scholarly journals Evolution and Diversity of Semaphorins and Plexins in Choanoflagellates

2021 ◽  
Vol 13 (3) ◽  
Author(s):  
Chrystian Junqueira Alves ◽  
Júlia Silva Ladeira ◽  
Theodore Hannah ◽  
Roberto J Pedroso Dias ◽  
Priscila V Zabala Capriles ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Salt Water ◽  
Water Environment ◽  
Three Dimensional ◽  
Ecological Factors ◽  
Sister Group ◽  
Heterotrophic Flagellates ◽  
Rich Domain ◽  
Cytoskeletal Dynamics ◽  
Structural Architecture

Abstract Semaphorins and plexins are cell surface ligand/receptor proteins that affect cytoskeletal dynamics in metazoan cells. Interestingly, they are also present in Choanoflagellata, a class of unicellular heterotrophic flagellates that forms the phylogenetic sister group to Metazoa. Several members of choanoflagellates are capable of forming transient colonies, whereas others reside solitary inside exoskeletons; their molecular diversity is only beginning to emerge. Here, we surveyed genomics data from 22 choanoflagellate species and detected semaphorin/plexin pairs in 16 species. Choanoflagellate semaphorins (Sema-FN1) contain several domain features distinct from metazoan semaphorins, including an N-terminal Reeler domain that may facilitate dimer stabilization, an array of fibronectin type III domains, a variable serine/threonine-rich domain that is a potential site for O-linked glycosylation, and a SEA domain that can undergo autoproteolysis. In contrast, choanoflagellate plexins (Plexin-1) harbor a domain arrangement that is largely identical to metazoan plexins. Both Sema-FN1 and Plexin-1 also contain a short homologous motif near the C-terminus, likely associated with a shared function. Three-dimensional molecular models revealed a highly conserved structural architecture of choanoflagellate Plexin-1 as compared to metazoan plexins, including similar predicted conformational changes in a segment that is involved in the activation of the intracellular Ras-GAP domain. The absence of semaphorins and plexins in several choanoflagellate species did not appear to correlate with unicellular versus colonial lifestyle or ecological factors such as fresh versus salt water environment. Together, our findings support a conserved mechanism of semaphorin/plexin proteins in regulating cytoskeletal dynamics in unicellular and multicellular organisms.

Electron Microscopy and image reconstruction reveal the structural basis for spectrin's elastic properties

1992 ◽  
Vol 50 (1) ◽  
pp. 510-511
Author(s):  
Amy M. McGough ◽  
Robert Josephs
Keyword(s):  
Electron Microscopy ◽  
Elastic Properties ◽  
Conformational Changes ◽  
Quaternary Structure ◽  
Three Dimensional ◽  
Membrane Skeleton ◽  
Projection Algorithm ◽  
Structural Basis ◽  
Iterative Approximation ◽  
Membrane Skeletons

The remarkable deformability of the erythrocyte derives in large part from the elastic properties of spectrin, the major component of the membrane skeleton. It is generally accepted that spectrin's elasticity arises from marked conformational changes which include variations in its overall length (1). In this work the structure of spectrin in partially expanded membrane skeletons was studied by electron microscopy to determine the molecular basis for spectrin's elastic properties. Spectrin molecules were analysed with respect to three features: length, conformation, and quaternary structure. The results of these studies lead to a model of how spectrin mediates the elastic deformation of the erythrocyte.Membrane skeletons were isolated from erythrocyte membrane ghosts, negatively stained, and examined by transmission electron microscopy (2). Particle lengths and end-to-end distances were measured from enlarged prints using the computer program MACMEASURE. Spectrin conformation (straightness) was assessed by calculating the particles’ correlation length by iterative approximation (3). Digitised spectrin images were correlation averaged or Fourier filtered to improve their signal-to-noise ratios. Three-dimensional reconstructions were performed using a suite of programs which were based on the filtered back-projection algorithm and executed on a cluster of Microvax 3200 workstations (4).

scholarly journals The Core and Holoenzyme Forms of RNA Polymerase from Mycobacterium smegmatis

