Force-Velocity Relations of a Two-State Crossbridge Model for Molecular Motors

We discuss the force-velocity relations obtained in a two-state crossbridge model for molecular motors. They can be calculated analytically in two limiting cases: for a large number and for one pair of motors. The effect of the strain-dependent detachment rate on the motor characteristics is studied. It can lead to linear, myosin-like, kinesin-like and anomalous curves. In particular, we specify the conditions under which oscillatory behavior may be found.Comment: 5 pages, 4 figures, REVTeX; thoroughly revised version; also available at http://www.physik.tu-muenchen.de/~frey

Predicting and harnessing protein flexibility in the design of species-specific inhibitors of thymidylate synthase1,21Escherichia coli thymidylate synthase numbering is used unless otherwise noted.2PDB coordinates have been deposited with the RCSB with accession ID: 1JG0.

AbstractBackground: Protein plasticity in response to ligand binding abrogates the notion of a rigid receptor site. Thus, computational docking alone misses important prospective drug design leads. Bacterial-specific inhibitors of an essential enzyme, thymidylate synthase (TS), were developed using a combination of computer-based screening followed by in-parallel synthetic elaboration and enzyme assay [Tondi et al. (1999) Chem. Biol. 6, 319–331]. Specificity was achieved through protein plasticity and despite the very high sequence conservation of the enzyme between species.Results: The most potent of the inhibitors synthesized, N,O-didansyl-L-tyrosine (DDT), binds to Lactobacillus casei TS (LcTS) with 35-fold higher affinity and to Escherichia coli TS (EcTS) with 24-fold higher affinity than to human TS (hTS). To reveal the molecular basis for this specificity, we have determined the crystal structure of EcTS complexed with DDT and 2′-deoxyuridine-5′-monophosphate (dUMP). The 2.0 Å structure shows that DDT binds to EcTS in a conformation not predicted by molecular docking studies and substantially differently than other TS inhibitors. Binding of DDT is accompanied by large rearrangements of the protein both near and distal to the enzyme’s active site with movement of Cα carbons up to 6 Å relative to other ternary complexes. This protein plasticity results in novel interactions with DDT including the formation of hydrogen bonds and van der Waals interactions to residues conserved in bacterial TS but not hTS and which are hypothesized to account for DDT’s specificity. The conformation DDT adopts when bound to EcTS explains the activity of several other LcTS inhibitors synthesized in-parallel with DDT suggesting that DDT binds to the two enzymes in similar orientations.Conclusions: Dramatic protein rearrangements involving both main and side chain atoms play an important role in the recognition of DDT by EcTS and highlight the importance of incorporating protein plasticity in drug design. The crystal structure of the EcTS/dUMP/DDT complex is a model system to develop more selective TS inhibitors aimed at pathogenic bacterial species. The crystal structure also suggests a general formula for identifying regions of TS and other enzymes that may be treated as flexible to aid in computational methods of drug discovery

Is famine exposure during developmental life in rural Bangladesh associated with a metabolic and epigenetic signature in young adulthood? A historical cohort study

Objectives Famine exposure in utero can ‘programme’ an individual towards type 2 diabetes and obesity in later life. We sought to identify, (1) whether Bangladeshis exposed to famine during developmental life are programmed towards diabetes and obesity, (2) whether this programming was specific to gestational or postnatal exposure windows and (3) whether epigenetic differences were associated with famine exposure. Design A historical cohort study was performed as part of a wider cross-sectional survey. Exposure to famine was defined through birth date and historical records and participants were selected according to: (A) exposure to famine in postnatal life, (B) exposure to famine during gestation and (C) unexposed. Setting Matlab, a rural area in the Chittagong division of Bangladesh. Participants Young adult men and women (n=190) recruited to a historical cohort study with a randomised subsample included in an epigenetic study (n=143). Outcome measures Primary outcome measures of weight, body mass index and oral glucose tolerance tests (0 and 120 min glucose). Secondary outcome measures included DNA methylation using genome-wide and targeted analysis of metastable epialleles sensitive to maternal nutrition. Results More young adults exposed to famine in gestation were underweight than those postnatally exposed or unexposed. In contrast, more young adults exposed to famine postnatally were overweight compared to those gestationally exposed or unexposed. Underweight adults exposed to famine in gestation in utero were hyperglycaemic following a glucose tolerance test, and those exposed postnatally had elevated fasting glucose, compared to those unexposed. Significant differences in DNA methylation at seven metastable epialleles (VTRNA2-1, PAX8, PRDM-9, near ZFP57, near BOLA, EXD3) known to vary with gestational famine exposure were identified. Conclusions Famine exposure in developmental life programmed Bangladeshi offspring towards diabetes and obesity in adulthood but gestational and postnatal windows of exposure had variable effects on phenotype. DNA methylation differences were replicated at previously identified metastable epialleles sensitive to periconceptual famine exposure

Divergent roles of Smad3 and PI3-kinase in murine adriamycin nephropathy indicate distinct mechanisms of proteinuria and fibrogenesis

