A Constant Proportion in Protein Structure

2018 ◽  
Author(s):  
Francisco Javier Lobo-Cabrera
Keyword(s):  
Protein Structure ◽  
Spatial Clustering ◽  
A Priori ◽  
Data Bank ◽  
X Ray ◽  
Protein Size ◽  
Protein Prediction ◽  
Quality Check ◽  
First Time ◽  
Secondary Structure Composition

The principles governing protein structure are largely unknown. Here, a structural proportion universal (R2 = 0.978) among proteins is reported. The model variance is shown to be independent from protein size, secondary structure composition, compactness or relative surface area. The structural characteristic under study --named here QUILLO-- quantifies residue-type spatial clustering. In this way, polar, hydrophobic, acidic and basic residues are evaluated individually and their values added up. For the analysis, all X-Ray currently determined structures deposited in the Protein Data Bank were studied. The QUILLO proportion offers for the first time an a priori protein prediction quality-check. Indeed, predictions with unexpected proportion values correspond to low ranks in the CASP12 experiment. The reason behind a specific, constant rule for protein folding remains unknown.

scholarly journals AlphaFold at CASP13

2019 ◽  
Vol 35 (22) ◽  
pp. 4862-4865 ◽  
Author(s):  
Mohammed AlQuraishi
Keyword(s):  
Protein Structure ◽  
Protein Sequence ◽  
Structure Prediction ◽  
Computational Prediction ◽  
Data Bank ◽  
Academic Community ◽  
Physical Contact ◽  
Evolutionary Analysis ◽  
History Of ◽  
First Time

Abstract Summary: Computational prediction of protein structure from sequence is broadly viewed as a foundational problem of biochemistry and one of the most difficult challenges in bioinformatics. Once every two years the Critical Assessment of protein Structure Prediction (CASP) experiments are held to assess the state of the art in the field in a blind fashion, by presenting predictor groups with protein sequences whose structures have been solved but have not yet been made publicly available. The first CASP was organized in 1994, and the latest, CASP13, took place last December, when for the first time the industrial laboratory DeepMind entered the competition. DeepMind's entry, AlphaFold, placed first in the Free Modeling (FM) category, which assesses methods on their ability to predict novel protein folds (the Zhang group placed first in the Template-Based Modeling (TBM) category, which assess methods on predicting proteins whose folds are related to ones already in the Protein Data Bank.) DeepMind's success generated significant public interest. Their approach builds on two ideas developed in the academic community during the preceding decade: (i) the use of co-evolutionary analysis to map residue co-variation in protein sequence to physical contact in protein structure, and (ii) the application of deep neural networks to robustly identify patterns in protein sequence and co-evolutionary couplings and convert them into contact maps. In this Letter, we contextualize the significance of DeepMind's entry within the broader history of CASP, relate AlphaFold's methodological advances to prior work, and speculate on the future of this important problem.

scholarly journals Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics programDivConinto thePHENIXrefinement package

2014 ◽  
Vol 70 (5) ◽  
pp. 1233-1247 ◽  
Author(s):  
Oleg Y. Borbulevych ◽  
Joshua A. Plumley ◽  
Roger I. Martin ◽  
Kenneth M. Merz ◽  
Lance M. Westerhoff
Keyword(s):  
Quantum Mechanics ◽  
A Priori ◽  
Data Bank ◽  
Linear Scaling ◽  
X Ray ◽  
Energy Functionals ◽  
The Past ◽  
Single Structure ◽  
Potential Ligand ◽  
High Throughput Crystallography

Macromolecular crystallographic refinement relies on sometimes dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the model of the macromolecule and any covalently bound ligand(s). The ligand stereochemical restraint file (CIF) requiresa prioriunderstanding of the ligand geometry within the active site, and creation of the CIF is often an error-prone process owing to the great variety of potential ligand chemistry and structure. Stereochemical restraints have been replaced with more robust functionals through the integration of the linear-scaling, semiempirical quantum-mechanics (SE-QM) programDivConwith thePHENIXX-ray refinement engine. ThePHENIX/DivConpackage has been thoroughly validated on a population of 50 protein–ligand Protein Data Bank (PDB) structures with a range of resolutions and chemistry. The PDB structures used for the validation were originally refined utilizing various refinement packages and were published within the past five years.PHENIX/DivCondoes not utilize CIF(s), link restraints and other parameters for refinement and hence it does not make as manya prioriassumptions about the model. Across the entire population, the method results in reasonable ligand geometries and low ligand strains, even when the original refinement exhibited difficulties, indicating thatPHENIX/DivConis applicable to both single-structure and high-throughput crystallography.

scholarly journals SCT: a suite of programs for comparing atomistic models with small-angle scattering data

