Inferring Subsystem Efficiencies in Bipartite Molecular Machines.

Molecular machines composed of coupled subsystems transduce free energy between different external reservoirs, in the process internally transducing energy and information. While subsystem efficiencies of these molecular machines have been measured in isolation, less is known about how they behave in their natural setting when coupled together and acting in concert. Here, we derive upper and lower bounds on the subsystem efficiencies of a bipartite molecular machine. We demonstrate their utility by estimating the efficiencies of the F_{o} and F_{1} subunits of ATP synthase and that of kinesin pulling a diffusive cargo.

Torsion and bistability of double-twist elastomers.

We investigate the elastic properties of anisotropic elastomers with a double-twist director field, which is a model for collagen fibrils or blue phases. We observe a significant Poynting-like effect, coupling torsion (fibril twist) and extension. For freely-rotating boundary conditions, we identify a structural bistability at very small extensional strains which undergoes a saddle-node bifurcation at a critical strain - at approximately 1% strain for a parameterization appropriate for collagen fibrils. With clamped boundary conditions appropriate for many experimental setups, the bifurcation is not present. We expect significant helical shape effects when fixed torsion does not equal the equilibrium torsion of freely-rotating boundary conditions, due to residual torques.

Dynamic and Thermodynamic Bounds for Collective Motor-Driven Transport.

Molecular motors work collectively to transport cargo within cells, with anywhere from one to several hundred motors towing a single cargo. For a broad class of collective-transport systems, we use tools from stochastic thermodynamics to derive a new lower bound for the entropy production rate which is tighter than the second law. This implies new bounds on the velocity, efficiency, and precision of general transport systems and a set of analytic Pareto frontiers for identical motors. In a specific model, we identify conditions for saturation of these Pareto frontiers.

Non-equilibrium growth and twist of cross-linked collagen fibrils.

The lysyl oxidase (LOX) enzyme that catalyses cross-link formation during the assembly of collagen fibrils in vivo is too large to diffuse within assembled fibrils, and so is incompatible with a fully equilibrium mechanism for fibril formation. We propose that enzymatic cross-links are formed at the fibril surface during the growth of collagen fibrils; as a consequence no significant reorientation of previously cross-linked collagen molecules occurs inside collagen fibrils during fibril growth in vivo. By imposing local equilibrium only at the fibril surface, we develop a coarse-grained quantitative model of in vivo fibril structure that incorporates a double-twist orientation of collagen molecules and a periodic D-band density modulation along the fibril axis. Radial growth is controlled by the concentration of available collagen molecules outside the fibril. In contrast with earlier equilibrium models of fibril structure, we find that all fibrils can exhibit a core-shell structure that is controlled only by the fibril radius. At small radii a core is developed with a linear double-twist structure as a function of radius. Within the core the double-twist structure is largely independent of the D-band. Within the shell at larger radii, the structure approaches a constant twist configuration that is strongly coupled with the D-band. We suggest a stable radius control mechanism that corneal fibrils can exploit near the edge of the linear core regime; while larger tendon fibrils use a cruder version of growth control that does not select a preferred radius.

Chiral phase-coexistence in compressed double-twist elastomers.

We adapt the theory of anisotropic rubber elasticity to model cross-linked double-twist liquid crystal cylinders such as exhibited in biological systems. In mechanical extension we recover strain-straightening, but with an exact expression in the small twist-angle limit. In compression, we observe coexistence between high and low twist phases. Coexistence begins at small compressive strains and is robustly observed for any anisotropic cross-links and for general double-twist functions - but disappears at large twist angles. Within the coexistence region, significant compression of double-twist cylinders is allowed at constant stress. Our results are qualitatively consistent with previous observations of swollen or compressed collagen fibrils, indicating that this phenomenon may be readily accessible experimentally.

Jensen bound for the entropy production rate in stochastic thermodynamics.

Bounding and estimating entropy production has long been an important goal of nonequilibrium thermodynamics. We recently derived a lower bound on the total and subsystem entropy production rates of continuous stochastic systems. This "Jensen bound" has led to fundamental limits on the performance of collective transport systems and permitted thermodynamic inference of free-energy transduction between components of bipartite molecular machines. Our original derivation relied on a number of assumptions, which restricted the bound's regime of applicability. Here we derive the Jensen bound far more generally for multipartite overdamped Langevin dynamics. We then consider several extensions, allowing for position-dependent diffusion coefficients, underdamped dynamics, and non-multipartite overdamped dynamics. Our results extend the Jensen bound to a far broader class of systems.

