Channeling by Proximity: The Catalytic Advantages of Active Site Colocalization Using Brownian Dynamics

Nature often colocalizes successive steps in a metabolic pathway. Such organization is predicted to increase the effective concentration of pathway intermediates near their recipient active sites and to enhance catalytic efficiency. Here, the pathway of a two-step reaction is modeled using a simple spherical approximation for the enzymes and substrate particles. Brownian dynamics are used to simulate the trajectory of a substrate particle as it diffuses between the active site zones of two different enzyme spheres. The results approximate distances for the most effective reaction pathways, indicating that the most effective reaction pathway is one in which the active sites are closely aligned. However, when the active sites are too close, the ability of the substrate to react with the first enzyme was hindered, suggesting that even the most efficient orientations can be improved for a system that is allowed to rotate or change orientation to optimize the likelihood of reaction at both sites

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

Change in Oral Health-Related Quality of Life Following Minimally Invasive Aesthetic Treatment for Children with Molar Incisor Hypomineralisation: A Prospective Study

Molar incisor hypomineralisation (MIH) is a common enamel condition, presenting with incisor opacities, which may be of psychosocial concern to children. This clinical study sought to determine whether minimally invasive treatment, aiming to improve incisor aesthetics, would also improve children's oral health-related quality of life (OHRQoL). 111 MIH patients, aged 7⁻16 years, referred to a UK Dental Hospital, were invited to complete the Child Oral Health Impact Profile (C-OHIP-SF19) prior to any intervention (T₀) and again at one-month following the intervention (T₁) for MIH. Treatment regimens included one or more of the following: Microabrasion; resin infiltration; tooth whitening; resin composite restoration. Data were obtained for 93 children with a mean age of 11 years. Mean total C-OHIP-SF19 score at T₀ was 47.00 (SD = 9.29; range = 0⁻76) and this increased significantly at T₁ to 58.24 (SD = 9.42; range = 0⁻76; p < 0.001, paired t-test), indicating a marked improvement in self-reported OHRQoL. There were no statistically significant differences according to gender. This is the first study to show that simple, minimally invasive dental treatment, to reduce the visibility of enamel opacities, in MIH, can have a positive impact on children's wellbeing

Determinants of children’s oral health-related quality of life following aesthetic treatment of enamel opacities

Objectives To identify clinical and psychosocial predictors of oral health-related quality of life (OHRQoL) in children with molar incisor hypomineralisation (MIH) following aesthetic treatment of incisor opacities. Methods Participants were 7- to 16-year-old children referred to a UK Dental Hospital for management of incisor opacities. Prior to treatment (To), participants completed validated questionnaires to assess OHRQoL and overall health status (C−OHIP-SF19), and self-concept (Harter’s Self-Perception Profile for Children [SPPC]). Interventions for MIH included microabrasion, resin infiltration, tooth whitening or composite resin restoration. Children were reviewed after six months (T1) when they re-completed the C−OHIP-SF19 and SPPC questionnaires. The relationships of predictors with improvement of children’s OHRQoL (T1-To) and children’s overall health status at T1 were assessed using linear and ordinal logistic regression respectively, guided by the Wilson and Cleary’s theoretical model. Results Of 103 participants, 86 were reviewed at T1 (83.5 % completion rate). Their mean age was 11-years (range = 7−16) and 60 % were female. Total and domain OHRQoL scores significantly increased (improved OHRQoL) following MIH treatment. There was a significant positive change in SPPC physical appearance subscale score between To and T1. A higher number of anterior teeth requiring aesthetic treatment were associated with poor improvement of socio-emotional wellbeing at T1 (Coef =-0.43). Higher self-concept at To was associated with greater improvement of socio-emotional wellbeing at T1 (ß = 3.44). Greater orthodontic treatment need (i.e. higher IOTN-AC score) at T0 was linked to worse overall oral health at T1 (OR = 0.43). Conclusions Psychosocial factors and dental clinical characteristics were associated with change in children’s OHRQoL following minimal interventions for incisor opacities. Clinical significance MIH is a common condition and clinicians should be aware of the negative impacts some children experience, particularly those with multiple anterior opacities, poor tooth alignment and low self-concept. However, simple, minimally invasive treatments can provide good clinical and psychosocial outcomes and should be offered to children reporting negative effects

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

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

Entropic Tension in Crowded Membranes

Unlike their model membrane counterparts, biological membranes are richly decorated with a heterogeneous assembly of membrane proteins. These proteins are so tightly packed that their excluded area interactions can alter the free energy landscape controlling the conformational transitions suffered by such proteins. For membrane channels, this effect can alter the critical membrane tension at which they undergo a transition from a closed to an open state, and therefore influence protein function \emph{in vivo}. Despite their obvious importance, crowding phenomena in membranes are much less well studied than in the cytoplasm. Using statistical mechanics results for hard disk liquids, we show that crowding induces an entropic tension in the membrane, which influences transitions that alter the projected area and circumference of a membrane protein. As a specific case study in this effect, we consider the impact of crowding on the gating properties of bacterial mechanosensitive membrane channels, which are thought to confer osmoprotection when these cells are subjected to osmotic shock. We find that crowding can alter the gating energies by more than $2\;k_BT$ in physiological conditions, a substantial fraction of the total gating energies in some cases. Given the ubiquity of membrane crowding, the nonspecific nature of excluded volume interactions, and the fact that the function of many membrane proteins involve significant conformational changes, this specific case study highlights a general aspect in the function of membrane proteins.Comment: 20 pages (inclduing supporting information), 4 figures, to appear in PLoS Comp. Bio

A Case of Thoracic Spondylosis Deformans and Multilevel Instrumented Spinal Fusion in an 84-Year-Old Male.

Spondylosis deformans is a type of spinal claw osteophytosis which can be found on the anterolateral vertebral bodies of any region, and which consists of protrusions of intervertebral disc tissue covered by a bony shell. We report here a case of thoracic spondylosis deformans and multilevel instrumented fusion found during routine dissection of a cadaver. Theories of the etiology of this condition are reviewed in general, and with respect to this specific case and the potential interaction of the presenting comorbidities. The clinical implications of these osteophytes, including musculoskeletal and visceral sequelae, are also discussed

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