Journal Articles

Mutations driving CLL and their evolution in progression and relapse

Nature - Tue, 10/13/2015 - 23:00

Mutations driving CLL and their evolution in progression and relapse

Nature 526, 7574 (2015). doi:10.1038/nature15395

Authors: Dan A. Landau, Eugen Tausch, Amaro N. Taylor-Weiner, Chip Stewart, Johannes G. Reiter, Jasmin Bahlo, Sandra Kluth, Ivana Bozic, Mike Lawrence, Sebastian Böttcher, Scott L. Carter, Kristian Cibulskis, Daniel Mertens, Carrie L. Sougnez, Mara Rosenberg, Julian M. Hess, Jennifer Edelmann, Sabrina Kless, Michael Kneba, Matthias Ritgen, Anna Fink, Kirsten Fischer, Stacey Gabriel, Eric S. Lander, Martin A. Nowak, Hartmut Döhner, Michael Hallek, Donna Neuberg, Gad Getz, Stephan Stilgenbauer & Catherine J. Wu

Which genetic alterations drive tumorigenesis and how they evolve over the course of disease and therapy are central questions in cancer biology. Here we identify 44 recurrently mutated genes and 11 recurrent somatic copy number variations through whole-exome sequencing of 538 chronic lymphocytic leukaemia (CLL)

Categories: Journal Articles

The vulnerability of Indo-Pacific mangrove forests to sea-level rise

Nature - Tue, 10/13/2015 - 23:00

The vulnerability of Indo-Pacific mangrove forests to sea-level rise

Nature 526, 7574 (2015). doi:10.1038/nature15538

Authors: Catherine E. Lovelock, Donald R. Cahoon, Daniel A. Friess, Glenn R. Guntenspergen, Ken W. Krauss, Ruth Reef, Kerrylee Rogers, Megan L. Saunders, Frida Sidik, Andrew Swales, Neil Saintilan, Le Xuan Thuyen & Tran Triet

Sea-level rise can threaten the long-term sustainability of coastal communities and valuable ecosystems such as coral reefs, salt marshes and mangroves. Mangrove forests have the capacity to keep pace with sea-level rise and to avoid inundation through vertical accretion of sediments, which allows them to maintain wetland soil elevations suitable for plant growth. The Indo-Pacific region holds most of the world’s mangrove forests, but sediment delivery in this region is declining, owing to anthropogenic activities such as damming of rivers. This decline is of particular concern because the Indo-Pacific region is expected to have variable, but high, rates of future sea-level rise. Here we analyse recent trends in mangrove surface elevation changes across the Indo-Pacific region using data from a network of surface elevation table instruments. We find that sediment availability can enable mangrove forests to maintain rates of soil-surface elevation gain that match or exceed that of sea-level rise, but for 69 per cent of our study sites the current rate of sea-level rise exceeded the soil surface elevation gain. We also present a model based on our field data, which suggests that mangrove forests at sites with low tidal range and low sediment supply could be submerged as early as 2070.

Categories: Journal Articles

Biodiversity increases the resistance of ecosystem productivity to climate extremes

Nature - Tue, 10/13/2015 - 23:00

Biodiversity increases the resistance of ecosystem productivity to climate extremes

Nature 526, 7574 (2015). doi:10.1038/nature15374

Authors: Forest Isbell, Dylan Craven, John Connolly, Michel Loreau, Bernhard Schmid, Carl Beierkuhnlein, T. Martijn Bezemer, Catherine Bonin, Helge Bruelheide, Enrica de Luca, Anne Ebeling, John N. Griffin, Qinfeng Guo, Yann Hautier, Andy Hector, Anke Jentsch, Jürgen Kreyling, Vojtěch Lanta, Pete Manning, Sebastian T. Meyer, Akira S. Mori, Shahid Naeem, Pascal A. Niklaus, H. Wayne Polley, Peter B. Reich, Christiane Roscher, Eric W. Seabloom, Melinda D. Smith, Madhav P. Thakur, David Tilman, Benjamin F. Tracy, Wim H. van der Putten, Jasper van Ruijven, Alexandra Weigelt, Wolfgang W. Weisser, Brian Wilsey & Nico Eisenhauer

