Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

How anisotropic and isotropic atomic displacement parameters monitor protein covalent bonds rigidity: isotropic B-factors underestimate bond rigidity.

ABSTRACT: Under the assumption that covalent bonds are rigid, it is possible to compare the estimations of rigidity based on anisotropic and isotropic B-factors. This is done by computing the difference of the mean-square displacements (Delta-u) of atoms A and Z along the covalent bond A-Z, which must be close to zero for a rigid bond. The analysis of a high-quality set of protein structures, refined at a resolution better than (or equal to) 0.8 Angstroms, showed that Delta-u is significantly close to zero when anisotropic B-factors are used, with an average 60% Delta-u reduction. This reduction is larger for larger B-factors and this suggests that care should be taken in data-mining procedures that involve isotropic B-factors, especially at lower resolution, when anisotropic B-factors cannot be determined and when the average B-factor increases.

SUBMITTER: Carugo O

PROVIDER: S-EPMC8128831 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

How anisotropic and isotropic atomic displacement parameters monitor protein covalent bonds rigidity: isotropic B-factors underestimate bond rigidity.

Carugo Oliviero O

Amino acids 20210429 5

Under the assumption that covalent bonds are rigid, it is possible to compare the estimations of rigidity based on anisotropic and isotropic B-factors. This is done by computing the difference of the mean-square displacements (Delta-u) of atoms A and Z along the covalent bond A-Z, which must be close to zero for a rigid bond. The analysis of a high-quality set of protein structures, refined at a resolution better than (or equal to) 0.8 Angstroms, showed that Delta-u is significantly close to zer ...[more]

PMID: 33928454

Similar Datasets

ForceGen: atomic covalent bond value derivation for Gromacs.

Project description:A large number of crystallographic protein structures include ligands, small molecules and post-translational modifications. Atomic bond force values for computational atomistic models of post-translational or non-standard amino acids, metal binding active sites, small molecules and drug molecules are not readily available in most simulation software packages. We present ForceGen, a Java tool that extracts the bond stretch and bond angle force values and equilibrium values from the Hessian of a Gaussian vibrational frequency analysis. The parameters are compatible with force fields derived using the second order tensor of the Hessian. The output is formatted with the Gromacs topology in mind. This study further demonstrates the use of ForceGen over the quantum mechanically derived structures of a small organic solvent, a naturally occurring protein crosslink derived from two amino acids following post-translational modification and the amino acid ligands of a zinc ion. We then derive Laplacian bond orders to understand how the resulting force values relate back to the quantum mechanical model. The parameterisation of the organic solvent, toluene, was verified using Molecular Mechanics simulations. The structural data from the simulation compared well with the quantum mechanical structure and the system density compared well with experimental values.

| S-EPMC5719132 | biostudies-literature

Anisotropic to Isotropic Transition in Monolayer Group-IV Tellurides.

Project description:Monolayer group-IV tellurides with phosphorene-derived structures are attracting increasing research interest because of their unique properties. Here, we systematically studied the quasiparticle electronic and optical properties of two-dimensional group-IV tellurides (SiTe, GeTe, SnTe, PbTe) using the GW and Bethe-Salpeter equation method. The calculations revealed that all group-IV tellurides are indirect bandgap semiconductors except for monolayer PbTe with a direct gap of 1.742 eV, while all of them are predicted to have prominent carrier transport ability. We further found that the excitonic effect has a significant impact on the optical properties for monolayer group-IV tellurides, and the predicted exciton binding energy is up to 0.598 eV for SiTe. Interestingly, the physical properties of monolayer group-IV tellurides were subject to an increasingly isotropic trend: from SiTe to PbTe, the differences of the calculated quasiparticle band gap, optical gap, and further exciton binding energy along different directions tended to decrease. We demonstrated that these anisotropic electronic and optical properties originate from the structural anisotropy, which in turn is the result of Coulomb repulsion between non-bonding electron pairs. Our theoretical results provide a deeper understanding of the anisotropic properties of group-IV telluride monolayers.

| S-EPMC8398135 | biostudies-literature

Polar molecules catalyze CO insertion into metal-alkyl bonds through the displacement of an agostic C-H bond.

