APROXIMACIÓN IN SILICO A LA ESTRUCTURA 3D DE LA PROTEÍNA ANTIVENENO DM64 DE LA ZARIGÜEYA (MAMMALIA: MARSUPIALIA: DIDELPHIDAE)
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Duque-Osorio, J.-F. ., Sánchez, A. ., Fierro, L. ., & Castaño, R. S. . (2023). APROXIMACIÓN IN SILICO A LA ESTRUCTURA 3D DE LA PROTEÍNA ANTIVENENO DM64 DE LA ZARIGÜEYA (MAMMALIA: MARSUPIALIA: DIDELPHIDAE). Revista De La Academia Colombiana De Ciencias Exactas, Físicas Y Naturales, 33(126), 103–123. https://doi.org/10.18257/raccefyn.33(126).2009.1815

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Abstract

Venomous snake byte accidents produce more than 50 thousand deaths each year, particularly in the tropics where these accidents have become a public health problem. Ophidic accidents produce, amongst other symptoms, hemorrhages (SVMPs), myonecrosis (PLAs) and pain, and conventional serotherapies are only partially effective and can produce immune adverse effects. Hence natural antivenom proteins from mammals are being investigated [DM43 (antihemorrhagin) and DM64 (antimyotoxic) from opossum serum (Maruspialia: Didelphis)] which have demonstrated to be more effective. Additionally, venomous PLAs and SVMPs have their normal non-venomous endogenous counterparts (MMPs and PLAs), and when the balance between the latter and their inhibitors is broken, the following pathologies can occur: arthritis, arteriosclerosis, asthma, diabetes, septic shocks, neoplasias, inflammations, psoriasis, etc. It’s because of all these reasons, that an approximation to the 3D structure of DM64 was made here, with in silico homology methods, using the Swiss Model-Deep View system. Besides obtaining a similar model to that previously published by another group for DM43, the work presented here allowed the standardization of the SM-DV modeling technique as a very useful tool in our countries, given its efficency and low costs (SM-DV is freely available).

https://doi.org/10.18257/raccefyn.33(126).2009.1815

Keywords

Mammal antivenom proteins (PLIs, anti-SVMP | DM64 | DM43) | Didelphis | structural homology model | Swiss Model-Deep View | veneno de serpientes (PLAs, SVMPs) | Viperidae
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References

Alberts B., Johnson A. Lewis J., Raff M., Roberts K. & P. Walter.2002. The Molecular Biology of the Cell. Garland Science, New York, USA.

Bazan J.F. 1990. Structural Design and Molecular Evolution of a Cytokine Receptor Superfamily. PNAS 87: 6934-6938.

Biardi J.E., Coss R.G. & D.G. Smith. 2000. California Ground Squirrel (Spermophilus beecheyi) Blood Sera Inhibits Crotalid Venom Proteolytic Activity. Toxicon 38(5): 713-721.

Bjarnason, J.B. & J.W. Fox. 1994. Hemorrhagic Metalloproteinases from Snake Venoms. Pharmac. Ther. 62(3): 325–372.

Bottino C., Vitale M., Pende D., Biassoni R. & A. Moretta. 1995. Receptors for HLA Class I Molecules in Human NK Cells. Seminars in Immunology 7: pp 67-73.

Catanese J.J. & L.F. Kress. 1992. Isolation from Opossum Serum of a Metalloproteinase Inhibitor Homologous to Human 1Bglycoprotein. Biochemistry 31: 410-418.

Chippaux J.P. & Goyfon M. 1998. Venoms, Antivenoms and Immunotherapy. Toxicon 36(6):823-846.

Contreras-Moreira B., Fitzjohn P.W. & P.A. Bates. 2002. Comparative Modelling: An Essential Methodology for Protein Structure Prediction in the Post-Genomic Era. Applied Bioinformatics 1(4): 177-190.

Contreras-Moreira B. & P.A. Bates. 2002. Domain Fishing: A First Step in Protein Comparative Modelling. Bioinformatics 18(8): 1141-1142.

