The structure of the hexameric atrazine chlorohydrolase AtzA

Atrazine chlorohydrolase (AtzA) was discovered and purified in the early 1990s from soil that had been exposed to the widely used herbicide atrazine. It was subsequently found that this enzyme catalyzes the first and necessary step in the breakdown of atrazine by the soil organism Pseudomonas sp. strain ADP. Although it has taken 20 years, a crystal structure of the full hexameric form of AtzA has now been obtained. AtzA is less well adapted to its physiological role (i.e. atrazine dechlorination) than the alternative metal-dependent atrazine chlorohydrolase (TrzN), with a substrate-binding pocket that is under considerable strain and for which the substrate is a poor fit

Hydrophobic and ionic-interactions in bulk and confined water with implications for collapse and folding of proteins

Water and water-mediated interactions determine thermodynamic and kinetics of protein folding, protein aggregation and self-assembly in confined spaces. To obtain insights into the role of water in the context of folding problems, we describe computer simulations of a few related model systems. The dynamics of collapse of eicosane shows that upon expulsion of water the linear hydrocarbon chain adopts an ordered helical hairpin structure with 1.5 turns. The structure of dimer of eicosane molecules has two well ordered helical hairpins that are stacked perpendicular to each other. As a prelude to studying folding in confined spaces we used simulations to understand changes in hydrophobic and ionic interactions in nano droplets. Solvation of hydrophobic and charged species change drastically in nano water droplets. Hydrophobic species are localized at the boundary. The tendency of ions to be at the boundary where water density is low increases as the charge density decreases. Interaction between hydrophobic, polar, and charged residue are also profoundly altered in confined spaces. Using the results of computer simulations and accounting for loss of chain entropy upon confinement we argue and then demonstrate, using simulations in explicit water, that ordered states of generic amphiphilic peptide sequences should be stabilized in cylindrical nanopores

Impact of RF mismatches on the performance of massive MIMO systems with ZF precoding

Thanks to the channel reciprocity, the time division duplex (TDD) operation is more preferred in massive multiple-input multiple-output (MIMO) systems. Avoiding the heavy feedback of downlink channel state information (CSI) from the user equipment (UE) to the base station (BS), the uplink CSI can be exploited for the downlink precoding. However, due to the mismatches of the radio frequency (RF) circuits at both sides of the link, the whole communication channels are usually not symmetric in practical systems. This paper is focused on the RF mismatches at the UEs and the BS for the multi-user massive MIMO systems with zero forcing (ZF) precoding. The closed-form expressions of the ergodic sum-rates are derived for evaluating the impact of RF mismatches on the system performance. Theoretical analysis and simulation results show that the RF mismatches at the UEs only lead to a negligible performance loss. However, it is imperative to perform reciprocity calibration at the BS, because the RF mismatches at the BS contribute to the inter-user interference (IUI) and result in a severe system performance degradation

Non-Bulk-Like Solvent Behavior in the Ribosome Exit Tunnel

As nascent proteins are synthesized by the ribosome, they depart via an exit tunnel running through the center of the large subunit. The exit tunnel likely plays an important part in various aspects of translation. Although water plays a key role in many bio-molecular processes, the nature of water confined to the exit tunnel has remained unknown. Furthermore, solvent in biological cavities has traditionally been characterized as either a continuous dielectric fluid, or a discrete tightly bound molecule. Using atomistic molecular dynamics simulations, we predict that the thermodynamic and kinetic properties of water confined within the ribosome exit tunnel are quite different from this simple two-state model. We find that the tunnel creates a complex microenvironment for the solvent resulting in perturbed rotational dynamics and heterogenous dielectric behavior. This gives rise to a very rugged solvation landscape and significantly retarded solvent diffusion. We discuss how this non-bulk-like solvent is likely to affect important biophysical processes such as sequence dependent stalling, co-translational folding, and antibiotic binding. We conclude with a discussion of the general applicability of these results to other biological cavities

Manipulating Biopolymer Dynamics by Anisotropic Nanoconfinement

How the geometry of nano-sized confinement affects dynamics of biomaterials is interesting yet poorly understood. An elucidation of structural details upon nano-sized confinement may benefit manufacturing pharmaceuticals in biomaterial sciences and medicine. The behavior of biopolymers in nano-sized confinement is investigated using coarse-grained models and molecular simulations. Particularly, we address the effects of shapes of a confinement on protein folding dynamics by measuring folding rates and dissecting structural properties of the transition states in nano-sized spheres and ellipsoids. We find that when the form of a confinement resembles the geometrical properties of the transition states, the rates of folding kinetics are most enhanced. This knowledge of shape selectivity in identifying optimal conditions for reactions will have a broad impact in nanotechnology and pharmaceutical sciences.Comment: to appear in Nano Letter

Adaptive and Outline-Based Subsampling of Images Containing Text and Binary Graphics Lawrence O’Gorman

For digital display of scanned documents containing text and other binary graphics including line drawings, there is often the need to reduce the image size so that it can be more completely viewed on a computer monitor. We present an approach entailing two complementary methods: adaptive subsampling and outline based subsampling. The adaptively subsampling method reduces image size by preferentially removing ‘‘low-information’ ’ or ‘‘silent’ ’ rows and columns. These lowinformation regions can be located in margins, between text lines, and even through lines of graphics and text. The outline-based subsampling method entails boundary determination, polygonal fitting, smoothing of this result, and finally reduction in size of these polygonal boundaries (rather than pixels as in the conventional approach). Together, or separately, these methods yield a higher quality, subsampled image. Results of the approach are shown. The limits in terms of image reduction versus readability are discussed. 1

Meltdown : a tool to help in the interpretation of thermal melt curves acquired by differential scanning fluorimetry

The output of a differential scanning fluorimetry (DSF) assay is a series of melt curves, which need to be interpreted to get value from the assay. An application that translates raw thermal melt curve data into more easily assimilated knowledge is described. This program, called “Meltdown,” conducts four main activities—control checks, curve normalization, outlier rejection, and melt temperature (Tm) estimation—and performs optimally in the presence of triplicate (or higher) sample data. The final output is a report that summarizes the results of a DSF experiment. The goal of Meltdown is not to replace human analysis of the raw fluorescence data but to provide a meaningful and comprehensive interpretation of the data to make this useful experimental technique accessible to inexperienced users, as well as providing a starting point for detailed analyses by more experienced users