It remains unclear whether biodiversity buffers ecosystems against climate extremes, which are becoming increasingly frequent worldwide. Early results suggested that the ecosystem productivity of diverse grassland plant communities was more resistant, changing less during drought, and more resilient, recovering more quickly after drought, than that of depauperate communities. However, subsequent experimental tests produced mixed results. Here we use data from 46 experiments that manipulated grassland plant diversity to test whether biodiversity provides resistance during and resilience after climate events. We show that biodiversity increased ecosystem resistance for a broad range of climate events, including wet or dry, moderate or extreme, and brief or prolonged events. Across all studies and climate events, the productivity of low-diversity communities with one or two species changed by approximately 50% during climate events, whereas that of high-diversity communities with 16–32 species was more resistant, changing by only approximately 25%. By a year after each climate event, ecosystem productivity had often fully recovered, or overshot, normal levels of productivity in both high- and low-diversity communities, leading to no detectable dependence of ecosystem resilience on biodiversity. Our results suggest that biodiversity mainly stabilizes ecosystem productivity, and productivity-dependent ecosystem services, by increasing resistance to climate events. Anthropogenic environmental changes that drive biodiversity loss thus seem likely to decrease ecosystem stability, and restoration of biodiversity to increase it, mainly by changing the resistance of ecosystem productivity to climate events.

Categories: Journal Articles

RAF inhibitors that evade paradoxical MAPK pathway activation

Nature - Tue, 10/13/2015 - 23:00

RAF inhibitors that evade paradoxical MAPK pathway activation

Nature 526, 7574 (2015). doi:10.1038/nature14982

Authors: Chao Zhang, Wayne Spevak, Ying Zhang, Elizabeth A. Burton, Yan Ma, Gaston Habets, Jiazhong Zhang, Jack Lin, Todd Ewing, Bernice Matusow, Garson Tsang, Adhirai Marimuthu, Hanna Cho, Guoxian Wu, Weiru Wang, Daniel Fong, Hoa Nguyen, Songyuan Shi, Patrick Womack, Marika Nespi, Rafe Shellooe, Heidi Carias, Ben Powell, Emily Light, Laura Sanftner, Jason Walters, James Tsai, Brian L. West, Gary Visor, Hamid Rezaei, Paul S. Lin, Keith Nolop, Prabha N. Ibrahim, Peter Hirth & Gideon Bollag

Oncogenic activation of BRAF fuels cancer growth by constitutively promoting RAS-independent mitogen-activated protein kinase (MAPK) pathway signalling. Accordingly, RAF inhibitors have brought substantially improved personalized treatment of metastatic melanoma. However, these targeted agents have also revealed an unexpected consequence: stimulated growth of certain cancers. Structurally diverse ATP-competitive RAF inhibitors can either inhibit or paradoxically activate the MAPK pathway, depending whether activation is by BRAF mutation or by an upstream event, such as RAS mutation or receptor tyrosine kinase activation. Here we have identified next-generation RAF inhibitors (dubbed ‘paradox breakers’) that suppress mutant BRAF cells without activating the MAPK pathway in cells bearing upstream activation. In cells that express the same HRAS mutation prevalent in squamous tumours from patients treated with RAF inhibitors, the first-generation RAF inhibitor vemurafenib stimulated in vitro and in vivo growth and induced expression of MAPK pathway response genes; by contrast the paradox breakers PLX7904 and PLX8394 had no effect. Paradox breakers also overcame several known mechanisms of resistance to first-generation RAF inhibitors. Dissociating MAPK pathway inhibition from paradoxical activation might yield both improved safety and more durable efficacy than first-generation RAF inhibitors, a concept currently undergoing human clinical evaluation with PLX8394.

Categories: Journal Articles

A 2-Approximation Algorithm for Finding a Spanning Tree with Maximum Number of Leaves

Algorithmica - Mon, 10/12/2015 - 23:00
Abstract

We study the problem of finding a spanning tree with maximum number of leaves. We present a simple, linear time 2-approximation algorithm for this problem, improving on the previous best known algorithm for the problem, which has approximation ratio 3.

