Molecular Dynamics Simulations of Tight Junction Proteins
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Molecular Dynamics Simulations of Tight Junction Proteins Eleni Fitsiou This dissertation is submitted for the degree of Doctor of Philosophy August 2020 Department of Chemistry I would like to dedicate this dissertation to my husband Antonios and sons Dimitrios and Ioannis. ii “Wisdom begins in wonder” Socrates iii Declaration I, Eleni Fitsiou, declare that this thesis titled ‘Molecular Dynamics Simulations of Tight Junction Proteins’ has not been submitted in support of an application for another degree at this or any other university. It is the result of my own work and includes nothing that is the outcome of work done in collaboration except where specifically indicated. Where I have quoted from the work of others, the source is always given. Lancaster University, UK iv Abstract Tight junctions (TJs) are specialised cell-cell structures that serve primarily as a barrier to molecular transport through the intercellular space between the cells. The claudin family of proteins are the main structural and functional components of the TJ strands that circumscribe the cells. The detailed molecular organisation at the TJs is not entirely resolved, being relatively inaccessible by current experimental methods. Here, we have employed molecular dynamics simulations using both atomistic and coarse-grained models to investigate the TJ structure formed by claudin-1 using self-assembly coupled with free energy calculations and enhanced sampling techniques. A feature of the studies is that the self-assembly simulations have been carried out using atomistic detail (a first) by simulating only the extracellular domains of claudin-1 in an implied membrane. The results show that the cis-interaction can occur in the absence of trans-interacting partners and that a claudin dimer is the smallest stable unit. The dimers further form higher-order aggregates with a plethora of interacting dimeric interfaces. The trans- interaction of claudins resulted in a compact structure with a minimal pore size confirming the barrier properties of claudin-1. The simulations also enabled the identification of the key regions of the claudin responsible for the trans-interaction, with the identified important amino acids being in agreement with experimental studies. The role of the lipid environment, with a focus on the skin lipids in the stratum granulosum, was also investigated, along with the effect of single-point mutations in claudin-1. The single-point mutation studies were consistent with experimental results. The simulation studies have enhanced our understanding of the assembly and structure of claudin-1 TJs, a notable finding being that kinetic locking is likely to be important in determining the TJ structure. The single-point mutation studies suggest that simulations could serve as screens towards defining potential gene-therapy strategies. v Acknowledgements First of all, I would like to sincerely thank my supervisor Prof. Jamshed Anwar for his support throughout the project. His expertise has been invaluable and his guidance and help has been much appreciated. I would also like to thank Dr Massimo Noro (STFC) for his advice, support and offered opportunities; Dr Gareth Tribello (Queen’s University Belfast) for his invaluable help with the metadynamics simulations; and Dr Mike Pacey for his assistance in resolving issues with HEC. I would like to acknowledge Unilever for funding this project and promoting research. In particular, I would like to thank Scott Singleton and Patrick Warren for organising my visit to Unilever and their valuable feedback on my work. Lastly, I would like to thank my colleagues and friends from the Chemistry Department at Lancaster University, for a very friendly and inclusive environment; especially, the Chemical Theory and Computation group, for their collaboration and assistance over these years. vi Contents 1 INTRODUCTION ..................................................................................................... 1 1.1 Overview .............................................................................................................. 1 1.2 Epithelial Cells, their Junctions and Cellular Transport ...................................... 4 1.2.1 Types of epithelial cells ................................................................................. 5 1.2.2 Cellular transport pathways ......................................................................... 6 1.2.3 Cell – cell junctions ...................................................................................... 7 1.3 Tight Junctions ................................................................................................... 10 1.3.1 Introduction - Tight junctions as multifunctional structures ...................... 10 1.3.2 Tight junctions: description and proposed models ..................................... 11 1.3.3 Claudins are the gate–keepers of tight junctions ........................................ 15 1.4 Structure and Function of Skin .......................................................................... 19 1.4.1 Layers of the skin ........................................................................................ 19 1.4.2 Epidermis layers ......................................................................................... 20 1.4.3 The terminal differentiation process ........................................................... 21 1.4.4 Epidermal barrier and the importance of TJs ............................................ 21 1.4.5 The diversity in lipid composition of plasma membranes ........................... 23 1.4.6 Lipids found in skin epidermis .................................................................... 24 1.5 Critical Review of Recent Literature and Outstanding Research Questions ..... 26 1.6 Aims of the Thesis ............................................................................................. 31 1.7 Thesis Outline .................................................................................................... 31 2 METHODOLOGY: MOLECULAR SIMULATION ......................................... 34 2.1 Molecular Mechanics (Force Field Methods) .................................................... 34 2.2 Statistical Mechanics.......................................................................................... 36 2.2.1 Phase space ................................................................................................. 36 2.2.2 Ergodic hypothesis ...................................................................................... 37 2.2.3 Common statistical ensembles .................................................................... 37 2.3 General Form of Potential Energy Function in Molecular Mechanics .............. 38 2.3.1 Force field terms ......................................................................................... 39 2.3.2 Parametrisation of force fields ................................................................... 43 2.3.3 Classical mechanics: the time evolution of a system .................................. 44 2.3.4 Thermostats and barostats .......................................................................... 46 2.4 Periodic Boundary Conditions ........................................................................... 47 2.4.1 Calculating interactions when PBC are applied ........................................ 48 2.4.2 Sampling phase space ................................................................................. 49 2.5 Thermodynamic Properties ................................................................................ 49 2.5.1 Free energy surface .................................................................................... 50 2.6 Enhanced Sampling Methods............................................................................. 51 2.6.1 Potential of mean force – umbrella sampling ............................................. 51 2.6.2 Metadynamics ............................................................................................. 52 2.6.3 Replica exchange method ........................................................................... 54 2.7 Free Energy Using Molecular Mechanics Poisson Boltzmann Surface Area Method ..................................................................................................................... 56 3 THE MUTUAL INTERACTION OF THE EXTRACELLULAR DOMAIN PARTICLES OF CLAUDIN-1 ................................................................................. 58 vii 3.1 Introduction ........................................................................................................ 58 3.2 Methodology ...................................................................................................... 63 3.2.1 Model building of claudin-1 ........................................................................ 64 3.2.2 MD simulation of a single extracellular domain particle in an implied membrane ............................................................................................................. 66 3.2.3 MD simulation of a full claudin-1 particle in an explicit bilayer membrane .............................................................................................................................. 66 3.2.4 Self-assembly of ECD particles in an implied membrane starting from a grid .............................................................................................................................. 67 3.2.5 The Suzuki 'face-to-face' interface .............................................................