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De-Simone SG, Lechuga GC, Napoleão-Pêgo P, Gomes LR, Provance DW, Nirello VD, Sodero ACR, Guedes HLDM. Small Angle X-ray Scattering, Molecular Modeling, and Chemometric Studies from a Thrombin-Like (Lmr-47) Enzyme of Lachesis m. rhombeata Venom. Molecules 2021; 26:3930. [PMID: 34203140 PMCID: PMC8271572 DOI: 10.3390/molecules26133930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/31/2021] [Accepted: 06/06/2021] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION Snakebite envenomation is considered a neglected tropical disease, and SVTLEs critical elements are involved in serious coagulopathies that occur on envenoming. Although some enzymes of this group have been structurally investigated, it is essential to characterize other proteins to better understand their unique properties such as the Lachesis muta rhombeata 47 kDa (Lmr-47) venom serine protease. METHODS The structure of Lmr-47 was studied in solution, using SAXS, DLS, CD, and in silico by homology modeling. Molecular docking experiments simulated 21 competitive inhibitors. RESULTS At pH 8.0, Lmr-47 has an Rg of 34.5 ± 0.6 Å, Dmax of 130 Å, and SR of 50 Å, according to DLS data. Kratky plot analysis indicates a rigid shape at pH 8.0. Conversely, the pH variation does not change the center of mass's intrinsic fluorescence, possibly indicating the absence of fluorescent amino acids in the regions affected by pH variation. CD experiments show a substantially random coiled secondary structure not affected by pH. The low-resolution model of Lmr-47 presented a prolate elongated shape at pH 8.0. Using the 3D structure obtained by molecular modeling, docking experiments identified five good and three suitable competitive inhibitors. CONCLUSION Together, our work provided insights into the structure of the Lmr-47 and identified inhibitors that may enhance our understanding of thrombin-like family proteins.
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Affiliation(s)
- Salvatore Giovanni De-Simone
- FIOCRUZ, Center of Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases Population (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (G.C.L.); (P.N.-P.); (L.R.G.); (D.W.P.J.)
- Department of Cellular and Molecular Biology, Biology Institute, Federal Fluminense University, Niterói 24020-141, Brazil
| | - Guilherme Curty Lechuga
- FIOCRUZ, Center of Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases Population (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (G.C.L.); (P.N.-P.); (L.R.G.); (D.W.P.J.)
| | - Paloma Napoleão-Pêgo
- FIOCRUZ, Center of Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases Population (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (G.C.L.); (P.N.-P.); (L.R.G.); (D.W.P.J.)
| | - Larissa Rodrigues Gomes
- FIOCRUZ, Center of Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases Population (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (G.C.L.); (P.N.-P.); (L.R.G.); (D.W.P.J.)
| | - David William Provance
- FIOCRUZ, Center of Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases Population (INCT-IDPN), Rio de Janeiro 21040-900, Brazil; (G.C.L.); (P.N.-P.); (L.R.G.); (D.W.P.J.)
- Interdisciplinary Medical Research Laboratory, Oswaldo Cruz Institute/FIOCRUZ, Rio de Janeiro 21040-900, Brazil;
| | - Vinícius Dias Nirello
- Faculty of Pharmacy, Federal of Rio de Janeiro University, Rio de Janeiro 21949-900, Brazil; (V.D.N.); (A.C.R.S.)
| | - Ana Carolina Rennó Sodero
- Faculty of Pharmacy, Federal of Rio de Janeiro University, Rio de Janeiro 21949-900, Brazil; (V.D.N.); (A.C.R.S.)