Categories: Journal Articles

Resilient Dynamic Programming

Algorithmica - Mon, 10/12/2015 - 23:00
Abstract

We investigate the design of dynamic programming algorithms in unreliable memories, i.e., in the presence of errors that lead the logical state of some bits to be read differently from how they were last written. Assuming that a limited number of memory faults can be inserted at run-time by an adversary with unbounded computational power, we obtain the first resilient algorithms for a broad range of dynamic programming problems, devising a general framework that can be applied to both iterative and recursive implementations. Besides all local dependency problems, where updates to table entries are determined by the contents of neighboring cells, we also settle challenging non-local problems, such as all-pairs shortest paths and matrix multiplication. All our algorithms are correct with high probability and match the running time of their standard non-resilient counterparts while tolerating a polynomial number of faults. The recursive algorithms are also cache-efficient and can tolerate faults at any level of the memory hierarchy. Our results exploit a careful combination of data replication, majority techniques, fingerprint computations, and lazy fault detection. To cope with the complex data access patterns induced by some of our algorithms, we also devise amplified fingerprints, which might be of independent interest in the design of resilient algorithms for different problems.

Categories: Journal Articles

An electron microscopy journey in the study of microtubule structure and dynamics

Protein Science - Sun, 10/11/2015 - 23:25
Eva Nogales is the winner of the 2015 Dorothy Crowfoot Hodgkin Award.Abstract

Structural characterization of microtubules has been the realm of three-dimensional electron microscopy and thus has evolved hand in hand with the progress of this technique, from the initial 3D reconstructions of stained tubulin assemblies, and the first atomic model of tubulin by electron crystallography of 2D sheets of protofilaments, to the ever more detailed cryoelectron microscopy structures of frozen-hydrated microtubules. Most recently, hybrid helical and single particle image processing techniques, and the latest detector technology, have lead to atomic models built directly into the density maps of microtubules in different functional states, shading new light into the critical process of microtubule dynamic instability.

Categories: Journal Articles

Crystal structure of the 500-kDa yeast acetyl-CoA carboxylase holoenzyme dimer

Nature - Sun, 10/11/2015 - 23:00

Crystal structure of the 500-kDa yeast acetyl-CoA carboxylase holoenzyme dimer

Nature 526, 7575 (2015). doi:10.1038/nature15375

Authors: Jia Wei & Liang Tong

Acetyl-CoA carboxylase (ACC) has crucial roles in fatty acid metabolism and is an attractive target for drug discovery against diabetes, cancer and other diseases. Saccharomyces cerevisiae ACC (ScACC) is crucial for the production of very-long-chain fatty acids and the maintenance of the nuclear envelope. ACC contains biotin carboxylase (BC) and carboxyltransferase (CT) activities, and its biotin is linked covalently to the biotin carboxyl carrier protein (BCCP). Most eukaryotic ACCs are 250-kilodalton (kDa), multi-domain enzymes and function as homodimers and higher oligomers. They contain a unique, 80-kDa central region that shares no homology with other proteins. Although the structures of the BC, CT and BCCP domains and other biotin-dependent carboxylase holoenzymes are known, there is currently no structural information on the ACC holoenzyme. Here we report the crystal structure of the full-length, 500-kDa holoenzyme dimer of ScACC. The structure is remarkably different from that of the other biotin-dependent carboxylases. The central region contains five domains and is important for positioning the BC and CT domains for catalysis. The structure unexpectedly reveals a dimer of the BC domain and extensive conformational differences compared to the structure of the BC domain alone, which is a monomer. These structural changes reveal why the BC domain alone is catalytically inactive and define the molecular mechanism for the inhibition of eukaryotic ACC by the natural product soraphen A and by phosphorylation of a Ser residue just before the BC domain core in mammalian ACC. The BC and CT active sites are separated by 80 Å, and the entire BCCP domain must translocate during catalysis.

Categories: Journal Articles

Observation of non-Hermitian degeneracies in a chaotic exciton-polariton billiard

Nature - Sun, 10/11/2015 - 23:00

Observation of non-Hermitian degeneracies in a chaotic exciton-polariton billiard

Nature 526, 7574 (2015). doi:10.1038/nature15522

Authors: T. Gao, E. Estrecho, K. Y. Bliokh, T. C. H. Liew, M. D. Fraser, S. Brodbeck, M. Kamp, C. Schneider, S. Höfling, Y. Yamamoto, F. Nori, Y. S. Kivshar, A. G. Truscott, R. G. Dall & E. A. Ostrovskaya

