scholarly journals Conserved Structural Features of Core Oligosaccharides among the Lipopolysaccharides of Respiratory Pathogens from the Genus Bordetella Analyzed Exclusively by NMR Spectroscopy

2021 ◽  
Vol 22 (3) ◽  
pp. 1029
Author(s):  
Karolina Ucieklak ◽  
Sabina Koj ◽  
Tomasz Niedziela
Keyword(s):  
Whooping Cough ◽  
Structural Data ◽  
Structural Features ◽  
Carbohydrate Antigen ◽  
Common Element ◽  
Gram Negative Bacteria ◽  
Respiratory Pathogens ◽  
Vaccine Component ◽  
Unique Identity ◽  
Main Components

Bacterial pathogens expose on the cell surface a variety of complex carbohydrate molecules. Gram-negative bacteria produce lipopolysaccharides, which are the main components of the outer membrane of bacterial envelopes and play a major role in host–pathogen interactions. B. pertussis, B. parapertussis, B. bronchiseptica, and B. holmesii, are mammalian respiratory pathogens, having substantial economic impact on human health and agriculture. B. pertussis is responsible for whooping cough (pertussis) and B. holmesii is the second pertussis etiological factor, but the current anti-pertussis vaccines do not provide cross-protection. The structural data on any given hypothetical carbohydrate antigen is a prerequisite for further analysis of structure-related activities and their interaction with hosts. 1H NMR spectra constitute fingerprints of the analyzed glycans and provide unique identity information. The concept of structure-reporter groups has now been augmented by 1H,13C-correlation spectra of the Bordetella oligosaccharides. The comparative analysis of Bordetellae oligosaccharides (OS) revealed that the hexasaccharide, comprising the α-GlcpN, α-GlcpA, 4,6-disubstituted-β-Glcp, 2,7-disubstituted-l-α-d-Hepp, 3,4-disubstituted-l-α-d-Hepp, and Kdo, constitute the least variable OS segment. This minimal common element in the structure of lipopolysaccharides of Bordetellae could be used to devise a universal cross-protective vaccine component against infections with various bacteria from the genus Bordetella.

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.

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.

ISSUES OF ETHNOCULTURAL TRADITIONS DEVELOPMENT IN MODERN ARTISTIC PRACTICE

2020 ◽  
Vol 1 (4) ◽  
pp. 50-54
Author(s):  
K. K. Murataev ◽  
◽  
S. M. Krykbayeva ◽  
Keyword(s):  
Folk Art ◽  
Structural Features ◽  
Artistic Practice ◽  
Creative Development ◽  
Traditional Art ◽  
Spatial Features ◽  
Applied Art ◽  
Main Components ◽  
Structurally Stable ◽  
Figurative Interpretation

The article deals with insufficiently studied theoretical aspects of revealing and analyzing new elements and motives of artistic and compositional means of expression in folk art, as well as topical issues concerning determining principles and possible options for their creative development in modern decorative and applied art, design, and artistic practice in general. The most important structural features of shaping in traditional art in the ontologically interrelated system "nature — man — object" are analyzed. The main structurally stable elements and components in Kazakh folk ornament are distinguished and characterized, these are the circle, S-shaped element, cruciform and triangular components. The evolution of their ideological and figurative interpretation and symbolism is traced, and their role in the genesis of folk art traditions formed over thousands of years is revealed. The selected basic elements of folk ornament, as the main components of means of artistic expression, are proposed to be defined and developed in line with modern interpretations of artistic and aesthetic categories — dynamics, statics, harmony and their decorative variations in accordance with the volumetric and spatial features of form.

