Lipid-anchored Ras oncoproteins assemble into transient, nano-sized substructures on the plasma membrane. These substructures, called nanoclusters, were proposed to be crucial for high-fidelity signal transmission in cells. However, the molecular basis of Ras nanoclustering is poorly understood. In this work, we used coarse-grained (CG) molecular dynamics simulations to investigate the molecula...

Cofilin is an actin-binding protein that depolymerizes and/or severs actin filaments. This dual function of cofilin makes it one of the major regulators of actin dynamics important for T-cell activation and migration. The activity of cofilin is spatio-temporally regulated. Its main control mechanisms comprise a molecular toolbox of phospho-, phospholipid, and redox regulation. Phosphorylated co...

In 2008, a successful computational design procedure was reported that yielded active enzyme catalysts for the Kemp elimination. Here, we studied these proteins together with a set of previously unpublished inactive designs to determine the sources of activity or lack thereof, and to predict which of the designed structures are most likely to be catalytic. Methods that range from quantum mechan...

Background. Obesity, through creating disorder in blood lipids and also, increase insulin resistance, has a main role in appearance high risk disease such as cardiovascular disease, diabetes and various kind of cancer. Objectives. The aim of this study was to survey effect of eight weeks continuous aerobic training accompanied with green tea consumption on lipid profile of inactive obese fe...

The epidermal growth factor receptor (EGFR) is aberrantly activated in various cancer cells and an important target for cancer treatment. Deep understanding of EGFR conformational changes between the active and inactive states is of pharmaceutical interest. Here we present a strategy combining multiply targeted molecular dynamics simulations, unbiased molecular dynamics simulations, and Bayesia...

Epidermal Growth Factor Receptor (EGFR), a tyrosine kinase receptor, is one of the main tumor markers in different types of cancers. The kinase native state is mainly composed of two populations of conformers: active and inactive. Several sequence variations in EGFR kinase region promote the differential enrichment of conformers with higher activity. Some structural characteristics have been pr...

An important step towards understanding biological systems is to relate simple biochemical elements to dynamics. Here, we present the arguably simplest dynamical element in biochemical networks. It consists of a single protein with two states (active and inactive) and an external signal that catalyses the conversion between these two states. Further, there is steady synthesis and degradation of...

TO THE EDITOR: Nguyen et al. (6) attempted to show the physiological significance of the coefficients of their linear regression fit to the data (6) of Edelman et al. (Table 1) and a similar one of Boling et al. (Table 2) in regard to understanding the physiological factors responsible for dysnatremias. An understanding of this clinical condition is very important, but this paper has a number o...