Exciton-polaritons are hybrid light–matter quasiparticles formed by strongly interacting photons and excitons (electron–hole pairs) in semiconductor microcavities. They have emerged as a robust solid-state platform for next-generation optoelectronic applications as well as for fundamental studies of quantum many-body physics. Importantly, exciton-polaritons are a profoundly open (that is, non-Hermitian) quantum system, which requires constant pumping of energy and continuously decays, releasing coherent radiation. Thus, the exciton-polaritons always exist in a balanced potential landscape of gain and loss. However, the inherent non-Hermitian nature of this potential has so far been largely ignored in exciton-polariton physics. Here we demonstrate that non-Hermiticity dramatically modifies the structure of modes and spectral degeneracies in exciton-polariton systems, and, therefore, will affect their quantum transport, localization and dynamical properties. Using a spatially structured optical pump, we create a chaotic exciton-polariton billiard—a two-dimensional area enclosed by a curved potential barrier. Eigenmodes of this billiard exhibit multiple non-Hermitian spectral degeneracies, known as exceptional points. Such points can cause remarkable wave phenomena, such as unidirectional transport, anomalous lasing/absorption and chiral modes. By varying parameters of the billiard, we observe crossing and anti-crossing of energy levels and reveal the non-trivial topological modal structure exclusive to non-Hermitian systems. We also observe mode switching and a topological Berry phase for a parameter loop encircling the exceptional point. Our findings pave the way to studies of non-Hermitian quantum dynamics of exciton-polaritons, which may uncover novel operating principles for polariton-based devices.

Categories: Journal Articles

Dynamic m6A mRNA methylation directs translational control of heat shock response

Nature - Sun, 10/11/2015 - 23:00

Dynamic m6A mRNA methylation directs translational control of heat shock response

Nature 526, 7574 (2015). doi:10.1038/nature15377

Authors: Jun Zhou, Ji Wan, Xiangwei Gao, Xingqian Zhang, Samie R. Jaffrey & Shu-Bing Qian

The most abundant mRNA post-transcriptional modification is N6-methyladenosine (m6A), which has broad roles in RNA biology. In mammalian cells, the asymmetric distribution of m6A along mRNAs results in relatively less methylation in the 5′ untranslated region (5′UTR) compared to other regions. However, whether and how 5′UTR methylation is regulated is poorly understood. Despite the crucial role of the 5′UTR in translation initiation, very little is known about whether m6A modification influences mRNA translation. Here we show that in response to heat shock stress, certain adenosines within the 5′UTR of newly transcribed mRNAs are preferentially methylated. We find that the dynamic 5′UTR methylation is a result of stress-induced nuclear localization of YTHDF2, a well-characterized m6A ‘reader’. Upon heat shock stress, the nuclear YTHDF2 preserves 5′UTR methylation of stress-induced transcripts by limiting the m6A ‘eraser’ FTO from demethylation. Remarkably, the increased 5′UTR methylation in the form of m6A promotes cap-independent translation initiation, providing a mechanism for selective mRNA translation under heat shock stress. Using Hsp70 mRNA as an example, we demonstrate that a single m6A modification site in the 5′UTR enables translation initiation independent of the 5′ end N7-methylguanosine cap. The elucidation of the dynamic features of 5′UTR methylation and its critical role in cap-independent translation not only expands the breadth of physiological roles of m6A, but also uncovers a previously unappreciated translational control mechanism in heat shock response.

Categories: Journal Articles

FEI’s direct electron detector developments: Embarking on a revolution in cryo-TEM

Journal of Structural Biology - Sun, 10/11/2015 - 00:04
Publication date: Available online 9 October 2015
Source:Journal of Structural Biology

Author(s): Maarten Kuijper, Gerald van Hoften, Bart Janssen, Rudolf Geurink, Sacha De Carlo, Matthijn Vos, Gijs van Duinen, Bart van Haeringen, Marc Storms

In early 2011 FEI Company launched the “Falcon”, its first commercial direct electron detector product intended for application in 3-D electron microscopy in the life sciences. In this paper we discuss the principle of direct electron detection and its implementation in Falcon cameras. We describe the signal formation in the sensor and its impact on the detection quantum efficiency (DQE) of the sensor. Insights into the signal formation led us to improved camera designs. Three significant improvements are discussed. (1) Back thinning of the sensor. This is implemented in the second-generation Falcon (Falcon 2), where the sensor thickness is reduced to 50μm, and in the latest generation Falcon 3 detector with further back-thinning down to 30μm. (2) The introduction of electron counting, a signal processing technology implemented in Falcon 3. (3) Dose fractionation mode, which allows the user to access intermediate results during the illumination of the sample.





