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Find video protocols related to scientific articles indexed in Pubmed.
Connection between the packing efficiency of binary hard spheres and the glass-forming ability of bulk metallic glasses.
Phys Rev E Stat Nonlin Soft Matter Phys
PUBLISHED: 09-29-2014
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We perform molecular dynamics simulations to compress binary hard spheres into jammed packings as a function of the compression rate R, size ratio ?, and number fraction x_{S} of small particles to determine the connection between the glass-forming ability (GFA) and packing efficiency in bulk metallic glasses (BMGs). We define the GFA by measuring the critical compression rate R_{c}, below which jammed hard-sphere packings begin to form "random crystal" structures with defects. We find that for systems with ??0.8 that do not demix, R_{c} decreases strongly with ??_{J}, as R_{c}?exp(-1/??_{J}^{2}), where ??_{J} is the difference between the average packing fraction of the amorphous packings and random crystal structures at R_{c}. Systems with ??0.8 partially demix, which promotes crystallization, but we still find a strong correlation between R_{c} and ??_{J}. We show that known metal-metal BMGs occur in the regions of the ? and x_{S} parameter space with the lowest values of R_{c} for binary hard spheres. Our results emphasize that maximizing GFA in binary systems involves two competing effects: minimizing ? to increase packing efficiency, while maximizing ? to prevent demixing.
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Computational studies of the glass-forming ability of model bulk metallic glasses.
J Chem Phys
PUBLISHED: 10-05-2013
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Bulk metallic glasses (BMGs) are produced by rapidly thermally quenching supercooled liquid metal alloys below the glass transition temperature at rates much faster than the critical cooling rate R(c) below which crystallization occurs. The glass-forming ability of BMGs increases with decreasing R(c), and thus good glass-formers possess small values of R(c). We perform molecular dynamics simulations of binary Lennard-Jones (LJ) mixtures to quantify how key parameters, such as the stoichiometry, particle size difference, attraction strength, and heat of mixing, influence the glass-formability of model BMGs. For binary LJ mixtures, we find that the best glass-forming mixtures possess atomic size ratios (small to large) less than 0.92 and stoichiometries near 50:50 by number. In addition, weaker attractive interactions between the smaller atoms facilitate glass formation, whereas negative heats of mixing (in the experimentally relevant regime) do not change R(c) significantly. These results are tempered by the fact that the slowest cooling rates achieved in our simulations correspond to ~10(11) K/s, which is several orders of magnitude higher than R(c) for typical BMGs. Despite this, our studies represent a first step in the development of computational methods for quantitatively predicting glass-formability.
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A general framework of persistence strategies for biological systems helps explain domains of life.
Front Genet
PUBLISHED: 01-28-2013
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The nature and cause of the division of organisms in superkingdoms is not fully understood. Assuming that environment shapes physiology, here we construct a novel theoretical framework that helps identify general patterns of organism persistence. This framework is based on Jacob von Uexkülls organism-centric view of the environment and James G. Millers view of organisms as matter-energy-information processing molecular machines. Three concepts describe an organisms environmental niche: scope, umwelt, and gap. Scope denotes the entirety of environmental events and conditions to which the organism is exposed during its lifetime. Umwelt encompasses an organisms perception of these events. The gap is the organisms blind spot, the scope that is not covered by umwelt. These concepts bring organisms of different complexity to a common ecological denominator. Ecological and physiological data suggest organisms persist using three strategies: flexibility, robustness, and economy. All organisms use umwelt information to flexibly adapt to environmental change. They implement robustness against environmental perturbations within the gap generally through redundancy and reliability of internal constituents. Both flexibility and robustness improve survival. However, they also incur metabolic matter-energy processing costs, which otherwise could have been used for growth and reproduction. Lineages evolve unique tradeoff solutions among strategies in the space of what we call "a persistence triangle." Protein domain architecture and other evidence support the preferential use of flexibility and robustness properties. Archaea and Bacteria gravitate toward the triangles economy vertex, with Archaea biased toward robustness. Eukarya trade economy for survivability. Protista occupy a saddle manifold separating akaryotes from multicellular organisms. Plants and the more flexible Fungi share an economic stratum, and Metazoa are locked in a positive feedback loop toward flexibility.
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Evolutionary optimization of protein folding.
PLoS Comput. Biol.
PUBLISHED: 01-17-2013
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Nature has shaped the make up of proteins since their appearance, [Formula: see text]3.8 billion years ago. However, the fundamental drivers of structural change responsible for the extraordinary diversity of proteins have yet to be elucidated. Here we explore if protein evolution affects folding speed. We estimated folding times for the present-day catalog of protein domains directly from their size-modified contact order. These values were mapped onto an evolutionary timeline of domain appearance derived from a phylogenomic analysis of protein domains in 989 fully-sequenced genomes. Our results show a clear overall increase of folding speed during evolution, with known ultra-fast downhill folders appearing rather late in the timeline. Remarkably, folding optimization depends on secondary structure. While alpha-folds showed a tendency to fold faster throughout evolution, beta-folds exhibited a trend of folding time increase during the last [Formula: see text]1.5 billion years that began during the "big bang" of domain combinations. As a consequence, these domain structures are on average slow folders today. Our results suggest that fast and efficient folding of domains shaped the universe of protein structure. This finding supports the hypothesis that optimization of the kinetic and thermodynamic accessibility of the native fold reduces protein aggregation propensities that hamper cellular functions.
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Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility.