Project description:The insertion of CO into metal-alkyl bonds is the key C-C bond-forming step in many of the most important organic reactions catalyzed by transition metal complexes. Polar organic molecules (e.g., tetrahydrofuran) have long been known to promote CO insertion reactions, but the mechanism of their action has been the subject of unresolved speculation for over five decades. Comprehensive computational studies [density functional theory (DFT)] on the prototypical system Mn(CO)5(arylmethyl) reveal that the polar molecules do not promote the actual alkyl migration step. Instead, CO insertion (i.e. alkyl migration) occurs rapidly and reversibly to give an acyl complex with a sigma-bound (agostic) C-H bond that is not easily displaced by typical ligands (e.g. phosphines or CO). The agostic C-H bond is displaced much more readily, however, by the polar promoter molecules, even though such species bind only weakly to the metal center and are themselves then easily displaced; the facile kinetics of this process are attributable to a hydrogen bonding-like interaction between the agostic C-H bond and the polar promoter. The role of the promoter is to thereby catalyze isomerization of the agostic product of CO insertion to give an [Formula: see text]-C,O-bound acyl product that is more easily trapped than the agostic species. This ability of such promoters to displace a strongly sigma-bound C-H bond and to subsequently undergo facile displacement themselves is without reported precedent, and could have implications for catalytic reactions beyond carbonylation.

| S-EPMC6397546 | biostudies-literature

Near-isotropic polariton heat transport along a polar anisotropic nanofilm.

Project description:The heat transport of surface phonon-polaritons propagating along a polar uniaxial anisotropic nanofilm is studied for different orientations of its optical axis, film thicknesses, and temperatures. For an hBN nanofilm, it is shown that i) the propagation of polaritons can be described in terms of even and odd modes that generalize the transverse magnetic and transverse electrical ones that typically appear in isotropic films. ii) The frequency spectrum of polaritons can efficiently be tuned with the angle between the film optical axis and their propagation direction. iii) The polariton thermal conductivity takes higher values for a thinner or hotter nanofilm. iv) The even and odd modes have a remarkable contribution to the total polariton thermal conductivity, which takes a value higher than 5.6 Wm-1K-1 for a 25-nm-thick nanofilm at 500 K. The obtained results thus uncover some key features of the propagation and heat transport of polaritons in uniaxial nanofilms.

| S-EPMC9420522 | biostudies-literature

Dumbbells, chains, and ribbons: anisotropic self-assembly of isotropic nanoparticles.

Project description:Functionalizing the surface of metal nanoparticles can assure their stability in solution or mediate their self-assembly into aggregates with controlled shapes. Here we present a computational study of the colloidal aggregation of gold nanoparticles (Au NPs) isotropically functionalized by a mixture of charged and hydrophobic ligands. We show that, by varying the relative proportion of the two ligands, the NPs form anisotropic aggregates with markedly different topologies: dumbbells, chains, or ribbons. In all cases, two kinds of connections keep the aggregates together: hydrophobic bonds and ion bridges. We show that the anisotropy of the aggregates derives from the NP shell reshaping due to the formation of the hydrophobic links, while ion bridges are accountable for the "secondary structure" of the aggregates. Our findings provide a general physical principle that can also be exploited in different self-assembled systems: anisotropic/directional aggregation can be achieved starting from isotropic objects with a soft, deformable surface.

| S-EPMC10540935 | biostudies-literature

Hybrid Silica-Based Fillers in Nanocomposites: Influence of Isotropic/Isotropic and Isotropic/Anisotropic Fillers on Mechanical Properties of Styrene-Butadiene (SBR)-Based Rubber.

Project description:The improvement of mechanical properties of polymer-based nanocomposites is usually obtained through a strong polymer-silica interaction. Most often, precipitated silica nanoparticles are used as filler. In this work, we study the synergetic effect occurring between dual silica-based fillers in a styrene-butadiene rubber (SBR)/polybutadiene (PBD) rubber matrix. Precipitated Highly Dispersed Silica (HDS) nanoparticles (10 nm) have been associated with spherical Stöber silica nanoparticles (250 nm) and anisotropic nano-Sepiolite. By imaging filler at nano scale through Scanning Transmission Electron Microscopy, we have shown that anisotropic fillers align only in presence of a critical amount of HDS. The dynamic mechanical analysis of rubber compounds confirms that this alignment leads to a stiffer nanocomposite when compared to Sepiolite alone. On the contrary, spherical 250 nm nanoparticles inhibit percolation network and reduce the nanocomposite stiffness.

| S-EPMC8348337 | biostudies-literature

Covalent bonds in positron dihalides.