Categories: Journal Articles

Simultaneous determination of sample thickness, tilt, and electron mean free path using tomographic tilt images based on Beer–Lambert law

Journal of Structural Biology - Sun, 10/11/2015 - 00:04
Publication date: Available online 9 October 2015
Source:Journal of Structural Biology

Author(s): Rui Yan, Thomas J. Edwards, Logan M. Pankratz, Richard J. Kuhn, Jason K. Lanman, Jun Liu, Wen Jiang

Cryo-electron tomography (cryo-ET) is an emerging technique that can elucidate the architecture of macromolecular complexes and cellular ultrastructure in a near-native state. Some important sample parameters, such as thickness and tilt, are needed for 3-D reconstruction. However, these parameters can currently only be determined using trial 3-D reconstructions. Accurate electron mean free path plays a significant role in modeling image formation process essential for simulation of electron microscopy images and model-based iterative 3-D reconstruction methods; however, their values are voltage and sample dependent and have only been experimentally measured for a limited number of sample conditions. Here, we report a computational method, tomoThickness, based on the Beer–Lambert law, to simultaneously determine the sample thickness, tilt and electron inelastic mean free path by solving an overdetermined nonlinear least square optimization problem utilizing the strong constraints of tilt relationships. The method has been extensively tested with both stained and cryo datasets. The fitted electron mean free paths are consistent with reported experimental measurements. The accurate thickness estimation eliminates the need for a generous assignment of Z-dimension size of the tomogram. Interestingly, we have also found that nearly all samples are a few degrees tilted relative to the electron beam. Compensation of the intrinsic sample tilt can result in horizontal structure and reduced Z-dimension of tomograms. Our fast, pre-reconstruction method can thus provide important sample parameters that can help improve performance of tomographic reconstruction of a wide range of samples.





Categories: Journal Articles

A fast cross-validation method for alignment of electron tomography images based on Beer–Lambert law

Journal of Structural Biology - Sun, 10/11/2015 - 00:04
Publication date: Available online 9 October 2015
Source:Journal of Structural Biology

Author(s): Rui Yan, Thomas J. Edwards, Logan M. Pankratz, Richard J. Kuhn, Jason K. Lanman, Jun Liu, Wen Jiang

In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer–Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography.





Categories: Journal Articles

Automated batch fiducial-less tilt-series alignment in Appion using Protomo

Journal of Structural Biology - Sun, 10/11/2015 - 00:04
Publication date: Available online 9 October 2015
Source:Journal of Structural Biology

Author(s): Alex J. Noble, Scott M. Stagg

The field of electron tomography has benefited greatly from manual and semi-automated approaches to marker-based tilt-series alignment that have allowed for the structural determination of multitudes of in situ cellular structures as well as macromolecular structures of individual protein complexes. The emergence of complementary metal-oxide semiconductor detectors capable of detecting individual electrons has enabled the collection of low dose, high contrast images, opening the door for reliable correlation-based tilt-series alignment. Here we present a set of automated, correlation-based tilt-series alignment, contrast transfer function (CTF) correction, and reconstruction workflows for use in conjunction with the Appion/Leginon package that are primarily targeted at automating structure determination with cryogenic electron microscopy.





Categories: Journal Articles

Mineral-bearing vesicle transport in sea urchin embryos

Journal of Structural Biology - Sun, 10/11/2015 - 00:04
Publication date: Available online 9 October 2015
Source:Journal of Structural Biology

Author(s): Netta Vidavsky, Admir Masic, Andreas Schertel, Steve Weiner, Lia Addadi

