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Coarse-Grained Modeling of the Assembly and Mechanical Properties of Viruses

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Coarse-Grained Modeling of the Assembly and Mechanical Properties of Viruses Coarse-Grained Modeling of the Assembly and Mechanical Properties of Viruses María Aznar Palenzuela ADVERTIMENT. La consulta d’aquesta tesi queda condicionada a l’acceptació de les següents condicions d'ús: La difusió d’aquesta tesi per mitjà del servei TDX (www.tdx.cat) i a través del Dipòsit Digital de la UB (diposit.ub.edu) ha estat autoritzada pels titulars dels drets de propietat intel·lectual únicament per a usos privats emmarcats en activitats d’investigació i docència. No s’autoritza la seva reproducció amb finalitats de lucre ni la seva difusió i posada a disposició des d’un lloc aliè al servei TDX ni al Dipòsit Digital de la UB. No s’autoritza la presentació del seu contingut en una finestra o marc aliè a TDX o al Dipòsit Digital de la UB (framing). Aquesta reserva de drets afecta tant al resum de presentació de la tesi com als seus continguts. En la utilització o cita de parts de la tesi és obligat indicar el nom de la persona autora. ADVERTENCIA. La consulta de esta tesis queda condicionada a la aceptación de las siguientes condiciones de uso: La difusión de esta tesis por medio del servicio TDR (www.tdx.cat) y a través del Repositorio Digital de la UB (diposit.ub.edu) ha sido autorizada por los titulares de los derechos de propiedad intelectual únicamente para usos privados enmarcados en actividades de investigación y docencia. No se autoriza su reproducción con finalidades de lucro ni su difusión y puesta a disposición desde un sitio ajeno al servicio TDR o al Repositorio Digital de la UB. No se autoriza la presentación de su contenido en una ventana o marco ajeno a TDR o al Repositorio Digital de la UB (framing). Esta reserva de derechos afecta tanto al resumen de presentación de la tesis como a sus contenidos. En la utilización o cita de partes de la tesis es obligado indicar el nombre de la persona autora. WARNING. On having consulted this thesis you’re accepting the following use conditions: Spreading this thesis by the TDX (www.tdx.cat) service and by the UB Digital Repository (diposit.ub.edu) has been authorized by the titular of the intellectual property rights only for private uses placed in investigation and teaching activities. Reproduction with lucrative aims is not authorized nor its spreading and availability from a site foreign to the TDX service or to the UB Digital Repository. Introducing its content in a window or frame foreign to the TDX service or to the UB Digital Repository is not authorized (framing). Those rights affect to the presentation summary of the thesis as well as to its contents. In the using or citation of parts of the thesis it’s obliged to indicate the name of the author. Coarse-Grained Modeling of the Assembly and Mechanical Properties of Viruses Mar´ıa Aznar Palenzuela Departament de F´ısica Fonamental Facultat de F´ısica Universitat de Barcelona 1 Facultat de F´ısica Departament de F´ısica Fonamental Coarse-Grained Modeling of the Assembly and Mechanical Properties of Viruses Programa de doctorado: F´ısica L´ınea de investigaci´on: F´ısica de la materia condensada Director y tutor de tesis: David Reguera L´opez Memoria presentada por Mar´ıa Aznar Palenzuela para optar al t´ıtulo de Doctor en F´ısica (25 de Septiembre de 2013). Agradecimientos Una gran parte de esta tesis es gracias a las personas que me han apoyado y acompa˜nado a lo largo de losultimos ´ a˜nos. Una gran parte es mi familia, espe- cialmente los m´as cercanos como mis padres, mi hermana y mi t´ıa Valle. Que casi se han alegrado de mis ´exitos m´as que yo, ag¨uita!. Tambi´en me gustar´ıa agradecer a esos amigos de la infancia (y no tan infancia) que pese a la distancia est´an en mi vida de una manera activa y para lo que se les necesite, como Jorge, Elia, Ulises, Carola, Emilio, Bea, Yonte y N´estor. Mucha gracias Churri por aguantarme en los momentos de llantina y los de jarana. Gracias a ese gran grupo, enorme, que son mis compaeros de F´ısica de ULL. MariPili, Carla, Yohana, Hector y Kike. Esos email colectivos en los que se ve que no s´oloamisemevaelbaifo,porqueesossue˜nos paranohicos de Kike o Hector, no tienen precio. Kike, gracias por esas chuletadas, moding mierda, noches del Skecht, Renes Barbier, etc ... Muchas gracias al 7 islas, la reina de Africa´ y Libelula y especialmente a su gente, por esos buenos momentos de cervezas y esparcimiento. Siempre me han dado todo lo que he necesitado, y m´as. No me puedo olvidar mencionar a esas maravillosos tangueros que me han ense˜nado tanto, Fernando, Gonzalo, Alex, Carmen, Yago, Pablo, Dr. Thomp- son, Lucia y Javier. Muchas gracias por esos buenos momentos de milonga y por sacarme a bailar cuando a´un me pisaba a mi misma, ahora s´olo les piso