scholarly journals In-silico study of Hesperidin, Epigallocatechin (EGCG ), Kaempferol and Quercetin

2021 ◽  
Author(s):  
Soham Chatterjee ◽  
Smrajit Maiti ◽  
Amrita Bannerjee ◽  
Mehak Kanwar
Keyword(s):  
Spatial Data ◽  
Chemical Structure ◽  
Three Dimensional ◽  
Rna Dependent Rna Polymerase ◽  
X Ray ◽  
X Ray Crystallography ◽  
Wide Range ◽  
In Silico Study ◽  
3Cl Protease ◽  
Conclusive Data

Abstract SARS-Cov-2 or COVID-19 has caused a global disaster and catastrophe which has consequently led to a pandemic for the last two decades, the world has faced coronaviruses similar to SARS-Cov-2 such as SARS-Cov and Mers-Cov. In this study, a wide range of proteins such as Plpro (Papain like Protease), Rdrp (RNA-Dependent-RNA-Polymerase), Mpro or 3cl Protease and Spike Protein. The selected proteins were listed retrieved from RCSB PDB(https://www.rcsb.org/) And Zhang lab (https://www.zhanglab.ccmb.med.umich.edu/COVID-19/) with their corresponding and respective PDB-ID. The 3d Structures or 2D Structures of these molecules were selected on the sole basis of resolved resolution (in Å)of the structures during the X-ray crystallography and Electron Microscopy. Structures were retrieved in .pdb format. The three dimensional ligand molecules were retrieved from PubChem chemical structure In Spatial Data Base (.SDF) format. The respective ligand molecules are; Hesperidin, Kaempferol, Quercetin, Epigallocatechin. This molecular docking shows significant data of polyphenols, flavonoids and bioflavonoids inhibiting SARS-Cov-2 proteins which could lead to conclusive data for treatment of polyphenols, flavonoids and bioflavonoids against SARS-Cov-2.

Ulrich Wolfgang Arndt. 23 April 1924 — 24 March 2006

2014 ◽  
Vol 60 ◽  
pp. 39-55
Author(s):  
R. A. Crowther ◽  
A. G. W. Leslie
Keyword(s):  
Protein Structures ◽  
Three Dimensional ◽  
Direct Methods ◽  
Biological Molecules ◽  
Data Generation ◽  
Data Set ◽  
X Ray ◽  
X Ray Crystallography ◽  
Whole Process ◽  
Wide Range

Ulrich (Uli) Arndt was a physicist and engineer whose contributions to the development of a wide range of instrumentation for X-ray crystallography played an important part in our ability to solve the atomic structure of large biological molecules. Such detailed information about protein structures has for the past 50 years underpinned the huge advances in the field of molecular biology. His innovations spanned all aspects of data generation and collection, from improvements in X-ray tubes, through novel designs for diffractometers and cameras to film scanners and more direct methods of X-ray detection. When he started in the field, the intensities of individual X-ray reflections were often estimated by eye from films. By the end of his career the whole process of collecting from a crystal a three-dimensional data set, possibly comprising hundreds of thousands of measurements, was fully automated and very rapid.

scholarly journals Covering complete proteomes with X-ray structures: a current snapshot

2014 ◽  
Vol 70 (11) ◽  
pp. 2781-2793 ◽  
Author(s):  
Marcin J. Mizianty ◽  
Xiao Fan ◽  
Jing Yan ◽  
Eric Chalmers ◽  
Christopher Woloschuk ◽  
...  
Keyword(s):  
Homology Modeling ◽  
Structure Determination ◽  
Large Scale ◽  
Structural Model ◽  
Target Selection ◽  
Three Dimensional ◽  
X Ray ◽  
X Ray Crystallography ◽  
Knowledge Based ◽  
Wide Range

Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.

3-D reconstruction of molecular shape from microcrystal thin sections

1983 ◽  
Vol 41 ◽  
pp. 748-749
Author(s):  
S. Cusack ◽  
J.-C. Jésior
Keyword(s):  
Three Dimensional ◽  
Molecular Shape ◽  
Biological Molecules ◽  
Fourier Space ◽  
Single Particles ◽  
Thin Sections ◽  
Standard Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).

