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We present molecular dynamics simulations of the interaction of fullerene-like, inhomogeneously charged proteins with polyelectrolyte brushes. A motivation of this work is the experimental observation that proteins, carrying an integral charge, may enter like-charged polymer brushes. Simulations of varying charge distributions on the protein surfaces are performed to unravel the physical mechanism of the adsorption. Our results prove that an overall neutral protein can be strongly driven into polyelectrolyte brush whenever the protein features patches of positive and negative charge. The findings reported here give further evidence that the strong adsorption of proteins is also driven by entropic forces due to counterion release, since charged patches on the surface of the proteins can act as multivalent counterions of the oppositely charged polyelectrolyte chains. A corresponding number of mobile co- and counterions is released from the brush and the vicinity of the proteins so that the entropy of the total system increases.

In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamical behavior of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense networks are created by a combined version of the bond fluctuation method and a Metropolis Monte Carlo algorithm. Semidilute behavior of the dense chain networks is shown. By comparing diffusion of particles in a static and a dynamical chain network, we demonstrate that chain diffusion does not alter the diffusion process of small particles. However, we prove that a dynamical network facilitates the transport of large particles. By weighting the mean square displacement trajectories of particles in the static chain, network data from the dynamical network can be reconstructed. Additionally, it is shown that subdiffusive behavior of particles on short time scales results from trapping processes in the crowded environment of the chain network. In the presented model a protein with 30 nm diameter has an effective diffusion coefficient of 1.24 x 10(-11) m2/s in a chromatin fiber network.

We investigate the accuracy of the binding modes predicted for 83 complexes of the high-resolution subset of the ASTEX/CCDC receptor-ligand database using the atomistic FlexScreen approach with a simple forcefield-based scoring function. The median RMS deviation between experimental and predicted binding mode was just 0.83 A. Over 80% of the ligands dock within 2 A of the experimental binding mode, for 60 complexes the docking protocol locates the correct binding mode in all of ten independent simulations. Most docking failures arise because (a) the experimental structure clashed in our forcefield and is thus unattainable in the docking process or (b) because the ligand is stabilized by crystal water., (2007 Wiley-Liss, Inc.)

Intermediate filament (IF) elongation proceeds via full-width “mini-filaments”, referred to as “unit-length” filaments (ULFs), which instantaneously form by lateral association of extended coiled-coil complexes after assembly is initiated. In a comparatively much slower process, ULFs longitudinally interact end-to-end with other ULFs to form short filaments, which further anneal with ULFs and with each other to increasingly longer filaments. This assembly concept was derived from time-lapse electron and atomic force microscopy data. We previously have quantitatively verified this concept through the generation of time-dependent filament length-profiles and an analytical model that describes assembly kinetics well for about the first ten minutes. In this time frame, filaments are shorter than one persistence length, i.e. ~1 μm, and thus filaments were treated as stiff rods associating via their ends. However, when filaments grow several μm in length over hours, their flexibility becomes a significant factor for the kinetics of the longitudinal annealing process. Incorporating now additional filament length distributions that we have recorded after extended assembly times by total internal reflection fluorescence microscopy (TIRFM), we developed a Monte Carlo simulation procedure that accurately describes the underlying assembly kinetics for large time scales. [ABSTRACT FROM AUTHOR]

An abstract of the article "High throughput in-silico screening against flexible protein receptors," by several researchers including, Bernhard Fischer, Daria Kokh, and Holger Merlitz is presented.