Computer simulation of the phase behavior of a model membrane protein: Annexin V

Role of protein interactions in defining HIV-1 viral capsid shape and stability: a coarse-grained analysis

Coarse-grained models of the HIV-1 CA dimer are constructed based on all-atom molecular dynamics simulations. Coarse-grained representations of the capsid shell, which is composed of approximately 1500 copies of CA proteins, are constructed and their stability is examined. A key interaction between carboxyl and hexameric amino terminal domains is shown to generate the curvature of the capsid shell. It is demonstrated that variation of the strength of this interaction for different subunits in the lattice can cause formation of asymmetric, conical-shaped closed capsid shells, and it is proposed that variations, in the structure of the additional carboxyl-amino terminal binding interface during self-assembly, are important aspects of capsid cone formation. These results are in agreement with recent structural studies of the capsid hexamer subunit, which suggest that variability in the binding interface is a cause of the differences in subunit environments that exist in a conical structure.

Simple model of membrane proteins including solvent

We report a numerical simulation for the phase diagram of a simple two-dimensional model, similar to the one proposed by Noro and Frenkel [J. Chem. Phys. 114, 2477 (2001)] for membrane proteins, but one that includes the role of the solvent. We first use Gibbs ensemble Monte Carlo simulations to determine the phase behavior of particles interacting via a square-well potential in two dimensions for various values of the interaction range. A phenomenological model for the solute-solvent interactions is then studied to understand how the fluid-fluid coexistence curve is modified by solute-solvent interactions. It is shown that such a model can yield systems with liquid-liquid phase separation curves that have both upper and lower critical points, as well as closed loop phase diagrams, as is the case with the corresponding three-dimensional model.

Two-dimensional structure in a generic model of triangular proteins and protein trimers

Motivated by the diversity and complexity of two-dimensional (2D) crystals formed by triangular proteins and protein trimers, we have investigated the structures and phase behavior of hard-disk trimers. In order to mimic specific binding interactions, each trimer possesses an "attractive" disk which can interact with similar disks on other trimers via an attractive square-well potential. At low density and low temperature, the fluid phase mainly consists of tetramers, pentamers, or hexamers. Hexamers provide the structural motif for a high-density, low-temperature periodic solid phase, but we also identify a metastable periodic structure based on a tetramer motif. At high density there is a transition between orientationally ordered and disordered solid phases. The connections between simulated structures and those of 2D protein crystals--as seen in electron microscopy--are briefly discussed.

Liquid crystalline behavior of a semifluorinated oligomer

Monte Carlo simulations with a coarse-grained model were performed to study the microstructure of a semifluoroalkane C20 diblock oligomer [F(CF(2))(10)(CH(2))(10)H]. The coarse-grained model adopted is based on previously reported united-atom force fields for alkanes and perfluoroalkanes and was first validated by simulating the phase behavior of a mixture of hexane and perfluorohexane. These preliminary simulations established the need of a significant correction factor in the Berthelot mixing rule between alkane and perfluoroalkane groups. Using such a force field, the semifluorinated C20 oligomer liquid was simulated using efficient Monte Carlo moves to sample different molecular arrangements and box dimensions so as to allow different layering structures to form. In qualitative agreement with experimental observations, a smectic-to-isotropic phase transition occurs as temperature is increased but the transition point and the structure of the smectic phase depend on the stiffness of the torsional potential and the model of van der Waals interactions adopted. We identify two smectic phases LC1' and LC2', whose structures do not agree with those that have been postulated before to explain x-ray diffraction data, namely, LC1 and LC2. LC1' has a layer spacing similar to LC1 but the antiparallel packing is not observed with individual chains but with groups of chains producing a checkerboard pattern. LC2' has fully microsegregated blocks such as LC2 but the alkyl tails are not fully stretched or interdigitated. Despite these inconsistencies, and considering that reported experimental data also reveal the presence of mixed phases, the simulated structures suggest other plausible ways how the semifluorinated chains could pack and microsegregate to best negotiate energetic and entropic constraints.

Elastic properties of dense solid phases of hard cyclic pentamers and heptamers in two dimensions

Systems of model planar, nonconvex, hard-body "molecules" of fivefold and sevenfold symmetry axes are studied by constant pressure Monte Carlo simulations with variable shape of the periodic box. The molecules, referred to as pentamers (heptamers), are composed of five (seven) identical hard disks "atoms" with centers forming regular pentagons (heptagons) of sides equal to the disk diameter. The elastic compliances of defect-free solid phases are computed by analysis of strain fluctuations and the reference (equilibrium) state is determined within the same run in which the elastic properties are computed. Results obtained by using pseudorandom number generators based on the idea proposed by Holian and co-workers [Holian et al., Phys. Rev. E 50, 1607 (1994)] are in good agreement with the results generated by DRAND48. It is shown that singular behavior of the elastic constants near close packing is in agreement with the free volume approximation; the coefficients of the leading singularities are estimated. The simulations prove that the highest density structures of heptamers (in which the molecules cannot rotate) are auxetic, i.e., show negative Poisson ratios.