scholarly journals Three-Dimensional Structures of Carbohydrates and Where to Find Them

2020 ◽  
Vol 21 (20) ◽  
pp. 7702 ◽  
Author(s):  
Sofya I. Scherbinina ◽  
Philip V. Toukach
Keyword(s):  
Experimental Data ◽  
Molecular Modeling ◽  
Computational Methods ◽  
Three Dimensional ◽  
Structural Diversity ◽  
Structural Data ◽  
Structural Features ◽  
Data Validation ◽  
Data Generation ◽  
Efficient Treatment

Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.

scholarly journals Structural Aspects of Phenylalanylation and Quality Control in Three Major Forms of Phenylalanyl-tRNA Synthetase

2010 ◽  
Vol 2010 ◽  
pp. 1-7 ◽  
Author(s):  
Liron Klipcan ◽  
Igal Finarov ◽  
Nina Moor ◽  
Mark G. Safro
Keyword(s):  
Quaternary Structure ◽  
Thermus Thermophilus ◽  
Three Dimensional ◽  
Structural Diversity ◽  
Structural Data ◽  
Trna Synthetase ◽  
Transfer Rnas ◽  
Trna Synthetases ◽  
Editing Activity ◽  
Structural Aspects

Aminoacyl-tRNA synthetases (aaRSs) are a canonical set of enzymes that specifically attach corresponding amino acids to their cognate transfer RNAs in the cytoplasm, mitochondria, and nucleus. The aaRSs display great differences in primary sequence, subunit size, and quaternary structure. Existence of three types of phenylalanyl-tRNA synthetase (PheRS)—bacterial (αβ)2, eukaryotic/archaeal cytosolic (αβ)2, and mitochondrial α—is a prominent example of structural diversity within the aaRSs family. Although archaeal/eukaryotic and bacterial PheRSs share common topology of the core domains and the B3/B4 interface, where editing activity of heterotetrameric PheRSs is localized, the detailed investigation of the three-dimensional structures from three kingdoms revealed significant variations in the local design of their synthetic and editing sites. Moreover, as might be expected from structural data eubacterial, Thermus thermophilus and human cytoplasmic PheRSs acquire different patterns of tRNAPhe anticodon recognition.

scholarly journals Membrane Protein Complex ExbB4-ExbD1-TonB1from Escherichia coli Demonstrates Conformational Plasticity

2015 ◽  
Vol 197 (11) ◽  
pp. 1873-1885 ◽  
Author(s):  
Aleksandr Sverzhinsky ◽  
Jacqueline W. Chung ◽  
Justin C. Deme ◽  
Lucien Fabre ◽  
Kristian T. Levey ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Iron Acquisition ◽  
Proton Translocation ◽  
Three Dimensional ◽  
Structural Data ◽  
Structural Features ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Content Type

ABSTRACTIron acquisition at the outer membrane (OM) of Gram-negative bacteria is powered by the proton motive force (PMF) of the cytoplasmic membrane (CM), harnessed by the CM-embedded complex of ExbB, ExbD, and TonB. Its stoichiometry, ensemble structural features, and mechanism of action are unknown. By panning combinatorial phage libraries, periplasmic regions of dimerization between ExbD and TonB were predicted. Using overexpression of full-length His6-taggedexbB-exbDand S-taggedtonB, we purified detergent-solubilized complexes of ExbB-ExbD-TonB fromEscherichia coli. Protein-detergent complexes of ∼230 kDa with a hydrodynamic radius of ∼6.0 nm were similar to previously purified ExbB4-ExbD2complexes. Significantly, they differed in electronegativity by native agarose gel electrophoresis. The stoichiometry was determined to be ExbB4-ExbD1-TonB1. Single-particle electron microscopy agrees with this stoichiometry. Two-dimensional averaging supported the phage display predictions, showing two forms of ExbD-TonB periplasmic heterodimerization: extensive and distal. Three-dimensional (3D) particle classification showed three representative conformations of ExbB4-ExbD1-TonB1. Based on our structural data, we propose a model in which ExbD shuttles a proton across the CM via an ExbB interprotein rearrangement. Proton translocation would be coupled to ExbD-mediated collapse of extended TonB in complex with ligand-loaded receptors in the OM, followed by repositioning of TonB through extensive dimerization with ExbD. Here we present the first report for purification of the ExbB-ExbD-TonB complex, molar ratios within the complex (4:1:1), and structural biology that provides insights into 3D organization.IMPORTANCEReceptors in the OM of Gram-negative bacteria allow entry of iron-bound siderophores that are necessary for pathogenicity. Numerous iron-acquisition strategies rely upon a ubiquitous and unique protein for energization: TonB. Complexed with ExbB and ExbD, the Ton system links the PMF to OM transport. Blocking iron uptake by targeting a vital nanomachine holds promise in therapeutics. Despite much research, the stoichiometry, structural arrangement, and molecular mechanism of the CM-embedded ExbB-ExbD-TonB complex remain unreported. Here we demonstratein vitroevidence of ExbB4-ExbD1-TonB1complexes. Using 3D EM, we reconstructed the complex in three conformational states that show variable ExbD-TonB heterodimerization. Our structural observations form the basis of a model for TonB-mediated iron acquisition.

