Identificación de sitios alostéricos en proteínas de Homo sapiens que interactúan con la molécula de ATP mediante la herramienta Deacon Active Site Profiler (DASP3)

Active proteins and allosteric sites are distinguished in proteins. The latter have their binding site within the enzyme in a diﬀerent place from the active site. Its importance lies in the contribution it makes in the inhibition and / or activation of its biological function, this, through molecule...

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Autores:: González Rosas, Adriana Camila

Tipo de recurso:: Trabajo de grado de pregrado

Fecha de publicación:: 2020

Institución:: Universidad Antonio Nariño

Repositorio:: Repositorio UAN

Idioma:: spa

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network_acronym_str	UAntonioN2
network_name_str	Repositorio UAN
repository_id_str
dc.title.es_ES.fl_str_mv	Identificación de sitios alostéricos en proteínas de Homo sapiens que interactúan con la molécula de ATP mediante la herramienta Deacon Active Site Profiler (DASP3)
title	Identificación de sitios alostéricos en proteínas de Homo sapiens que interactúan con la molécula de ATP mediante la herramienta Deacon Active Site Profiler (DASP3)
spellingShingle	Identificación de sitios alostéricos en proteínas de Homo sapiens que interactúan con la molécula de ATP mediante la herramienta Deacon Active Site Profiler (DASP3) Proteínas Sitio alostérico ATP Bioinformática DASP3 Docking Proteins Allosteric Site ATP Bioinformatics DASP3 Docking
title_short	Identificación de sitios alostéricos en proteínas de Homo sapiens que interactúan con la molécula de ATP mediante la herramienta Deacon Active Site Profiler (DASP3)
title_full	Identificación de sitios alostéricos en proteínas de Homo sapiens que interactúan con la molécula de ATP mediante la herramienta Deacon Active Site Profiler (DASP3)
title_fullStr	Identificación de sitios alostéricos en proteínas de Homo sapiens que interactúan con la molécula de ATP mediante la herramienta Deacon Active Site Profiler (DASP3)
title_full_unstemmed	Identificación de sitios alostéricos en proteínas de Homo sapiens que interactúan con la molécula de ATP mediante la herramienta Deacon Active Site Profiler (DASP3)
title_sort	Identificación de sitios alostéricos en proteínas de Homo sapiens que interactúan con la molécula de ATP mediante la herramienta Deacon Active Site Profiler (DASP3)
dc.creator.fl_str_mv	González Rosas, Adriana Camila
dc.contributor.advisor.spa.fl_str_mv	Duarte González, Mario Enrique
dc.contributor.author.spa.fl_str_mv	González Rosas, Adriana Camila
dc.subject.es_ES.fl_str_mv	Proteínas Sitio alostérico ATP Bioinformática DASP3 Docking
topic	Proteínas Sitio alostérico ATP Bioinformática DASP3 Docking Proteins Allosteric Site ATP Bioinformatics DASP3 Docking
dc.subject.keyword.es_ES.fl_str_mv	Proteins Allosteric Site ATP Bioinformatics DASP3 Docking
description	Active proteins and allosteric sites are distinguished in proteins. The latter have their binding site within the enzyme in a diﬀerent place from the active site. Its importance lies in the contribution it makes in the inhibition and / or activation of its biological function, this, through molecules (ligands) that act as allosteric modulators, being a basis for the design of drugs, since they provide fewer adverse eﬀects than traditional ones. (active regulators). One of the main molecules that can act as an allosteric regulator is adenosine triphosphate (ATP), since it is essential for obtaining cellular energy. Among the public databases that have information on the structure of proteins, is the National Center for Biotechnology Information (NCBI), there are 1,364,990 proteins in Homo sapiens, some of which have not been studied and therefore it is not known if there is an allosteric site, nor its molecular position. In the work that follows, the creation of an allosteric site proﬁle (ASP) is presented, from three proteins and with the help of the Deacon Active Site Proﬁler 3 tool (DASP3), which allows identify active sites by creating an active site proﬁle; these proteins, through the reviewed literature, are known allosteric site in interaction with the ATP ligand.