Ultrastructure of the osphradium of the Tertiary relict snail, Campanile symbolicum Iredale (Mollusca, Streptoneura)

1992 ◽  
Vol 337 (1282) ◽  
pp. 457-469 ◽  
Keyword(s):  
Smooth Endoplasmic Reticulum ◽  
Sense Organ ◽  
Central Zone ◽  
Structural Data ◽  
Structural Features ◽  
Sensory Epithelium ◽  
Sensory Cells ◽  
Cell Type ◽  
Sensory Cilia ◽  
A Cell

The osphradium of Campanile symbolicum Iredale, 1917 is a gill-like, bipectinate sense organ, which is located at the left side of the mantle roof. The mass of the deeply clefted sensory epithelium of the leaflets is built up by sensory cells, which are provided with deeply invaginated aberrant cilia and large cytosomes containing pigment formations. In addition, many free nerve processes are present, bearing a single or few sensory cilia with accessory centrioles. Polyciliary cells are interspersed. A cell type with netlike or concentrically arranged smooth endoplasmic reticulum is commonly found near the central axis of the osphradium . The central zone of each leaflet includes nervous tissue and a complicated muscular grid, with pore cells and fibroblasts also present. Based on the fine-structural data the functional and ecological significance of the osphradium of Campanile symbolicum is discussed. The com bination of herbivory and a lamellar osphradium is rare among the Gastropoda, suggesting that the osphradium of Campanile might also be involved in reproductive biology. Many fine-structural features of the osphradium of Campanile symbolicum are unique among the gastropods and reflect the phylogenetic isolation of this relict snail. The net-like cell type, however, is probably homologous with the so-called Si4 cell in the rem aining caenogastropods, for which a largely different osphradial fine-structure is diagnostic. The affinities of Campanile symbolicum are probably closer to the Caenogastropoda than to the Allogastropoda and Euthyneura. With present knowledge it might be best classified near the base or even as the first clade within the Caenogastropoda.

scholarly journals A g-Type Lysozyme from Deep-Sea Hydrothermal Vent Shrimp Kills Selectively Gram-Negative Bacteria

Molecules ◽  
2021 ◽  
Vol 26 (24) ◽  
pp. 7624
Author(s):  
Jing-Chang Luo ◽  
Jian Zhang ◽  
Li Sun
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Binding Capacity ◽  
Cellular Membrane ◽  
Structural Features ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Bacterial Binding ◽  
Muramidase Activity

Lysozyme is a key effector molecule of the innate immune system in both vertebrate and invertebrate. It is classified into six types, one of which is the goose-type (g-type). To date, no study on g-type lysozyme in crustacean has been documented. Here, we report the identification and characterization of a g-type lysozyme (named LysG1) from the shrimp inhabiting a deep-sea hydrothermal vent in Manus Basin. LysG1 possesses conserved structural features of g-type lysozymes. The recombinant LysG1 (rLysG1) exhibited no muramidase activity and killed selectively Gram-negative bacteria in a manner that depended on temperature, pH, and metal ions. rLysG1 bound target bacteria via interaction with bacterial cell wall components, notably lipopolysaccharide (LPS), and induced cellular membrane permeabilization, which eventually caused cell lysis. The endotoxin-binding capacity enabled rLysG1 to alleviate the inflammatory response induced by LPS. Mutation analysis showed that the bacterial binding and killing activities of rLysG1 required the integrity of the conserved α3 and 4 helixes of the protein. Together, these results provide the first insight into the activity and working mechanism of g-type lysozyme in crustacean and deep-sea organisms.

scholarly journals Insights into AMS/PCAT transporters from biochemical and structural characterization of a double Glycine motif protease

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Silvia C Bobeica ◽  
Shi-Hui Dong ◽  
Liujie Huo ◽  
Nuria Mazo ◽  
Martin I McLaughlin ◽  
...  
Keyword(s):  
Structural Data ◽  
Leader Peptide ◽  
Gram Negative Bacteria ◽  
Protease Domain ◽  
Peptide Recognition ◽  
Gram Positive Bacteria ◽  
Dual Functional ◽  
Signaling Peptides