Recent Trends in Drug Design and Discovery

2020 ◽  
Vol 20 (19) ◽  
pp. 1761-1770
Author(s):  
Devadasan Velmurugan ◽  
R. Pachaiappan ◽  
Chandrasekaran Ramakrishnan
Keyword(s):  
Machine Learning ◽  
Data Analysis ◽  
Molecular Modeling ◽  
Drug Design ◽  
Computational Methods ◽  
Data Analytics ◽  
Drug Targets ◽  
Structural Data ◽  
Target Protein ◽  
Structure Based Drug Design

Introduction: Structure-based drug design is a wide area of identification of selective inhibitors of a target of interest. From the time of the availability of three dimensional structure of the drug targets, mostly the proteins, many computational methods had emerged to address the challenges associated with drug design process. Particularly, drug-likeness, druggability of the target protein, specificity, off-target binding, etc., are the important factors to determine the efficacy of new chemical inhibitors. Objective: The aim of the present research was to improve the drug design strategies in field of design of novel inhibitors with respect to specific target protein in disease pathology. Recent statistical machine learning methods applied for structural and chemical data analysis had been elaborated in current drug design field. Methods: As the size of the biological data shows a continuous growth, new computational algorithms and analytical methods are being developed with different objectives. It covers a wide area, from protein structure prediction to drug toxicity prediction. Moreover, the computational methods are available to analyze the structural data of varying types and sizes of which, most of the semi-empirical force field and quantum mechanics based molecular modeling methods showed a proven accuracy towards analysing small structural data sets while statistics based methods such as machine learning, QSAR and other specific data analytics methods are robust for large scale data analysis. Results: In this present study, the background has been reviewed for new drug lead development with respect specific drug targets of interest. Overall approach of both the extreme methods were also used to demonstrate with the plausible outcome. Conclusion: In this chapter, we focus on the recent developments in the structure-based drug design using advanced molecular modeling techniques in conjunction with machine learning and other data analytics methods. Natural products based drug discovery is also discussed.

scholarly journals Sequence-dependent structural changes in a self-assembling DNA oligonucleotide

2015 ◽  
Vol 71 (12) ◽  
pp. 2471-2478 ◽  
Author(s):  
Maithili Saoji ◽  
Paul J. Paukstelis
Keyword(s):  
Structural Changes ◽  
Three Dimensional ◽  
Structural Diversity ◽  
Structural Features ◽  
Base Pairing ◽  
Base Pairs ◽  
Dna Oligonucleotides ◽  
Self Assembling ◽  
Structure Relationship ◽  
Noncanonical Base Pairs

DNA has proved to be a remarkable molecule for the construction of sophisticated two-dimensional and three-dimensional architectures because of its programmability and structural predictability provided by complementary Watson–Crick base pairing. DNA oligonucleotides can, however, exhibit a great deal of local structural diversity. DNA conformation is strongly linked to both environmental conditions and the nucleobase identities inherent in the oligonucleotide sequence, but the exact relationship between sequence and local structure is not completely understood. This study examines how a single-nucleotide addition to a class of self-assembling DNA 13-mers leads to a significantly different overall structure under identical crystallization conditions. The DNA 13-mers self-assemble in the presence of Mg2+through a combination of Watson–Crick and noncanonical base-pairing interactions. The crystal structures described here show that all of the predicted Watson–Crick base pairs are present, with the major difference being a significant rearrangement of noncanonical base pairs. This includes the formation of a sheared A–G base pair, a junction of strands formed from base-triple interactions, and tertiary interactions that generate structural features similar to tandem sheared G–A base pairs. The adoption of this alternate noncanonical structure is dependent in part on the sequence in the Watson–Crick duplex region. These results provide important new insights into the sequence–structure relationship of short DNA oligonucleotides and demonstrate a unique interplay between Watson–Crick and noncanonical base pairs that is responsible for crystallization fate.

