Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins

Hydrophobicity is thought to be one of the primary forces driving the folding of proteins. On average, hydrophobic residues occur preferentially in the core, whereas polar residues tends to occur at the surface of a folded protein. By analyzing the known protein structures, we quantify the degree to which the hydrophobicity sequence of a protein correlates with its pattern of surface exposure. We have assessed the statistical significance of this correlation for several hydrophobicity scales in the literature, and find that the computed correlations are significant but far from optimal. We show that this less than optimal correlation arises primarily from the large degree of mutations that naturally occurring proteins can tolerate. Lesser effects are due in part to forces other than hydrophobicity and we quantify this by analyzing the surface exposure distributions of all amino acids. Lastly we show that our database findings are consistent with those found from an off-lattice hydrophobic-polar model of protein folding.Comment: 16 pages, 2 tables, 8 figure

Kosmotropes and chaotropes: modelling preferential exclusion, binding and aggregate stability

Kosmotropic cosolvents added to an aqueous solution promote the aggregation of hydrophobic solute particles, while chaotropic cosolvents act to destabilise such aggregates. We discuss the mechanism for these phenomena within an adapted version of the two-state Muller-Lee-Graziano model for water, which provides a complete description of the ternary water/cosolvent/solute system for small solute particles. This model contains the dominant effect of a kosmotropic substance, which is to enhance the formation of water structure. The consequent preferential exclusion both of cosolvent molecules from the solvation shell of hydrophobic particles and of these particles from the solution leads to a stabilisation of aggregates. By contrast, chaotropic substances disrupt the formation of water structure, are themselves preferentially excluded from the solution, and thereby contribute to solvation of hydrophobic particles. We use Monte Carlo simulations to demonstrate at the molecular level the preferential exclusion or binding of cosolvent molecules in the solvation shell of hydrophobic particles, and the consequent enhancement or suppression of aggregate formation. We illustrate the influence of structure-changing cosolvents on effective hydrophobic interactions by modelling qualitatively the kosmotropic effect of sodium chloride and the chaotropic effect of urea.Comment: 13 pages, 12 figures; inclusion of review material, parameter analysis and comparison of kosmotropic and chaotropic effect

The Minority Game with interactions

We partially modify the rules of the Minority Game (MG) by introducing some degree of local information in the game, which is only available for some agents, called the interacting agents. Our work shows that, for small values of the new parameter of the model (the fraction of interacting agents), there is an improvement of the use of the resources with respect to the MG, while as this number grows the response of the system changes, and ends up behaving worst than the usual MG.Comment: 9 pages, 4 figures; typoos corrected; references upadted; Physica A -like LaTe

The Local Minority Game

Ecologists and economists try to explain collective behavior in terms of competitive systems of selfish individuals with the ability to learn from the past. Statistical physicists have been investigating models which might contribute to the understanding of the underlying mechanisms of these systems. During the last three years one intuitive model, commonly referred to as the Minority Game, has attracted broad attention. Powerful yet simple, the minority game has produced encouraging results which can explain the temporal behaviour of competitive systems. Here we switch the interest to phenomena due to a distribution of the individuals in space. For analyzing these effects we modify the Minority Game and the Local Minority Game is introduced. We study the system both numerically and analytically, using the customary techniques already developped for the ordinary Minority Game

Order and disorder in the Local Evolutionary Minority Game

We study a modification of the Evolutionary Minority Game (EMG) in which agents are placed in the nodes of a regular or a random graph. A neighborhood for each agent can thus be defined and a modification of the usual relaxation dynamics can be made in which each agent updates her decision scheme depending upon the options made in her immediate neighborhood. We name this model the Local Evolutionary Minority Game (LEMG). We report numerical results for the topologies of a ring, a torus and a random graph changing the size of the neighborhood. We focus our discussion in a one dimensional system and perform a detailed comparison of the results obtained from the random relaxation dynamics of the LEMG and from a linear chain of interacting spin-like variables at a finite temperature. We provide a physical interpretation of the surprising result that in the LEMG a better coordination (a lower frustration) is achieved if agents base their actions on local information. We show how the LEMG can be regarded as a model that gradually interpolates between a fully ordered, antiferromagnetic system and a fully disordered system that can be assimilated to a spin glass.Comment: 12 pages, 8 figures, RevTex; omission of a relevant reference correcte

Solvent-induced micelle formation in a hydrophobic interaction model

We investigate the aggregation of amphiphilic molecules by adapting the two-state Muller-Lee-Graziano model for water, in which a solvent-induced hydrophobic interaction is included implicitly. We study the formation of various types of micelle as a function of the distribution of hydrophobic regions at the molecular surface. Successive substitution of non-polar surfaces by polar ones demonstrates the influence of hydrophobicity on the upper and lower critical solution temperatures. Aggregates of lipid molecules, described by a refinement of the model in which a hydrophobic tail of variable length interacts with different numbers of water molecules, are stabilized as the length of the tail increases. We demonstrate that the essential features of micelle formation are primarily solvent-induced, and are explained within a model which focuses only on the alteration of water structure in the vicinity of the hydrophobic surface regions of amphiphiles in solution.Comment: 11 pages, 10 figures; some rearrangement of introduction and discussion sections, streamlining of formalism and general compression; to appear in Phys. Rev.

Boolean Game on Scale-free Networks

Inspired by the local minority game, we propose a network Boolean game and investigate its dynamical properties on scale-free networks. The system can self-organize to a stable state with better performance than random choice game, although only the local information is available to the agent. By introducing the heterogeneity of local interactions, we find the system has the best performance when each agent's interaction frequency is linear correlated with its information capacity. Generally, the agents with more information gain more than those with less information, while in the optimal case, each agent almost has the same average profit. In addition, we investigate the role of irrational factor and find an interesting symmetrical behavior.Comment: 12 pages and 6 figure

The Emergence of Leadership in Social Networks

We study a networked version of the minority game in which agents can choose to follow the choices made by a neighbouring agent in a social network. We show that for a wide variety of networks a leadership structure always emerges, with most agents following the choice made by a few agents. We find a suitable parameterisation which highlights the universal aspects of the behaviour and which also indicates where results depend on the type of social network.Comment: 22 pages (as in Physica A but with a few extra references to supplementary material) plus 11 pages of supplementary material not in Physica A versio

Structure-preserving desynchronization of minority games

Perfect synchronicity in $N$-player games is a useful theoretical dream, but communication delays are inevitable and may result in asynchronous interactions. Some systems such as financial markets are asynchronous by design, and yet most theoretical models assume perfectly synchronized actions. We propose a general method to transform standard models of adaptive agents into asynchronous systems while preserving their global structure under some conditions. Using the Minority Game as an example, we find that the phase and fluctuations structure of the standard game subsists even in maximally asynchronous deterministic case, but that it disappears if too much stochasticity is added to the temporal structure of interaction. Allowing for heterogeneous communication speeds and activity patterns gives rise to a new information ecology that we study in details.Comment: 6 pages, 7 figures. New version removed a section and found a new phase transitio

Statistical Mechanics of Dilute Batch Minority Games with Random External Information

We study the dynamics and statics of a dilute batch minority game with random external information. We focus on the case in which the number of connections per agent is infinite in the thermodynamic limit. The dynamical scenario of ergodicity breaking in this model is different from the phase transition in the standard minority game and is characterised by the onset of long-term memory at finite integrated response. We demonstrate that finite memory appears at the AT-line obtained from the corresponding replica calculation, and compare the behaviour of the dilute model with the minority game with market impact correction, which is known to exhibit similar features.Comment: 22 pages, 6 figures, text modified, references updated and added, figure added, typos correcte