| | - Herbert Leonel de Mattos Guedes
- Interdisciplinary Medical Research Laboratory, Oswaldo Cruz Institute/FIOCRUZ, Rio de Janeiro 21040-900, Brazil;
- Laboratory of Immunopharmacology, Federal of Rio de Janeiro University, Duque de Caxias 25245-390, Brazil
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Tang Y, Huang M, Hu Q, Wu H, Yao J, Sun K, Li X. Agkihpin, a Distinct SVTLE from the Venom of Gloydius halys Pallas: Purification, Characterization and Structure-Activity Determination. Chem Biodivers 2018; 15:e1800122. [PMID: 29696792 DOI: 10.1002/cbdv.201800122] [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: 03/20/2018] [Accepted: 04/20/2018] [Indexed: 11/05/2022]
Abstract
Blood clots produced by snake-venom thrombin-like enzymes (SVTLEs) are cleared rapidly, which makes SVTLEs attractive as potential candidates for antithrombotic therapy. We isolated a SVTLE, agkihpin, from the venom of Gloydius halys Pallas. Agkihpin was confirmed to a single-chain TLE with molecular mass of 25.5 kD, pI of 7.43, optimal pH of 8.0 (hydrolyzing TAME), linked carbohydrate absent, and weak fibrinogen clotting activity. It was also found that (i) G. halys might be the latest species in SVTLEs phylogenetic tree; (ii) different level of conservation was shown among the SVTLEs from the Viperidae snakes. Some of those site may account for different activities exhibited by those SVTLEs, especially position 181, at which a fibrinogenolytic activity increase was found when a basic and larger amino acid substituted by a neutral and smaller one; (iii) an extra α-helix constructed with a 'Pro + acidic amino acid + aromatic amino acid' pattern was found in the SVTLEs from Gloydius and Agkistrodon snakes, although it does not necessarily imply an effect on the fibrinogenolytic activity of the SVTLEs. This study provided some new insight into the activity of SVTLE.
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Affiliation(s)
- Yulu Tang
- Department of Cell Biology and Genetics, School of Pre-clinical Medicine, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, P. R. China
| | - Miao Huang
- Department of Radiology, Affiliated Cancer Hospital of Guangxi Medical University, Nanning, 530021, P. R. China
| | - Qiping Hu
- Department of Cell Biology and Genetics, School of Pre-clinical Medicine, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, P. R. China
| | - Huayu Wu
- Department of Cell Biology and Genetics, School of Pre-clinical Medicine, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, P. R. China
| | - Jiali Yao
- Department of Cell Biology and Genetics, School of Pre-clinical Medicine, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, P. R. China
| | - Kejian Sun
- Department of Cell Biology and Genetics, School of Pre-clinical Medicine, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, P. R. China
| | - Xiaolong Li
- Department of Cell Biology and Genetics, School of Pre-clinical Medicine, Guangxi Medical University, 22 Shuangyong Road, Nanning, 530021, P. R. China
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Song H, Chen C, Zhao S, Ge F, Liu D, Shi D, Zhang T. Interaction of gallic acid with trypsin analyzed by spectroscopy. J Food Drug Anal 2015; 23:234-242. [PMID: 28911378 PMCID: PMC9351775 DOI: 10.1016/j.jfda.2014.09.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 09/03/2014] [Accepted: 09/30/2014] [Indexed: 11/18/2022] Open
Abstract
The interactions between trypsin and gallic acid (GA) were investigated by means of fluorescence spectroscopy, UV-vis absorption spectroscopy, resonance light scattering (RLS) spectroscopy, synchronous fluorescence spectroscopy, and enzymatic inhibition assay. It was found that GA can cause the fluorescence quenching of trypsin during the process of formation of GA-trypsin complex, resulting in inhibition of trypsin activity (IC50 = 3.9 × 10−6 mol/L). The fluorescence spectroscopic data showed that the quenching efficiency can reach about 80%. The binding constants were 1.9371 × 104 L/mol, 1.8192 × 104 L/mol, and 1.7465 × 104 L/mol at three temperatures, respectively. The thermodynamic parameters revealed that hydrogen bonds, van der Waals, hydrophobic, and electrostatic interactions were involved in the binding process of GA to trypsin. Molecular modeling studies illustrated a specific display of binding information and explained most of the experiment phenomena. The microenvironments of tryptophan and tyrosine residue in trypsin were changed by the GA. Results indicated that GA was a strong quencher and inhibitor of trypsin.