scholarly journals Cysteine Mutagenesis and Computer Modeling of the S6 Region of an Intermediate Conductance IKCa Channel

2002 ◽  
Vol 120 (1) ◽  
pp. 99-116 ◽  
Author(s):  
Manuel Simoes ◽  
Line Garneau ◽  
Hélène Klein ◽  
Umberto Banderali ◽  
Fadi Hobeila ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Structural Data ◽  
Structural Features ◽  
K Channel ◽  
Crystallographic Structure ◽  
Channel Pore ◽  
State Dependent ◽  
Cysteine Scanning Mutagenesis ◽  
Three Dimensional Models ◽  
State Configuration

Cysteine-scanning mutagenesis (SCAM) and computer-based modeling were used to investigate key structural features of the S6 transmembrane segment of the calcium-activated K+ channel of intermediate conductance IKCa. Our SCAM results show that the interaction of [2-(trimethylammonium)ethyl] methanethiosulfonate bromide (MTSET) with cysteines engineered at positions 275, 278, and 282 leads to current inhibition. This effect was state dependent as MTSET appeared less effective at inhibiting IKCa in the closed (zero Ca2+ conditions) than open state configuration. Our results also indicate that the last four residues in S6, from A283 to A286, are entirely exposed to water in open IKCa channels, whereas MTSET can still reach the 283C and 286C residues with IKCa maintained in a closed state configuration. Notably, the internal application of MTSET or sodium (2-sulfonatoethyl) methanethiosulfonate (MTSES) caused a strong Ca2+-dependent stimulation of the A283C, V285C, and A286C currents. However, in contrast to the wild-type IKCa, the MTSET-stimulated A283C and A286C currents appeared to be TEA insensitive, indicating that the MTSET binding at positions 283 and 286 impaired the access of TEA to the channel pore. Three-dimensional structural data were next generated through homology modeling using the KcsA structure as template. In accordance with the SCAM results, the three-dimensional models predict that the V275, T278, and V282 residues should be lining the channel pore. However, the pore dimensions derived for the A283–A286 region cannot account for the MTSET effect on the closed A283C and A286 mutants. Our results suggest that the S6 domain extending from V275 to V282 possesses features corresponding to the inner cavity region of KcsA, and that the COOH terminus end of S6, from A283 to A286, is more flexible than predicted on the basis of the closed KcsA crystallographic structure alone. According to this model, closure by the gate should occur at a point located between the T278 and V282 residues.

scholarly journals Synthesis, magneto-structural features and thermal behavior of a new MOF

2014 ◽  
Vol 70 (a1) ◽  
pp. C1232-C1232
Author(s):  
Khadidja Aliouane ◽  
Belkacem Benmerad ◽  
Narimène Rahahlia ◽  
Hamza Kherfi ◽  
Achoura Guehria-Laïdoudi ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Structural Data ◽  
Structural Features ◽  
Crystal Structure Analysis ◽  
Magnetic Interactions ◽  
Rare Earth Complex ◽  
Polymeric Compound ◽  
Thermal Stabilities ◽  
Synthesis Conditions ◽  
Weight Losses

By applying soft synthesis conditions, in presence of a mixture that contains malonic acid, (3 mmol), lanthanide salt CeCl3.7H2O (1 mmol), alkaline-earth hydroxide Ca(OH)2 (1 mmol), and at pH below 4, we have obtained single crystals of a novel rare-earth complex which includes the dianion [L2-], {[Ce2(C3H2O4)3(H2O)3].2H2O}.The given formula was deduced from the single crystal structure analysis. The asymmetric unit corresponds to chemical formula (Figure 1). This novel polymeric compound is a three-dimensional MOF, built up from cross-linked infinite chains of one-edge-shared CeO7(H2O)3 and CeO9 polyhedrons embedding solvent molecules. Each crystallographically different metal is connected to two neighbouring ones, through four μ2-oxo bridges, to form repeat four-membered typical Ce/O/Ce/O rings. The three independant ligands show different conformations of their end functional groups: syn-syn, syn-anti, anti-anti, giving explanation for the concomitant magnetic interactions and interesting magneto-structural data. These studies are still in progress. The TG curve shows five successive weight losses. The material begins losing weight directly upon starting the thermal gravimetric experiments. It is one of the more unstable lanthanide malonates known. The correlative thermal behaviour data and X-Ray structural sub-features of the novel Ce(III)-based MOF obtained, brought out the great supramolecular effects: decarboxylation process, crystalline, and thermal stabilities are much more related to the specific infinite hydrogen patterns, than the size, shape, and embedding capability of voids accommodated in the 3D packing.