publishDate	2020
dc.date.issued.spa.fl_str_mv	2020-07-21
dc.date.accessioned.none.fl_str_mv	2021-03-02T15:15:48Z
dc.date.available.none.fl_str_mv	2021-03-02T15:15:48Z
dc.type.spa.fl_str_mv	Trabajo de grado (Pregrado y/o Especialización)
dc.type.coar.spa.fl_str_mv	http://purl.org/coar/resource_type/c_7a1f
dc.type.coarversion.none.fl_str_mv	http://purl.org/coar/version/c_970fb48d4fbd8a85
format	http://purl.org/coar/resource_type/c_7a1f
dc.identifier.uri.none.fl_str_mv	http://repositorio.uan.edu.co/handle/123456789/2216
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dc.identifier.instname.spa.fl_str_mv	instname:Universidad Antonio Nariño
dc.identifier.reponame.spa.fl_str_mv	reponame:Repositorio Institucional UAN
dc.identifier.repourl.spa.fl_str_mv	repourl:https://repositorio.uan.edu.co/
url	http://repositorio.uan.edu.co/handle/123456789/2216
identifier_str_mv	O Flores Herrera, E Rendón Huerta, H Riveros Rosas, A Sosa Peinado, E Vázquez Contreras, and I Velázquez López. La estructura y la visualización molecular de proteínas. Mensaje bioquímico, 29, 2005. David L Nelson, Michael M Cox, and Albert L Lehninger. Principles of biochemistry. Freeman New York, 2008. HN Curtis. Ns barnes biología. Editorial M´edica Panamericana, 2002. Homero Saénz-Suárez, Leonardo René Lareo, Carlos Oribio-Quinto, Juan Martínez Mendoza, and Aura Chávez-Zobel. Predicción computacional de estructura terciaria de las proteínas humanas hsp27, ab-cristalina y hspb8. Universitas Scientiarum, 16(1):15– 28, 2011. Victoria Luque Guillén. Estructura y propiedades de las proteínas, 2009. Luis A Chel Guerrero, Luis Corzo Ríos, and David A Betancur Ancona. Estructura y propiedades funcionales de proteínas de leguminosas. Revista de la Universidad Autónoma de Yucatán, pages 34–43, 2003. O Martínez Augustin and E Martínez de Victoria. Proteínas y péptidos en nutrición enteral. Nutrición Hospitalaria, 21:01–14, 2006. Ángel Gil and FermÍn SÁnchez de Medina Contreras. Tratado de Nutrición: Bases ﬁsiológicas y bioquímicas de la nutrición. Acción Médica, 2005. Micaela Anahí Santucho Cordoba. Proteínas. Monografía, 2014. Jesús Merino Pérez and Maria José Noriega Borge. Enzimas. universidad de cantabria, 2011. Trudy McKee and James R Mckee. Enzimas. In Bioqu´ımica: la base molecular de la vida, chapter 6, pages 184–226. McGraw-Hill/Interamericana,, 5 edition, 2003. Yael Avissar, Jung Choi, Jean DeSaix, Vladimir Jurukovski, Robert Wise, Connie Rye, et al. Atp: Adenosine triphosphate. In Biology. OpenStax, 2018. Elizabeth Lira Silva, Ricardo Jasso Chávez, and Juan Pablo Pardo Vázquez. Respuestas al problema bioquímico. REB. Revista de educación bioquímica, 33(2):68–72, 2014. Ismael Lares-Asseﬀ and Francisca Trujillo-Jiménez. La farmacogenética y su importancia en la clínica. Gaceta medica de Mexico, 137(3), 2001. Claude Denson Pepper. National center for biotechnology information (ncbi). [citado 17 marzo 2020]. Disponible en: https://www.ncbi.nlm.nih.gov/, 1988. Janelle B Leuthaeuser, John H Morris, Angela F Harper, Thomas E Ferrin, Patricia C Babbitt, and Jacquelyn S Fetrow. Dasp3: identiﬁcation of protein sequences belonging to functionally relevant groups. BMC bioinformatics, 17(1):458, 2016. Richard D Taylor, Philip J Jewsbury, and Jonathan W Essex. A review of protein-small molecule docking methods. Journal of computer-aided molecular design, 16(3):151–166, 2002. Ruifeng Qi, Evans Boateng Sarbeng, Qun Liu, Katherine Quynh Le, Xinping Xu, Hongya Xu, Jiao Yang, Jennifer Li Wong, Christina Vorvis, Wayne A Hendrickson, et al. Allosteric opening of the polypeptide-binding site when an hsp70 binds atp. Nature structural & molecular biology, 