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Affiliation(s)
- Hao Song
- Faculty of Life Science, Kunming University of Science and Technology, Kunming 650500, People's Republic of China
| | - Chaoyin Chen
- Faculty of Life Science, Kunming University of Science and Technology, Kunming 650500, People's Republic of China.
| | - Shenglan Zhao
- Faculty of Traditional Chinese Medicine, Yunnan University of Traditional Chinese Medicine, Kunming 650200, People's Republic of China.
| | - Feng Ge
- Faculty of Life Science, Kunming University of Science and Technology, Kunming 650500, People's Republic of China
| | - Diqiu Liu
- Faculty of Life Science, Kunming University of Science and Technology, Kunming 650500, People's Republic of China
| | - Dandan Shi
- Faculty of Life Science, Kunming University of Science and Technology, Kunming 650500, People's Republic of China
| | - Tiancai Zhang
- Faculty of Life Science, Kunming University of Science and Technology, Kunming 650500, People's Republic of China
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The structure–function relationship of thrombin-like enzymes from the green pit viper (Trimeresurus albolabris). Toxicon 2015; 100:53-9. [DOI: 10.1016/j.toxicon.2015.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 04/06/2015] [Accepted: 04/21/2015] [Indexed: 10/23/2022]
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Garro HA, García C, Martín VS, Tonn CE, Pungitore CR. Chemistry and Biological Activity of Coumarins at Molecular Level. Nat Prod Commun 2014. [DOI: 10.1177/1934578x1400900808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Synthetic coumarins were prepared in high yields using ionic liquids as an environmental friendly alternative. 3,4-Dimethyl-7-hydroxycoumarin (3ab) and 3-isopropyl-4-methyl-5,7-dihydroxycoumarin (3bc) showed interesting activity against Taq DNA polymerase with IC50 values of 115.7 μM and 82.2 μM, respectively. Also, 4-methyl-7-hydroxycoumarin (3aa) and 4-methyl-5,7-dihydroxycoumarin (3ba) exhibited inhibitory activity against MMLV-RT with IC50 values of 23.5 μM and 18.3 μM, respectively. These inhibitors could have importance as antiretroviral chemotherapeutic agents and also for the development of antitumor drugs.
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Affiliation(s)
- Hugo A. Garro
- INTEQUI-CONICET, Fac. Qca., Bioqca. y Fcia., Univ. Nac. de San Luis (U.N.S.L.). Chacabuco y Pedernera, 5700 San Luis, Argentina
| | - Celina García
- Instituto Universitario de Bio-Orgánica Antonio González, Dpto. Química Orgánica, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez 2, 38206 La Laguna, Spain
| | - Víctor S. Martín
- Instituto Universitario de Bio-Orgánica Antonio González, Dpto. Química Orgánica, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez 2, 38206 La Laguna, Spain
| | - Carlos E. Tonn
- INTEQUI-CONICET, Fac. Qca., Bioqca. y Fcia., Univ. Nac. de San Luis (U.N.S.L.). Chacabuco y Pedernera, 5700 San Luis, Argentina
| | - Carlos R. Pungitore
- INTEQUI-CONICET, Fac. Qca., Bioqca. y Fcia., Univ. Nac. de San Luis (U.N.S.L.). Chacabuco y Pedernera, 5700 San Luis, Argentina
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Biochemical and functional properties of a thrombin-like enzyme isolated from Bothrops pauloensis snake venom. Toxicon 2009; 54:725-35. [PMID: 19539638 DOI: 10.1016/j.toxicon.2009.05.040] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Revised: 05/22/2009] [Accepted: 05/27/2009] [Indexed: 11/22/2022]
Abstract
In the present study, a thrombin-like enzyme named BpSP-I was isolated from Bothrops pauloensis snake venom and its biochemical, enzymatic and pharmacological characteristics were determined. BpSP-I is a glycoprotein that contains both N-linked carbohydrates and sialic acid in its structure, with M(r)=34,000 under reducing conditions and pI approximately 6.4. The N-terminal sequence of the enzyme (VIGGDECDINEHPFL) showed high similarity with other thrombin-like enzymes from snake venoms. BpSP-I showed high clotting activity upon bovine and human plasma and was inhibited by PMSF, benzamidine and leupeptin. Moreover, this enzyme showed stability when examined at different temperatures (-70 to 37 degrees C), pH values (3-9) or in the presence of divalent metal ions (Ca(2+), Mg(2+), Zn(2+) and Mn(2+)). BpSP-I showed high catalytic activity upon substrates, such as fibrinogen, TAME, S-2238 and S-2288. It also showed kallikrein-like activity, but was unable to act upon factor Xa and plasmin substrates. Indeed, the enzyme did not induce hemorrhage, myotoxicity or edema. Taken together, our data showed that BpSP-I is in fact a thrombin-like enzyme isoform isolated from Bothrops pauloensis snake venom.
