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dc.contributor.advisorRamírez-Vick, Jaime E.
dc.contributor.authorAcevedo-Morantes, Claudia Y.
dc.date.accessioned2018-03-26T15:55:06Z
dc.date.available2018-03-26T15:55:06Z
dc.date.issued2007
dc.identifier.urihttps://hdl.handle.net/20.500.11801/306
dc.description.abstractRhodobacter sphaeroides is a facultative photoheterotroph organism, belonging to the α-3 subdivision of the Proteobacteria. It has many modes of growth conferring advantage when the environmental conditions change. These different metabolic pathways involve a diversity of hemoproteins like cytochrome c2 (cyt c2). Within the cyt c2 maturation pathway a diversity of proteins is involved. CcmE is a chaperone protein involved in the covalent binding of a heme group through a histidine (H) residue, and delivering it to the CX2CH motif of the apo-cytochrome c2.. This study involves an in silico analysis of a hypothetical CcmE protein from Rhodobacter sphaeroides 2.4.1. Primers were designed based on the predicted ccmE gene sequence at GenBank and the translation was made using the ExPASy server. One hundred twenty-five CcmE sequences obtained from diverse organisms and related to CcmE from R. sphaeroides were used to generate a Multiple Sequence Alignment (MSA) using the ProbCons and T-Coffee applications. Two well conserved motifs Y*TGILPDLF*REG and LAKH*DE are found to be present in all sequences analyzed. A selection of conserved blocks from the MSA was used to generate a phylogenetic tree resulting in seven groups. The GEnt application found that tyrosine (Y*) and phenylalanine (F*) at the first motif and histidine (H*) at the second motif have the highest entropy score, implying a key functional role in the CcmE protein family. Finally, using the VMD application, the structure of the CcmE protein is compared: one from CcmE sequence obtained from in silico analysis against the CcmE obtained from the database of E. coli. All of these sequences have the six stranded β-sheet and histidine (H) and tyrosine (Y) residues iii involved in interactions between CcmE and the heme group. Our results for motifs of CCME_Rhodo are also in agreement with preliminary studies from CcmE obtained from database of E. coli. Our analysis suggest the presence of two well conserved motifs with internal gaps of variable length, consistent with previously published predictions. Using the predicted consensus sequences obtained from MEME analysis, we were able to predict the structure of CCME_Rhodo (obtained in silico) and compare it with the CcmE protein from E. coli (PDB ID 1SR3). These newly identified sequences are now more amenable for study using classic protein expression that may experimentally elucidate its structure and function.en_US
dc.description.abstractRhodobacter sphaeroides es un organismo fotoheterótrofo, que pertenece a la subdivisión α-3 de las proteobacterias. Este organismo tiene diversos modos de crecimiento, lo que le confiere ventaja adaptativa cuando las condiciones ambientales cambian. Éstas diversas rutas metabólicas involucran un gran número de hemoproteínas, una de las cuales es citocromo c2. Durante la maduración de citocromo c2, participan una gran variedad de proteínas. CcmE es una proteína chaperona involucrada en la unión covalente de un grupo hemo por medio del residuo histidina (H) y su posterior liberación del grupo hemo, al motivo CX2CH de la apo-citocromo c2. Éste estudio consiste del análisis in silico de una proteína hipotética obtenida de Rhodobacter sphaeroides 2.4.1. Se diseñaron iniciadores teniendo en cuenta la secuencia del gen ccmE obtenida de GenBank y su traducción se llevó a cabo usando el servidor ExPASy. Ciento-veinticinco secuencias obtenidas de diversos organismos y relacionadas con CcmE de R. sphaeroides fueron usadas para generar un Alineamiento Múltiple de Secuencias (MSA), empleando los programas ProbCons y TCoffee. Dos motivos bien conservados, Y*TGILPDLF*REG y LAKH*DE, se encontraron presentes en todas las secuencias analizadas. Se seleccionaron bloques de secuencias conservadas en el MSA para generar un árbol filogenético que produjo siete grupos. El programa GEnt encontró que los amino ácidos tirosina (Y*) y fenilalanina (F*), ubicados en el primer motivo, e histidina (H*), ubicada en el segundo motivo, presentan el mayor valor de entropía, implicando que éstos amino ácidos juegan un papel clave en la función de la familia de CcmE. Finalmente, usando el programa VMD, se comparó la estructura de la proteína CcmE obtenida del analisis in silico con una CcmE obtenida de la base de datos de E. coli. Nuestro análisis sugiere la presencia de dos motivos conservados con intervalos internos de longitud variable, consistente con predicciones publicadas previamente. Usando las secuencias consenso que se habian predecido obtenidas del análisis de MEME, se pudo predecir la estructura de CCME_Rhodo (obtenida in silico) y se comparó con la proteína CcmE de E. coli (PDB ID 1SR3). Ésta nueva secuencia identificada, está ahora accesible para estudio usando ensayos clásico de expresión de proteínas dirigidos a elucidar experimentalmente su estructura y su función.en_US
dc.description.sponsorshipEngineer department and to the Biology department of the University of Puerto Rico, for financial supporten_US
dc.language.isoenen_US
dc.subjectRhodobacter sphaeroidesen_US
dc.subjectFacultative photoheterotroph organismen_US
dc.subjectProteobacteriaen_US
dc.subjectCytochrome c2 (cyt c2)en_US
dc.subjectCcmEen_US
dc.subject.lcshBiochemical genetics.en_US
dc.subject.lcshComputational biology.en_US
dc.subject.lcshProteins--Analysis.en_US
dc.subject.lcshHemoproteins.en_US
dc.subject.lcshCytochrome c.en_US
dc.subject.lcshBacteria, Autotrophic.en_US
dc.titleIn silico analysis of the putative CcmE protein from Rhodobacter sphaeroides 2.4.1en_US
dc.typeThesisen_US
dc.rights.licenseAll rights reserveden_US
dc.rights.holder(c) 2007 Claudia Yaneth Acevedo Morantesen_US
dc.contributor.committeeMartínez-Cruzado, Juan Carlos
dc.contributor.committeeRíos-Velázquez, Carlos
dc.contributor.representativePérez-Muñoz, Carlos A.
thesis.degree.levelM.S.en_US
thesis.degree.disciplineBiologyen_US
dc.contributor.collegeCollege of Arts and Sciences - Sciencesen_US
dc.contributor.departmentDepartment of Biologyen_US
dc.description.graduationYear2007en_US


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