Sea urchin embryos sequester calcium from the sea water. This calcium is deposited in a concentrated form in granule bearing vesicles both in the epithelium and in mesenchymal cells. Here we use in vivo calcein labeling and confocal Raman spectroscopy, as well as cryo-FIB-SEM 3D structural reconstructions, to investigate the processes occurring in the internal cavity of the embryo, the blastocoel. We demonstrate that calcein stained granules are also present in the filopodial network within the blastocoel. Simultaneous fluorescence imaging and Raman spectroscopy show that these granules do contain a calcium mineral. By tracking the movements of these granules, we show that the granules in the epithelium and primary mesenchymal cells barely move, but those in the filopodial network move long distances. We could however not detect any unidirectional movement of the filopodial granules. We also show the presence of mineral containing multivesicular vesicles that also move in the filopodial network. We conclude that the filopodial network is an integral part of the mineral transport process, and possibly also for sequestering calcium and other ions. Although much of the sequestered calcium is deposited in the mineralized skeleton, a significant amount is used for other purposes, and this may be temporarily stored in these membrane-delineated intracellular deposits.





Categories: Journal Articles

Reassessment of MxiH subunit orientation and fold within native Shigella T3SS needles using surface labelling and solid-state NMR

Journal of Structural Biology - Sun, 10/11/2015 - 00:04
Publication date: Available online 6 October 2015
Source:Journal of Structural Biology

Author(s): Joeri Verasdonck, Da-Kang Shen, Alexander Treadgold, Christopher Arthur, Anja Böckmann, Beat H. Meier, Ariel J. Blocker

T3SSs are essential virulence determinants of many Gram-negative bacteria, used to inject bacterial effectors of virulence into eukaryotic host cells. Their major extracellular portion, a ∼50nm hollow, needle-like structure, is essential to host cell sensing and the conduit for effector secretion. It is formed of a small, conserved subunit arranged as a helical polymer. The structure of the subunit has been studied by electron cryomicroscopy within native polymers and by solid-state NMR in recombinant polymers, yielding two incompatible atomic models. To resolve this controversy, we re-examined the native polymer used for electron cryomicroscopy via surface labelling and solid-state NMR. Our data show the orientation and overall fold of the subunit within this polymer is as established by solid-state NMR for recombinant polymers.





Categories: Journal Articles

Analysis of distinct molecular assembly complexes of keratin K8 and K18 by hydrogen–deuterium exchange

Journal of Structural Biology - Sun, 10/11/2015 - 00:04
Publication date: Available online 3 October 2015
Source:Journal of Structural Biology

Author(s): Aiswarya Premchandar, Anna Kupniewska, Krzysztof Tarnowski, Norbert Mücke, Monika Mauermann, Magdalena Kaus-Drobek, Aleksander Edelman, Harald Herrmann, Michał Dadlez

Keratins are intermediate filament (IF) proteins that form complex filament systems in epithelial cells, thus serving as scaffolding elements and mechanical stress absorbers. The building blocks of keratin IFs are parallel coiled-coil dimers of two distinct sequence-related proteins distinguished as type I and type II keratins. To gain more insight into their structural dynamics, we resorted to hydrogen–deuterium exchange mass spectrometry of keratins K8 and K18, which are characteristic for simple epithelial cells. Using this powerful technique not employed with IFs before, we mapped patterns of protected versus unprotected regions in keratin complexes at various assembly levels. In particular, we localized protein segments exhibiting different hydrogen exchange patterns in tetramers versus filaments. We observed a general pattern of precisely positioned regions of stability intertwining with flexible regions, mostly represented by the non-α-helical segments. Notably, some regions within the coiled-coil domains are significantly more dynamic than others, while the IF-consensus motifs at the end domains of the central α-helical “rod” segment, which mediate the “head-to-tail” dimer–dimer interaction in the filament elongation process, become distinctly more protected upon formation of filaments. Moreover, to gain more insight into the dynamics of the individual keratins, we investigated the properties of homomeric preparations of K8 and K18. The physiological importance of keratins without a partner is encountered in both pathological and experimental situations when one of the two species is present in robust excess or completely absent, such as in gene-targeted mice.