2015 ◽  
Vol 48 (3) ◽  
pp. 953-961 ◽  
Author(s):  
David W. Wright ◽  
Stephen J. Perkins
Keyword(s):  
Small Angle ◽  
Data Bank ◽  
Scattering Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Angle Scattering ◽  
Atomistic Models ◽  
First Time ◽  
Best Fit ◽  
Theoretical Scattering

Small-angle X-ray and neutron scattering techniques characterize proteins in solution and complement high-resolution structural studies. They are of particular utility when large proteins cannot be crystallized or when the structure is altered by solution conditions. Atomistic models of the averaged structure can be generated through constrained modelling, a technique in which known domain or subunit structures are combined with linker models to produce candidate global conformations. By randomizing the configuration adopted by the different elements of the model, thousands of candidate structures are produced. Next, theoretical scattering curves are generated for each model for trial-and-error fits to the experimental data. From these, a small family of best-fit models is identified. In order to facilitate both the computation of theoretical scattering curves from atomistic models and their comparison with experiment, theSCTsuite of tools was developed.SCTalso includes programs that provide sequence-based estimates of protein volume (either incorporating hydration or not) and add a hydration layer to models for X-ray scattering modelling. The originalSCTsoftware, written in Fortran, resulted in the first atomistic scattering structures to be deposited in the Protein Data Bank, and 77 structures for antibodies, complement proteins and anionic oligosaccharides were determined between 1998 and 2014. For the first time, this software is publicly available, alongside an easier-to-use reimplementation of the same algorithms in Python. Both versions ofSCThave been released as open-source software under the Apache 2 license and are available for download from https://github.com/dww100/sct.

scholarly journals 2. X-Ray Astronomy

1985 ◽  
Vol 19 (1) ◽  
pp. 616-625
Author(s):  
K A Pounds
Keyword(s):  
Data Bank ◽  
The United States ◽  
Scientific Output ◽  
Absorption Feature ◽  
Burst Source ◽  
X Ray ◽  
Proportional Counters ◽  
Large Satellite ◽  
Storage Problem ◽  
First Time

The period leading up to the last IAU General Assembly was dominated in X-ray Astronomy by the results from the Einstein Observatory. This first application of a large, satellite-borne, high resolution X-ray telescope to the study of cosmic sources had led, by the end of orbital operation in April 1981, to the detection of X-ray fluxes from a wide variety of astronomical objects and the full maturing of X-ray Astronomy. During the past three years a strong scientific output has continued to flow from the analysis of the more than 5600 separate Einstein observations, many of which are now widely available via the Einstein Data Bank. In sharp contrast, the peak of activity and scientific output from Einstein will apparently be followed, in the United States, by almost a decade with no new X-ray satellite. Fortunately, successful launches have been achieved in both the Japanese and European programmes, with Tenma launched in February 1983 (to join Hakucho in orbit) followed by EXOSAT three months later. Both these new missions have attracted world-wide interest and observing time on both is at a premium. Of a range of instruments on board the Tenma satellite the most productive is proving to be the large (~800 cm2) array of gas scintillation proportional counters. These detectors, flown for the first time on Tenma (and EXOSAT), provide a factor-of-two increase in spectral resolution over the more conventional proportional counters, an advantage which is particularly valuable in resolving the key emission line and absorption features associated with the K-shell of iron, near ~7 keV. One particularly exciting result reported from this Tenma instrument was an apparent absorption feature at ~4.1 keV in X-ray burst spectra from the source 2S 1636-536 (later supported by EXOSAT observations), the feature being attributed to red-shifted iron absorption in the strong gravitational field close to the neutron star burst source! At the time of writing (December 1984) a power storage problem is limiting the operational efficiency of Tenma, but the scientific payload continues to function well.

scholarly journals Homology-based loop modelling yields more complete crystallographic protein structures

2018 ◽  
Author(s):  
Bart van Beusekom ◽  
Krista Joosten ◽  
Maarten L. Hekkelman ◽  
Robbie P. Joosten ◽  
Anastassis Perrakis
Keyword(s):  
Protein Structure ◽  
Protein Function ◽  
Model Building ◽  
Protein Structures ◽  
Data Bank ◽  
X Ray ◽  
New Methods ◽  
Density Maps ◽  
Complete Protein ◽  
Automated Procedures

AbstractInherent protein flexibility, poor or low-resolution diffraction data, or poor electron density maps, often inhibit building complete structural models during X-ray structure determination. However, advances in crystallographic refinement and model building nowadays often allow to complete previously missing parts. Here, we present algorithms that identify regions missing in a certain model but present in homologous structures in the Protein Data Bank (PDB), and “graft” these regions of interest. These new regions are refined and validated in a fully automated procedure. Including these developments in our PDB-REDO pipeline, allowed to build 24,962 missing loops in the PDB. The models and the automated procedures are publically available through the PDB-REDO databank and web server (https://pdb-redo.eu). More complete protein structure models enable a higher quality public archive, but also a better understanding of protein function, better comparison between homologous structures, and more complete data mining in structural bioinformatics projects.SynopsisThousands of missing regions in existing protein structure models are completed using new methods based on homology.