20(7):900, 2013. Marta Acebro´n Garc´ıa de Eulate. Fragment based ligand discovery on Focal Adhesion Kinase. PhD thesis, Universidad Auto´noma de Madrid, 2018. Alejandro Reyes. ANÁLISIS FUNCIONAL DE MUTANTES PUNTUALES EN SITIOS ALOSTÉRICOS ENDO Y EXOFACIALES EN EL TRANSPORTADOR DE GLUCOSA GLUT1. PhD thesis, Universidad de Concepci´on, 2009. Joerg Klepper and Baerbel Leiendecker. Glut1 deﬁciency syndrome–2007 update. Developmental Medicine & Child Neurology, 49(9):707–716, 2007. Rafael Lahoz-Beltr´a. Bioinform´atica: Simulaci´on, vida artiﬁcial e inteligencia artiﬁcial. Ediciones Díaz de Santos, 2010. Vincent Le Guilloux, Peter Schmidtke, and Pierre Tuﬀery. Fpocket: an open source platform for ligand pocket detection. BMC bioinformatics, 10(1):168, 2009. Joe G Greener, Ioannis Filippis, and Michael JE Sternberg. Predicting protein dynamics and allostery using multi-protein atomic distance constraints. Structure, 25(3):546–558, 2017. Declan Clarke, Anurag Sethi, Shantao Li, Sushant Kumar, Richard WF Chang, Jieming Chen, and Mark Gerstein. Identifying allosteric hotspots with dynamics: Application to inter-and intra-species conservation. Structure, 24(5):826–837, 2016. Leslie B Poole and Kimberly J Nelson. Distribution and features of the six classes of peroxiredoxins. Molecules and cells, 39(1):53, 2016. Jacquelyn S Fetrow. Active site proﬁling to identify protein functional sites in sequences and structures using the deacon active site proﬁler (dasp). Current protocols in bioinformatics, 14(1):8–10, 2006. Laura Soito, Chris Williamson, Stacy T Knutson, Jacquelyn S Fetrow, Leslie B Poole, and Kimberly J Nelson. Prex: Peroxiredoxin classiﬁcation index, a database of subfamily assignments across the diverse peroxiredoxin family. Nucleic acids research, 39(suppl 1):D332–D337, 2011. Ryan G Huﬀ, Ersin Bayram, Huan Tan, Stacy T Knutson, Michael H Knaggs, Allen B Richon, Peter Santago, and Jacquelyn S Fetrow. Chemical and structural diversity in cyclooxygenase protein active sites. 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Carlos Roca, Carlos Requena, Víctor Sebastián-Pérez, Sony Malhotra, Chris Radoux, Concepción Pérez, Ana Martinez, Juan Antonio Paez, Tom L Blundell, and Nuria E Campillo. Identiﬁcation of new allosteric sites and modulators of ache through computational and experimental tools. Journal of enzyme inhibition and medicinal chemistry, 33(1):1034–1047, 2018. Garrett M Morris, Ruth Huey, William Lindstrom, Michel F Sanner, Richard K Belew, David S Goodsell, and Arthur J Olson. Autodock4 and autodocktools4: Automated docking with selective receptor ﬂexibility. Journal of computational chemistry, 30(16):2785–2791, 2009. Marcelo Adrian Marti and Adrian Turjanski. La bioinformática estructural o la realidad virtual de los medicamentos. Química Viva, 2009. Ruth Nussinov and Chung-Jung Tsai. The diﬀerent ways through which speciﬁcity works in orthosteric and allosteric drugs. Current pharmaceutical design, 18(9):1311– 1316, 2012. Shaoyong Lu, Shuai Li, and Jian Zhang. 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spelling	Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)Acceso abiertohttps://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Duarte González, Mario EnriqueGonzález Rosas, Adriana Camila2021-03-02T15:15:48Z2021-03-02T15:15:48Z2020-07-21http://repositorio.uan.edu.co/handle/123456789/2216O Flores Herrera, E Rendón Huerta, H Riveros Rosas, A Sosa Peinado, E Vázquez Contreras, and I Velázquez López. La estructura y la visualización molecular de proteínas. Mensaje bioquímico, 29, 2005.David L Nelson, Michael M Cox, and Albert L Lehninger. Principles of biochemistry. Freeman New York, 2008.HN Curtis. Ns barnes biología. Editorial M´edica Panamericana, 2002.Homero Saénz-Suárez, Leonardo René Lareo, Carlos Oribio-Quinto, Juan Martínez Mendoza, and Aura Chávez-Zobel. Predicción computacional de estructura terciaria de las proteínas humanas hsp27, ab-cristalina y hspb8. 