2018 ◽  
Vol 201 (4) ◽  
Author(s):  
Tomáš Kouba ◽  
Jiří Pospíšil ◽  
Jarmila Hnilicová ◽  
Hana Šanderová ◽  
Ivan Barvík ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Rna Polymerase ◽  
Conformational Changes ◽  
Mycobacterium Smegmatis ◽  
Drug Target ◽  
Conformational Dynamics ◽  
Three Dimensional ◽  
Cryo Electron Microscopy ◽  
Bacterial Rna ◽  
High Degree

ABSTRACT Bacterial RNA polymerase (RNAP) is essential for gene expression and as such is a valid drug target. Hence, it is imperative to know its structure and dynamics. Here, we present two as-yet-unreported forms of Mycobacterium smegmatis RNAP: core and holoenzyme containing σA but no other factors. Each form was detected by cryo-electron microscopy in two major conformations. Comparisons of these structures with known structures of other RNAPs reveal a high degree of conformational flexibility of the mycobacterial enzyme and confirm that region 1.1 of σA is directed into the primary channel of RNAP. Taken together, we describe the conformational changes of unrestrained mycobacterial RNAP. IMPORTANCE We describe here three-dimensional structures of core and holoenzyme forms of mycobacterial RNA polymerase (RNAP) solved by cryo-electron microscopy. These structures fill the thus-far-empty spots in the gallery of the pivotal forms of mycobacterial RNAP and illuminate the extent of conformational dynamics of this enzyme. The presented findings may facilitate future designs of antimycobacterial drugs targeting RNAP.

scholarly journals Biophysical and functional characterization of Norrin signaling through Frizzled4

2018 ◽  
Vol 115 (35) ◽  
pp. 8787-8792 ◽  
Author(s):  
Injin Bang ◽  
Hee Ryung Kim ◽  
Andrew H. Beaven ◽  
Jinuk Kim ◽  
Seung-Bum Ko ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Wnt Signaling ◽  
Conformational Changes ◽  
Cellular Response ◽  
Transmembrane Domain ◽  
Functional Characterization ◽  
Intracellular Loop ◽  
Ligand Interaction ◽  
Rich Domain ◽  
Linker Domain

Wnt signaling is initiated by Wnt ligand binding to the extracellular ligand binding domain, called the cysteine-rich domain (CRD), of a Frizzled (Fzd) receptor. Norrin, an atypical Fzd ligand, specifically interacts with Fzd4 to activate β-catenin–dependent canonical Wnt signaling. Much of the molecular basis that confers Norrin selectivity in binding to Fzd4 was revealed through the structural study of the Fzd4CRD–Norrin complex. However, how the ligand interaction, seemingly localized at the CRD, is transmitted across full-length Fzd4 to the cytoplasm remains largely unknown. Here, we show that a flexible linker domain, which connects the CRD to the transmembrane domain, plays an important role in Norrin signaling. The linker domain directly contributes to the high-affinity interaction between Fzd4 and Norrin as shown by ∼10-fold higher binding affinity of Fzd4CRD to Norrin in the presence of the linker. Swapping the Fzd4 linker with the Fzd5 linker resulted in the loss of Norrin signaling, suggesting the importance of the linker in ligand-specific cellular response. In addition, structural dynamics of Fzd4 associated with Norrin binding investigated by hydrogen/deuterium exchange MS revealed Norrin-induced conformational changes on the linker domain and the intracellular loop 3 (ICL3) region of Fzd4. Cell-based functional assays showed that linker deletion, L430A and L433A mutations at ICL3, and C-terminal tail truncation displayed reduced β-catenin–dependent signaling activity, indicating the functional significance of these sites. Together, our results provide functional and biochemical dissection of Fzd4 in Norrin signaling.

scholarly journals Investigation of Environmental Degradation on Joint Properties of Polymer Adhesive Joints in Salt Water Environment

2019 ◽  
Vol 11 (4) ◽  
Author(s):  
Shirish Kerur ◽  
Shivakumar S
Keyword(s):  
Vinyl Ester ◽  
Salt Water ◽  
Research Work ◽  
Water Environment ◽  
Adhesive Joints ◽  
Reinforced Plastics ◽  
Double Shear ◽  
Joint Properties ◽  
Polymer Adhesive ◽  
Glass Fibre Reinforced

The objective of research work is to establish the influence of environmental factors such as moisture and temperature on the shear properties of metal and polymer joints. The specimens of metal and polymer joints were prepared with aluminium plate and glass fibre reinforced plastics. Here three types of resins were used for joining the metal and polymer composites viz. epoxy vinyl ester and polyester. The joint specimens were exposed to 80 C temperature and relative humidity of 90% for 25 days in environmental chamber. The single and double shear strength of the joints for ascast and hygrothermal exposed specimens are investigated. The results showed that the strength of hydrothermal specimens decreased about 25%, 18% and 33% for epoxy, vinyl ester and polymer adhesive joints respectively. The result also shows that vinyl ester joints exhibit lower water absorption and property degradation of the joints.

