The Native 3D Organization of Bacterial Polysomes

SummaryRecent advances have led to insights into the structure of the bacterial ribosome, but little is known about the 3D organization of ribosomes in the context of translating polysomes. We employed cryoelectron tomography and a template-matching approach to map 70S ribosomes in vitrified bacterial translation extracts and in lysates of active E. coli spheroplasts. In these preparations, polysomal arrangements were observed in which neighboring ribosomes are densely packed and exhibit preferred orientations. Analysis of characteristic examples of polysomes reveals a staggered or pseudohelical organization of ribosomes along the mRNA trace, with the transcript being sequestered on the inside, the tRNA entrance sites being accessible, and the polypeptide exit sites facing the cytosol. Modeling of elongating nascent polypeptide chains suggests that this arrangement maximizes the distance between nascent chains on adjacent ribosomes, thereby reducing the probability of intermolecular interactions that would give rise to aggregation and limit productive folding

Diffusional Channeling in the Sulfate-Activating Complex: Combined Continuum Modeling and Coarse-Grained Brownian Dynamics Studies

Enzymes required for sulfur metabolism have been suggested to gain efficiency by restricted diffusion (i.e., channeling) of an intermediate APS2– between active sites. This article describes modeling of the whole channeling process by numerical solution of the Smoluchowski diffusion equation, as well as by coarse-grained Brownian dynamics. The results suggest that electrostatics plays an essential role in the APS2– channeling. Furthermore, with coarse-grained Brownian dynamics, the substrate channeling process has been studied with reactions in multiple active sites. Our simulations provide a bridge for numerical modeling with Brownian dynamics to simulate the complicated reaction and diffusion and raise important questions relating to the electrostatically mediated substrate channeling in vitro, in situ, and in vivo

Capturing the essence of folding and functions of biomolecules using Coarse-Grained Models

The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such diverse length, and also time scales, requires models that capture the underlying physics for the particular length scale of interest. Theoretical ideas, in particular, concepts from polymer physics, have guided the development of coarse-grained models to study folding of DNA, RNA, and proteins. More recently, such models and their variants have been applied to the functions of biological nanomachines. Simulations using coarse-grained models are now poised to address a wide range of problems in biology.Comment: 37 pages, 8 figure

Safeguarding children in dentistry: 1. Child protection training, experience and practice of dental professionals with an interest in paediatric dentistry

* Few dental professionals with child protection training have experience of making referrals. * There is a wide gap in practice between recognising signs of child abuse and neglect and responding effectively. * This may indicate missed opportunities to save children from continuing abuse. * There is a need for improved child protection information, support and training for dental professionals. Abstract Following several highly publicised inquiries into the deaths of children from abuse and neglect, there has been much recent interest in the role and responsibility of all health professionals to protect children at risk of maltreatment. The findings of a postal questionnaire, sent in March 2005 to 789 dentists and dental care professionals with an interest in paediatric dentistry working in varied settings in the UK, are presented in a two-part report and discussed in the context of current multi-agency good practice in safeguarding and promoting the welfare of children. This first part explores reported child protection training, experience and practice. There was a significant gap between recognising signs of abuse and responding effectively: 67% of respondents had suspected abuse or neglect of a child patient at some time in their career but only 29% had ever made a child protection referral. The dental profession is alerted to the need to ensure necessary appropriate action to safeguard children is always taken when child abuse or neglect are suspected

Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide

Understanding the influence of macromolecular crowding and nanoparticles on the formation of in-register $\beta$-sheets, the primary structural component of amyloid fibrils, is a first step towards describing \emph{in vivo} protein aggregation and interactions between synthetic materials and proteins. Using all atom molecular simulations in implicit solvent we illustrate the effects of nanoparticle size, shape, and volume fraction on oligomer formation of an amyloidogenic peptide from the transthyretin protein. Surprisingly, we find that inert spherical crowding particles destabilize in-register $\beta$-sheets formed by dimers while stabilizing $\beta$-sheets comprised of trimers and tetramers. As the radius of the nanoparticle increases crowding effects decrease, implying smaller crowding particles have the largest influence on the earliest amyloid species. We explain these results using a theory based on the depletion effect. Finally, we show that spherocylindrical crowders destabilize the ordered $\beta$-sheet dimer to a greater extent than spherical crowders, which underscores the influence of nanoparticle shape on protein aggregation

Disposal of NORM-contaminated oil field wastes in salt caverns -- Legality, technical feasibility, economics, and risk

