FACULTE DES SCIENCES INSTITUT DE PHYSIQUE THEORIQUE The Hydrophobic Interaction Modeling Hydrophobic Interactions and Aggregation of Non-Polar Particles in Aqueous Solutions These` de doctorat present´ ee´ a` la Faculte´ des Sciences de l’Universite´ de Lausanne par Susanne Molber¨ t Diplomˆ ee´ en Physique Universite´ de Fribourg Jury Prof. Jean Hernandez, President´ Prof. Paolo De Los Rios, Directeur de These` Prof. Giovanni Dietler, Rapporteur Dr. Chao Tang, Expert Dr. Pierpaolo Bruscolini, Expert Lausanne 2003 Acknowledgments I have benefited from long-term collaborations, discussions, and exchange of ideas and results with a large number of people. Most importantly, I am indebted to Paolo De Los Rios for his many ideas, useful suggestions, and interesting comments. He provided the motivation to begin the work, guidance in the methods to use, and constant reality checks for my results. I wish to thank all my collaborators at the Institute of Theoretical Physics at the University of Lausanne for their support, in particular Shin Miyahara and Franc¸ois Vernay, not least for their useful comments, valuable input, and help with specific problems. I am grateful to Chao Tang at the NEC Research Institute in Princeton, NJ (USA), in whose group the study of hydrophobicity in proteins was performed. I also wish to thank Eldon Emberly and Jonathan Miller for many helpful discussions. This piece of research was supported in part by The Swiss Study Foundation. I am particularly indebted to Bruce Normand for his encouragement, enlightening discussions, and constructive criticism, and especially for sacrificing so much of his time to the careful reading of this thesis. This work was supported financially by the Swiss National Science Foundation through grants FNRS 21-61397.00 and 2000-67886.02. 1 Abstract Hydration of hydrophobic solutes in water is the cause of different phenomena, in- cluding the hydrophobic heat-capacity anomaly. We use a simple yet powerful mixture model for water, an adapted two-state Muller-Lee-Graziano model, to describe the energy levels of water molecules as a function of their proximity to non-polar solute molecules. The model is shown to provide an appropriate description of many-body interactions between the hydrophobic solute particles. The solubility and aggregation of hydrophobic substances is studied by evaluating detailed Monte Carlo simulations in the vicinity of the first-order aggregation phase transition. A closed-loop coexis- tence curve is found, which is consistent with a mean-field calculation carried out for the same system. In addition, we have studied the aggregation of hydrophobic particles in aqueous solutions in the presence of cosolvents. Here we have demonstrated that the important features of the effect of cosolvents on hydrophobic aggregates may be described within the same two-state model, with adaptations to focus on the ability of such substances to alter the structure of water. The relevant phenomena include a significant change in solubility of non-polar solute particles and preferential binding or exclusion of such substances to solute molecules. We have further adapted the MLG model to include the solvation of amphiphilic solute particles in water. By allowing different distributions of hydrophobic regions at the molecular surface, we have found aggregation of the amphiphiles, and formation of various types of micelle as a function of the hydrophobicity pattern. We demonstrate that the essential features of micelle formation, usually attributed to the amphiphilic nature of the solute particles, are primarily solvent-induced. Hydrophobicity remains a controversial quantity also in protein science. Statistical studies have shown that some amino-acids are found preferentially either in the core or on the surface of native folds, whereas many are present at all positions with equal probability. Based on these results we have presented the average surface-accessibility scale, which may lead to an improvement in the comparison of experimental data with the results from theoretical HP models. We verify the validity of the new scale on secondary-structure elements. 3 Contents Prologue 7 1 Introduction 9 1.1 Aqueous Solutions . 9 1.2 Hydrophobic-Polar Model . 10 1.3 Cosolvent Effects . 13 1.4 Solutions of Amphiphilic Molecules . 15 1.5 Hydrophobicity in Protein Folding . 18 1.6 Overview . 20 2 Model and Methods 21 2.1 Energy Levels . 22 2.2 Coarse-Grained Model . 25 2.3 Hydrophobic Interaction . 27 2.4 Mean-Field Calculation . 28 2.5 Molecular-Level Simulations . 29 2.5.1 Monte Carlo Simulation . 29 2.6 Pair Approximation . 30 2.6.1 Cluster-Variation Method . 31 3 Solution of Hydrophobic Particles in Water 35 3.1 Mean-Field Calculation . 35 3.2 Molecular-Level Simulations . 40 3.3 Discussion . 43 4 Chaotropic Effect 49 4.1 Model including Chaotropic Cosolvent . 49 4.2 Mean-Field Approximation . 54 4.2.1 Single Mean Cosolvent Concentration . 54 4.2.2 Distinct Mean Bulk and Shell Concentrations . 