Browse
Submit Data
Databases
API
Help

Dataset Information

28 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Geometrical prediction of cleavage planes in crystal structures.

ABSTRACT: Cleavage is the ability of single crystals to split easily along specifically oriented planes. This phenomenon is of great interest for materials' scientists. Acquiring the data regarding cleavage is essential for the understanding of brittle fracture, plasticity and strength, as well as for the prevention of catastrophic device failures. Unfortunately, theoretical calculations of cleavage energy are demanding and often unsuitable for high-throughput searches of cleavage planes in arbitrary crystal structures. A simplified geometrical approach (GALOCS = gaps locations in crystal structures) is suggested for predicting the most promising cleavage planes. GALOCS enumerates all the possible reticular lattice planes and calculates the plane-average electron density as a function of the position of the planes in the unit cell. The assessment of the cleavage ability of the planes is based on the width and depth of planar gaps in crystal structures, which appear when observing the planes lengthwise. The method is demonstrated on two-dimensional graphene and three-dimensional silicon, quartz and LiNbO₃ structures. A summary of planar gaps in a few more inorganic crystal structures is also presented.

SUBMITTER: Vaknin U

PROVIDER: S-EPMC8420770 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Development of epithelial tissues: How are cleavage planes chosen?

Project description:The cross-section of a cell in a monolayer epithelial tissue can be modeled mathematically as a k-sided polygon. Empirically studied distributions of the proportions of k-sided cells in epithelia show remarkable similarities in a wide range of evolutionarily distant organisms. A variety of mathematical models have been proposed for explaining this phenomenon. The highly parsimonious simulation model of (Patel et al., PLoS Comput. Biol., 2009) that takes into account only the number of sides of a given cell and cell division already achieves a remarkably good fit with empirical distributions from Drosophila, Hydra, Xenopus, Cucumber, and Anagallis. Within the same modeling framework as in that paper, we introduce additional options for the choice of the endpoints of the cleavage plane that appear to be biologically more realistic. By taking the same data sets as our benchmarks, we found that combinations of some of our new options consistently gave better fits with each of these data sets than previously studied ones. Both our algorithm and simulation data are made available as research tools for future investigations.

| S-EPMC6221281 | biostudies-literature

Crystal structures of a meta-cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) complexed with cleavage products.

Project description:2-Hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase (CumD) from Pseudomonas fluorescens IP01 hydrolyzes a meta-cleavage product generated in the cumene (isopropylbenzene) degradation pathway. The crystal structures of the inactive S103A mutant of the CumD enzyme complexed with isobutyrate and acetate ions were determined at 1.6 and 2.0 A resolution, respectively. The isobutyrate and acetate ions were located at the same position in the active site, and occupied the site for a part of the hydrolysis product with CumD, which has the key determinant group for the substrate specificity of related hydrolases. One of the oxygen atoms of the carboxyl group of the isobutyrate ion was hydrogen bonded with a water molecule and His252. Another oxygen atom of the carboxyl group was situated in an oxyanion hole formed by the two main-chain N atoms. The isopropyl group of the isobutyric acid was recognized by the side-chains of the hydrophobic residues. The substrate-binding pocket of CumD was long, and the inhibition constants of various organic acids corresponded well to it. In comparison with the structure of BphD from Rhodococcus sp. RHA1, the structural basis for the substrate specificity of related hydrolases, is revealed.

| S-EPMC2373588 | biostudies-literature

Data-driven prediction of complex crystal structures of dense lithium.

Project description:Lithium (Li) is a prototypical simple metal at ambient conditions, but exhibits remarkable changes in structural and electronic properties under compression. There has been intense debate about the structure of dense Li, and recent experiments offered fresh evidence for yet undetermined crystalline phases near the enigmatic melting minimum region in the pressure-temperature phase diagram of Li. Here, we report on an extensive exploration of the energy landscape of Li using an advanced crystal structure search method combined with a machine-learning approach, which greatly expands the scale of structure search, leading to the prediction of four complex Li crystal structures containing up to 192 atoms in the unit cell that are energetically competitive with known Li structures. These findings provide a viable solution to the observed yet unidentified crystalline phases of Li, and showcase the predictive power of the global structure search method for discovering complex crystal structures in conjunction with accurate machine learning potentials.

| S-EPMC10203143 | biostudies-literature

Crystal structures of human caspase 6 reveal a new mechanism for intramolecular cleavage self-activation.