The secretion of peptides and proteins is essential for survival and ecological adaptation of bacteria. Dual-functional ATP-binding cassette transporters export antimicrobial or quorum signaling peptides in Gram-positive bacteria. Their substrates contain a leader sequence that is excised by an N-terminal peptidase C39 domain at a double Gly motif. We characterized the protease domain (LahT150) of a transporter from a lanthipeptide biosynthetic operon in Lachnospiraceae and demonstrate that this protease can remove the leader peptide from a diverse set of peptides. The 2.0 Å resolution crystal structure of the protease domain in complex with a covalently bound leader peptide demonstrates the basis for substrate recognition across the entire class of such transporters. The structural data also provide a model for understanding the role of leader peptide recognition in the translocation cycle, and the function of degenerate, non-functional C39-like domains (CLD) in substrate recruitment in toxin exporters in Gram-negative bacteria.

scholarly journals Composition of the Essential Oils and Antibacterial Activities of Hymenocrater yazdianus, Stachys obtusicrena and Nepeta asterotricha Three Labiatae Herbs Growing Wild in Iran

2012 ◽  
Vol 7 (1) ◽  
pp. 1934578X1200700 ◽  
Author(s):  
Shiva Masoudi ◽  
Abdolhossein Rustaiyan ◽  
Razieh Mohebat ◽  
Mohammad Hossein Mosslemin
Keyword(s):  
Essential Oils ◽  
Antibacterial Activities ◽  
Gram Negative Bacteria ◽  
Inhibitory Zone ◽  
Growth Inhibitory ◽  
Germacrene D ◽  
Leaf Oil ◽  
Main Components ◽  
Total Oil ◽  
Stem Leaf

Water-distilled essential oils from leaves of Hymenocrater yazdianus Rech.f., flowers of Stachys obtusicrena Boiss., and stems and flowers of Nepeta asterotricha Rech.f, which are endemic to Iran, were analyzed by GC and GC/MS. Fifty-five components of the leaf oil of H. yazdianus were characterized, representing 95.1% of the total components detected. The major constituents were identified as 1,8-cineole (17.6%), β-caryophyllene (13.9%), α-pinene (10.6%) and caryophyllene oxide (10.4%). Germacrene-D (37.5%) and α-bisabolol (23.5%) were the main components among the twenty constituents characterized in the flower oil of S. obtusicrena, representing 90.8% of the total components detected. Thirty-five compounds representing 93.0% of the stem oil of N. asterotrica were identified among which terpinen-4-ol (22.8%) and γ-terpinene (14.1%) were the major ones. The flower oil of the species was characterized by higher amounts of terpinen-4-ol (24.8%), 4aα, 7aβ-nepetalactone (18.2%) and 1,8-cineole (11.6%) among the thirty-three components comprising 98.5% of the total oil detected. The antibacterial activity of the stem, leaf and flower oils of Hymenocrater yazdianus, Stachys obtusicrena and Nepeta asterotricha against seven Gram-positive and Gram-negative bacteria were determined using the MIC method. The growth inhibitory zone (mm) was also measured.

scholarly journals Determination of Chemical Composition and Antimicrobial Activity of Melaleuca cajuputi Essential Oil from Quang Tri Province, Vietnam

2020 ◽  
Vol 32 (9) ◽  
pp. 2203-2207
Author(s):  
TRAN QUOC TOAN ◽  
LAI PHUONG PHUONG THAO ◽  
NGUYEN QUYET CHIEN ◽  
NGUYEN THI HONG VAN ◽  
ÐOAN LAN PHUONG ◽  
...  
Keyword(s):  
Essential Oil ◽  
Maximum Yield ◽  
Batch Process ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Qualitative And Quantitative ◽  
Melaleuca Cajuputi ◽  
Main Components ◽  
Bactericidal Agent

The essential oil of Melaleuca cajuputi was obtained by hydrodistillation method. This work aims to adopt water as a solvent in a batch process to extract essential oil from Melaleuca cajuputi fresh leaves. The leaves are collected from Quang Tri Province, Vietnam. Analysis of constituents was performed by GC/MS. The maximum yield ranged from 0.6 to 0.7%. Several compounds have been identified in high quantities and meaningful qualitative and quantitative differences have been observed under different conditions. The main components of the M. cajuputi essential oil included eucalyptol (27.512%), γ-terpinene (8.59%), terpinolene (9.047%), β-eudesmene (3.359%), α- selinene (3.889%), α-terpineol (4.108%), 1R-α-pinene (2.158%), caryophyllene (6.48%) and α-caryophyllene (3.522%). This study has confirmed that the essential oil of M. cajuputi essential oil is a promising bactericidal agent on several Gram-positive and Gram-negative bacteria.