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Acta biochimica et biophysica Sinica, 48(1):3–10, 2016.Alexander L Perryman, Daniel N Santiago, Stefano Forli, Diogo Santos-Martins, and Arthur J Olson. Virtual screening with autodock vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of hiv integrase: participation in the sampl4 protein–ligand binding challenge. Journal of computer-aided molecular design, 28(4):429–441, 2014.Carlos Roca, Carlos Requena, Víctor Sebastián-Pérez, Sony Malhotra, Chris Radoux, Concepción Pérez, Ana Martinez, Juan Antonio Paez, Tom L Blundell, and Nuria E Campillo. Identiﬁcation of new allosteric sites and modulators of ache through computational and experimental tools. Journal of enzyme inhibition and medicinal chemistry, 33(1):1034–1047, 2018.Garrett M Morris, Ruth Huey, William Lindstrom, Michel F Sanner, Richard K Belew, David S Goodsell, and Arthur J Olson. Autodock4 and autodocktools4: Automated docking with selective receptor ﬂexibility. Journal of computational chemistry, 30(16):2785–2791, 2009.Marcelo Adrian Marti and Adrian Turjanski. La bioinformática estructural o la realidad virtual de los medicamentos. Química Viva, 2009.Ruth Nussinov and Chung-Jung Tsai. The diﬀerent ways through which speciﬁcity works in orthosteric and allosteric drugs. Current pharmaceutical design, 18(9):1311– 1316, 2012.Shaoyong Lu, Shuai Li, and Jian Zhang. Harnessing allostery: a novel approach to drug discovery. Medicinal research reviews, 34(6):1242–1285, 2014.Alejandro Panjkovich and Xavier Daura. Exploiting protein ﬂexibility to predict the location of allosteric sites. BMC bioinformatics, 13(1):273, 2012.Fernanda Saldívar-González, Fernando D Prieto-Martínez, and José L Medina-Franco. Descubrimiento y desarrollo de fármacos: un enfoque computacional. Educación química, 28(1):51–58, 2017.Carlos Roca Magad´an. Estrategias computacionales en el desarrollo de neurofármacos: una tecnología de éxito. PhD thesis, Universidad Complutense de Madrid, 2018.Shaoyong Lu, Mingfei Ji, Duan Ni, and Jian Zhang. Discovery of hidden allosteric sites as novel targets for allosteric drug design. Drug discovery today, 23(2):359–365, 2018.Ruth Nussinov and Chung-Jung Tsai. The design of covalent allosteric drugs. Annual review of pharmacology and toxicology, 55:249–267, 2015.Gerard J Tortora and Bryan Derrickson. Principios de anatomía y ﬁsiología. Médica Panamericana,, 2013.W Sperl, P Jeˇsina, J Zeman, JA Mayr, L Demeirleir, Rudy VanCoster, A Pickova, H Hansikova, H Houˇst’kov´a, Z Krejˇc´ık, et al. Deﬁciency of mitochondrial atp synthase of nuclear genetic origin. Neuromuscular Disorders, 16(12):821–829, 2006.Paolo Cremonesi. L’ambiente acquoso per il trattamento di opere policrome. il prato publishing house srl, 2012.Marcela Ayala Aceves. Enzimas:¿ qué son y cómo funcionan? 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Método acoplado autodock-pm6 para seleccionar la mejor pose en estudios de acoplamiento molecular. Revista Colombiana de Química, 42(1), 2013.instname:Universidad Antonio Nariñoreponame:Repositorio Institucional UANrepourl:https://repositorio.uan.edu.co/Active proteins and allosteric sites are distinguished in proteins. The latter have their binding site within the enzyme in a diﬀerent place from the active site. Its importance lies in the contribution it makes in the inhibition and / or activation of its biological function, this, through molecules (ligands) that act as allosteric modulators, being a basis for the design of drugs, since they provide fewer adverse eﬀects than traditional ones. (active regulators). One of the main molecules that can act as an allosteric regulator is adenosine triphosphate (ATP), since it is essential for obtaining cellular energy. Among the public databases that have information on the structure of proteins, is the National Center for Biotechnology Information (NCBI), there are 