binding proteins of the related family are conserved but the residues Glu126/120 are replaced by lysine at the corresponding sites in the alpha and beta-subunits.
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Affiliation(s)
- Jayasankar Jasti
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, 110 029, New Delhi, India
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Horii K, Okuda D, Morita T, Mizuno H. Structural Characterization of EMS16, an Antagonist of Collagen Receptor (GPIa/IIa) from the Venom of Echis multisquamatus,. Biochemistry 2003; 42:12497-502. [PMID: 14580195 DOI: 10.1021/bi034890h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Snake venoms contain a number of hemostatically active C-type lectin-like proteins (CLPs), which affect the blood coagulation system, endothelial cells, and platelets. CLPs have broad similarities in structure and possess distinct biological functions. EMS16, a CLP from Echis multisquamatus venom, which is a potent and selective inhibitor of the collagen receptor, glycoprotein Ia/IIa (integrin alpha2beta1), has been used in the present study to examine structure-function relationships in venom CLPs by X-ray crystallography. The structure of EMS16, determined at a resolution of 1.9 A, revealed a heterodimer involved with domain swapping of the central loop as observed in the structures of other CLPs. A part of the glycan was observed and identified as N-acetyl-D-glucosamine (GlcNAc) in the electron density map at Asn21 of subunit B, an expected glycosylation site. EMS16 had a unique, positively charged electrostatic potential patch on the concave surface that may qualify as a site for interaction with the I-domain of the glycoprotein Ia/IIa.
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Affiliation(s)
- Katsunori Horii
- Department of Biochemistry, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
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