Categories: Journal Articles

Structural and biochemical insights into the DNA-binding mode of MjSpt4p:Spt5 complex at the exit tunnel of RNAPII

Journal of Structural Biology - Sun, 10/11/2015 - 00:04
Publication date: Available online 2 October 2015
Source:Journal of Structural Biology

Author(s): Gongrui Guo, Yongxiang Gao, Zhongliang Zhu, Debiao Zhao, Zhihong Liu, Huihao Zhou, Liwen Niu, Maikun Teng

Spt5 (NusG in bacteria) is the only RNA polymerase-associated factor known to be conserved in all three domains of life. In archaea and eukaryotes, Spt5 associates with Spt4, an elongation factor that is absent in bacteria, to form a functional heterodimeric complex. Previous studies suggest that the Spt4:Spt5 complex interacts directly with DNA at the double-stranded DNA exit tunnel of RNA polymerase to regulate gene transcription. In this study, the DNA-binding ability of Spt4:Spt5 from the archaeon Methanocaldococcus jannaschii was confirmed via nuclear magnetic resonance chemical shift perturbation and fluorescence polarization assays. Crystallographic analysis of the full-length MjSpt4:Spt5 revealed two distinct conformations of the C-terminal KOW domain of Spt5. A similar alkaline region was found on the Spt4:Spt5 surface in both crystal forms, and identified as double-stranded DNA binding patch through mutagenesis-fluorescence polarization assays. Based on these structural and biochemical data, the Spt4:Spt5-DNA binding model was built for the first time.





Categories: Journal Articles

The giant keyhole limpet radular teeth: a naturally-grown harvest machine

Journal of Structural Biology - Sun, 10/11/2015 - 00:04
Publication date: Available online 2 October 2015
Source:Journal of Structural Biology

Author(s): Tina Ukmar-Godec, Gregor Kapun, Paul Zaslansky, Damien Faivre

The limpet radula is a feeding organ, which contains more than 100 rows of teeth. During their growth the teeth mature and advance in position along the radula. The simpler doccoglossan radulae operate by grinding rocky substrates, extracting the algae by rasping and scraping with the teeth functioning as shovels. Less is known about the rhipidoglossan radulae, used as rakes or brooms that brush and collect loose marine debris. This type of radula is found in the giant keyhole limpet (Megathura crenulata). The large size of this organism suggests that the rhipidoglossan radula entails a technological superiority for Megathura crenulata in its habitat. The structure and function of the radulae teeth have however not been reported in detail. Using a combination of 2D and 3D microscopy techniques coupled with amino acid analysis and X-ray scattering, we reveal the working components of Megathura crenulata’s radula. It is characterized by numerous marginal teeth surrounding a pair of major hook-like lateral teeth, two pairs of minor lateral teeth and a large central tooth. The mature major lateral teeth show pronounced signs of wear, which gradually increase towards the very front end of the radula and are evidence for scraping. An abrupt change in the amino acid composition in the major lateral teeth and the concurrent formation of a chitinous fiber-network mark the onset of tooth maturation. In comparison to the simpler rock-scraping doccoglossate limpets, the radula of Megathura crenulata forms an elaborate feeding apparatus, which can be seen as a natural harvest machine.





Categories: Journal Articles

Molecular events during the early stages of aggregation of GNNQQNY: An all atom MD simulation study of randomly dispersed peptides

Journal of Structural Biology - Sun, 10/11/2015 - 00:04
Publication date: Available online 2 October 2015
Source:Journal of Structural Biology

Author(s): Alka Srivastava, Petety V. Balaji

This study probes the early events during lag phase of aggregation of GNNQQNY using all atom MD simulations in explicit solvent. Simulations were performed by varying system size, temperature and starting configuration. Peptides dispersed randomly in the simulation box come together early on in the simulation and form aggregates. These aggregates are dynamic implying the absence of stabilizing interactions. This facilitates the exploration of alternate arrangements. The constituent peptides sample a variety of conformations, frequently re-orient and re-arrange with respect to each other and dissociate from/re-associate with the aggregate. The size and lifetime of aggregates vary depending upon the number of inter-peptide backbone H-bonds. Most of the aggregates formed are amorphous but crystalline aggregates of smaller size (mainly 2-mers) do appear and sustain for varying durations of time. The peptides in crystalline 2-mers are mostly anti-parallel. The largest crystalline aggregate that appears is a 4-mer in a single sheet and a 4-, 5-, or 6-mer in double layered arrangement. Crystalline aggregates grow either by the sequential addition of peptides, or by the head-on or lateral collision-adhesion of 2-mers. The formation of various smaller aggregates suggests the polymorphic nature of oligomers and heterogeneity in the lag phase.





Categories: Journal Articles
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