Project description:Dimeric effectors caspase 3 and caspase 7 are activated by initiator caspase processing. In this study, we report the crystal structures of effector caspase 6 (CASP6) zymogen and N-Acetyl-Val-Glu-Ile-Asp-al-inhibited CASP6. Both of these forms of CASP6 have a dimeric structure, and in CASP6 zymogen the intersubunit cleavage site (190)TEVD(193) is well structured and inserts into the active site. This positions residue Asp 193 to be easily attacked by the catalytic residue Cys 163. We demonstrate biochemically that intramolecular cleavage at Asp 193 is a prerequisite for CASP6 self-activation and that this activation mechanism is dependent on the length of the L2 loop. Our results indicate that CASP6 can be activated and regulated through intramolecular self-cleavage.

| S-EPMC2966951 | biostudies-literature

Single crystalline Co3O4 nanocrystals exposed with different crystal planes for Li-O2 batteries.

Project description:Single crystalline Co3O4 nanocrystals exposed with different crystal planes were synthesised, including cubic Co3O4 nanocrystals enclosed by {100} crystal planes, pseudo octahedral Co3O4 enclosed by {100} and {110} crystal planes, Co3O4 nanosheets exposed by {110} crystal planes, hexagonal Co3O4 nanoplatelets exposed with {111} crystal planes, and Co3O4 nanolaminar exposed with {112} crystal planes. Well single crystalline features of these Co3O4 nanocrystals were confirmed by FESEM and HRTEM analyses. The electrochemical performance for Li-O2 batteries shows that Co3O4 nanocrystals can significantly reduce the discharge-charge over-potential via the effect on the oxygen evolution reaction (OER). From the comparison on their catalytic performances, we found that the essential factor to promote the oxygen evolution reactions is the surface crystal planes of Co3O4 nanocrystals, namely, crystal planes-dependent process. The correlation between different Co3O4 crystal planes and their effect on reducing charge-discharge over-potential was established: {100} < {110} < {112} < {111}.

| S-EPMC5385818 | biostudies-literature

Image-Based Geometrical Characterization of Nodes in Additively Manufactured Lattice Structures.

Project description:Additive manufacturing (AM) enables the fabrication of lattice structures with optimal mechanical, fluid, and thermal properties. However, during the AM fabrication process, defects are produced in the strut and node elements, which comprise the lattice structure. This leads to discrepancies between the AM fabricated lattice and its idealized computer-aided design (CAD) model, negatively affecting the ability to predict the mechanical behavior of the fabricated lattice via numerical models. Current research is focused on quantification of geometric uncertainties in the strut elements of the lattice; as-manufactured node geometries remain relatively unexplored on an individual scale, despite their criticality to the mechanical response of the structure. Understanding the geometrical properties of as-manufactured nodes relative to CAD idealizations can be used to improve lattice designs and numerical models. In this research, X-ray microcomputed tomography (μCT) is used to analyze and quantify the as-manufactured nodal geometry, found in face-centered cubic and face-centered cubic with axial struts lattices fabricated via selective laser melting. A custom tool is developed that enables auto-isolation and classification of nodal joints from μCT-derived cross-sectional slices. Geometrical properties are extracted from the isolated nodal cross sections and compared with their idealized CAD model counterpart. Quantification of geometrical defects provides insight into how nodes within an AM lattice structure differ from each other and their idealized design. Overall, this research is an initial step toward developing accurate and efficient numerical models, as well as better node design for AM.

| S-EPMC9828589 | biostudies-literature

Generation of crystal structures using known crystal structures as analogues.