a ustedes. Unas de las personas que m´as me han animado con este trabajo es Sebasti´an. Sin ´el, entre otras muchas cosas, no existir´ıa esta maravillosa portada y probable- mente mucho del trabajo de esta tesis. En los a˜nos que llevo form´andome, los primeros que me hicieron apasionar por las matem´aticas y la f´ısica fueron Cutillas y Luis Balbuena, en el instituto. Estoy especialmente agradecida a Javier Hernand´ez Rojas por poner en mis manos el primer paper de virus. Gracias a mis primeros compa˜neros en Barcelona, Nuria Tabener, Mary, Irina, Ronald, Nuria Amig´o, Jordi, Xavi, Fabiana. Con especial cari˜no a Ignasi que a parte de compa˜nero y amigo, compa˜nero de piso durante 3 a˜nosyqueportanto le ha tocado aguantarme un poco m´as que el resto. Durante estosultimos ´ 4 a˜nos he tenido muchos buenos amigos compartiendo despacho con Nidal, Nico, Martin, Adriana, Guillem e Iv´an. Compa˜neros de al- iii muerzos siempre muy animados como Alvaro,´ Ricard, Noela, Cristina, Benedetta, Xavi, Andrea, Pau, Joaquin, Thomas, Paolo, Valentino, Fabio, Carlos, Marco. A Carlos y los juguitos y en especial a Paquito con el que he pasado tan buenos momentos de mezcales, pozole y las veces que casi me echan del Shang´o, darle las gracias por estar ah´ı. No me puedo olvidar de compa˜neros del departamento de ECM, Laura, Xavi, Guillermo, Carles, Jordi y porsupues´ısimo Claudia. Claudia y las infinitas horas que habremos pasado tomando juguitos, terremoteando, luchando con rosas y salu- dando a Pepe. Sin ti todo hubiera sido mucho m´as aburrido. Especialmente quisiera dar las gracias a mi director David Reguera por lo much´ısimo que he aprendido con ´el y sobretodo por la paciencia que me ha tenido. Gracias a todo el laboratorio de AFM de la Autonoma de Madrid, especial- mente a los componentes de la mesa de los ni˜nos, Alvaro,´ Pablo, Gabriela, Ana, Merche. Gracias Merche por esas ca˜nas y por la ayuda con los cap´ıtulos de AFM. iv Table of Contents Introduction ................................. 1 I Physical modeling of viruses 17 1 Viral architecture ........................... 2 1.1Introduction............................. 19 1.2TheCasparandKlugconstructionandtheT-number...... 20 1.3TheP-class............................. 23 1.4 Generalization of the CK construction to classify prolate viruses 25 1.5Theoriginoficosahedralsymmetryinviralcapsids....... 28 1.6Discussion.............................. 29 1.7Conclusions............................. 30 References ................................. 31 2 Theoretical description of viral assembly kinetics ....... 36 2.1Introduction............................. 37 2.2 Common features of viral assembly . ............... 39 2.3 Master equation approach to viral assembly kinetics . ...... 40 2.4 Classical Nucleation Theory applied to viral assembly . ..... 42 2.4.1 Viral assembly as a phase transition ............ 42 2.4.2 Freeenergybarrierforcapsidformation.......... 43 2.4.3 Kinetics of viral assembly and disassembly . ....... 46 2.4.4 Nucleation theorem and the size of the critical nucleus . 47 2.5Conclusions............................. 48 References ................................. 49 ....................................... 52 3 Coarse-grained modeling of capsids ................ 54 3.1Introduction............................. 55 3.2Previouscoarse-grainedmodels.................. 56 3.2.1 Minimal model for capsid architecture ........... 58 3.3Modelproposedinthisthesis................... 59 3.4Conclusions............................. 65 Appendix A . ............................... 67 Appendix B . ............................... 68 References ................................. 70 4 Elastic modeling of viral capsids .................. 74 4.1Introduction............................. 75 4.2 Bending and stretching model . .................. 76 4.2.1 Stretching-dominated limit . ................ 78 4.2.2 Bending-dominated limit . ................. 78 4.2.3 Generalcase......................... 79 4.2.4 Optimalsizeandmetastablesolutions........... 81 4.3Conclusions............................. 86 References ................................. 90 5 Simulation methods .......................... 92 5.1Introduction............................. 93 5.2MonteCarlosimulations...................... 93 5.3BrownianDynamics......................... 97 5.4 Finite Element Methods ...................... 99 5.5Conclusions.............................101 5.6 Appendix A . ............................103 Appendix A . ...............................103 References .................................108 II Self-assembly of viruses 112 6 Physical ingredients controlling the stability of capsids ....114 6.1Introduction.............................115 6.2ModelandMonteCarlosimulations................116 6.3 Stability of all-pentamer viruses . .................117 6.3.1 Stability of different structures . ..............118 6.3.2
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