Multiple transforming growth factor (TGF)-β-induced fibrogenic signals have been described in vitro. To evaluate mechanisms in vivo, we used an adriamycin nephropathy model in 129x1/Svj mice that display massive proteinuria by day 5 to7 and pathological findings similar to human focal segmental glomerulosclerosis by day 14. TGF-β mRNA expression increased after day 7 along with nuclear translocation of the TGF-β receptor-specific transcription factor Smad3. Inhibiting TGF-β prevented both pathological changes and type-I collagen and fibronectin mRNA expression, but proteinuria persisted. Renal Akt was phosphorylated in adriamycin-treated mice, suggesting PI3-kinase activation. Expression of mRNA for the p110γ isozyme of PI3-kinase was specifically increased and p110γ colocalized with nephrin by immunohistochemistry early in disease. Nephrin levels subsequently decreased. Inhibition of p110γ by AS605240 preserved nephrin expression and prevented proteinuria. In cultured podocytes, adriamycin stimulated p110γ expression. AS605240, but not a TGF-β receptor kinase inhibitor, prevented adriamycin-induced cytoskeletal disorganization and apoptosis, supporting a role for p110γ in podocyte injury. AS605240, at a dose that decreased proteinuria, prevented renal collagen mRNA expression in vivo but did not affect TGF-β-stimulated collagen induction in vitro. Thus, PI3-kinase p110γ mediates initial podocyte injury and proteinuria, both of which precede TGF-β-mediated glomerular scarring

Fluctuating-friction molecular motors

We show that the correlated stochastic fluctuation of the friction coefficient can give rise to long-range directional motion of a particle undergoing Brownian random walk in a constant periodic energy potential landscape. The occurrence of this motion requires the presence of two additional independent bodies interacting with the particle via friction and via the energy potential, respectively, which can move relative to each other. Such three-body system generalizes the classical Brownian ratchet mechanism, which requires only two interacting bodies. In particular, we describe a simple two-level model of fluctuating-friction molecular motor that can be solved analytically. In our previous work [M.K., L.M and D.P. 2000 J. Nonlinear Opt. Phys. Mater. vol. 9, 157] this model has been first applied to understanding the fundamental mechanism of the photoinduced reorientation of dye-doped liquid crystals. Applications of the same idea to other fields such as molecular biology and nanotechnology can however be envisioned. As an example, in this paper we work out a model of the actomyosin system based on the fluctuating-friction mechanism.Comment: to be published in J. Physics Condensed Matter (http://www.iop.org/Journals/JPhysCM

Steps in the bacterial flagellar motor

The bacterial flagellar motor is a highly efficient rotary machine used by many bacteria to propel themselves. It has recently been shown that at low speeds its rotation proceeds in steps [Sowa et al. (2005) Nature 437, 916--919]. Here we propose a simple physical model that accounts for this stepping behavior as a random walk in a tilted corrugated potential that combines torque and contact forces. We argue that the absolute angular position of the rotor is crucial for understanding step properties, and show this hypothesis to be consistent with the available data, in particular the observation that backward steps are smaller on average than forward steps. Our model also predicts a sublinear torque-speed relationship at low torque, and a peak in rotor diffusion as a function of torque

Implementation and delivery of group consultations for young people with diabetes in socioeconomically deprived, ethnically diverse settings

BACKGROUND: Young people with diabetes experience poor clinical and psychosocial outcomes, and consider the health service ill-equipped in meeting their needs. Improvements, including alternative consulting approaches, are required to improve care quality and patient engagement. We examined how group-based, outpatient diabetes consultations might be delivered to support young people (16-25 years old) in socio-economically deprived, ethnically diverse settings. METHODS: This multi-method, comparative study recruited a total of 135 young people with diabetes across two implementation and two comparison sites (2017-2019). Informed by a 'researcher-in-residence' approach and complexity theory, we used a combination of methods: (a) 31 qualitative interviews with young people and staff and ethnographic observation in group and individual clinics, (b) quantitative analysis of sociodemographic, clinical, service use, and patient enablement data, and (c) micro-costing analysis. RESULTS: Implementation sites delivered 29 group consultations in total. Overall mean attendance per session was low, but a core group of young people attended repeatedly. They reported feeling better understood and supported, gaining new learning from peers and clinicians, and being better prepared to normalise diabetes self-care. Yet, there were also instances where peer comparison proved difficult to manage. Group consultations challenged deeply embedded ways of thinking about care provision and required staff to work flexibly to achieve local tailoring, sustain continuity, and safely manage complex interdependencies with other care processes. Set-up and delivery were time-consuming and required in-depth clinical and relational knowledge of patients. Facilitation by an experienced youth worker was instrumental. There was indication that economic value could derive from preventing at least one unscheduled consultation annually. CONCLUSIONS: Group consulting can provide added value when tailored to meet local needs rather than following standardised approaches. This study illustrates the importance of adaptive capability and self-organisation when integrating new models of care, with young people as active partners in shaping service provision. TRIAL REGISTRATION: ISRCTN reference 27989430