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Samy RP, Gopalakrishnakone P, Chow VTK, Ho B. Viper metalloproteinase (Agkistrodon halys pallas) with antimicrobial activity against multi-drug resistant human pathogens. J Cell Physiol 2008; 216:54-68. [PMID: 18297685 DOI: 10.1002/jcp.21373] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Metalloproteinases are abundant enzymes in crotalidae and viperidae snake venoms. Snake venom metalloproteinases (SVMPs) comprise a family of zinc-dependent enzymes, which display many different biological activities. A 23.1 kDa protein was isolated from Agkistrodon halys (pallas, Chinese viper) snake venom. The toxin is a single chain polypeptide with a molecular weight of 23146.61 and an N-terminal sequence (MIQVLLVTICLAVFPYQGSSIILES) relatively similar to that of other metalloprotein-like proteases isolated from the snake venoms of the Viperidae family. The antibacterial effect of Agkistrodon halys metalloproteinase (AHM) on Burkholderia pseudomallei (strains TES and KHW), Escherichia coli, Enterobacter aerogenes, Proteus vulgaris, Proteus mirabilis, Pseudomonas aeruginosa (Gram-negative bacteria) and Staphylococcus aureus (Gram-positive bacterium) was studied at a concentration 120 microM. Interestingly, we found that the metalloproteinase exhibited antibacterial properties and was more active against S. aureus, P. vulgaris, P. mirabilis and multi-drug resistant B. pseudomallei (strain KHW) bacteria. AHM variants with high bacteriostatic activity (MIC 1.875-60 microM) also tended to be less cytotoxic against U-937 human monocytic cells up to 1 mM concentrations. These results suggest that this metalloprotein exerts its antimicrobial effect by altering membrane packing and inhibiting mechanosensitive targets.
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Affiliation(s)
- Ramar Perumal Samy
- Venom and Toxin Research Programme, Yong Loo Lin School of Medicine, Department of Anatomy, National University of Singapore, Singapore, Singapore
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Oligopeptidase B from Leishmania amazonensis: molecular cloning, gene expression analysis and molecular model. Parasitol Res 2008; 101:865-75. [PMID: 18074461 DOI: 10.1007/s00436-007-0630-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Serine oligopeptidases of trypanosomatids are emerging as important virulence factors and therapeutic targets in trypanosome infections. A complete open reading frame of oligopeptidase B from Leishmania amazonensis was amplified with polymerase chain reaction with gradient annealing temperatures using primers designed for the oligopeptidase B gene from L. major. The 2,196-bp fragment coded for a protein of 731 amino acids with a predicted molecular mass of 83.49 KDa. The encoded protein (La_OpB) shares a 90% identity with oligopeptidases of L. major and L. infantum, 84% with L. braziliensis, and approximately 62% identity with Trypanosoma peptidases. The oligopeptidase B gene is expressed in all cycle stages of L. amazonensis. The three dimensional model of La_OpB was obtained by homology modeling based on the structure of prolyl oligopeptidases. We mapped a La_OpB model that presents a greater negative charge than prolyl oligopeptidases; our results suggest a difference in the S2 subsite when compared to oligopeptidases B from Trypanosoma and bacterial oligopeptidases B. The La_OpB model serves as a starting point for its exploration as a potential target source for a rational chemotherapy.