A novel form of chondrocyte stress is triggered by a COMP mutation causing pseudoachondroplasia.

Pseudoachondroplasia (PSACH) results from mutations in cartilage oligomeric matrix protein (COMP) and the p.D469del mutation within the type III repeats of COMP accounts for approximately 30% of PSACH. To determine disease mechanisms of PSACH in vivo, we introduced the Comp D469del mutation into the mouse genome. Mutant animals were normal at birth but grew slower than their wild-type littermates and developed short-limb dwarfism. In the growth plates of mutant mice chondrocyte columns were reduced in number and poorly organized, while mutant COMP was retained within the endoplasmic reticulum (ER) of cells. Chondrocyte proliferation was reduced and apoptosis was both increased and spatially dysregulated. Previous studies on COMP mutations have shown mutant COMP is co-localized with chaperone proteins, and we have reported an unfolded protein response (UPR) in mouse models of PSACH-MED (multiple epiphyseal dysplasia) harboring mutations in Comp (T585M) and Matn3, Comp etc (V194D). However, we found no evidence of UPR in this mouse model of PSACH. In contrast, microarray analysis identified expression changes in groups of genes implicated in oxidative stress, cell cycle regulation, and apoptosis, which is consistent with the chondrocyte pathology. Overall, these data suggest that a novel form of chondrocyte stress triggered by the expression of mutant COMP is central to the pathogenesis of PSACH.

D-band strain underestimates fibril strain for twisted collagen fibrils at low strains.

Collagen fibrils are the main structural component of load-bearing tissues such as tendons, ligaments, skin, the cornea of the eye, and the heart. The D-band of collagen fibrils is an axial periodic density modulation that can be easily characterized by tissue-level X-ray scattering. During mechanical testing, D-band strain is often used as a proxy for fibril strain. However, this approach ignores the coupling between strain and molecular tilt. We examine the validity of this approximation using an elastomeric collagen fibril model that includes both the D-band and a molecular tilt field. In the low strain regime, we show that the D-band strain substantially underestimates fibril strain for strongly twisted collagen fibrils - such as fibrils from skin or corneal tissue.

Multiple epiphyseal dysplasia mutations in MATN3 cause misfolding of the A-domain and prevent secretion of mutant matrilin-3.

Multiple epiphyseal dysplasia (MED) is a relatively common skeletal dysplasia that can present in childhood with a variable phenotype of short stature and pain and stiffness in the large joints, and often progresses to early-onset osteoarthritis in adulthood. Mutations in the matrilin-3 gene (MATN3) have recently been shown to underlie some forms of autosomal dominant MED. To date all MED mutations in matrilin-3 cluster in the single A-domain, suggesting that they may disrupt the structure and/or function of this important domain. To determine the effects of MATN3 mutations on the structure and function of matrilin-3 we expressed both normal and mutant matrilin-3 in mammalian cells. Wild-type (wt) matrilin-3 was efficiently secreted into conditioned medium, whereas mutant matrilin-3 was retained and accumulated within the cell. Furthermore, when the mutant A-domains were examined individually, they existed primarily in an unfolded conformation. Co-immunoprecipitation experiments demonstrated that the mutant A-domains were specifically associated with ERp72, a chaperone protein known to be involved in mediating disulfide bond formation. Light microscopy of cartilage from an MED patient with a MATN3 mutation showed the presence of intracellular material within the chondrocytes, whilst the overall matrix appeared normal. On electron micrographs, the inclusions noted at the light microscopy level appeared to be dilated cisternae of rough endoplasmic reticulum and immunohistochemical analysis confirmed that the retained protein was matrilin-3. In summary, the data presented in this paper suggest that MED caused by MATN3 mutations is the result of an intracellular retention of the mutant protein.

Efficacy and mode of action of mesalazine in the treatment of diarrhoea-predominant irritable bowel syndrome (IBS-D): study protocol for a randomised controlled trial.