scholarly journals Structural diversity in copper(I) iodide complexes with 6-thioxopiperidin-2-one, piperidine-2,6-dithione and isoindoline-1,3-dithione ligands

2020 ◽  
Vol 76 (8) ◽  
pp. 1336-1344
Author(s):  
Amelia M. Wheaton ◽  
Ilia A. Guzei ◽  
John F. Berry
Keyword(s):  
Three Dimensional ◽  
Structural Diversity ◽  
Structural Features ◽  
Acta Cryst ◽  
Bridging Ligands ◽  
Hydrogen Bonding Interactions ◽  
Scattering Effects ◽  
Internuclear Distances ◽  
Solvent Molecules ◽  
The Given

Copper(I) iodide complexes are well known for displaying a diverse array of structural features even when only small changes in ligand design are made. This structural diversity is well displayed by five copper(I) iodide compounds reported here with closely related piperidine-2,6-dithione (SNS), isoindoline-1,3-dithione (SNS6), and 6-thioxopiperidin-2-one (SNO) ligands: di-μ-iodido-bis[(acetonitrile-κN)(6-sulfanylidenepiperidin-2-one-κS)copper(I)], [Cu2I2(CH3CN)2(C5H7NOS)2] (I), bis(acetonitrile-κN)tetra-μ3-iodido-bis(6-sulfanylidenepiperidin-2-one-κS)-tetrahedro-tetracopper(I), [Cu4I4(CH3CN)4(C5H7NOS)4] (II), catena-poly[[(μ-6-sulfanylidenepiperidin-2-one-κ2 O:S)copper(I)]-μ3-iodido], [CuI(C5H7NOS)] n (III), poly[[(piperidine-2,6-dithione-κS)copper(I)]-μ3-iodido], [CuI(C5H7NS2)] n (IV), and poly[[(μ-isoindoline-1,3-dithione-κ2 S:S)copper(I)]-μ3-iodido], [CuI(C8H5NS2)] n (V). Compounds I and II crystallize as discrete dimeric and tetrameric complexes, whereas III, IV, and V crystallize as polymeric two-dimensional sheets. To the best of our knowledge, compound III is the first instance of an extended hexagonal [Cu3I3] structure that is not supported by bridging ligands. Structures I, II, and IV display weak to moderately strong Cu...Cu cuprophilic interactions [Cu...Cu internuclear distances range between 2.5803 (10) and 2.8485 (14) Å]. All structures except III display weak hydrogen-bonding interactions between the N—H of the ligand and the μ2 and μ3-I− atoms. Structure III contains classical N–H...O interactions between the SNO ligands that connect the molecules in a three-dimensional framework. Complex V features π–π stacking interactions between the aryl rings of the SNS6 ligands within the same polymeric sheet. In structure IV, there were three partially occupied solvent molecules of dichloromethane and one partially occupied molecule of acetonitrile present in the asymmetric unit. The SQUEEZE routine [Spek (2015). Acta Cryst. C71, 9–18] was used to correct the diffraction data for diffuse scattering effects and to identify the solvent molecules. The given chemical formula and other crystal data do not take into account the solvent molecules.

scholarly journals Time for a Plant Structural Economics Spectrum

2020 ◽  
Author(s):  
Hans Verbeeck ◽  
Marijn Bauters ◽  
Jackson Toby ◽  
Alexander Schenkin ◽  
Mathias Disney ◽  
...  
Keyword(s):  
Woody Plants ◽  
Laser Scanning ◽  
Three Dimensional ◽  
Structural Diversity ◽  
Functional Trait ◽  
Structural Features ◽  
Dimensional Structure ◽  
Leaf Economics Spectrum ◽  
Tree Form ◽  
Structural Trait