56 4.2.3 Results . 57 4.3 Molecular-Level Simulations . 60 4.4 Pair Approximation . 65 4.4.1 Model in Pair Approximation . 66 4 Contents 4.4.2 Results . 69 4.5 Discussion . 71 5 Kosmotropic Effect 75 5.1 Model including Kosmotropic Cosolvent . 76 5.2 Methods . 78 5.3 Results and Discussion . 79 6 Micelle Formation 85 6.1 Hydrophobic-Polar Model for Amphiphiles . 86 6.1.1 Method . 89 6.1.2 Results . 90 6.2 Surfactant Model . 95 6.2.1 Methods . 99 6.2.2 Results . 100 6.3 Discussion . 102 7 Hydrophobicity in Protein Folding 109 7.1 Protein-Structure Classification . 112 7.2 Testing Hydrophobicity Scales . 114 7.3 Surface-Accessibility Scale . 118 7.4 Hydrophobic-Polar Model . 122 7.5 Secondary-Structure Analysis . 125 7.6 Discussion . 128 8 Summary 133 Resum´ e´ en franc¸ais 137 Bibliography 139 5 Prologue Life as we know it originated in water, and could not exist in its absence. It has been conditioned by the abnormal properties of water, because water was present on this planet long before the evolution of life. Water forms a necessary constituent of the cells of all animal and plant tissues, and is essential for the maintenance of organic life. Natural processes are characterized by the economy with which energy (matter) is used. However, organisms consist of up to ¢¡¤£ water, and it seems permissible to conclude that this liquid must fulfil a function other than that of an inert substrate. Only little is known about the manner in which water acts in the formation of organized biological structures at the subcellular, cellular, and multicellular level, while at the molecular level the role of water in the stabilization of native conformations of biopolymers has only recently begun to receive attention. The importance of the unique physical properties of water, and in particular of its unique solvent power, has been cited frequently [1, 2, 3, 4]. However, the equally great importance of its unique lack of solvent power for many non-polar substances has attracted far less attention. Many of these non-polar molecules are soluble in alcohol and other solvents, but not in water. This poor solubility of non-polar substances in water, which is known as the hydrophobic (from the Greek “hydro” = “water” and “phobia” = “dread”) effect, is perhaps the most important single factor in the organization of the constituent molecules of living matter into complex structural entities such as cell membranes and organelles. Specifically, particles of dual nature, consisting of one part which is soluble in water and another part which is expelled from it, are forced by their duality to adopt unique orientations with respect to the aqueous medium, and to form suitably organized structures. The self-assembling properties of such molecules are crucial in the formation of living matter. The cell membrane, which in effect defines the living cell and allows it to exist as a coherent entity, is perhaps the best example [4, 5]. There can be little doubt that its formation is spontaneous, dependent only on the fact that its constituent molecules are partly hydrophilic (“water-loving”) and partly hydrophobic (“water-fearing”). Despite its importance for life, the physical mechanisms underlying the hy- drophobic effect and the resulting hydrophobic interaction, which is the interaction of non-polar particles in aqueous media, are at present not well understood and require further investigation. The aim of this study is to clarify the origin of the hydrophobic 7 Prologue interaction using a simple yet powerful model of water, which includes the essential features of aqueous solutions of hydrophobic molecules and reproduces various aspects of their behavior. 8 Chapter 1 Introduction 1.1 Aqueous Solutions Hydrophobic substances are defined as those which are readily soluble in many non-polar solvents, but only barely soluble in water, in contrast to substances which form solids with strong intermolecular cohesion, and thus generally exhibit low solubility in all solvents. This distinction is especially important from the biological point of view, because it means that molecules expelled from water as a result of their hydrophobicity will tend to remain in a fluid, deformable state. The existence of hydrophobic substances, and of dual-nature organic molecules containing polar and non-polar portions, has been known for a long time, but the mechanism underlying the hydrophobic effect remains controversial. For a consider- able period, the association between hydrocarbon chains in the formation of micelles was believed to arise from their “like to like” attraction [6, 7]. However, it has been recognized more recently that the attraction of non-polar groups (such as hydrocarbon chains) plays only a minor role in the hydrophobic effect [8, 9]. The effect rather arises primarily from the strong attractive forces between isotropically arranged water molecules. These arrangements must be disrupted or distorted when any solute is dissolved in the water.