A estrutura líquida da elastina: mero acaso, fortuita necessidade ou design inteligente?

sábado, janeiro 13, 2018

The liquid structure of elastin

Sarah Rauscher, Régis Pomès

The Hospital for Sick Children, Canada University of Toronto, Canada

RESEARCH ARTICLE Nov 9, 2017

Peptide hydration in the liquid-like aggregate.

Abstract

The protein elastin imparts extensibility, elastic recoil, and resilience to tissues including arterial walls, skin, lung alveoli, and the uterus. Elastin and elastin-like peptides are hydrophobic, disordered, and undergo liquid-liquid phase separation upon self-assembly. Despite extensive study, the structure of elastin remains controversial. We use molecular dynamics simulations on a massive scale to elucidate the structural ensemble of aggregated elastin-like peptides. Consistent with the entropic nature of elastic recoil, the aggregated state is stabilized by the hydrophobic effect. However, self-assembly does not entail formation of a hydrophobic core. The polypeptide backbone forms transient, sparse hydrogen-bonded turns and remains significantly hydrated even as self-assembly triples the extent of non-polar side chain contacts. Individual chains in the assembly approach a maximally-disordered, melt-like state which may be called the liquid state of proteins. These findings resolve long-standing controversies regarding elastin structure and function and afford insight into the phase separation of disordered proteins.

https://doi.org/10.7554/eLife.26526.001

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A mobilidade da cinesina é conduzida por dinâmicas de sub regiões: mero acaso, fortuita necessidade ou design inteligente?

Kinesin motility is driven by subdomain dynamics

Wonmuk Hwang, Matthew J Lang, Martin Karplus

Texas A&M University, United States Korea Institute for Advanced Study, Korea Vanderbilt University, United States Vanderbilt University School of Medicine, United States Harvard University, United States ISIS, Université de Strasbourg, France

RESEARCH ARTICLE Nov 7, 2017

Motility of a Kin-1 dimer driven by subdomain dynamics.

Abstract

The microtubule (MT)-associated motor protein kinesin utilizes its conserved ATPase head to achieve diverse motility characteristics. Despite considerable knowledge about how its ATPase activity and MT binding are coupled to the motility cycle, the atomic mechanism of the core events remain to be found. To obtain insights into the mechanism, we performed 38.5 microseconds of all-atom molecular dynamics simulations of kinesin-MT complexes in different nucleotide states. Local subdomain dynamics were found to be essential for nucleotide processing. Catalytic water molecules are dynamically organized by the switch domains of the nucleotide binding pocket while ATP is torsionally strained. Hydrolysis products are 'pulled' by switch-I, and a new ATP is 'captured' by a concerted motion of the α0/L5/switch-I trio. The dynamic and wet kinesin-MT interface is tuned for rapid interactions while maintaining specificity. The proposed mechanism provides the flexibility necessary for walking in the crowded cellular environment.

https://doi.org/10.7554/eLife.28948.001

eLife digest

Motor proteins called kinesins perform a number of different roles inside cells, including transporting cargo and organizing filaments called microtubules to generate the force needed for a cell to divide. Kinesins move along the microtubules, with different kinesins moving in different ways: some ‘walk’, some jump, and some destroy the microtubule as they travel along it. All kinesins power their movements using the same molecule as fuel – adenosine triphosphate, known as ATP for short.

Energy stored in ATP is released by a chemical reaction known as hydrolysis, which uses water to break off specific parts of the ATP molecule. The site to which ATP binds in a kinesin has a similar structure to the ATP binding site of many other proteins that use ATP. However, little was known about the way in which kinesin uses ATP as a fuel, including how ATP binds to kinesin and is hydrolyzed, and how the products of hydrolysis are released. These events are used to power the motor protein.

Hwang et al. have used powerful computer simulation methods to examine in detail how ATP interacts with kinesin whilst moving across a microtubule. The simulations suggest that regions (or 'domains') of kinesin near the ATP binding site move around to help in processing ATP. These kinesin domains trap a nearby ATP molecule from the environment and help to deliver water molecules to ATP for hydrolysis. Hwang et al. also found that the domain motion subsequently helps in the release of the hydrolysis products by kinesin.