Cooper G.M. 2000. The Cell: A Molecular Approach. Second Edition, Sinauer Associates, Inc., Sunderland, Missachusetts, USA. de Vos A.M., Ultsch M. & A.A. Kosslakoff. 1992. Human Growth Hormone and Extracellular Domain of its Receptor: Crystal Structure of the Complex. Science 255: 306-312

Domont G.B., Perales J. & H. Moussatche. 1991. Natural Anti- Snake Venom Proteins. Toxicon 29(10):1183-94.

Duque-Osorio J.F., Sánchez A., Fierro L., Garzón S. & R.S. Castaño. 2007. Venenos de Serpientes y Moléculas Antiveneno. Revista de la Academia Colombiana de Ciencias Físicas Exactas y Naturales (ACCEFYN) 31(118): 109-137.

Gold B.S., Dart R.C. & R.A. Barish. 2002. Bites of Venomous Snakes. N. Engl. J. Med. 347: 347 - 356.

Guex N. & M.C. Peitsch. 1997. SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling.Electrophoresis 18 (15): 2714-2723.

Guex N. & M.C. Peitsch. 2009. Principles of Protein Structure, Comparative Protein Modelling and Visualisation. [publicación en línea]. Disponible desde Internet en: <http://swissmodel.expasy.org/course/course-index.htm> [con acceso el 06-May-2009].

Guex N., Diemand A. and M.C. Peitsch. 1999. Protein Modelling for All. Elsevier TIBS 24: 364-367.

Guex N., Diemand A., M.C. Peitsch & T. Schwede. 2008. The Swiss Institute of Bioinformatics Presents Deep View (Swiss PDB Viewer). [publicación en línea]. Disponible desde Internet en: <http://swissmodel.expasy.org/spdbv/> [con acceso el 06-May-2009].

Gunsteren W.F., Billeter S.R., Eising A.A., Hünenberger P.H., Krüger P., Mark A.E., Scott A.M. & I.G. Tironi. 2009.Biomolecular Simulation: The Gromos Manual. [publicación en línea]. Disponible desde Internet en: <http://www.igc.ethz.ch/GROMOS/manual> [con acceso el 06-May-2009].

Gutiérrez J.M. & A. Rucavado. 2000. Snake Venom Metalloproteinases: Their Role in the Pathogenesis of Local Tissue Damage. Biochimie 82(9-10): 841-50.

Gutiérrez J.M. & C.L. Ownby. 2003. Skeletal Muscle Degeneration Induced by Venom Phospholipases A2: Insights Into the Mechanisms of Local and Systemic Myotoxicity. Toxicon42(8): 915-931.

Hains P.G. & K.W. Broady. 2000. Purification and Inhibitory Profile of Phospholipase A2 Inhibitors from Australian Elapid Sera. Biochem J 346: 139-146.

Hains P.G., Sung K.L., Tseng A. & K.W. Broady. 2000. Functional Characteristics of a Phospholipase A2 Inhibitor from Notechis ater Serum. J Biol Chem 275: 983-991.

Hains P.G., Nield B., Skuloski S., Dunn R. & K. Broady. 2001.Sequencing and Two-dimensional Structure Prediction of a Phospholipase A2 Inhibitor from the Serum of the Common Tiger Snake (Notechis scutatus). J Mol Biol 312: 875-884.

Halaby D.M. & J.P.E. Mornon. 1998. The ImmunoglobulinSuperfamily: An Insight on Its Tissular, Species, and Functional Diversity. J Mol Evol 46: 389-400.

Halaby D.M., Poupon A. & J.P. Mornon. 1999. The Immunoglobulin Fold Family: Sequence Analysis and 3D Structure Comparisons. Protein Engineering 12(7): 563 - 571. Harpaz Y. & C. Chothia. 1994. Many of the Immunoglobulin Superfamily Domains in Cell Adhesion Molecules and Surface Receptors Belong to a New Structural Set Which is Close to that Containing Variable Domains. J Mol Biol 238: 528-539.