Project description:This analysis attempts to answer the question of whether similar molecules crystallize in a similar manner. An analysis of structures in the Cambridge Structural Database shows that the answer is yes - sometimes they do, particularly for single-component structures. However, one does need to define what we mean by similar in both cases. Building on this observation we then demonstrate how this correlation between shape similarity and packing similarity can be used to generate potential lattices for molecules with no known crystal structure. Simple intermolecular interaction potentials can be used to minimize these potential lattices. Finally we discuss the many limitations of this approach.

| S-EPMC4971547 | biostudies-literature

Ice-binding proteins that accumulate on different ice crystal planes produce distinct thermal hysteresis dynamics.

Project description:Ice-binding proteins that aid the survival of freeze-avoiding, cold-adapted organisms by inhibiting the growth of endogenous ice crystals are called antifreeze proteins (AFPs). The binding of AFPs to ice causes a separation between the melting point and the freezing point of the ice crystal (thermal hysteresis, TH). TH produced by hyperactive AFPs is an order of magnitude higher than that produced by a typical fish AFP. The basis for this difference in activity remains unclear. Here, we have compared the time dependence of TH activity for both hyperactive and moderately active AFPs using a custom-made nanolitre osmometer and a novel microfluidics system. We found that the TH activities of hyperactive AFPs were time-dependent, and that the TH activity of a moderate AFP was almost insensitive to time. Fluorescence microscopy measurement revealed that despite their higher TH activity, hyperactive AFPs from two insects (moth and beetle) took far longer to accumulate on the ice surface than did a moderately active fish AFP. An ice-binding protein from a bacterium that functions as an ice adhesin rather than as an antifreeze had intermediate TH properties. Nevertheless, the accumulation of this ice adhesion protein and the two hyperactive AFPs on the basal plane of ice is distinct and extensive, but not detectable for moderately active AFPs. Basal ice plane binding is the distinguishing feature of antifreeze hyperactivity, which is not strictly needed in fish that require only approximately 1°C of TH. Here, we found a correlation between the accumulation kinetics of the hyperactive AFP at the basal plane and the time sensitivity of the measured TH.

| S-EPMC4233703 | biostudies-literature

Protemot: prediction of protein binding sites with automatically extracted geometrical templates.

Project description:Geometrical analysis of protein tertiary substructures has been an effective approach employed to predict protein binding sites. This article presents the Protemot web server that carries out prediction of protein binding sites based on the structural templates automatically extracted from the crystal structures of protein-ligand complexes in the PDB (Protein Data Bank). The automatic extraction mechanism is essential for creating and maintaining a comprehensive template library that timely accommodates to the new release of PDB as the number of entries continues to grow rapidly. The design of Protemot is also distinctive by the mechanism employed to expedite the analysis process that matches the tertiary substructures on the contour of the query protein with the templates in the library. This expediting mechanism is essential for providing reasonable response time to the user as the number of entries in the template library continues to grow rapidly due to rapid growth of the number of entries in PDB. This article also reports the experiments conducted to evaluate the prediction power delivered by the Protemot web server. Experimental results show that Protemot can deliver a superior prediction power than a web server based on a manually curated template library with insufficient quantity of entries.http://protemot.csie.ntu.edu.tw/step1.cgi http://bioinfo.mc.ntu.edu.tw/protemot/step1.cgi.

| S-EPMC1538868 | biostudies-literature

Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway.

Project description:I-SceI is a homing endonuclease that specifically cleaves an 18-bp double-stranded DNA. I-SceI exhibits a strong preference for cleaving the bottom strand DNA. The published structure of I-SceI bound to an uncleaved DNA substrate provided a mechanism for bottom strand cleavage but not for top strand cleavage. To more fully elucidate the I-SceI catalytic mechanism, we determined the X-ray structures of I-SceI in complex with DNA substrates that are nicked in either the top or bottom strands. The structures resemble intermediates along the DNA cleavage reaction. In a structure containing a nick in the top strand, the spatial arrangement of metal ions is similar to that observed in the structure that contains uncleaved DNA, suggesting that cleavage of the bottom strand occurs by a common mechanism regardless of whether this strand is cleaved first or second. In the structure containing a nick in the bottom strand, a new metal binding site is present in the active site that cleaves the top strand. This new metal and a candidate nucleophilic water molecule are correctly positioned to cleave the top strand following bottom strand cleavage, providing a plausible mechanism for top strand cleavage.

| S-EPMC2425494 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data