The domains around the ATP pocket vary among the kinesins and these differences may enable kinesins to fine-tune how they use ATP to move. Further investigations will help us understand why different kinesin families behave differently. They will also contribute to exploring how kinesin inhibitors might be used as anti-cancer drugs.

https://doi.org/10.7554/eLife.28948.002

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Redução de genoma, novidade fisiológica, e a dominância global das plantas com flores

sexta-feira, janeiro 12, 2018

Genome downsizing, physiological novelty, and the global dominance of flowering plants

Kevin A. Simonin , Adam B. Roddy 

Published: January 11, 2018https://doi.org/10.1371/journal.pbio.2003706

Source/Font: Casa de Sobra

Abstract

The abrupt origin and rapid diversification of the flowering plants during the Cretaceous has long been considered an “abominable mystery.” While the cause of their high diversity has been attributed largely to coevolution with pollinators and herbivores, their ability to outcompete the previously dominant ferns and gymnosperms has been the subject of many hypotheses. Common among these is that the angiosperms alone developed leaves with smaller, more numerous stomata and more highly branching venation networks that enable higher rates of transpiration, photosynthesis, and growth. Yet, how angiosperms pack their leaves with smaller, more abundant stomata and more veins is unknown but linked—we show—to simple biophysical constraints on cell size. Only angiosperm lineages underwent rapid genome downsizing during the early Cretaceous period, which facilitated the reductions in cell size necessary to pack more veins and stomata into their leaves, effectively bringing actual primary productivity closer to its maximum potential. Thus, the angiosperms' heightened competitive abilities are due in no small part to genome downsizing.

Author summary

The angiosperms, commonly referred to as the flowering plants, are the dominant plants in most terrestrial ecosystems, but how they came to be so successful is considered one of the most profound mysteries in evolutionary biology. Prevailing hypotheses have suggested that the angiosperms rose to dominance through an increase in their maximum potential photosynthesis and whole-plant carbon gain, allowing them to outcompete the ferns and gymnosperms that had previously dominated terrestrial ecosystems. Using a combination of anatomy, cytology, and modelling of liquid water transport and CO2 exchange between leaves and the atmosphere, we now provide strong evidence that the success and rapid spread of flowering plants around the world was the result of genome downsizing. Smaller genomes permit the construction of smaller cells that allow for greater CO2 uptake and photosynthetic carbon gain. Genome downsizing occurred only among the angiosperms, and we propose that it was a necessary prerequisite for rapid growth rates among land plants.

Citation: Simonin KA, Roddy AB (2018) Genome downsizing, physiological novelty, and the global dominance of flowering plants. PLoS Biol 16(1): e2003706. https://doi.org/10.1371/journal.pbio.2003706

Academic Editor: Andrew Tanentzap, University of Cambridge, United Kingdom of Great Britain and Northern Ireland

Received: July 13, 2017; Accepted: December 8, 2017; Published: January 11, 2018

Copyright: © 2018 Simonin, Roddy. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All relevant data are within the paper and its Supporting Information files.

Funding: The authors received no specific funding for this work.

Competing interests: The authors have declared that no competing interests exist.

Abbreviations: AIC, Akaike Information Criterion; ci, leaf intercellular CO2 concentrations; Ds, stomatal density; Dv, leaf vein density; gs, max, maximum stomatal conductance; gs, op, operational stomatal conductance; lg, guard cell length; W, guard cell width

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Quem disse que água e óleo não se misturam, seu hidrofóbico!

quinta-feira, janeiro 11, 2018

Creating nanoscale emulsions using condensation

Ingrid F. Guha, Sushant Anand & Kripa K. Varanasi

Nature Communications 8, Article number: 1371 (2017)