PLoS ONE
PUBLISHED: 01-01-2013
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The genetic code shapes the genetic repository. Its origin has puzzled molecular scientists for over half a century and remains a long-standing mystery. Here we show that the origin of the genetic code is tightly coupled to the history of aminoacyl-tRNA synthetase enzymes and their interactions with tRNA. A timeline of evolutionary appearance of protein domain families derived from a structural census in hundreds of genomes reveals the early emergence of the operational RNA code and the late implementation of the standard genetic code. The emergence of codon specificities and amino acid charging involved tight coevolution of aminoacyl-tRNA synthetases and tRNA structures as well as episodes of structural recruitment. Remarkably, amino acid and dipeptide compositions of single-domain proteins appearing before the standard code suggest archaic synthetases with structures homologous to catalytic domains of tyrosyl-tRNA and seryl-tRNA synthetases were capable of peptide bond formation and aminoacylation. Results reveal that genetics arose through coevolutionary interactions between polypeptides and nucleic acid cofactors as an exacting mechanism that favored flexibility and folding of the emergent proteins. These enhancements of phenotypic robustness were likely internalized into the emerging genetic system with the early rise of modern protein structure.
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Reductive evolution of proteomes and protein structures.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 07-05-2011
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The lengths of orthologous protein families in Eukarya are almost double the lengths found in Bacteria and Archaea. Here we examine protein structures in 745 genomes and show that protein length differences between superkingdoms arise as much shorter prokaryotic nondomain linker sequences. Eukaryotic, bacterial, and archaeal linkers are 250, 86, and 73 aa residues in length, respectively, whereas folded domain sequences are 281, 280, and 256 residues, respectively. Cryptic domains match linkers (P < 0.0001) with probabilities ranging between 0.022 and 0.042; accordingly, they do not affect length estimates significantly. Linker sequences support intermolecular binding within proteomes and they are probably enriched in intrinsically disordered regions as well. Reductively evolved linker sequence lengths in growth rate maximized cells should be proportional to proteome diversity. By using total in-frame coding capacity of a genome [i.e., coding sequence (CDS)] as a reliable measure of proteome diversity, we find linker lengths of prokaryotes clearly evolve in proportion to CDS values, whereas those of eukaryotes are more randomly larger than expected. Domain lengths scarcely change over the entire range of CDS values. Thus, the protein linkers of prokaryotes evolve reductively whereas those of eukaryotes do not.
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A universal molecular clock of protein folds and its power in tracing the early history of aerobic metabolism and planet oxygenation.
Mol. Biol. Evol.
PUBLISHED: 08-30-2010
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The standard molecular clock describes a constant rate of molecular evolution and provides a powerful framework for evolutionary timescales. Here, we describe the existence and implications of a molecular clock of folds, a universal recurrence in the discovery of new structures in the world of proteins. Using a phylogenomic structural census in hundreds of proteomes, we build phylogenies and time lines of domains at fold and fold superfamily levels of structural complexity. These time lines correlate approximately linearly with geological timescales and were here used to date two crucial events in life history, planet oxygenation and organism diversification. We first dissected the structures and functions of enzymes in simulated metabolic networks. The placement of anaerobic and aerobic enzymes in the time line revealed that aerobic metabolism emerged about 2.9 billion years (giga-annum; Ga) ago and expanded during a period of about 400 My, reaching what is known as the Great Oxidation Event. During this period, enzymes recruited old and new folds for oxygen-mediated enzymatic activities. Remarkably, the first fold lost by a superkingdom disappeared in Archaea 2.6 Ga ago, within the span of oxygen rise, suggesting that oxygen also triggered diversification of life. The implications of a molecular clock of folds are many and important for the neutral theory of molecular evolution and for understanding the growth and diversity of the protein world. The clock also extends the standard concept that was specific to molecules and their timescales and turns it into a universal timescale-generating tool.
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The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world.
Structure
PUBLISHED: 01-15-2009
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Protein domains are compact evolutionary units of structure and function that usually combine in proteins to produce complex domain arrangements. In order to study their evolution, we reconstructed genome-based phylogenetic trees of architectures from a census of domain structure and organization conducted at protein fold and fold-superfamily levels in hundreds of fully sequenced genomes. These trees defined timelines of architectural discovery and revealed remarkable evolutionary patterns, including the explosive appearance of domain combinations during the rise of organismal lineages, the dominance of domain fusion processes throughout evolution, and the late appearance of a new class of multifunctional modules in Eukarya by fission of domain combinations. Our study provides a detailed account of the history and diversification of a molecular interactome and shows how the interplay of domain fusions and fissions defines an evolutionary mechanics of domain organization that is fundamentally responsible for the complexity of the protein world.
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The origin, evolution and structure of the protein world.
Biochem. J.
PUBLISHED: 01-13-2009
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Contemporary protein architectures can be regarded as molecular fossils, historical imprints that mark important milestones in the history of life. Whereas sequences change at a considerable pace, higher-order structures are constrained by the energetic landscape of protein folding, the exploration of sequence and structure space, and complex interactions mediated by the proteostasis and proteolytic machineries of the cell. The survey of architectures in the living world that was fuelled by recent structural genomic initiatives has been summarized in protein classification schemes, and the overall structure of fold space explored with novel bioinformatic approaches. However, metrics of general structural comparison have not yet unified architectural complexity using the shared and derived tenet of evolutionary analysis. In contrast, a shift of focus from molecules to proteomes and a census of protein structure in fully sequenced genomes were able to uncover global evolutionary patterns in the structure of proteins. Timelines of discovery of architectures and functions unfolded episodes of specialization, reductive evolutionary tendencies of architectural repertoires in proteomes and the rise of modularity in the protein world. They revealed a biologically complex ancestral proteome and the early origin of the archaeal lineage. Studies also identified an origin of the protein world in enzymes of nucleotide metabolism harbouring the P-loop-containing triphosphate hydrolase fold and the explosive discovery of metabolic functions that recapitulated well-defined prebiotic shells and involved the recruitment of structures and functions. These observations have important implications for origins of modern biochemistry and diversification of life.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.