The self-assembly and evolution of homomeric protein complexes

We introduce a simple "patchy particle" model to study the thermodynamics and dynamics of self-assembly of homomeric protein complexes. Our calculations allow us to rationalize recent results for dihedral complexes. Namely, why evolution of such complexes naturally takes the system into a region of interaction space where (i) the evolutionarily newer interactions are weaker, (ii) subcomplexes involving the stronger interactions are observed to be thermodynamically stable on destabilization of the protein-protein interactions and (iii) the self-assembly dynamics are hierarchical with these same subcomplexes acting as kinetic intermediates.Comment: 4 pages, 4 figure

Experimental and theoretical evidence for bilayer-by-bilayer surface melting of crystalline ice

On the surface of water ice, a quasi-liquid layer (QLL) has been extensively reported at temperatures below its bulk melting point at 273 K. Approaching the bulk melting temperature from below, the thickness of the QLL is known to increase. To elucidate the precise temperature variation of the QLL, and its nature, we investigate the surface melting of hexagonal ice by combining noncontact, surface-specific vibrational sum frequency generation (SFG) spectroscopy and spectra calculated from molecular dynamics simulations. Using SFG, we probe the outermost water layers of distinct single crystalline ice faces at different temperatures. For the basal face, a stepwise, sudden weakening of the hydrogen-bonded structure of the outermost water layers occurs at 257 K. The spectral calculations from the molecular dynamics simulations reproduce the experimental findings; this allows us to interpret our experimental findings in terms of a stepwise change from one to two molten bilayers at the transition temperature

Computation times for the construction of neighbor lists: simple vs. grid search.

<p>Shown are the results for the Lennard-Jones fluid as a function of particles in the system. In addition to the data points for the simple and grid search algorithms, lines indicate the scaling law with 2 and 1 as the exponent, respectively. These exponents result from the cost of the simple and grid search algorithm:</p

Average computational cost per iteration step (in seconds) for simplex and relative entropy-based coarse-graining.

<p>For the simplex methods the number in the bracket denote the time spend in energy minimization before the actual molecular dynamics part.</p

Comparisons of CG potentials (a) and RDFs (b) for bulk water.

<p>All methods fit the target RDF sufficiently well and lead to potential of similar shape. The relative entropy method has a slightly smaller error due the fact that more parameter are available in the potential form.</p

Absolute computation time for the radial distribution function calculation as a function of threads.

<p>The small system holds 5324, the medium 17687 and the big system 60132 particles. The dashed line shows the ideal scaling line. Also shown are the results from the script-based parallelization of multi_g_rdf.</p

Simulated water-methanol mixtures.

<p>Simulated water-methanol mixtures.</p