Download Citation

Chemical engineering Fluids Microfluidics

Received: 04 May 2017 Accepted: 12 September 2017

Published online: 08 November 2017


Abstract

Nanoscale emulsions are essential components in numerous products, ranging from processed foods to novel drug delivery systems. Existing emulsification methods rely either on the breakup of larger droplets or solvent exchange/inversion. Here we report a simple, scalable method of creating nanoscale water-in-oil emulsions by condensing water vapor onto a subcooled oil-surfactant solution. Our technique enables a bottom-up approach to forming small-scale emulsions. Nanoscale water droplets nucleate at the oil/air interface and spontaneously disperse within the oil, due to the spreading dynamics of oil on water. Oil-soluble surfactants stabilize the resulting emulsions. We find that the oil-surfactant concentration controls the spreading behavior of oil on water, as well as the peak size, polydispersity, and stability of the resulting emulsions. Using condensation, we form emulsions with peak radii around 100 nm and polydispersities around 10%. This emulsion formation technique may open different routes to creating emulsions, colloidal systems, and emulsion-based materials.

Acknowledgements

We thank the MIT Energy Initiative for financial support. I.F.G. is grateful for support from the NSF Graduate Research Fellowship Program. S.A. thanks the Society in Science—Branco Weiss Fellowship for financial support. The Biophysical Instrumentation Facility for the Study of Complex Macromolecular Systems (NSF-0070319) is gratefully acknowledged. We thank Dr. Arindam Das for his help with fabricating the sample container and Mr. Hassan Bararnia for assistance with DLS measurements (Supplementary Figs. 5, 6).

Author information

Author notes

Ingrid F. Guha and Sushant Anand contributed equally to this work.

Affiliations

Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA

Ingrid F. Guha

Department of Mechanical & Industrial Engineering, University of Illinois at Chicago, Chicago, IL, 60607, USA

Sushant Anand

Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA

Sushant Anand & Kripa K. Varanasi

Contributions

K.K.V and S.A. conceived the research; S.A., I.F.G., and K.K.V designed the research; I.F.G. and S.A. conducted the research; I.F.G., S.A., and K.K.V. prepared the manuscript.

Competing interests
The authors declare no competing financial interests.

Corresponding authors
Correspondence to Sushant Anand or Kripa K. Varanasi.

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Nature Communications Sup. Info. 1 Additional Sup. Info. Movie 1 Movie 2

A crença em Deus não está ligada à intuição ou pensamento racional?

Supernatural Belief Is Not Modulated by Intuitive Thinking Style or Cognitive Inhibition

Miguel Farias, Valerie van Mulukom, Guy Kahane, Ute Kreplin, Anna Joyce, Pedro Soares, Lluis Oviedo, Mathilde Hernu, Karolina Rokita, Julian Savulescu & Riikka Möttönen

Scientific Reports 7, Article number: 15100 (2017)


Download Citation

Cognitive controlHuman behaviour

Received: 24 April 2017 Accepted: 29 September 2017

Published online: 08 November 2017


Abstract

According to the Intuitive Belief Hypothesis, supernatural belief relies heavily on intuitive thinking—and decreases when analytic thinking is engaged. After pointing out various limitations in prior attempts to support this Intuitive Belief Hypothesis, we test it across three new studies using a variety of paradigms, ranging from a pilgrimage field study to a neurostimulation experiment. In all three studies, we found no relationship between intuitive or analytical thinking and supernatural belief. We conclude that it is premature to explain belief in gods as ‘intuitive’, and that other factors, such as socio-cultural upbringing, are likely to play a greater role in the emergence and maintenance of supernatural belief than cognitive style.

Acknowledgements

Supported by awards from the BIAL Foundation (62/06 and 380/14) to M.F., U.K., the John Templeton Foundation (57676) to M.F., R.M., G.K., J.S., and the Medical Research Council, UK (G1000566) to R.M. We thank Sangeetha Santhanam for her assistance with data collection for study 2.

