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Universidad Católica De Santa María Facultad De Ciencias Farmacéuticas, Bioquímicas Y Biotecnológicas Escuela Profesional De Ingeniería Biotecnológica

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Universidad Católica De Santa María Facultad De Ciencias Farmacéuticas, Bioquímicas Y Biotecnológicas Escuela Profesional De Ingeniería Biotecnológica Universidad Católica de Santa María Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas Escuela Profesional de Ingeniería Biotecnológica EVALUACIÓN DE LA DEPENDENCIA ESTRUCTURAL TERMOESTABLE RESPECTO A LOS PUENTES DISULFURO PRESENTES EN LOS CICLÓTIDOS DE LA FAMILIA RUBIACEAE Y SU CORRELACIÓN RESPECTO A LOS POTENCIALES ELECTROSTÁTICOS CLÁSICOS Y CUÁNTICOS Tesis presentada por el Bachiller: Morales Fernández, Dante Alexander Para optar el Título Profesional de: Ingeniero Biotecnólogo Asesor: Dr. Gómez Valdez, Badhin Arequipa – Perú 2018 DEDICATORIA Dedico esta tesis al centro de investigación en Ingeniería Molecular quienes fueron un gran apoyo durante el tiempo en que escribía esta tesis, a mis compañeros de proyecto y en especial a mi compañera de cálculo quien me ayudo concluir con mi investigación. A mis padres y personas cercanas quienes me apoyaron todo el tiempo. A mis maestros quienes nunca desistieron al enseñarme, aun sin importar el poco conocimiento que tenía en ciencia teórica, a ellos que continuaron depositando su esperanza en mí. A los sinodales quienes estudiaron mi tesis y la aprobaron. A todos los que me apoyaron para escribir y concluir esta tesis. Para ellos es esta dedicatoria de tesis, pues es a ellos a quienes se las debo por su apoyo incondicional. II AGRADECIMIENTOS Gracias a mi universidad, gracias por haberme permitido formarme y en ella, gracias a todas las personas que fueron participes de este proceso, ya sea de manera directa o indirecta, gracias a todos ustedes, fueron ustedes los responsables de realizar su pequeño aporte, que el día de hoy se vería reflejado en la culminación de mi paso por la universidad. Gracias a mis padres, que fueron mis mayores promotores durante este proceso. Este es un momento muy especial que espero, perduré en el tiempo, no solo en la mente de las personas a quienes agradecí, sino también a quienes invirtieron su tiempo en el proceso y desarrollo de mi investigación, a ellos asimismo les agradezco con todo mí ser. III CONTENIDO DEDICATORIA…………………………………………………………………...………..II AGRADECIMIENTOS…………………………………………………………………... III CONTENIDO………………………………………………………………………………IV ÍNDICE DE FIGURAS…………………………………………………………………. VIII ÍNDICE DE TABLAS……………………………………………………………………XIII GLOSARIO……………………………………………………………………………... XIV RESUMEN………………………………………………………………………………..XVI ABSTRACT…………………………………………………………………………….. XVII INTRODUCCIÓN…………………………………………………………………….. XVIII OBJETIVOS……………………………………………………………………………... XX OBJETIVO GENERAL…………………………………………………………. XX OBJETIVOS ESPECÍFICOS…………………………………………………… XX HIPÓTESIS…………………………………………………………………………….... XXI CÁPITULO I……………………………………………….…………………...……….…. 1 MARCO TEÓRICO……………………………………………………………….… 1 1.1. Familia Rubiaceae...………………………………………………………………1 1.1.1. Distribución Geográfica..................................................................................... 1 1.1.2. Taxonomía .......................................................................................................... 1 1.2. Ciclótidos.................................................................................................................2 1.2.1. Ciclótidos en la clase Eudicots .......................................................................... 3 IV 1.2.2. Ciclótidos en la Familia Rubiaceae ................................................................... 4 2.2.2.1. División de los Ciclótidos ...................................................................... 5 1.3. Estructura y características de los ciclótidos de Rubiaceae .............................. 6 1.3.1. Enlace peptídico ................................................................................................. 8 1.3.2. Enlace disulfuro .................................................................................................. 9 1.3.3. Nudo ciclico de cisteínas .................................................................................. 11 1.3.4. Influencia de los puentes disulfuro en el plegamiento .................................. 13 1.3.5. Plegamiento y flexibilidad de las proteínas cíclicas ....................................... 13 1.3.6. Termoestabilidad .............................................................................................. 14 1.3.7. Biosíntesis de los ciclótidos .............................................................................. 15 1.3.7.1. Secuenciación de los ciclótidos de Rubiaceae .................................... 16 1.3.7.2. Aplicación biólogica de los ciclótidos ................................................ 17 1.3.7.3. Polipéptidos cíclicos y defensinas ....................................................... 