Structure of protochlorophyllide reductase reveals a mechanism for greening in the dark

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Continuum Mechanical Parameterisation of Cytoplasmic Dynein from Atomistic Simulation

Cytoplasmic dynein is responsible for intra-cellular transport in eukaryotic cells. Using Fluctuating Finite Element Analysis (FFEA), a novel algorithm that represents proteins as continuum viscoelastic solids subject to thermal noise, we are building computational tools to study the mechanics of these molecular machines. Here we present a methodology for obtaining the material parameters required to represent the flexibility of cytoplasmic dynein within FFEA from atomistic molecular dynamics (MD) simulations, and show this continuum representation is sufficient to capture the principal dynamic properties of the motor

A Theory of Anisotropic Semiconductor of Heavy Fermions

It is demonstrated that a {\veck}-dependence of the hybridization matrix element between $f$- and conduction electrons can give rise to an anisotropic hybridization gap of heavy fermions if the filling of electrons corresponds to that of the band insulator. The most interesting case occurs when the hybridization vanishes along some symmetry axis of the crystal reflecting a particular symmetry of the crystal field. The results of a model calculation are consistent with wide range of anomalous properties observed in CeNiSn and its isostructural compounds, the anisotropic semiconductor of heavy fermions. In particular, highly sensitive effect of impurity scattering on the residual density of states for zero energy excitation and the anisotropic temperature dependence of the resistivity are well explained. It is also discussed that a weak semimetallic behavior arises through the weak \veck-dependence of the $f$-electron self-energy \Sigma_{f}(\veck,0).Comment: 21 pages, LaTeX (JPSJ style file) and 13 postscript figures, To appear in J. Phys. Soc. Jp

Electron transport pathways in isolated chromoplasts from Narcissus pseudonarcissus L.

During daffodil flower development, chloroplasts differentiate into photosynthetically inactive chromoplasts having lost functional photosynthetic reaction centers. Chromoplasts exhibit a respiratory activity reducing oxygen to water and generating ATP. Immunoblots revealed the presence of the plastid terminal oxidase (PTOX), the NAD(P)H dehydrogenase (NDH) complex, the cytochrome b(6)f complex, ATP synthase and several isoforms of ferredoxin-NADP(+) oxidoreductase (FNR), and ferredoxin (Fd). Fluorescence spectroscopy allowed the detection of chlorophyll a in the cytochrome b(6)f complex. Here we characterize the electron transport pathway of chromorespiration by using specific inhibitors for the NDH complex, the cytochrome b(6)f complex, FNR and redox-inactive Fd in which the iron was replaced by gallium. Our data suggest an electron flow via two separate pathways, both reducing plastoquinone (PQ) and using PTOX as oxidase. The first oxidizes NADPH via FNR, Fd and cytochrome b(h) of the cytochrome b(6)f complex, and does not result in the pumping of protons across the membrane. In the second, electron transport takes place via the NDH complex using both NADH and NADPH as electron donor. FNR and Fd are not involved in this pathway. The NDH complex is responsible for the generation of the proton gradient. We propose a model for chromorespiration that may also be relevant for the understanding of chlororespiration and for the characterization of the electron input from Fd to the cytochrome b(6)f complex during cyclic electron transport in chloroplasts.Significance Statement Chromorespiration takes place via two pathways, one depends on FNR, ferredoxin, the cytochrome b6f complex, and the other depends on the NDH complex and is ferredoxin independent. We propose an electron transport via the cytochrome b6f complex that involves neither a Q-cycle nor a high potential electron transport chai

ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models

ModelCIF (github.com/ihmwg/ModelCIF) is a data information framework developed for and by computational structural biologists to enable delivery of Findable, Accessible, Interoperable, and Reusable (FAIR) data to users worldwide. ModelCIF describes the specific set of attributes and metadata associated with macromolecular structures modeled by solely computational methods and provides an extensible data representation for deposition, archiving, and public dissemination of predicted three-dimensional (3D) models of macromolecules. It is an extension of the Protein Data Bank Exchange / macromolecular Crystallographic Information Framework (PDBx/mmCIF), which is the global data standard for representing experimentally-determined 3D structures of macromolecules and associated metadata. The PDBx/mmCIF framework and its extensions (e.g., ModelCIF) are managed by the Worldwide Protein Data Bank partnership (wwPDB, wwpdb.org) in collaboration with relevant community stakeholders such as the wwPDB ModelCIF Working Group (wwpdb.org/task/modelcif). This semantically rich and extensible data framework for representing computed structure models (CSMs) accelerates the pace of scientific discovery. Herein, we describe the architecture, contents, and governance of ModelCIF, and tools and processes for maintaining and extending the data standard. Community tools and software libraries that support ModelCIF are also described

Lectin-like bacteriocins from pseudomonas spp. utilise D-rhamnose containing lipopolysaccharide as a cellular receptor