Hood L., Kronenberg M. & T. Hunkapiller. 1985. T Cell Antigen Receptors and the Immunoglobulin Supergene Family. Cell 40: 225-229.

Ishioka N., Takahashi N. & F.W. Putnam. 1986. Amino Acid Sequence of Human Plasma -1B-glycoprotein: Homology to the Immunoglobulin Supergene Family. PNAS 83: 2363-2367.

Jia L.G., Shimokawa K., Bjarnason J.B. & J.W. Fox. 1996. Snake Venom Metalloproteinases: Structure, Function and Relationship to the ADAMs Family of Proteins. Toxicon 34(11-12): 1269-1276.

Jurgilas P.B., Neves-Ferreira A.G.C., Domont G.B. & J. Perales. 2003. PO41, a Snake Venom Metalloproteinase Inhibitor Isolated From Philander Opossum Serum. Toxicon 42: 621-628.

Kamiguti A.S., Hay C.R., Theakston R.D. & M. Zuzel. 1996. Insights into the Mechanism of Haemorrhage Caused by Snake Venom Metalloproteinases. Toxicon 34(6): 627-642.

Kamiguti A.S., Zuzel M. & R.D. Theakston. 1998. Snake Venom Metalloproteinases and Disintegrins: Interactions With Cells. Braz J Med Biol Res 31(7): 853-62.

Kaplan W. & T.G. Littlejohn. 2001. Swiss-PDB viewer (Deep View). Briefings in Bioinformatics 2(2): 195-197.

Kopp J. & T. Schwede. 2004. The SWISS-MODEL Repository of Annotated Three-Dimensional Protein Structure Homology Models. Nucleic Acids Research 32: D230-D234.

Kumar S., Tamura K. & M. Nei. 2004. MEGA 3: Integrated Software for Molecular Evolutionary Genetics Analysis and Sequence Alignment Briefings in Bioinformatics 5:150-163.

Lehtinen M.J., Meri S. and T.S. Jokiranta. 2004. Interdomain Contact Regions and Angles Between Adjacent Short Consensus Repeat Domains. J. Mol. Biol. 344(5): 1385-1396.

Letunic I., Copley R.R., Schmidt S., Ciccarelli F.D., Doerks T., Schultz J., Ponting C.P. & P. Bork. 2004. SMART 4.0: Towards Genomic Data Integration. Nucleic Acids Research 32: D142-D144.

Lizano S., Domont G. & J. Perales. 2003. Natural Phospholipase A2 Myotoxin Inhibitor Proteins from Snakes, Mammals and Plants.Toxicon 42: 963-977.

Lomonte B., Ángulo Y. & L. Calderón. 2003. An Overview of Lysine-Phospholipase A2 Myotoxins from Crotalid Snake Venoms and their Structural Determinants of Myotoxic Action. Toxicon 42(8): 885–901.

Martínez R.R., Pérez J.C., Sánchez E.E. & R. Campos. 1999. The Antihemorrhagic Factor of the Mexican Ground Squirrel,(Spermophilus mexicanus). Toxicon 37: 949-954.

Matsui T., Fujimura Y. & K. Titani. 2000. Snake Venom Proteases Affecting Hemostasis and Thrombosis. Biochim Biophys Acta 1477(1-2): 146-156.

Mattison C. 1995. The Encyclopedia of Snakes. Facts on Life, Inc. New York. 256 pp.

Melo P.A. & G. Suarez-Kurtz. 1988. Release of Sarcoplasmic Enzymes from Skeletal Muscle by Bothrops jaracussu venom: Antagonism by Heparin and by the Serum of South American Marsupials. Toxicon 26:87-95.

Moretta A., Bottino C., Vitale M., Pende D., Biassoni R., Mingari M.C. & L. Moretta. 1996. Receptors for HLA Class-I Molecules in Human Natural Killer Cells. Annu Rev Immunol 14:619-648.