Diphosphinoazine Rhodium(I) and Iridium(I) Complexes

2006 ◽  
Vol 71 (2) ◽  
pp. 197-206 ◽  
Author(s):  
Martin Pošta ◽  
Jan Čermák ◽  
Pavel Vojtíšek ◽  
Ivana Císařová
Keyword(s):  
Rhodium Complexes ◽  
Iridium Complexes ◽  
X Ray ◽  
First Time

The first rhodium complexes of diphosphinoazines [{RhCl(1,2-η:5,6-η-CH=CHCH2CH2CH=CHCH2CH2)}2 {μ-R2PCH2C(But)=NN=C(But)CH2PR2] (R = Ph, Cy, Pri) were prepared by cleavage of the bridge in chloro(cycloocta-1,5-diene)rhodium(I) dimer, the analogous iridium(I) complexes were also prepared for the first time. The X-ray structures of isostructural rhodium and iridium complexes with bis(dicyclohexylphosphino)pinacoloneazine were determined. Diphosphinoazine ligands in the complexes remained in (Z,Z) configuration bridging two RhCl(C8H12) units.

scholarly journals Quartz Crystallite Size and Moganite Content as Indicators of the Mineralogical Maturity of the Carboniferous Chert: The Case of Cherts from Eastern Asturias (Spain)

Minerals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 611
Author(s):  
Celia Marcos ◽  
María de Uribe-Zorita ◽  
Pedro Álvarez-Lloret ◽  
Alaa Adawy ◽  
Patricia Fernández ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Crystallite Size ◽  
Archaeological Sites ◽  
X Ray Diffraction ◽  
X Ray ◽  
Transmission Electron ◽  
Infrared And Raman Spectroscopy ◽  
First Time ◽  
Geological Formations

Chert samples from different coastal and inland outcrops in the Eastern Asturias (Spain) were mineralogically investigated for the first time for archaeological purposes. X-ray diffraction, X-ray fluorescence, transmission electron microscopy, infrared and Raman spectroscopy and total organic carbon techniques were used. The low content of moganite, since its detection by X-ray diffraction is practically imperceptible, and the crystallite size (over 1000 Å) of the quartz in these cherts would be indicative of its maturity and could potentially be used for dating chert-tools recovered from archaeological sites. Also, this information can constitute essential data to differentiate the cherts and compare them with those used in archaeological tools. However, neither composition nor crystallite size would allow distinguishing between coastal and inland chert outcrops belonging to the same geological formations.

scholarly journals First Report on the Geologic Occurrence of Natural Na–A Zeolite and Associated Minerals in Cretaceous Mudstones of the Paja Formation of Vélez (Santander), Colombia

Crystals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 218
Author(s):  
Carlos Alberto Ríos-Reyes ◽  
German Alfonso Reyes-Mendoza ◽  
José Antonio Henao-Martínez ◽  
Craig Williams ◽  
Alan Dyer
Keyword(s):  
Natural Zeolite ◽  
Scanning Electron Micrographs ◽  
Total Sulfur ◽  
Zeolite A ◽  
X Ray Diffraction ◽  
X Ray ◽  
Mineral Phases ◽  
The World ◽  
Porosity And Permeability ◽  
First Time

This study reports for the first time the geologic occurrence of natural zeolite A and associated minerals in mudstones from the Cretaceous Paja Formation in the urban area of the municipality of Vélez (Santander), Colombia. These rocks are mainly composed of quartz, muscovite, pyrophyllite, kaolinite and chlorite group minerals, framboidal and cubic pyrite, as well as marcasite, with minor feldspar, sulphates, and phosphates. Total organic carbon (TOC), total sulfur (TS), and millimeter fragments of algae are high, whereas few centimeters and not biodiverse small ammonite fossils, and other allochemical components are subordinated. Na–A zeolite and associated mineral phases as sodalite occur just beside the interparticle micropores (honeycomb from framboidal, cube molds, and amorphous cavities). It is facilitated by petrophysical properties alterations, due to processes of high diagenesis, temperatures up to 80–100 °C, with weathering contributions, which increase the porosity and permeability, as well as the transmissivity (fluid flow), allowing the geochemistry remobilization and/or recrystallization of pre-existing silica, muscovite, kaolinite minerals group, salts, carbonates, oxides and peroxides. X-ray diffraction analyses reveal the mineral composition of the mudstones and scanning electron micrographs show the typical cubic morphology of Na–A zeolite of approximately 0.45 mμ in particle size. Our data show that the sequence of the transformation of phases is: Poorly crystalline aluminosilicate → sodalite → Na–A zeolite. A literature review shows that this is an unusual example of the occurrence of natural zeolites in sedimentary marine rocks recognized around the world.

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