Lectin-like bacteriocins consist of tandem monocot mannose-binding domains and display a genus-specific killing activity. Here we show that pyocin L1, a novel member of this family from Pseudomonas aeruginosa, targets susceptible strains of this species through recognition of the common polysaccharide antigen (CPA) of P. aeruginosa lipopolysaccharide that is predominantly a homopolymer of d-rhamnose. Structural and biophysical analyses show that recognition of CPA occurs through the C-terminal carbohydrate-binding domain of pyocin L1 and that this interaction is a prerequisite for bactericidal activity. Further to this, we show that the previously described lectin-like bacteriocin putidacin L1 shows a similar carbohydrate-binding specificity, indicating that oligosaccharides containing d-rhamnose and not d-mannose, as was previously thought, are the physiologically relevant ligands for this group of bacteriocins. The widespread inclusion of d-rhamnose in the lipopolysaccharide of members of the genus Pseudomonas explains the unusual genus-specific activity of the lectin-like bacteriocins

Takotsubo cardiomyopathy after a dancing session: a case report

<p>Abstract</p> <p>Introduction</p> <p>Stress-induced (Takotsubo) cardiomyopathy is a rare form of cardiomyopathy which presents in a manner similar to that of acute coronary syndrome. This sometimes leads to unnecessary thrombolysis therapy. The pathogenesis of this disease is still poorly understood. We believe that reporting all cases of Takotsubo cardiomyopathy will contribute to a better understanding of this disease. Here, we report a patient who, in the absence of any recent stressful events in her life, developed the disease after a session of dancing.</p> <p>Case presentation</p> <p>A 69-year-old Caucasian woman presented with features suggestive of acute coronary syndrome shortly after a session of dancing. Echocardiography and a coronary angiogram showed typical features of Takotsubo cardiomyopathy and our patient was treated accordingly. Eight weeks later, her condition resolved completely and the results of echocardiography were totally normal.</p> <p>Conclusions</p> <p>Takotsubo cardiomyopathy, though transient, is a rare and serious condition. Although it is commonly precipitated by stressful life events, these are not necessarily present. Our patient was enjoying one of her hobbies (that is, dancing) when she developed the disease. This case has particular interest in medicine, especially for the specialties of cardiology and emergency medicine. We hope that it will add more information to the literature about this rare condition.</p

Dobutamine stress echocardiography for assessing the role of dynamic intraventricular obstruction in left ventricular ballooning syndrome

<p>Abstract</p> <p>Background</p> <p>Dynamic intraventricular obstruction has been observed in patients with left ventricular ballooning syndrome (LVBS) and has been hypothesized as a possible mechanism of the syndrome. The aim of this study was to assess the prevalence and significance of dynamic intraventricular obstruction in patients with LVBS.</p> <p>Methods and Results</p> <p>Dobutamine stress echocardiography was carried out in 22 patients with LVBS (82% apical), all women, aged 68 ± 9 years. At baseline 1 patient had a > 30 mmHg LV gradient; during stress a LV gradient > 30 mm Hg developed in 6/21 patients (28%) and was caused by systolic anterior motion of the mitral valve in the 3 patients with severe gradient (mean 116 ± 29 mmHg), who developed mitral regurgitation and impaired apical wall motion and by obstruction at mid-ventricular level in the other 3 with a moderate gradient (mean 46 ± 16 mmHg). Compared with patients without obstruction those with obstruction had a greater mean septal thickness (11.6 ± .6 vs 9.8. ± 3, p < .01), a higher prevalence of septal hypertrophy (71% vs 7%, p < .005) and a higher peak wall motion score index (1.62 ± .4 vs 1.08 ± .4, p < .01).</p> <p>Conclusion</p> <p>Spontaneous or dobutamine-induced dynamic LV obstruction is documented in 32% of patients with LVBS, is correlated with the presence of septal hypertrophy and may play a role in the development of LVBS in this subset of patients. In those without septal hypertrophy a dynamic obstruction is rarely induced with dobutamine and is unlikely to be a major pathogenetic factor of the syndrome.</p

Migration and actin protrusion in melanoma cells are regulated by EB1 protein

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Cancer Letters 284 (2009): 30-36, doi:10.1016/j.canlet.2009.04.007.Remodeling of actin and microtubule cytoskeletons is thought to be coupled; however, the interplay between these two systems is not fully understood. We show a microtubule end-binding protein, EB1, is required for formation of polarized morphology and motility of melanoma cells. EB1 depletion decreased lamellipodia protrusion, and resulted in loss of opposed protruding and retracting cell edges. Lamellipodia attenuation correlated with mis-localization of filopodia throughout the cell and decreased Arp3 localization. EB1-depleted cells displayed less persistent migration and reduced velocity in singlecell motility experiments. We propose EB1 coordinates melanoma cell migration through regulating the balance between lamellipodial and filopodial protrusion.This work was supported by American Heart Association grant 0525660Z (J.M.S.) and Southern Illinois University Edwardsville FUR grant