Purifying selection shaping the evolution of the Toll-like receptor 2 TIR domain in brown hares (Lepus europaeus) from Europe and the Middle East

Molecular Biology Reports - Toll-like receptors (TLRs) are transmembrane proteins of the innate immune system, composed of the ectodomain involved in pathogen recognition and the intracellular...     

Molecular dynamics of leucine and dopamine transporter proteins in a model cell membrane lipid bilayer

The dopamine transporter (DAT) operates via facilitated diffusion, harnessing an inward Na⁺ gradient to drive dopamine from the extracellular synaptic cleft to the neuron interior. The DAT is relevant to central nervous system disorders such as Parkinson disease and attention‐deficit hyperactivity disorder and is the primary site of action for the abused psychostimulants cocaine and amphetamines. Crystallization of a DAT homolog, the bacterial leucine transporter LeuT, provided the first reliable 3‐D DAT template. Here, the LeuT crystal structure and the DAT molecular model have been combined with their respective substrates, leucine and dopamine, in lipid bilayer molecular dynamics simulations toward tracking substrate movement along the protein's substrate/ion permeation pathway. Specifically, movement of residue pairs that comprise the “external gate” was followed as a function of substrate presence. The transmembrane (TM) 1 arginine‐TM 10 aspartate strut formed less readily in DAT compared with LeuT, with or without substrate present. For LeuT but not DAT, the addition of substrate enhanced the chances of forming the TM 1‐10 bridge. Also, movement of the fourth extracellular loop EL‐4 in the presence of substrate was more pronounced for DAT, the EL‐4 unwinding to a degree. The overall similarity between the LeuT and DAT molecular dynamics simulations indicated that LeuT was a legitimate model to guide DAT structure‐function predictions. There were, nevertheless, differences significant enough to allow for DAT‐unique insights, which may include how cocaine, methylphenidate (Ritalin, NIDA Drug Supply, Rockville, MD), and other DAT blockers are not recognized as substrates even though they can access the primary substrate binding pocket. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

A novel hybrid simulation for study of multiscale phenomena

A novel multiscale model and simulation has been developed by combining the algorithms from a course grained 2D lattice model with Brownian dynamics (BD). The lattice model incorporates Lennard-Jones and coulombic interactions between particles, as well as nearest-neighbor interactions. The BD simulation allows the particles to move in solution before they adsorb to the surface. This hybrid simulation is used to study the behavior of nanoparticles in the presence of a surface and evaporation of solvent. The simulation is able to produce amorphous topologies of nanoparticles on the surface.     

Identification and characterisation of a novel adhesin Ifp in <Emphasis Type="Italic">Yersinia pseudotuberculosis</Emphasis>

Background  

In order to identify new virulence determinants in Y. pseudotuberculosis a comparison between its genome and that of Yersinia pestis was undertaken. This reveals dozens of pseudogenes in Y. pestis, which are still putatively functional in Y. pseudotuberculosis and may be important in the enteric lifestyle. One such gene, YPTB1572 in the Y. pseudotuberculosis IP32953 genome sequence, encodes a protein with similarity to invasin, a classic adhesion/invasion protein, and to intimin, the attaching and effacing protein from enteropathogenic (EPEC) and enterohaemorraghic (EHEC) Escherichia coli.     

Modification of chitosan-methylcellulose composite films with meso-tetrakis(4-sulfonatophenyl)porphyrin

Polysaccharide films containing chitosan, methylcellulose, and a mixture of these polysaccharides in various ratios were prepared and modified with meso-tetrakis(4-sulfonatophenyl)porphyrin in an aqueous medium at pH 7. The modified films were compared with the initial films using spectroscopic methods and microscopic imaging. Electronic (UV-vis absorption, electronic circular dichroism (ECD)) and vibrational (FTIR and Raman) spectra showed that the porphyrin macrocycles had a strong affinity toward chitosan and did not interact with the methylcellulose. The total porphyrin uptake depended on the chitosan: methylcellulose ratio and pure methylcellulose films did not retain porphyrin macrocycles. ECD measurements detected the presence of optically active porphyrin species bound to the films. SEM and AFM images confirmed that the porphyrin macrocycles caused structural changes on the film surface and within the film layer.     

Modeling arthropod filiform hair motion using the penalty immersed boundary method

Crickets are able to sense their surrounding environment through about 2000 filiform hairs located on a pair of abdominal cerci. The mechanism by which the cricket is able to sense a wide range of input signals using these filiform hairs of different length and orientation is of great interest. Most of the previous filiform hair models have focused on a single, rigid hair in an idealized air field. Here, we present a model of the cercus and filiform hairs that are mechanically coupled to the surrounding air, and the model equations are based on the penalty immersed boundary method. The key difference between the penalty immersed boundary method and the traditional immersed boundary method is the addition of forces to account for density differences between the immersed solid (the filiform hairs) and the surrounding fluid (air). The model is validated by comparing the model predictions to experimental results, and then the model is used to examine the interactions between multiple hairs. With multiple hairs, there is little interaction when the hairs are separated by more than 1mm, and, as they move closer, they interact through viscous coupling, which reduces the deflection of the hairs due to the air movement. We also examine the computational scalability of the algorithm and show that the computational costs grow linearly with the number of hairs being modeled.     

Accessible and total molecular surfaces of unsmooth protein globules

A method for the calculation of accessible and total molecular surfaces of protein globules is proposed. It is based on consideration of structuring of protein globule surface. As a whole, the protein globule is approximated by ellipsoids. By computer imitations, the areas of accessible and total molecular surfaces as well as the volumes for 58 globular proteins were calculated. The calculation showed that the best agreement between the calculated areas and volumes and the experimental results is obtained at the radii of protein surface structures of 1-2 A.     

Dynamics of a simple regulatory switch

We consider the dynamics of a model toggle switch abstracted from the genetic interactions operative in a fungal stress response circuit. The switch transduces an external signal and propagates it forward by mediating the transport between compartments of two interacting gene products. The transport between compartments is assumed to be related to the degree of association between the interacting proteins, a fact for which there exists a wealth of biological evidence. The ubiquity and modularity of this cellular control mechanism warrants a detailed study of the dynamics entailed by various modelling assumptions. Specifically, we consider a general gate model in which both of the associating proteins are freely transportable between compartments. A more restrictive, but biologically supported model, is considered in which only one of the two proteins undergoes transport. Under the strong assumption that the disassociation of the interacting proteins is unidirectional we show that the qualitative dynamics of the two models are similar; that is they both converge to unique periodic orbits. From a biophysical perspective the assumption of unidirectional dissociation is unrealistic. We show that the same result holds for the more restrictive model when one weakens the assumption of unidirectional binding or disassociation. We speculate that this is not true for the more general model. This difference in dynamics may have important biological implications and certainly points to promising avenues of research.