In Silico Identification of a Potent Arsenic Based Approved Drug Darinaparsin against SARS-CoV-2: Inhibitor of RNA Dependent RNA polymerase (RdRp) and Essential Proteases

2020 ◽  
Vol 20 ◽  
Author(s):  
Trinath Chowdhury ◽  
Gourisankar Roymahapatra ◽  
Santi M. Mandal
Keyword(s):  
Rna Polymerase ◽  
Viral Entry ◽  
In Silico ◽  
Rna Dependent Rna Polymerase ◽  
Replication Complex ◽  
In Silico Study ◽  
Life Threatening ◽  
In Vivo Analysis ◽  
3Cl Protease

Background: COVID-19 is a life threatening novel corona viral infection to our civilization and spreading rapidly. Terrific efforts are generous by the researchers to search for a drug to control SARS-CoV-2. Methods: Here, a series of arsenical derivatives were optimized and analyzed with in silico study to search the inhibitor of RNA dependent RNA polymerase (RdRp), the major replication factor of SARS-CoV-2. All the optimized derivatives were blindly docked with RdRp of SARS-CoV-2 using iGEMDOCK v2.1. Results: Based on the lower idock score in the catalytic pocket of RdRp, darinaparsin (-82.52 kcal/mol) revealed most effective among them. Darinaparsin strongly binds with both Nsp9 replicase protein (-8.77 kcal/mol) and Nsp15 endoribonuclease (-8.3 kcal/mol) of SARS-CoV-2 as confirmed from the AutoDock analysis. During infection, the ssRNA of SARS-CoV2 is translated into large polyproteins forming viral replication complex by specific proteases like 3CL protease and papain protease. This is also another target to control the virus infection where darinaparsin also perform the inhibitory role to proteases of 3CL protease (-7.69 kcal/mol) and papain protease (-8.43 kcal/mol). Conclusion: In host cell, the furin protease serves as a gateway to the viral entry and darinaparsin docked with furin protease which revealed a strong binding affinity. Thus, screening of potential arsenic drugs would help in providing the fast invitro to in-vivo analysis towards development of therapeutics against SARS-CoV-2.

Turbulent three-dimensional dielectric electrohydrodynamic convection between two plates

2012 ◽  
Vol 696 ◽  
pp. 228-262 ◽  
Author(s):  
A. Kourmatzis ◽  
J. S. Shrimpton
Keyword(s):  
Spatial Data ◽  
Three Dimensional ◽  
Reynolds Numbers ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Energy Budgets ◽  
Turbulent Regime ◽  
Scalar Flux ◽  
Wide Range ◽  
Scalar Variance

AbstractThe fundamental mechanisms responsible for the creation of electrohydrodynamically driven roll structures in free electroconvection between two plates are analysed with reference to traditional Rayleigh–Bénard convection (RBC). Previously available knowledge limited to two dimensions is extended to three-dimensions, and a wide range of electric Reynolds numbers is analysed, extending into a fully inherently three-dimensional turbulent regime. Results reveal that structures appearing in three-dimensional electrohydrodynamics (EHD) are similar to those observed for RBC, and while two-dimensional EHD results bear some similarities with the three-dimensional results there are distinct differences. Analysis of two-point correlations and integral length scales show that full three-dimensional electroconvection is more chaotic than in two dimensions and this is also noted by qualitatively observing the roll structures that arise for both low (${\mathit{Re}}_{E} = 1$) and high electric Reynolds numbers (up to ${\mathit{Re}}_{E} = 120$). Furthermore, calculations of mean profiles and second-order moments along with energy budgets and spectra have examined the validity of neglecting the fluctuating electric field ${ E}_{i}^{\ensuremath{\prime} } $ in the Reynolds-averaged EHD equations and provide insight into the generation and transport mechanisms of turbulent EHD. Spectral and spatial data clearly indicate how fluctuating energy is transferred from electrical to hydrodynamic forms, on moving through the domain away from the charging electrode. It is shown that ${ E}_{i}^{\ensuremath{\prime} } $ is not negligible close to the walls and terms acting as sources and sinks in the turbulent kinetic energy, turbulent scalar flux and turbulent scalar variance equations are examined. Profiles of hydrodynamic terms in the budgets resemble those in the literature for RBC; however there are terms specific to EHD that are significant, indicating that the transfer of energy in EHD is also attributed to further electrodynamic terms and a strong coupling exists between the charge flux and variance, due to the ionic drift term.

Three-dimensional crystallization of membrane proteins

1988 ◽  
Vol 21 (4) ◽  
pp. 429-477 ◽  
Author(s):  
W. Kühlbrandt
Keyword(s):  
High Resolution ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Crystallography ◽  
Membrane Protein Complexes ◽  
Essential Prerequisite

As recently as 10 years ago, the prospect of solving the structure of any membrane protein by X-ray crystallography seemed remote. Since then, the threedimensional (3-D) structures of two membrane protein complexes, the bacterial photosynthetic reaction centres of Rhodopseudomonas viridis (Deisenhofer et al. 1984, 1985) and of Rhodobacter sphaeroides (Allen et al. 1986, 1987 a, 6; Chang et al. 1986) have been determined at high resolution. This astonishing progress would not have been possible without the pioneering work of Michel and Garavito who first succeeded in growing 3-D crystals of the membrane proteins bacteriorhodopsin (Michel & Oesterhelt, 1980) and matrix porin (Garavito & Rosenbusch, 1980). X-ray crystallography is still the only routine method for determining the 3-D structures of biological macromolecules at high resolution and well-ordered 3-D crystals of sufficient size are the essential prerequisite.