<p>We argue that tree and crown structural diversity can and should be integrated in the whole-plant economics spectrum. Ecologists have found that certain functional trait combinations have been more viable than others during evolution, generating a trait trade-off continuum which can be summarized along a few axes of variation, such as the “worldwide leaf economics spectrum” and the “wood economics spectrum”. However, for woody plants the crown structural diversity should be included as well in the recently introduced “global spectrum of plant form and function”, which now merely focusses on plant height as structural factor. The recent revolution in terrestrial laser scanning (TLS) unlocks the possibility to describe the three dimensional structure of trees quantitatively with unprecedented detail. We demonstrate that based on TLS data, a multidimensional structural trait space can be constructed, which can be decomposed into a few descriptive axes or spectra. We conclude that the time has come to develop a “structural economics spectrum” for woody plants based on structural trait data across the globe. We make suggestions as to what structural features might lie on this spectrum and how these might help improve our understanding of tree form-function relationships.</p>

scholarly journals Structure of the EphB6 receptor ectodomain

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0247335
Author(s):  
Emilia O. Mason ◽  
Yehuda Goldgur ◽  
Dorothea Robev ◽  
Andrew Freywald ◽  
Dimitar B. Nikolov ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Mechanism Of Action ◽  
Tyrosine Kinases ◽  
Three Dimensional ◽  
Structural Data ◽  
Structural Features ◽  
Dimensional Structure ◽  
Eph Receptors ◽  
X Ray Crystallography ◽  
General Importance

Eph receptors are the largest group amongst the receptor tyrosine kinases and are divided into two subgroups, A and B, based on ligand binding specificities and sequence conservation. Through ligand-induced and ligand-independent activities, Ephs play central roles in diverse biological processes, including embryo development, regulation of neuronal signaling, immune responses, vasculogenesis, as well as tumor initiation, progression, and metastasis. The Eph extracellular regions (ECDs) are constituted of multiple domains, and previous structural studies of the A class receptors revealed how they interact with ephrin ligands and simultaneously mediate Eph-Eph clustering necessary for biological activity. Specifically, EphA structures highlighted a model, where clustering of ligand-bound receptors relies on two distinct receptor/receptor interfaces. Interestingly, most unliganded A class receptors also form an additional, third interface, between the ligand binding domain (LBD) and the fibronectin III domain (FN3) of neighboring molecules. Structures of B-class Eph ECDs, on the other hand, have never been reported. To further our understanding of Eph receptor function, we crystallized the EphB6-ECD and determined its three-dimensional structure using X-ray crystallography. EphB6 has important functions in both normal physiology and human malignancies and is especially interesting because this atypical receptor innately lacks kinase activity and our understanding of the mechanism of action is still incomplete. Our structural data reveals the overall EphB6-ECD architecture and shows EphB6-LBD/FN3 interactions similar to those observed for the unliganded A class receptors, suggesting that these unusual interactions are of general importance to the Eph group. We also observe unique structural features, which likely reflect the atypical signaling properties of EphB6, namely the need of co-receptor(s) for this kinase-inactive Eph. These findings provide new valuable information on the structural organization and mechanism of action of the B-class Ephs, and specifically EphB6, which in the future will assist in identifying clinically relevant targets for cancer therapy.

Methods for making stereoslides and -prints, with freeze-etched olfactory epithelium as example

1984 ◽  
Vol 42 ◽  
pp. 704-705
Author(s):  
Bert Ph. M. Menco ◽  
Ido F. Menco ◽  
Frans L.T. Verdonk
Keyword(s):  
Electron Microscope ◽  
Olfactory Epithelium ◽  
Three Dimensional ◽  
Supporting Cell ◽  
Structural Features ◽  
Extensive Study ◽  
Sprague Dawley ◽  
Freezing Method ◽  
Respiratory Epithelia ◽  
Three Dimensional Presentation

Previously we presented an extensive study of the distributions of intramembranous particles of structures in apical surfaces of nasal olfactory and respiratory epithelia of the Sprague-Dawley rat. For the same structures these distributions were compared in samples which were i) chemically fixed and cryo-protected with glycerol before cryo-fixation, after excision, and ii)ultra-rapidly frozen by means of the slam-freezing method. Since a three-dimensional presentation markedly improves visualization of structural features micrographs were presented as stereopairs. Two exposures were made by tiling the sample stage of the electron microscope 6° in either direction with an eucentric goniometer. The negatives (Agfa Pan 25 Professional) were reversed with Kodak Technical Pan Film 2415 developed in D76 1:1. The prints were made from these reversed negatives. As an example tight-junctional features of an olfactory supporting cell in a region where this cell conjoined with two other cells are presented (Fig. 1).

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