BACKGROUND: Irritable bowel syndrome (IBS) is reported by one in ten of the population accounting for up to 40% of new referrals to gastroenterology outpatients. Patients characteristically have abdominal discomfort and disturbed bowel habit. Diarrhoea-predominant IBS is characterised by frequent loose stools with associated urgency and abdominal cramps. Current symptomatic treatments can reduce bowel frequency but often fail to reduce discomfort.Mesalazine is an anti-inflammatory drug used to treat patients with inflammatory bowel disease. There is one pilot study suggesting it may be beneficial to patients who have diarrhoea-predominant IBS but these findings need to be confirmed in a larger trial. The current study aims to test the effectiveness of mesalazine to reduce symptoms in diarrhoea-predominant IBS patients. The study will also investigate the mode of action of the drug, especially its impact on mast cell activation. METHODS/DESIGN: This is a multicentre randomised, double-blind, placebo-controlled trial using a parallel group design. At least 108 participants with diarrhoea-predominant IBS will be recruited through at least six hospitals. The intervention is a 12-week course of 2g mesalazine granules taken up to twice a day. The comparator is a blinded placebo granule formulation.Outcome measures include stool diaries, symptom questionnaires, stool and blood samples together with rectal mucosal biopsies. The daily stool diary will record stool frequency and form, urgency, bloating, abdominal pain and a global satisfaction with control of IBS scored each week. The questionnaires will assess bowel symptoms, while the samples and biopsies will be used to analyse underlying mechanisms of any response.Primary outcome will be the average stool frequency during weeks 11 and 12 of the treatment period and will be compared between treatment arms using an analysis of covariance in the form of a general linear model incorporating baseline characteristics that are thought a priori to strongly predict outcome. The primary efficacy parameter will be the difference in mean frequency between treatment arms. DISCUSSION: This report describes a randomised controlled trial that will provide evidence of any benefit of treating diarrhoea-predominant IBS patients with mesalazine. The results will be available toward the end of 2013. TRIAL REGISTRATION: ISRCTN76612274.

Decreased chondrocyte proliferation and dysregulated apoptosis in the cartilage growth plate are key features of a murine model of epiphyseal dysplasia caused by a matn3 mutation.

Disruption to endochondral ossification leads to delayed and irregular bone formation and can result in a heterogeneous group of genetic disorders known as the chondrodysplasias. One such disorder, multiple epiphyseal dysplasia (MED), is characterized by mild dwarfism and early-onset osteoarthritis and can result from mutations in the gene encoding matrilin-3 (MATN3). To determine the disease mechanisms that underpin the pathophysiology of MED we generated a murine model of epiphyseal dysplasia by knocking-in a matn3 mutation. Mice that are homozygous for the mutation develop a progressive dysplasia and have short-limbed dwarfism that is consistent in severity with the relevant human phenotype. Mutant matrilin-3 is retained within the rough endoplasmic reticulum of chondrocytes and is associated with an unfolded protein response. Eventually, there is reduced proliferation and spatially dysregulated apoptosis of chondrocytes in the cartilage growth plate, which is likely to be the cause of disrupted linear bone growth and the resulting short-limbed dwarfism in the mutant mice.

An NMR and enzyme study of the carbon metabolism of Neisseria meningitidis.

The pathogenic neisseriae are fastidious bacteria that are only able to grow on a restricted range of carbon sources. The genome sequence of Neisseria meningitidis strain MC58 predicts the presence of a complete citric acid cycle (CAC), but there have been no detailed biochemical studies of carbon metabolism in this important pathogen. In this study, both NMR and conventional enzyme assays were used to investigate the central metabolic pathways of a serogroup B strain (K454). (13)C-NMR labelling patterns of amino acids from hydrolysed cell proteins after growth with either 2- or 3-[(13)C]pyruvate were consistent with the operation of a complete oxidative CAC. Enzyme assays showed that cell-free extracts contained all the CAC enzymes predicted from the genome sequence, including a membrane-bound malate:quinone oxidoreductase which is present in place of the conventional NAD-linked cytoplasmic malate dehydrogenase. (1)H-NMR studies showed that growth on glucose, lactate and, especially, pyruvate, resulted in the excretion of significant amounts of acetate into the culture supernatant. This occurred via the phosphotransacetylase (PTA)-acetate kinase (ACK) pathway. Extremely high specific activities of PTA (7-14 micromol min(-1) mg(-1)) were detected in cell-free extracts, although ACK activities were much lower (46-298 nmol min(-1) mg(-1)). Expression of PTA and ACK activities was not co-ordinately regulated during growth on combinations of carbon sources. This may be related to the presence of two ackA paralogues in N. meningitidis which are, unusually, unlinked to the pta gene.