Nei M., Gu X. & T. Sitnikova. 1997. Evolution by the Birth-and-Death Process in Multigene Families of the Vertebrate Immune System. PNAS 94: 7799–7806.

Neves-Ferreira A.G.C., Perales J., Ovadia M., Moussatché H. & G.B. Domont. 1997. Inhibitory Properties of the Antibothropic Complex from the South American Opossum (Didelphis marsupialis) Serum. Toxicon 35(6): 849-863.

Neves-Ferreira A.G.C., Cardinale N.; Rocha S.L.G., Perales J. & G.B. Domont. 2000. Isolation and Characterization of DM40 and DM43, Two Snake Venom Metalloproteinase Inhibitors from Didelphis marsupialis Serum. Biochim Biophys Acta 1474: 309-320.

Neves-Ferreira A.G.C., Perales J., Fox J.W., Shannon J.D., Makino D.L., Garratt R.C. & G.B. Domont. 2002. Structural and Functional Analyses of DM43, a Snake Venom Metalloproteinase Inhibitor from Didelphis marsupialis Serum. J Biol Chem 277: 13129-13137.

Núñez C.C., Ángulo Y. & B. Lomonte. 2001. Identification of the Myotoxic site of the Lys49 Phospholipase A2 from Agkistrodon piscivorus piscivorus Snake Venom: Synthetic C-terminal Peptides from Lys49, but not from Asp49 Myotoxins, Exert Membrane-damaging Activities. Toxicon 39(10): 1587-1594.

Ohno M., Chijiwa T., Oda-Ueda N., Ogawa T. & S. Hattori. 2003. Molecular Evolution of Myotoxic Phospholipases A2 from Snake Venom. Toxicon 42(8): 841-854.

Omori-Satoh T., Yamakawa Y. & D. Mebs. 2000. The Antihemorrhagic Factor, Erinacin, from the European Hedgehog (Erinaceus europaeus), a Metalloprotease Inhibitor of Large Molecular Size Possessing Ficolin/Opsonin P35 Lectin Domains. Toxicon 38(11): 1561-1580.

Ownby C.L., Colberg T.R. & H.S. Selistre-de-Araujo. 1998. Phospholipase A2 Toxins: Diversity in Structure and Function. 12th World Congress on Animal, Plant and Microbial Toxins. Toxicon 36(9):1219-1232.

Peitsch M.C. 2002. About the Use of Protein Models. Bioinformatics 18 (7): 934-938.

Perales J., Moussatche H., Oliveira B., Marangoni S. & G.B. Domont. 1994. Isolation and Partial Characterization of an Antibothropic Complex From Serum of South American Didelphidae. Toxicon 32: 1237-1249.

Perales J. & G.B. Domont. 2002. Are Inhibitors of Metalloproteinases, Phospholipases A2 and Myotoxins Members of the Innate Immune System?. Pp: 435-455 En: Menéz A. (ed.). Perspectives in Molecular Toxinology. John Wiley & Sons. 485 pp.

Pérez J.C. & E.E. Sanchez. 1999. Natural Protease Inhibitors to Hemorrhagins in Snake Venoms and Their Potential use in Medicine. Toxicon 37(5): 703-28.

Pruess M. & R. Apweiler. 2003. Bioinformatics Resources for In Silico Proteome Analysis. Journal of Biomedicine and Biotechnology 4 (2003): 231-236. Qi Z.Q., Yonaha K., Tomihara Y. & S. Toyama. 1994. Characterization of the Antihemorrhagic Factors of Mongoose (Herpestes edwardsii). Toxicon 32(11): 1459-1469.