Author information

Affiliations

Brain, Belief, & Behaviour Lab, Centre for Advances in Behavioural Science, Coventry University, Coventry, UK

Miguel Farias, Valerie van Mulukom & Anna Joyce
Philosophy Faculty, University of Oxford, Oxford, UK

Guy Kahane & Julian Savulescu
Department of Psychology, Massey University, Palmerston, New Zealand

Ute Kreplin
Faculty of Social and Human Sciences, Universidade Nova de Lisboa, Lisbon, Portugal

Pedro Soares
Pontificia Universita Antonianum, Rome, Italy

Lluis Oviedo
Institute of Cognitive and Culture, Queen’s University, Belfast, Ireland

Mathilde Hernu
National University of Ireland, Galway, Ireland

Karolina Rokita
Department of Experimental Psychology, University of Oxford, Oxford, UK

Riikka Möttönen
School of Psychology, The University of Nottingham, Nottingham, UK

Contributions

M.F., R.M., and G.K. designed overall research. M.F., V.M., R.M., G.K., and J.S. wrote the first draft. Study 1: M.F. designed research; M.F., P.S., and L.O. performed research; M.F. and V.M. analysed data and wrote it up. Study 2: M.F. and R.M. designed and performed research; M.F. and V.M. analysed data and wrote it up. Study 3: M.F., R.M., and G.K. designed research; U.K., A.J., K.R., and M.H. performed research. V.M., U.K., A.J., R.M. and M.F. analysed data and wrote it up.

Competing Interests

The authors declare that they have no competing interests.

Corresponding author

Correspondence to Miguel Farias.

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Evolução do torque maior em motores flagelares bacterianos tipo Campylobacter: mero acaso, fortuita necessidade ou design inteligente?

quarta-feira, janeiro 10, 2018

Evolution of higher torque in Campylobacter-type bacterial flagellar motors

Bonnie Chaban, Izaak Coleman & Morgan Beeby

Scientific Reports 8, Article number: 97 (2018)


Download Citation

Bacterial evolution Cryoelectron tomography Molecular evolution

Received: 13 October 2017 Accepted: 05 December 2017

Published online: 08 January 2018

3-D model images of the eight studied bacterial motors. 
Source/Fonte: Morgan Beeby/Imperial College London

Abstract

Understanding the evolution of molecular machines underpins our understanding of the development of life on earth. A well-studied case are bacterial flagellar motors that spin helical propellers for bacterial motility. Diverse motors produce different torques, but how this diversity evolved remains unknown. To gain insights into evolution of the high-torque ε-proteobacterial motor exemplified by the Campylobacter jejuni motor, we inferred ancestral states by combining phylogenetics, electron cryotomography, and motility assays to characterize motors from Wolinella succinogenes, Arcobacter butzleri and Bdellovibrio bacteriovorus. Observation of ~12 stator complexes in many proteobacteria, yet ~17 in ε-proteobacteria suggest a “quantum leap” evolutionary event. Campylobacter-type motors have high stator occupancy in wider rings of additional stator complexes that are scaffolded by large proteinaceous periplasmic rings. We propose a model for motor evolution wherein independent inner- and outer-membrane structures fused to form a scaffold for additional stator complexes. Significantly, inner- and outer-membrane associated structures have evolved independently multiple times, suggesting that evolution of such structures is facile and poised the ε-proteobacteria to fuse them to form the high-torque Campylobacter-type motor.

Acknowledgements

The authors gratefully thank Tillmann Pape for electron microscopy assistance, Liz Sockett from the University of Nottingham for the gift of Bdellovibrio bacteriovorus, Erin Gaynor from the University of British Columbia for the gift of the straight Campylobacter mutant strain, and Bertus Beaumont, Josie Ferreira, and Florian Rossmann for critical reading of the manuscript. This work was supported by a Biotechnology and Biological Sciences Research Council Grant BB/L023091/1 (to M.B.).

Author information

Author notes

Bonnie Chaban

Present address: Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, 4556, QLD, Australia

Affiliations

Department of Life Sciences, Imperial College of London, London, SW7 2AZ, UK

Bonnie Chaban, Izaak Coleman & Morgan Beeby

Contributions

B.C. and I.C. performed phylogenetic analysis, B.C. collected tomographic and motility data, B.C., I.C. and M.B. analysed data. B.C. and M.B. wrote the main manuscript text and prepared figures. All authors reviewed the manuscript.

Competing Interests

The authors declare that they have no competing interests.

Corresponding author

Correspondence to Morgan Beeby.