2D X-ray diffraction and molecular modelling of the crystalline structure of polyesters under uniaxial stress

2021 ◽  
pp. 096739112199822
Author(s):  
Ahmed I Abou-Kandil ◽  
Gerhard Goldbeck
Keyword(s):  
Crystalline Structure ◽  
Molecular Modelling ◽  
Three Dimensional ◽  
Uniaxial Stress ◽  
X Ray Diffraction ◽  
X Ray ◽  
Wide Range ◽  
Modelling Techniques ◽  
Diffraction Patterns

Studying the crystalline structure of uniaxially and biaxially drawn polyesters is of great importance due to their wide range of applications. In this study, we shed some light on the behaviour of PET and PEN under uniaxial stress using experimental and molecular modelling techniques. Comparing experiment with modelling provides insights into polymer crystallisation with extended chains. Experimental x-ray diffraction patterns are reproduced by means of models of chains sliding along the c-axis leading to some loss of three-dimensional order, i.e. moving away from the condition of perfect register of the fully extended chains in triclinic crystals of both PET and PEN. This will help us understand the mechanism of polymer crystallisation under uniaxial stress and the appearance of mesophases in some cases as discussed herein.

scholarly journals Low-Zpolymer sample supports for fixed-target serial femtosecond X-ray crystallography

2015 ◽  
Vol 48 (4) ◽  
pp. 1072-1079 ◽  
Author(s):  
Geoffrey K. Feld ◽  
Michael Heymann ◽  
W. Henry Benner ◽  
Tommaso Pardini ◽  
Ching-Ju Tsai ◽  
...  
Keyword(s):  
Protective Antigen ◽  
Three Dimensional ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
Fixed Target ◽  
X Ray ◽  
X Ray Crystallography ◽  
Transmission Electron ◽  
Linac Coherent Light Source ◽  
Efficient Alternative

X-ray free-electron lasers (XFELs) offer a new avenue to the structural probing of complex materials, including biomolecules. Delivery of precious sample to the XFEL beam is a key consideration, as the sample of interest must be serially replaced after each destructive pulse. The fixed-target approach to sample delivery involves depositing samples on a thin-film support and subsequent serial introductionviaa translating stage. Some classes of biological materials, including two-dimensional protein crystals, must be introduced on fixed-target supports, as they require a flat surface to prevent sample wrinkling. A series of wafer and transmission electron microscopy (TEM)-style grid supports constructed of low-Zplastic have been custom-designed and produced. Aluminium TEM grid holders were engineered, capable of delivering up to 20 different conventional or plastic TEM grids using fixed-target stages available at the Linac Coherent Light Source (LCLS). As proof-of-principle, X-ray diffraction has been demonstrated from two-dimensional crystals of bacteriorhodopsin and three-dimensional crystals of anthrax toxin protective antigen mounted on these supports at the LCLS. The benefits and limitations of these low-Zfixed-target supports are discussed; it is the authors' belief that they represent a viable and efficient alternative to previously reported fixed-target supports for conducting diffraction studies with XFELs.

scholarly journals Serial Electron Diffraction Data Processing With diffractem and CrystFEL

2021 ◽  
Vol 8 ◽  
Author(s):  
Robert Bücker ◽  
Pascal Hogan-Lamarre ◽  
R. J. Dwayne Miller
Keyword(s):  
Electron Diffraction ◽  
Data Processing ◽  
Three Dimensional ◽  
Electron Diffraction Data ◽  
New Techniques ◽  
X Ray ◽  
X Ray Crystallography ◽  
Level Of Automation ◽  
Rotation Method ◽  
High Level

Serial electron diffraction (SerialED) is an emerging technique, which applies the snapshot data-collection mode of serial X-ray crystallography to three-dimensional electron diffraction (3D Electron Diffraction), forgoing the conventional rotation method. Similarly to serial X-ray crystallography, this approach leads to almost complete absence of radiation damage effects even for the most sensitive samples, and allows for a high level of automation. However, SerialED also necessitates new techniques of data processing, which combine existing pipelines for rotation electron diffraction and serial X-ray crystallography with some more particular solutions for challenges arising in SerialED specifically. Here, we introduce our analysis pipeline for SerialED data, and its implementation using the CrystFEL and diffractem program packages. Detailed examples are provided in extensive supplementary code.

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