Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ionic scattering factors of atoms that compose biological molecules.

ABSTRACT: Ionic scattering factors of atoms that compose biological molecules have been computed by the multi-configuration Dirac-Fock method. These ions are chemically unstable and their scattering factors had not been reported except for O-. Yet these factors are required for the estimation of partial charges in protein molecules and nucleic acids. The electron scattering factors of these ions are particularly important as the electron scattering curves vary considerably between neutral and charged atoms in the spatial-resolution range explored in structural biology. The calculated X-ray and electron scattering factors have then been parameterized for the major scattering curve models used in X-ray and electron protein crystallography and single-particle cryo-EM. The X-ray and electron scattering factors and the fitting parameters are presented for future reference.

SUBMITTER: Yonekura K

PROVIDER: S-EPMC5929380 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Ionic scattering factors of atoms that compose biological molecules.

Yonekura Koji K Matsuoka Rei R Yamashita Yoshiki Y Yamane Tsutomu T Ikeguchi Mitsunori M Kidera Akinori A Maki-Yonekura Saori S

IUCrJ 20180427 Pt 3

Ionic scattering factors of atoms that compose biological molecules have been computed by the multi-configuration Dirac-Fock method. These ions are chemically unstable and their scattering factors had not been reported except for O<sup>-</sup>. Yet these factors are required for the estimation of partial charges in protein molecules and nucleic acids. The electron scattering factors of these ions are particularly important as the electron scattering curves vary considerably between neutral and c ...[more]

PMID: 29755750

Similar Datasets

Evaluating elastic network models of crystalline biological molecules with temperature factors, correlated motions, and diffuse x-ray scattering.

Project description:In this study, the variance-covariance matrix of protein motions is used to compare several elastic network models within the theoretical framework of x-ray scattering from crystals. A set of 33 ultra-high resolution structures is used to characterize the average scaling behavior of the vibrational density of states and make comparisons between experimental and theoretical temperature factors. Detailed investigations of the vibrational density of states, correlations, and predicted diffuse x-ray scatter are carried out for crystalline Staphylococcal nuclease; correlations and diffuse x-ray scatter are also compared to predictions from the translation, libration, screw model and a liquid-like dynamics model. We show that elastic network models developed to best predict temperature factors without regard for the crystal environment have relatively strong long-range interactions that yield very short-ranged atom-atom correlations. Further, we find that the low-frequency modes dominate the variance-covariance matrix only for those models with a physically reasonable vibrational density of states, and the fraction of modes required to converge the correlations is higher than that typically used for elastic network model studies. The practical implications are explored using computed diffuse x-ray scatter, which can be measured experimentally.

| S-EPMC2955396 | biostudies-literature

Reducing dynamical electron scattering reveals hydrogen atoms.

Project description:Compared with X-rays, electron diffraction faces a crucial challenge: dynamical electron scattering compromises structure solution and its effects can only be modelled in specific cases. Dynamical scattering can be reduced experimentally by decreasing crystal size but not without a penalty, as it also reduces the overall diffracted intensity. In this article it is shown that nanometre-sized crystals from organic pharmaceuticals allow positional refinement of the hydrogen atoms, even whilst ignoring the effects of dynamical scattering during refinement. To boost the very weak diffraction data, a highly sensitive hybrid pixel detector was employed. A general likelihood-based computational approach was also introduced for further reducing the adverse effects of dynamic scattering, which significantly improved model accuracy, even for protein crystal data at substantially lower resolution.

| S-EPMC6302931 | biostudies-literature

Single-Molecule X-ray Scattering Used to Visualize the Conformation Distribution of Biological Molecules via Single-Object Scattering Sampling.

Project description:Biological macromolecules, the fundamental building blocks of life, exhibit dynamic structures in their natural environment. Traditional structure determination techniques often oversimplify these multifarious conformational spectra by capturing only ensemble- and time-averaged molecular structures. Addressing this gap, in this work, we extend the application of the single-object scattering sampling (SOSS) method to diverse biological molecules, including RNAs and proteins. Our approach, referred to as "Bio-SOSS", leverages ultrashort X-ray pulses to capture instantaneous structures. In Bio-SOSS, we employ two gold nanoparticles (AuNPs) as labels, which provide strong contrast in the X-ray scattering signal, to ensure precise distance determinations between labeled sites. We generated hypothetical Bio-SOSS images for RNAs, proteins, and an RNA-protein complex, each labeled with two AuNPs at specified positions. Subsequently, to validate the accuracy of Bio-SOSS, we extracted distances between these nanoparticle labels from the images and compared them with the actual values used to generate the Bio-SOSS images. Specifically, for a representative RNA (1KXK), the standard deviation in distance discrepancies between molecular dynamics snapshots and Bio-SOSS retrievals was found to be optimally around 0.2 Å, typically within 1 Å under practical experimental conditions at state-of-the-art X-ray free-electron laser facilities. Furthermore, we conducted an in-depth analysis of how various experimental factors, such as AuNP size, X-ray properties, and detector geometry, influence the accuracy of Bio-SOSS. This comprehensive investigation highlights the practicality and potential of Bio-SOSS in accurately capturing the diverse conformation spectrum of biological macromolecules, paving the way for deeper insights into their dynamic natures.