Corrosion Resistance of Nitrided Gray Cast Iron （FC） in Salt Water Environment

2020 ◽  
Vol 69 (12) ◽  
pp. 329-332
Author(s):  
Hisao Fujikawa ◽  
Souhei Nishisaka ◽  
Teruhiko Nishikawa
Keyword(s):  
Corrosion Resistance ◽  
Cast Iron ◽  
Gray Cast Iron ◽  
Salt Water ◽  
Water Environment ◽  
Gray Cast

Deepstar Hull Fabrication

1965 ◽  
Vol 2 (04) ◽  
pp. 360-369
Author(s):  
George F. Gayer
Keyword(s):  
Salt Water ◽  
Water Environment ◽  
Welding Process ◽  
High Strength ◽  
Automatic Welding ◽  
Electric Motors ◽  
Camera Port ◽  
Ac Power ◽  
Welding Alloy ◽  
Private Venture

Deepstar is a self-propelled, manned vehicle for deep-sea research. It is being built as a private venture by Westinghouse Underseas Division, Baltimore, under a technical exchange license with Captain Cousteau and the OFRS (Office Francais de Recherches Sous-Marines) of Marseilles, France. Deepstar is designed to carry a crew of three to depths of 4000 ft for periods up to 24 hr. It is powered by two 4½-hpbattery-operated electric motors which propel it at about 3 knots, with a maximum range of about 20 miles. Overall dimensions of the vehicle are 13 ft long by 7 ft high by 11½ft wide over the fairing. The pressure sphere which houses the crew was built for our Baltimore Underseas Division by Westinghouse, Sunnyvale Marine Division. It measures 70 in. od and was fabricated from two hemispheres of high-strength steel. These hemispheres were spun from alloy plates 1?in. and then machined both inside and outside to 1.2 in. thick. Accurate machining was essential to maintain the sphericity required for pressure stability. After machining, the two hemispheres were welded together by an automatic welding process. The sphere has a total of 11 penetrations through the shell, including an access hatch, 2 viewports, a camera port, 2 electrical passages and 5 shaft openings. Reinforcements for the larger openings were made by welding alloy-steel forgings into the shell. Small openings were reinforced by weld metal buildup through which holes were drilled. All reinforcements were then machined to provide accurate penetrations and sealing surfaces. An extensive metallurgical testing program was conducted to insure that all material and welding used in the sphere had the strength and toughness required for operation at maximum depths. Pressure tests have been conducted in a chamber to 1.2 maximum operating depth. Sunnyvale also made the electric motors for Deepstar. These free-flooded ac motors are suspended outside the pressure hull. Unusual problems solved by special processing included electrical insulation in the salt water environment and water-lubricated bearings. AC power for the motors is provided from the batteries through a rotary inverter with semi-conductor controls.

scholarly journals Chemical Decorations of “MARs” Residents in Orchestrating Eukaryotic Gene Regulation

2020 ◽  
Vol 8 ◽  
Author(s):  
Tanaya Roychowdhury ◽  
Samit Chattopadhyay
Keyword(s):  
Gene Regulation ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Protein Function ◽  
Functional Outcomes ◽  
Three Dimensional ◽  
Limited Information ◽  
Post Translational Modification ◽  
Cellular Functions ◽  
3D Matrix