Some types of oil and gas production and processing wastes contain naturally occurring radioactive materials (NORM). If NORM is present at concentrations above regulatory levels in oil field waste, the waste requires special disposal practices. The existing disposal options for wastes containing NORM are limited and costly. This paper evaluates the legality, technical feasibility, economics, and human health risk of disposing of NORM-contaminated oil field wastes in salt caverns. Cavern disposal of NORM waste is technically feasible and poses a very low human health risk. From a legal perspective, there are no fatal flaws that would prevent a state regulatory agency from approaching cavern disposal of NORM. On the basis of the costs charged by caverns currently used for disposal of nonhazardous oil field waste (NOW), NORM waste disposal caverns could be cost competitive with existing NORM waste disposal methods when regulatory agencies approve the practice

Disposal of NORM-Contaminated Oil Field Wastes in Salt Caverns

In 1995, the U.S. Department of Energy (DOE), Office of Fossil Energy, asked Argonne National Laboratory (Argonne) to conduct a preliminary technical and legal evaluation of disposing of nonhazardous oil field waste (NOW) into salt caverns. That study concluded that disposal of NOW into salt caverns is feasible and legal. If caverns are sited and designed well, operated carefully, closed properly, and monitored routinely, they can be a suitable means of disposing of NOW (Veil et al. 1996). Considering these findings and the increased U.S. interest in using salt caverns for NOW disposal, the Office of Fossil Energy asked Argonne to conduct further research on the cost of cavern disposal compared with the cost of more traditional NOW disposal methods and on preliminary identification and investigation of the risks associated with such disposal. The cost study (Veil 1997) found that disposal costs at the four permitted disposal caverns in the United States were comparable to or lower than the costs of other disposal facilities in the same geographic area. The risk study (Tomasko et al. 1997) estimated that both cancer and noncancer human health risks from drinking water that had been contaminated by releases of cavern contents were significantly lower than the accepted risk thresholds. Since 1992, DOE has funded Argonne to conduct a series of studies evaluating issues related to management and disposal of oil field wastes contaminated with naturally occurring radioactive material (NORM). Included among these studies were radiological dose assessments of several different NORM disposal options (Smith et al. 1996). In 1997, DOE asked Argonne to conduct additional analyses on waste disposal in salt caverns, except that this time the wastes to be evaluated would be those types of oil field wastes that are contaminated by NORM. This report describes these analyses. Throughout the remainder of this report, the term ''NORM waste'' is used to mean ''oil field waste contaminated by NORM''

Thermodynamics of Nonstoichiometric Nickel Tellurides. I. Heat Capacity and Thermodynamic Functions of the δ Phase from 5 to 350°K

Heat capacities of the nickel tellurides were measured at compositions NiTe1.1 and NiTe2.0 (near limits of homogeneity of the δ phase) and at one intermediate composition, NiTe1.5, from 5 to 350°K. Heat capacity values and entropy and enthalpy increments are tabulated. No evidence of order‐disorder transitions, or thermal anomalies, or of contributions to the thermal properties from the anisotropy or phonon scattering by the holes in the structure on approaching the composition NiTe2 was observed. Although simple additivity of the heat capacities of the constituent elements failed to represent that of the solution compositions adequately, a Kopp‐Neumann treatment in terms of the limiting compositions of the δ phase gives good agreement with the experimental heat capacity and entropy of NiTe1.5 and hence is useful in interpolating to other intermediate compositions.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/70090/2/JCPSA6-28-3-497-1.pd

Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm

A longstanding question in molecular biology is the extent to which the behavior of macromolecules observed in vitro accurately reflects their behavior in vivo. A number of sophisticated experimental techniques now allow the behavior of individual types of macromolecule to be studied directly in vivo; none, however, allow a wide range of molecule types to be observed simultaneously. In order to tackle this issue we have adopted a computational perspective, and, having selected the model prokaryote Escherichia coli as a test system, have assembled an atomically detailed model of its cytoplasmic environment that includes 50 of the most abundant types of macromolecules at experimentally measured concentrations. Brownian dynamics (BD) simulations of the cytoplasm model have been calibrated to reproduce the translational diffusion coefficients of Green Fluorescent Protein (GFP) observed in vivo, and “snapshots” of the simulation trajectories have been used to compute the cytoplasm's effects on the thermodynamics of protein folding, association and aggregation events. The simulation model successfully describes the relative thermodynamic stabilities of proteins measured in E. coli, and shows that effects additional to the commonly cited “crowding” effect must be included in attempts to understand macromolecular behavior in vivo