| S-EPMC10743147 | biostudies-literature

The COUP-TFs compose a family of functionally related transcription factors.

Project description:The chicken ovalbumin upstream promoter transcription factors (COUP-TFs) are members of the steroid/thyroid hormone receptor superfamily and function in transcriptional regulation of a wide variety of genes. The COUP-TFs purified from HeLa nuclear extract by COUP-affinity chromatography are composed of multiple M(r) forms. The Low M(r) COUP-TFs (43,000, 44,000, 46,000, and 47,000 M(r)) produce a relatively fast migrating complex (C1) with DNA in electrophoresis mobility shift assays, while the high M(r) forms (66,000, 68,000, 72,000, and 74,000 M(r)) produce a slower migrating (C2) complex. The high M(r) COUP-TFs were purified by gel filtration chromatography and independently formed the C2 DNA complex, probably acting as dimers. The high M(r) forms are indistinguishable from the low M(r) COUP-TFs in DNA binding and in enhancement of in vitro transcription from the ovalbumin promoter. The finding of multiple COUP-TF forms led us to clone a second low M(r) COUP-TF, "COUP-TF2." The COUP-TF2 sequence has very strong homology with COUP-TF1. The N-termini of COUP-TF1 and COUP-TF2 are least similar, but both contain glutamine-rich and proline-rich motifs, putative activation domains.

| S-EPMC5952191 | biostudies-literature

Interactions in Model Ionic Dyads and Triads Containing Tetrel Atoms.

Project description:The interactions in model ionic YTX3···Z (Y = NC, F, Cl, Br; X = F, Cl, Br, Z = F-, Cl-, Br-, Li+) dyads containing the tetrel atoms, T = C, Si, Ge, were studied using ab initio computational methods, including an energy decomposition analysis, which found that the YTX3 molecules were stabilized by both anions (via tetrel bonding) and cations (via polarization). For the tetrel-bonded dyads, both the electrostatic and polarization forces make comparable contributions to the binding in the C-containing dyads, whereas, electrostatic forces are by far the largest contributor to the binding in the Si- and Ge-containing analogues. Model metastable Li+···NCTCl3···F- (T = C, Si, Ge) triads were found to be lower in energy than the combined energy of the Li+ + NCTCl3 + F- fragments. The pair energies and cooperative energies for these highly polar triads were also computed and discussed.

| S-EPMC7570900 | biostudies-literature

Form factor determination of biological molecules with X-ray free electron laser small-angle scattering (XFEL-SAS).

Project description:Free-electron lasers (FEL) are revolutionizing X-ray-based structural biology methods. While protein crystallography is already routinely performed at FELs, Small Angle X-ray Scattering (SAXS) studies of biological macromolecules are not as prevalent. SAXS allows the study of the shape and overall structure of proteins and nucleic acids in solution, in a quasi-native environment. In solution, chemical and biophysical parameters that have an influence on the structure and dynamics of molecules can be varied and their effect on conformational changes can be monitored in time-resolved XFEL and SAXS experiments. We report here the collection of scattering form factors of proteins in solution using FEL X-rays. The form factors correspond to the scattering signal of the protein ensemble alone; the scattering contributions from the solvent and the instrument are separately measured and accurately subtracted. The experiment was done using a liquid jet for sample delivery. These results pave the way for time-resolved studies and measurements from dilute samples, capitalizing on the intense and short FEL X-ray pulses.

| S-EPMC10585004 | biostudies-literature

Spectroscopy of lithium atoms and molecules on helium nanodroplets.