18 1.3.7.4. Potencial inmunosupresor de los ciclótidos ...................................... 19 1.4. Bioinformática ...................................................................................................... 19 1.4.1. Mecánica Molecular ........................................................................................ 20 1.4.1.1. Modelamiento proteico ....................................................................... 20 1.4.1.2. Estructura conformacional ................................................................ 21 1.4.1.3. Plegamiento oxidativo ......................................................................... 22 1.4.1.4. Dinámica Molecular ............................................................................ 22 1.4.1.4.1. Elementos de la Dinámica Molecular ........................................ 24 1.4.1.4.2. Optimización Geométrica ........................................................... 26 1.4.1.4.3. Integrador Steepest descent ....................................................... 26 1.4.1.4.4. Gradiente de Conjugación .......................................................... 27 V 1.4.1.5. Potencial Electrostatico APBS ........................................................... 27 1.4.2. Mecánica Cuántica .......................................................................................... 27 1.4.2.1. Ecuación de Schrödinger .................................................................... 28 1.4.2.2. Teoría funciona de la densidad .......................................................... 28 1.4.2.3. Funcional CAM-B3LYP ..................................................................... 29 1.4.3. Validación de estructuras ................................................................................ 29 1.4.3.1. Calculo de la convergencia del sistema (RMSD) .............................. 30 1.4.3.2. Calculo de la raiz cuadrada media de las fluctuaciones (RMSF) ... 30 1.4.2.1. Diagrama Ramachandran .................................................................. 30 CAPÍTULO II………………………………………………………………………………32 METODOLOGÍA Y DETALLES COMPUTACIONALES………………………..32 2.1. Equipos y Software ............................................................................................... 32 2.2. Metodología ......................................................................................................... 36 2.2.1. Recopilación de información sobre las estructuras de los ciclótidos ............ 36 2.2.2. Dinámica molecular en un ensamble Canónico (NVT) ................................. 37 2.2.3. Minimización a nivel de mecánica cuántica.................................................... 45 2.2.4. Evaluación de la estabilidad térmica de los ciclótidos ................................... 46 2.2.5. Determinación de la estabilidad de los puentes disulfuro de los ciclótidos .. 46 2.2.6. Potencial electrostático ..................................................................................... 46 2.2.7. Validacion de las distancias de los enlaces disulfuro ..................................... 48 CAPÍTULO III……………………………………………………………………………..49 RESULTADOS Y DISCUSIÓN………………………………………………………49 3.1. Recopilación de información de las estructuras de los ciclótidos ..................... 49 VI 3.1.1. Ciclótidos en la Familia Rubiaceae .................................................................. 53 3.2. Estados fundamentales de los ciclótidos .............................................................. 55 3.2.1. Estructura lineal de los ciclótidos de Rubiaceae ............................................. 55 3.2.2. Estructura terciaria de los Ciclótidos de Rubiaceae ...................................... 55 3.2.3. Optimización geométrica de los Ciclótidos ..................................................... 62 3.3. Minimización a nivel de mécanica cuántica ....................................................... 88 3.4. Estabilidad térmica de los ciclótidos en la simulación annealing ..................... 89 3.5. Variación de los puentes disulfuro de los ciclótidos ........................................... 99 3.6. Evaluación del potencial electrostático ……………… ................................... 103 3.6.1. Comparación de los Potenciales electrostáticos de los ciclótidos ................ 105 3.7. Validación de las distancias de enlaces disulfuro…...……………………….…108 CONCLUSIONES ........................................................................................................ 110 BIBLIOGRAFÍA ......................................................................................................... 111 APÉNDICE A …….. .................................................................................................... 120 APÉNDICE B …….. .................................................................................................... 121 APÉNDICE C …….. ...................................................................................................
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