scholarly journals Understanding Structural Features of Microbial Lipases–-An Overview

2008 ◽  
Vol 3 ◽  
pp. ACI.S551 ◽  
Author(s):  
John Geraldine Sandana Mala ◽  
Satoru Takeuchi
Keyword(s):  
Structural Analysis ◽  
Candida Rugosa ◽  
Structural Data ◽  
Data Bank ◽  
Candida Rugosa Lipase ◽  
Structural Features ◽  
X Ray Crystallography ◽  
Versatile Tool ◽  
Microbial Lipases

The structural elucidations of microbial lipases have been of prime interest since the 1980s. Knowledge of structural features plays an important role in designing and engineering lipases for specific purposes. Significant structural data have been presented for few microbial lipases, while, there is still a structure-deficit, that is, most lipase structures are yet to be resolved. A search for ‘lipase structure’ in the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) returns only 93 hits (as of September 2007) and, the NCBI database ( http://www.ncbi.nlm.nih.gov ) reports 89 lipase structures as compared to 14719 core nucleotide records. It is therefore worthwhile to consider investigations on the structural analysis of microbial lipases. This review is intended to provide a collection of resources on the instrumental, chemical and bioinformatics approaches for structure analyses. X-ray crystallography is a versatile tool for the structural biochemists and is been exploited till today. The chemical methods of recent interests include molecular modeling and combinatorial designs. Bioinformatics has surged striking interests in protein structural analysis with the advent of innumerable tools. Furthermore, a literature platform of the structural elucidations so far investigated has been presented with detailed descriptions as applicable to microbial lipases. A case study of Candida rugosa lipase (CRL) has also been discussed which highlights important structural features also common to most lipases. A general profile of lipase has been vividly described with an overview of lipase research reviewed in the past.

scholarly journals The structure of the proteinaceous inhibitor PliI fromAeromonas hydrophilain complex with its target lysozyme

2015 ◽  
Vol 71 (2) ◽  
pp. 344-351 ◽  
Author(s):  
Seppe Leysen ◽  
Joris M. Van Herreweghe ◽  
Kazunari Yoneda ◽  
Makoto Ogata ◽  
Taichi Usui ◽  
...  
Keyword(s):  
Structural Data ◽  
Gram Negative Bacteria ◽  
Conserved Residues ◽  
New Class ◽  
Rational Development ◽  
Lysozyme Inhibitor ◽  
Meretrix Lusoria ◽  
Binding Groove ◽  
Proteinaceous Inhibitor ◽  
Microbiological Data

Recent microbiological data have revealed that Gram-negative bacteria are able to protect themselves against the lytic action of host lysozymes by secreting proteinaceous inhibitors. Four distinct classes of such inhibitors have been discovered that specifically act against c-type, g-type and i-type lysozymes. Here, the 1.24 Å resolution crystal structure of the periplasmic i-type lysozyme inhibitor fromAeromonas hydrophila(PliI-Ah) in complex with the i-type lysozyme fromMeretrix lusoriais reported. The structure is the first to explain the inhibitory mechanism of the PliI family at the atomic level. A distinct `ridge' formed by three exposed PliI loops inserts into the substrate-binding groove of the lysozyme, resulting in a complementary `key–lock' interface. The interface is principally stabilized by the interactions made by the PliI-Ah residues Ser104 and Tyr107 belonging to the conserved SGxY motif, as well as by the other conserved residues Ser46 and Asp76. The functional importance of these residues is confirmed by inhibition assays with the corresponding point mutants of PliI-Ah. The accumulated structural data on lysozyme–inhibitor complexes from several classes indicate that in all cases an extensive interface of either a single or a double `key–lock' type is formed, resulting in highly efficient inhibition. These data provide a basis for the rational development of a new class of antibacterial drugs.

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