1,364,990 proteins in Homo sapiens, some of which have not been studied and therefore it is not known if there is an allosteric site, nor its molecular position. In the work that follows, the creation of an allosteric site proﬁle (ASP) is presented, from three proteins and with the help of the Deacon Active Site Proﬁler 3 tool (DASP3), which allows identify active sites by creating an active site proﬁle; these proteins, through the reviewed literature, are known allosteric site in interaction with the ATP ligand.En las proteínas se distinguen los sitios activos y los sitios alostéricos. Estos últimos poseen su sitio de unión dentro de la enzima en un lugar diferente al del sitio activo. Su importancia radica en la contribución que realiza en la inhibición y/o activación de su función biológica, esto, mediante moléculas (ligandos) que actúan como moduladores alostéricos, siendo una base para el diseño de fármacos, pues proporcionan menos efectos adversos que los tradicionales (reguladores activos). Una de las principales moléculas que puede actuar como regulador alostérico es el adenosín trifosfato (ATP), ya que es fundamental para la obtención de energía celular. Entre las bases de datos públicas que cuentan con información sobre la estructura de las proteínas, se encuentra el National Center for Biotechnology Information (NCBI), allí existen 1’364.990 proteínas en Homo sapiens, algunas de estas no han sido estudiadas y por tanto no se conoce si existe un sitio alostérico, ni su posición molecular. En el trabajo que se desarrolla a continuación, se presenta la creación de un perﬁl de sitio alostérico (ASP), a partir de tres proteínas y con la ayuda de la herramienta Deacon Active Site Proﬁler 3 (DASP3), que permite identiﬁcar sitios activos a partir de la creación de un perﬁl de sitio activo; a dichas proteínas, por medio de la literatura revisada, se les conoce sitio alostérico en interacción con el ligando ATP.OtroIngeniero(a) Biomédico(a)PregradoCosto del proyecto $ 2’260.000. Financiación propia $ 1’010.000. Financiación UAN $ 1’250.000.PresencialspaUniversidad Antonio NariñoIngeniería BiomédicaFacultad de Ingeniería Mecánica, Electrónica y BiomédicaBogotá - SurProteínasSitio alostéricoATPBioinformáticaDASP3DockingProteinsAllosteric SiteATPBioinformaticsDASP3DockingIdentificación de sitios alostéricos en proteínas de Homo sapiens que interactúan con la molécula de ATP mediante la herramienta Deacon Active Site Profiler (DASP3)Trabajo de grado (Pregrado y/o Especialización)http://purl.org/coar/resource_type/c_7a1fhttp://purl.org/coar/version/c_970fb48d4fbd8a85CC-LICENSElicense_rdflicense_rdfapplication/rdf+xml; charset=utf-8811https://repositorio.uan.edu.co/bitstreams/56945e2c-099d-4cdc-92bd-ecf0a398a9c7/download9868ccc48a14c8d591352b6eaf7f6239MD515LICENSElicense.txtlicense.txttext/plain; charset=utf-82710https://repositorio.uan.edu.co/bitstreams/4569adbc-fbc7-42c3-b3e0-424d71390ba0/download2e388663398085f69421c9e4c5fcf235MD516ORIGINAL2020AutorizacióndeAutores.pdf2020AutorizacióndeAutores.pdfAutorización de autoresapplication/pdf665533https://repositorio.uan.edu.co/bitstreams/6b98455d-8683-4bbe-8b62-19b05fe966d7/downloadf4991e38807900ad3546571a51390703MD5122020AdrianaCamilaGonzalezRosas.pdf2020AdrianaCamilaGonzalezRosas.pdfTrabajo integral de gradoapplication/pdf4084872https://repositorio.uan.edu.co/bitstreams/ffda075a-c5c5-4be8-a414-d5982a86dd20/download1ffa012ec7dc76814014583eb316cf4aMD513123456789/2216oai:repositorio.uan.edu.co:123456789/22162024-10-09 22:36:27.676https://creativecommons.org/licenses/by-nc-nd/4.0/Acceso abiertorestrictedhttps://repositorio.uan.edu.coRepositorio Institucional 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Identificación de sitios alostéricos en proteínas de Homo sapiens que interactúan con la molécula de ATP mediante la herramienta Deacon Active Site Profiler (DASP3)

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