Descoberta nova receita plausível para a origem da vida primeva na Terra

terça-feira, janeiro 09, 2018

Linked cycles of oxidative decarboxylation of glyoxylate as protometabolic analogs of the citric acid cycle

Greg Springsteen, Jayasudhan Reddy Yerabolu, Julia Nelson, Chandler Joel Rhea & Ramanarayanan Krishnamurthy

Nature Communications 9, Article number: 91 (2018)


Download Citation

Metabolic pathwaysOrganic chemistryChemical origin of lifeReaction mechanisms

Received: 23 August 2017 Accepted: 08 December 2017

Published online: 08 January 2018


Abstract

The development of metabolic approaches towards understanding the origins of life, which have focused mainly on the citric acid (TCA) cycle, have languished—primarily due to a lack of experimentally demonstrable and sustainable cycle(s) of reactions. We show here the existence of a protometabolic analog of the TCA involving two linked cycles, which convert glyoxylate into CO2 and produce aspartic acid in the presence of ammonia. The reactions proceed from either pyruvate, oxaloacetate or malonate in the presence of glyoxylate as the carbon source and hydrogen peroxide as the oxidant under neutral aqueous conditions and at mild temperatures. The reaction pathway demonstrates turnover under controlled conditions. These results indicate that simpler versions of metabolic cycles could have emerged under potential prebiotic conditions, laying the foundation for the appearance of more sophisticated metabolic pathways once control by (polymeric) catalysts became available.

Darwin, quem diria: a metafísica da evolução

segunda-feira, janeiro 08, 2018

Interface Focus. 2017 Oct 6; 7(5): 20160148.

Published online 2017 Aug 18. doi: 10.1098/rsfs.2016.0148 ReadCube 

PMCID: PMC5566809

The metaphysics of evolution

John Dupré

Egenis, University of Exeter, Exeter, UK

e-mail: ku.ca.retexe@erpud.a.j


Source/Fonte: New Scientist

ABSTRACT

This paper briefly describes process metaphysics, and argues that it is better suited for describing life than the more standard thing, or substance, metaphysics. It then explores the implications of process metaphysics for conceptualizing evolution. After explaining what it is for an organism to be a process, the paper takes up the Hull/Ghiselin thesis of species as individuals and explores the conditions under which a species or lineage could constitute an individual process. It is argued that only sexual species satisfy these conditions, and that within sexual species the degree of organization varies. This, in turn, has important implications for species' evolvability. One important moral is that evolution will work differently in different biological domains.

Keywords: process ontology, evolution, species, lineage, individual

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As redes de RNA nas origens da vida

sexta-feira, janeiro 05, 2018

RNA networks at the origins of life

Jessica A.M. Yeates and Niles Lehman (Portland State University, USA)


The origin of life has often been viewed as the advent of a single self-replicating molecular species, such as RNA. We propose a somewhat different approach in that a network of co-operating molecules could have kick-started life. This view has both theoretical and experimental support. The foundations for life, as we understand it on our planet, began some 4.5 billion years ago with the formation of the Earth 1 and by 4.0 billion years ago evidence for the presence of life existed. Within that timeframe, physical and chemical processes would have produced increasingly more complex interactions, moving from simple inorganic molecules to biopolymers capable of replication and variation. In order to answer the question of how life originated and to even understand what life is, empirical proof-ofconcept simple abiotic pathways demonstrating these transitions are needed. In this article, we discuss how networks of molecules, rather than single replicating molecular species, is an emerging view that may unlock some longstanding problems in the origins field. 

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A vida sem água

Life without water

Kazuharu Arakawa and Mark Blaxter

(Keio University, Japan and University of Edinburgh, UK)

Tardigrade - Source/Fonte: Extreme Marine Org.

From space our planet is blue, and life here has evolved in the presence of abundant water. However, on land, water remains one of life’s major challenges. Fully two-fifths of the land surface is classified as arid: the hot and cold deserts, where water is largely unavailable. Even in biomes where water availability is generally good, seasonal, daily and sporadic conditions can mean that life has to be able to survive its absence. Surprisingly, some organisms are able to survive complete loss of all their body water, to undergo anhydrobiosis. This surprising ability has evolved many times, and is particularly prevalent in very small animals. The biochemistry of anhydrobiosis challenges ideas of what ‘being alive’ really means and promises exciting biotechnological applications.
....

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