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10
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Guedes HLM, Silva FP, Netto CC, de Salles CMC, Alexandre G, Oliveira CLP, Torriani I, De Simone SG. Structural characterization and low-resolution model of BJ-48, a thrombin-like enzyme from Bothrops jararacussu venom. Biophys Chem 2007; 132:159-64. [PMID: 18069115 DOI: 10.1016/j.bpc.2007.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Revised: 11/08/2007] [Accepted: 11/08/2007] [Indexed: 11/16/2022]
Abstract
Thrombin-like enzymes (TLEs) are important components of snake venoms due to their involvement in coagulopathies occurring on envenoming. Structural characterization of this group of serine proteases is of utmost importance for better understanding their unique properties. However, the high carbohydrate content of some members of this group prevents successful crystallization for structural determination. Circumventing this difficulty, the structure of BJ-48, a highly glycosylated TLE from Bothrops jararacussu venom, was studied in solution. At pH 8.0, where the enzyme displays maximum activity, BJ-48 has a radius of gyration (Rg) of 37 A and a maximum dimension (D(max)) of 130 A as measured by small-angle X-ray scattering (SAXS) and a Stokes radius (SR) of 50 A according to dynamic light scattering (DLS) data. At the naturally more acidic pH (6.0) of the B. jararacussu venom BJ-48 behaves as a more compact particle as evidenced by SAXS (R(g)=27.9 A and D(max)=82 A) and DLS (SR=30 A) data. In addition, Kratky plot analysis indicates a rigid shape at pH 8.0 and a flexible shape at pH 6.0. On the other hand, the center of mass of intrinsic fluorescence was not changed while varying pH, possibly indicating the absence of fluorescent amino acids in the regions affected by pH variation. Circular dichroism experiments carried out with BJ-48 indicate a substantially random coiled secondary structure that is not affected by pH. Low-resolution model of BJ-48 presented a prolate elongated shape at pH 8.0 and a U-shape at 6.0. BJ-48 tertiary structure at pH 6.0 was maintained on heating up to 52 degrees C and was completely lost at 75 degrees C. The possible existence of two pH-induced folding states for BJ-48 and its importance for the biological role and stability of this enzyme was discussed.
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Affiliation(s)
- Herbert L M Guedes
- Laboratório de Bioquímica de Proteínas e Peptídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, RJ, Brazil
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de Matos Guedes HL, Carneiro MPD, Gomes DCDO, Rossi-Bergmanmn B, Giovanni de Simone S. Oligopeptidase B from L. amazonensis: molecular cloning, gene expression analysis and molecular model. Parasitol Res 2007; 101:853-63. [PMID: 17530480 DOI: 10.1007/s00436-007-0552-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2007] [Accepted: 04/17/2007] [Indexed: 11/25/2022]
Abstract
Serine oligopeptidases of trypanosomatids are emerging as important virulence factors and therapeutic targets in trypanosome infections. A complete open reading frame of oligopeptidase B from Leishmania amazonensis was amplified with polymerase chain reaction with gradient annealing temperatures using primers designed for the oligopeptidase B gene from L. major. The 2,196-bp fragment coded for a protein of 731 amino acids with a predicted molecular mass of 83.49 KDa. The encoded protein (La_OpB) shares a 90% identity with oligopeptidases of L. major and L. infantum, 84% with L. braziliensis, and approximately 62 identity with Trypanosoma peptidases. The oligopeptidase B gene is expressed in all cycle stages of L. amazonensis. The three dimensional model of La_OpB was obtained by homology modeling based on the structure of prolyl oligopeptidases. We mapped a La_OpB model that presents a greater negative charge than prolyl oligopeptidases; our results suggest a difference in the S2 subsite when compared to oligopeptidases B from Trypanosoma and bacterial oligopeptidases B. The La_OpB model serves as a starting point for its exploration as a potential target source for a rational chemotherapy.