Project description:We report on the spectroscopic investigation of lithium atoms and lithium dimers in their triplet manifold on the surface of helium nanodroplets (He(N)). We present the excitation spectrum of the 3p ← 2s and 3d ← 2s two-photon transitions for single Li atoms on He(N). The atoms are excited from the 2S(Σ) ground state into Δ, Π, and Σ pseudodiatomic molecular substates. Excitation spectra are recorded by resonance enhanced multiphoton ionization time-of-flight (REMPI-TOF) mass spectroscopy, which allows an investigation of the exciplex (Li*–He(m), m = 1–3) formation process in the Li–He(N) system. Electronic states are shifted and broadened with respect to free atom states, which is explained within the pseudodiatomic model. The assignment is assisted by theoretical calculations, which are based on the Orsay–Trento density functional where the interaction between the helium droplet and the lithium atom is introduced by a pairwise additive approach. When a droplet is doped with more than one alkali atom, the fragility of the alkali–He(N) systems leads preferably to the formation of high-spin molecules on the droplets. We use this property of helium nanodroplets for the preparation of Li dimers in their triplet ground state (13Σu(+)). The excitation spectrum of the 23Πg(ν′ = 0–11) ← 13Σu(+)(ν″ = 0) transition is presented. The interaction between the molecule and the droplet manifests in a broadening of the transitions with a characteristic asymmetric form. The broadening extends to the blue side of each vibronic level, which is caused by the simultaneous excitation of the molecule and vibrations of the droplet (phonons). The two isotopes of Li form 6Li2 and 7Li2 as well as isotope mixed 6Li7Li molecules on the droplet surface. By using REMPI-TOF mass spectroscopy, isotope-dependent effects could be studied.

| S-EPMC3839407 | biostudies-other

Atomic Charges in Highly Ionic Diatomic Molecules.

Project description:Atomic charges were investigated as functions of detectable atomic and molecular constants at equilibrium structures. It was found based upon the variation idea that atomic charges in highly ionic molecules can be expressed as a function of molecular dipole moments, polarizabilities of free cations, and polarizabilities of free neutral atoms of the corresponding anions. The function can be given in the form of classical Rittner's relationship (J. Chem. Phys. 1951, 19, 1030). For the ground states of alkali halide molecules, the predicted atomic charges are close to an elementary charge e and the predicted dipole moments are in good agreement with the observed values; for spin-restricted high-ionic systems such as the lowest 9Σ electronic states of BN, AlN, GaN, BP, AlP, GaP, BAs, AlAs, and GaAs molecules, the predicted atomic charges are also near 1e and in good agreement with the results of natural population analysis at MRCI/cc-pvqz and HF/6-311+G(3df) levels. Polarizabilities for the lowest quintet states of B-, Al-, Ga-, N+, P+, and As+ ions were also obtained based upon high-level ab initio computations. Atomic charges from other related methods are also investigated for comparison. The results demonstrate that high-quality atomic charges can be obtained with detectable variables, such as molecular dipole moment, vibrational frequency, as well as polarizabilities of the related free atoms and ions.

| S-EPMC6643469 | biostudies-literature

Unique identifiers for small molecules enable rigorous labeling of their atoms.

Project description:Rigorous characterization of small organic molecules in terms of their structural and biological properties is vital to biomedical research. The three-dimensional structure of a molecule, its 'photo ID', is inefficient for searching and matching tasks. Instead, identifiers play a key role in accessing compound data. Unique and reproducible molecule and atom identifiers are required to ensure the correct cross-referencing of properties associated with compounds archived in databases. The best approach to this requirement is the International Chemical Identifier (InChI). However, the current implementation of InChI fails to provide a complete standard for atom nomenclature, and incorrect use of the InChI standard has resulted in the proliferation of non-unique identifiers. We propose a methodology and associated software tools, named ALATIS, that overcomes these shortcomings. ALATIS is an adaptation of InChI, which operates fully within the InChI convention to provide unique and reproducible molecule and all atom identifiers. ALATIS includes an InChI extension for unique atom labeling of symmetric molecules. ALATIS forms the basis for improving reproducibility and unifying cross-referencing across databases.

| S-EPMC5441290 | biostudies-literature

Universal diffraction of atoms and molecules from a quantum reflection grating.

Project description:Since de Broglie's work on the wave nature of particles, various optical phenomena have been observed with matter waves of atoms and molecules. However, the analogy between classical and atom/molecule optics is not exact because of different dispersion relations. In addition, according to de Broglie's formula, different combinations of particle mass and velocity can give the same de Broglie wavelength. As a result, even for identical wavelengths, different molecular properties such as electric polarizabilities, Casimir-Polder forces, and dissociation energies modify (and potentially suppress) the resulting matter-wave optical phenomena such as diffraction intensities or interference effects. We report on the universal behavior observed in matter-wave diffraction of He atoms and He2 and D2 molecules from a ruled grating. Clear evidence for emerging beam resonances is observed in the diffraction patterns, which are quantitatively the same for all three particles and only depend on the de Broglie wavelength. A model, combining secondary scattering and quantum reflection, permits us to trace the observed universal behavior back to the peculiar principles of quantum reflection.

| S-EPMC4803490 | 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