Genome organization plays a crucial role in gene regulation, orchestrating multiple cellular functions. A meshwork of proteins constituting a three-dimensional (3D) matrix helps in maintaining the genomic architecture. Sequences of DNA that are involved in tethering the chromatin to the matrix are called scaffold/matrix attachment regions (S/MARs), and the proteins that bind to these sequences and mediate tethering are termed S/MAR-binding proteins (S/MARBPs). The regulation of S/MARBPs is important for cellular functions and is altered under different conditions. Limited information is available presently to understand the structure–function relationship conclusively. Although all S/MARBPs bind to DNA, their context- and tissue-specific regulatory roles cannot be justified solely based on the available information on their structures. Conformational changes in a protein lead to changes in protein–protein interactions (PPIs) that essentially would regulate functional outcomes. A well-studied form of protein regulation is post-translational modification (PTM). It involves disulfide bond formation, cleavage of precursor proteins, and addition or removal of low-molecular-weight groups, leading to modifications like phosphorylation, methylation, SUMOylation, acetylation, PARylation, and ubiquitination. These chemical modifications lead to varied functional outcomes by mechanisms like modifying DNA–protein interactions and PPIs, altering protein function, stability, and crosstalk with other PTMs regulating subcellular localizations. S/MARBPs are reported to be regulated by PTMs, thereby contributing to gene regulation. In this review, we discuss the current understanding, scope, disease implications, and future perspectives of the diverse PTMs regulating functions of S/MARBPs.

scholarly journals The three-dimensional structure of a class-Pi glutathione S-transferase complexed with glutathione: the active-site hydration provides insights into the reaction mechanism

1998 ◽  
Vol 333 (3) ◽  
pp. 811-816 ◽  
Author(s):  
Antonio PÁRRAGA ◽  
Isabel GARCÍA-SÁEZ ◽  
Sinead B. WALSH ◽  
Timothy J. MANTLE ◽  
Miquel COLL
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Glutathione S Transferase ◽  
X Ray ◽  
The Right

The structure of mouse liver glutathione S-transferase P1-1 complexed with its substrate glutathione (GSH) has been determined by X-ray diffraction analysis. No conformational changes in the glutathione moiety or in the protein, other than small adjustments of some side chains, are observed when compared with glutathione adduct complexes. Our structure confirms that the role of Tyr-7 is to stabilize the thiolate by hydrogen bonding and to position it in the right orientation. A comparison of the enzyme–GSH structure reported here with previously described structures reveals rearrangements in a well-defined network of water molecules in the active site. One of these water molecules (W0), identified in the unliganded enzyme (carboxymethylated at Cys-47), is displaced by the binding of GSH, and a further water molecule (W4) is displaced following the binding of the electrophilic substrate and the formation of the glutathione conjugate. The possibility that one of these water molecules participates in the proton abstraction from the glutathione thiol is discussed.

scholarly journals New insights on human IRE1 tetramer structures based on molecular modeling

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Antonio Carlesso ◽  
Johanna Hörberg ◽  
Anna Reymer ◽  
Leif A. Eriksson
Keyword(s):  
Conformational Changes ◽  
Three Dimensional ◽  
Protein Docking ◽  
Activation Mechanism ◽  
Crystallographic Structure ◽  
Face To Face ◽  
Unfolded Protein ◽  
Dynamics Simulations ◽  
The Unfolded Protein Response ◽  
Protein Response

Abstract Inositol-Requiring Enzyme 1α (IRE1α; hereafter IRE1) is a transmembrane kinase/ribonuclease protein related with the unfolded protein response (UPR) signaling. Experimental evidence suggests that IRE1 forms several three dimensional (3D) structural variants: dimers, tetramers and higher order oligomers, where each structural variant can contain different IRE1 conformers in different arrangements. For example, studies have shown that two sets of IRE1 dimers exist; a face-to-face dimer and a back-to-back dimer, with the latter considered the important unit for UPR signaling propagation. However, the structural configuration and mechanistic details of the biologically important IRE1 tetramers are limited. Here, we combine protein–protein docking with molecular dynamics simulations to derive human IRE1 tetramer models and identify a molecular mechanism of IRE1 activation. To validate the derived models of the human IRE1 tetramer, we compare the dynamic behavior of the models with the yeast IRE1 tetramer crystallographic structure. We show that IRE1 tetramer conformational changes could be linked to the initiation of the unconventional splicing of mRNA encoding X-box binding protein-1 (XBP1), which allows for the expression of the transcription factor XBP1s (XBP1 spliced). The derived IRE1 tetrameric models bring new mechanistic insights about the IRE1 molecular activation mechanism by describing the IRE1 tetramers as active protagonists accommodating the XBP1 substrate.

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