Project description:We report a computational study on homo- and heteronuclear e+[X-Y-] compounds formed by two halide anions (X-, Y- = F-, Cl-, Br-) and one positron. Our results indicate the formation of energetically stable positronic molecules in all cases. Analysis of the electron and positron densities points out that the formation of positron covalent bonds underlies the stabilization of the otherwise repelling dihalides, revealing that positronic bonding can reach far beyond the previously addressed e+[H-H-] molecule [J. Charry, M. T. do N. Varella and A. Reyes, Angew. Chem. Int. Ed., 2018, 57, 8859-8864.]. To a significant extent, the properties of the positron dihalides are similar to those of the purely electronic analogs, e-[A+B+], molecular cations with isoelectronic atomic cores (A+, B+ = Na+, K+, Rb+) bound by one electron. The positron bonds in the e+[X-Y-] complexes are however stronger than those in the isoelectronic e-[A+B+] counterparts, as the former have shorter bond lengths and higher bond energies. While an energy decomposition analysis points out that both electronic and positronic bonds essentially arise from electrostatic interactions, the more stable positron bonds are partly due to the higher polarizabilities of the dihalide anions, and partly to more significant contributions from correlation and relaxation effects.

| S-EPMC7472554 | biostudies-literature

Isotropic Failure Criteria Are Not Appropriate for Anisotropic Fibrous Biological Tissues.

Project description:The von Mises (VM) stress is a common stress measure for finite element models of tissue mechanics. The VM failure criterion, however, is inherently isotropic, and therefore may yield incorrect results for anisotropic tissues, and the relevance of the VM stress to anisotropic materials is not clear. We explored the application of a well-studied anisotropic failure criterion, the Tsai–Hill (TH) theory, to the mechanically anisotropic porcine aorta. Uniaxial dogbones were cut at different angles and stretched to failure. The tissue was anisotropic, with the circumferential failure stress nearly twice the axial (2.67 ± 0.67 MPa compared to 1.46 ± 0.59 MPa). The VM failure criterion did not capture the anisotropic tissue response, but the TH criterion fit the data well (R2 = 0.986). Shear lap samples were also tested to study the efficacy of each criterion in predicting tissue failure. Two-dimensional failure propagation simulations showed that the VM failure criterion did not capture the failure type, location, or propagation direction nearly as well as the TH criterion. Over the range of loading conditions and tissue geometries studied, we found that problematic results that arise when applying the VM failure criterion to an anisotropic tissue. In contrast, the TH failure criterion, though simplistic and clearly unable to capture all aspects of tissue failure, performed much better. Ultimately, isotropic failure criteria are not appropriate for anisotropic tissues, and the use of the VM stress as a metric of mechanical state should be reconsidered when dealing with anisotropic tissues.

| S-EPMC5467028 | biostudies-literature

Visualization of anisotropic-isotropic phase transformation dynamics in battery electrode particles.

Project description:Anisotropy, or alternatively, isotropy of phase transformations extensively exist in a number of solid-state materials, with performance depending on the three-dimensional transformation features. Fundamental insights into internal chemical phase evolution allow manipulating materials with desired functionalities, and can be developed via real-time multi-dimensional imaging methods. Here, we report a five-dimensional imaging method to track phase transformation as a function of charging time in individual lithium iron phosphate battery cathode particles during delithiation. The electrochemically driven phase transformation is initially anisotropic with a preferred boundary migration direction, but becomes isotropic as delithiation proceeds further. We also observe the expected two-phase coexistence throughout the entire charging process. We expect this five-dimensional imaging method to be broadly applicable to problems in energy, materials, environmental and life sciences.

| S-EPMC4990630 | biostudies-literature

Nucleic-acid structural deformability deduced from anisotropic displacement parameters.

Project description:The growing numbers of very well resolved nucleic-acid crystal structures with anisotropic displacement parameters provide an unprecedented opportunity to learn about the natural motions of DNA and RNA. Here we report a new Monte-Carlo approach that takes direct account of this information to extract the distortions of covalent structure, base pairing, and dinucleotide geometry intrinsic to regularly organized double-helical molecules. We present new methods to test the validity of the anisotropic parameters and examine the apparent deformability of a variety of structures, including several A, B, and Z DNA duplexes, an AB helical intermediate, an RNA, a ligand-DNA complex, and an enzyme-bound DNA. The rigid-body parameters characterizing the positions of the bases in the structures mirror the mean parameters found when atomic motion is taken into account. The base-pair fluctuations intrinsic to a single structure, however, differ from those extracted from collections of nucleic-acid structures, although selected base-pair steps undergo conformational excursions along routes suggested by the ensembles. The computations reveal surprising new molecular insights, such as the stiffening of DNA and concomitant separation of motions of contacted nucleotides on opposite strands by the binding of Escherichia coli endonuclease VIII, which suggest how the protein may direct enzymatic action.

| S-EPMC4163913 | 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