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Affiliation(s)
- Herbert Leonel de Matos Guedes
- Laboratório de Bioquímica de Proteínas e Peptídeos, Departamento de Bioquímica e Biologia Molecular, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
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Sakai J, Zhang S, Chen H, Atsumi F, Matsui T, Shiono H, Sanada S, Okada T. Primary structure of a thrombin-like serine protease, kangshuanmei, from the venom of Agkistrodon halys brevicaudus stejneger. Toxicon 2006; 48:313-22. [DOI: 10.1016/j.toxicon.2006.06.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2006] [Accepted: 06/01/2006] [Indexed: 11/30/2022]
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Vitorino-Cardoso AF, Pereira Ramos OH, Homsi-Brandeburgo MI, Selistre-de-Araujo HS. Insights into the substrate specificity of a novel snake venom serine peptidase by molecular modeling. Comp Biochem Physiol B Biochem Mol Biol 2006; 144:334-42. [PMID: 16716626 DOI: 10.1016/j.cbpb.2006.03.010] [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: 11/28/2005] [Revised: 03/23/2006] [Accepted: 03/25/2006] [Indexed: 11/24/2022]
Abstract
The cDNA encoding BthaTL, a serine peptidase from the venom of the snake Bothrops alternatus, was cloned and sequenced. The deduced primary structure shows over 62% of identity with snake venom thrombin-like enzymes (SVTLEs), molecules with high substrate specificity toward different natural substrates. Indeed, a phylogenetic reconstruction by two different methods clustered this enzyme close to other SVTLEs. These enzymes generally affect the hemostatic system in several ways, and therefore are used as tools in pharmacology and clinical diagnosis. A three-dimensional model of BthaTL was built by homology modeling using TSV-PA (Trimeresurus stejnegeri venom plasminogen activator) crystal structure as template. BthaTL model showed that the typical catalytic triad conformation of serine peptidases was preserved. The calcium coordination ligands were absent or adopt an unfavorable conformation, preventing interactions with metals. On the other hand, the Asp97-Arg174 saline bridge of TSV-PA was not found and its specificity determinant Phe193 is replaced by a Gly in BthaTL. The substitution of essential residues in the neighborhoods of the catalytic site cleft of BthaTL indicates that these two proteins do not share the same enzymatic specificity, what means that BthaTL will probably not activate plasminogen. Such observations may be helpful in the understanding of the molecular mechanism for substrate specificity of these enzymes.
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Affiliation(s)
- Ana Flávia Vitorino-Cardoso
- Laboratório de Química de Proteínas e Produtos Naturais, Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Uberlândia-MG, Brazil
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Silva FP, Antunes OAC, de Alencastro RB, De Simone SG. The Na+ binding channel of human coagulation proteases: novel insights on the structure and allosteric modulation revealed by molecular surface analysis. Biophys Chem 2005; 119:282-94. [PMID: 16288954 DOI: 10.1016/j.bpc.2005.10.001] [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] [Received: 07/21/2005] [Revised: 09/30/2005] [Accepted: 10/01/2005] [Indexed: 11/17/2022]
Abstract
Thrombovascular diseases result from imbalanced haemostasis and comprise important health problems in the aging population worldwide. The activity of enzymes pertaining to the coagulation cascade of mammalians exhibit several control mechanisms in order to maintain a proper balance between bleeding and thrombosis. For instance, human coagulation serine proteases carrying a F225 or Y225 are allosteric modulated by the binding of Na+ in a water-filled channel connected to the primary specificity pocket (S1 subsite) of these enzymes. We have characterized the structure, topography and lipophilicity of this channel in the ligand-free fast (sodium-bound) and slow (sodium-free) forms of thrombin, in the sole available structure of activated protein C and in several structures of the coagulation factors VIIa, IXa and Xa, differing in the nature of the bound inhibitor and in the occupancy of exosite-I as well as the Ca2+ and Na+ binding sites. Opposite to thrombin, the aqueous channels in all other coagulation enzymes sheltering a Na+ binding site do not have an aperture on the enzyme surface opposite to the S1 subsite entrance. In these enzymes, the lack of the three-residue insertion in loop 1 (183-189) as found in thrombin allied to compensatory mutations in the positions 187-185 and 222 effects a constriction in the water-filled channel that ends up by segregating the ion binding site from the S1 subsite. We also disclosed major topographical changes on the thrombin's surface upon sodium release and transition to the slow form that culminate in the narrowing of the S1 subsite entrance and, strikingly, in the loss of communication between the primary specificity pocket and the exosite-I. Such observation is in accordance with existing experimental data demonstrating thermodynamic linkage between these distant regions on the thrombin surface. Conformational changes in F34, L40, R73 and T74 were the main responsible for this effect. A path by which these changes in the vicinity of exosite-I could be transmitted to the S1 subsite and, consequently, to the sodium binding site is proposed.