Rhodes G. 2000. Judging the Quality of Macromolecular Models: A Glossary of Terms from Crystallography, NMR, and Homology Modeling. [publicación en línea]. Disponible desde Internet en: <http://spdbv.vital-it.ch/TheMolecularLevel/ModQual/>[con acceso el 06-May-2009]

Rhodes G. 2008. Molecular Modeling for Beginners: Tutorial For Deep View (Swiss-PdbViewer). Disponible desde Internet en:<http://spdbv.vital-it.ch/TheMolecularLevel/SPVTut/> [con acceso el 06-May-2009]

Rocha S.L.G., Lomonte B., Neves-Ferreira A.G.C., Trugilho M.R.O., Junqueira-de-Azevedo I.L.M., Ho P.L., Domont G.B., Gutiérrez J.M. & J. Perales. 2002. Functional Analysis of DM64, an Antimyotoxic Protein with immunoglobulin-like Structure from Didelphis marsupialis serum. Eur J Biochem 269: 6052-6062.

Rueda-Borrego M. 2005. Estudio Teórico Sobre la Influencia del Solvente en la Estructura y Dinámica del ADN. Universidad de Barcelona, Departamento de Bioquímica y Biología Molecular.

[publicación en línea]. Disponible desde Internet en: <http://www.tesisenxarxa.net/TESIS_UB/AVAILABLE/TDX-0629106-135551//MRB_TESIS.pdf> [con acceso el 06-May-2009].

Sali A. 2009. Modeller: A Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. [publicación en línea]. Disponible desde Internet en: <http://salilab.org/modeller/> [con acceso el 06-May-2009].

Scott W.R.P., Hünenberger P.H., Tironi I.G., Mark A.E., Billeter S.R., Fennen J., Torda A.E., Huber T., Krüger P. & W.F. vanGunsteren. 1999. The GROMOS Biomolecular Simulation Program Package. J Phys Chem A 103(19):3596–3607.

Schultz J., Milpetz, F., Bork, P. & C.P. Ponting. 1998. SMART, a Simple Modular Architecture Research Tool: Identification of Signalling Domains. PNAS 95(11): 5857-5864.

Schwede T., Diemand A., Guex N. & M.C. Peitsch. 2000. Protein Structure Computing in the Genomic Era. Res Microbiol 151: 107-112.

Schwede T., Kopp J., Guex N. & Peitsch M.C. 2003. SWISS-MODEL: An Automated Protein Homology-Modeling Server. Nucleic Acids Research 31 (13): 3381-3385.

Soares A.M., Rodrigues V.M., Borges M.H., Andriao-Escarso S.H., Cunha O.A., Homsi-Brandeburgo M.I. & J.R. Giglio. 1997. Inhibition of Proteases, Myotoxins and Phospholipases A2 from Bothrops Venoms by the Heteromeric Protein Complex of Didelphis Albiventris Opossum Serum. Biochem Mol Biol Int 43(5): 1091-1099.

Soares A.M., Marcussi S., Stábeli R.G., França S.C., Giglio J.R., Ward R.J. & E.C. Arantes. 2003. Structural and Functional Análisis of BmjMIP, a Phospholipase A2 Myotoxin Inhibitor Protein from Bothrops moojeni plasma. Biochem Biophys Res Comm 302:193-200.

Somers W., Ultsch M., De Vos A.M. & A.A. Kossiakoff. 1994. The X-Ray Structure of A Growth Hormone-Prolactin Receptor Complex. Nature 372(6505): 478-81.

Thwin M.M. & P. Gopalakrishnakone. 1998. Snake Envenomation and Protective Natural Endogenous Proteins: A Mini Review of Recent Developments. Toxicon 36(11): 1471-1482.

Thwin M.M., Gopalakrishnakone P., Kini R.M., Armugam A. & K. Jeyaseelan. 2000. Recombinant Antitoxic and Anti-inflamatory Factor from the Nonvenomous Snake Python reticulatus: Phospholipase A2 Inhibition and Venom Neutralizing Potential.Biochemistry 39: 9604-9611.

Weissenberg S., Ovadia M., Fleminger G. & E. Kochva. 1991. Antihemorrhagic Factors from the Blood Serum of the Western Diamondback Rattlesnake Crotalus atrox. Toxicon Volume 29(7): 807-818.

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