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Affiliation(s)
- Floriano P Silva
- Laboratório de Bioquímica de Proteínas e Peptídeos, Departamento de Bioquímica e Biologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, 21045-900, Rio de Janeiro, RJ, Brazil.
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De-Simone SG, Correa-Netto C, Antunes OAC, De-Alencastro RB, Silva FP. Biochemical and molecular modeling analysis of the ability of two p-aminobenzamidine-based sorbents to selectively purify serine proteases (fibrinogenases) from snake venoms. J Chromatogr B Analyt Technol Biomed Life Sci 2005; 822:1-9. [PMID: 15994137 DOI: 10.1016/j.jchromb.2005.04.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2004] [Revised: 04/06/2005] [Accepted: 04/16/2005] [Indexed: 11/16/2022]
Abstract
Snake venoms contain several trypsin-like enzymes with equivalent physicochemical characteristics and similar inhibition profiles. These are rather difficult to separate by classical purification procedures and therefore constitute a good model for affinity chromatography analysis. Some of these trypsin homologues present fibrinogenase activity, mimicking one or more features of the central mammalian coagulation enzyme, thrombin. It was previously demonstrated that a number of amidine derivatives are able to interact specifically with some of these serine proteases. To understand the enzyme-sorbent interactions we have investigated the ability of two commercially available benzamidine affinity matrices to purify thrombin-like serine proteases (TLSP) with similar biological properties from two snake venoms (Bothrops jararacussu and Lachesis muta rhombeata). Curiously, each sorbent retained a single but distinct TLSP from each venom with high yield. Molecular modeling analysis suggested that hydrophobic interactions within a specific region on the surface of these enzymes could be generated to explain this exquisite specificity. In addition, it was demonstrated that a specific tandem alignment of the two benzamidine sorbents enables the purification of three other enzymes from B. jararacussu venom.
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Affiliation(s)
- S G De-Simone
- Laboratório de Bioquímica de Proteínas e Peptídeos, Departamento de Bioquímica e Biologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, 21045-900 Rio de Janeiro, RJ, Brazil.
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Zeng Q, Yin Q, Zhao Y. The study on the interaction between seryl-histidine dipeptide and proteins by circular dichroism and molecular modeling. Bioorg Med Chem 2005; 13:2679-89. [PMID: 15755667 DOI: 10.1016/j.bmc.2004.12.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Revised: 12/21/2004] [Accepted: 12/23/2004] [Indexed: 11/22/2022]
Abstract
The selective cleavage of proteins is very important in key biological processes. Chemical (nonenzymatic) reagents such as cyanogen bromide and transition metal complexes are used extensively with great defects. In this paper, the binding of seryl-histidine dipeptide (abbreviated as SH) with bovine serum albumin (BSA) and lysozyme were investigated by the circular dichroism spectroscopy (CD) at 298K, molecular docking studies and quantum chemical calculations based on the previous results of polyacrylamide gel electrophoresis (PAGE). From the studies of CD, it showed that SH interacted strongly with BSA and lysozyme. The change percentages of the secondary structures of BSA and lysozyme were calculated. The contents of the beta-sheets decreased remarkably. It indicated that the interactions between SH and proteins could break the hydrogen bonds of beta-sheets selectively. The docking studies between SH and BSA showed that the position of the oxygen atom of the hydroxyl group of SH (O(12)) was in favor of a nucleophilic attack on carbon atom of the amide bond of a beta-sheet (C(34)) because the distance between O(12) and C(34) was 3.37A. Natural charges, natural atomic hybrid percentages and square sums of HOMO coefficients calculated by the NBO and population analysis at HF/6-31G* supported the suggested mechanism. And so SH may be an interesting agent for the therapeutic use.
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Affiliation(s)
- Qing Zeng
- The Key Laboratory of Bioorganic Phosphorus Chemistry, Ministry of Education, China
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