scholarly journals The CXC Chemokine Receptors in Four-Eyed Sleeper (Bostrychus sinensis) and Their Involvement in Responding to Skin Injury

2021 ◽  
Vol 22 (18) ◽  
pp. 10022
Author(s):  
Mengdan Dong ◽  
Hong Zhang ◽  
Chengyu Mo ◽  
Wenjing Li ◽  
Wanwan Zhang ◽  
...  
Keyword(s):  
Wound Healing ◽  
Chemokine Receptors ◽  
De Novo ◽  
Protein Structures ◽  
Perinuclear Region ◽  
Skin Injury ◽  
Skin Ulceration ◽  
Chemokine Signaling ◽  
Cxc Chemokine ◽  
Early Inflammatory Response

CXC Chemokine signaling plays an important role in wound healing. The four-eyed sleeper (Bostrychus sinensis) is a commercially important marine fish, which is prone to suffer skin ulceration at high temperature seasons, leading to mass mortality of fish in aquaculture farms. The genetic background related to skin ulceration and wound healing has remained unknown in this fish. Herein, we identified 10 differentially expressed Bostrychus sinensis CXC chemokine receptors (BsCXCRs) in skin ulcerated fish by de novo transcriptome sequencing. The transcripts of these BsCXCRs were classified in seven types, including BsCXCR1a/1b, BsCXCR2, BsCXCR3a1/3a2, BsCXCR4a/4b, and BsCXCR5-7, and BsCXCR6 was the first CXCR6 homologue experimentally identified in teleost fish. These BsCXCRs were further characterized in gene and protein structures, as well as phylogenetics, and the results revealed that BsCXCRs have expanded to divergent homologues. Our results showed that, in healthy fish, the BsCXCR transcripts was mainly distributed in the muscle and immune related organs, and that BsCXCR1a/1b proteins located in the cytomembrane, BsCXCR4a/4b/5/6 in the cytomembrane and perinuclear region, and BsCXCR3a1/3a2/7 in the cytomembrane, perinuclear region, and nuclear membrane, respectively. In skin injured fish, the transcripts of all BsCXCRs were transiently increased within one hour after injury, suggesting the involvement of BsCXCRs into the early inflammatory response to skin injury in the four-eyed sleeper. These results are valuable for understanding the evolutionary events of fish CXCR genes and provide insights into the roles of CXCR family in fish skin injury.

scholarly journals Profiling of Sub-Lethal in Vitro Effects of Multi-Walled Carbon Nanotubes Reveals Changes in Chemokines and Chemokine Receptors

Nanomaterials ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 883 ◽  
Author(s):  
Sandeep Keshavan ◽  
Fernando Torres Andón ◽  
Audrey Gallud ◽  
Wei Chen ◽  
Knut Reinert ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Chemokine Receptors ◽  
Research Centre ◽  
Target Cells ◽  
Joint Research ◽  
Chemokine Signaling ◽  
Multi Walled Carbon Nanotubes ◽  
Downstream Analysis ◽  
Walled Carbon Nanotubes

Engineered nanomaterials are potentially very useful for a variety of applications, but studies are needed to ascertain whether these materials pose a risk to human health. Here, we studied three benchmark nanomaterials (Ag nanoparticles, TiO2 nanoparticles, and multi-walled carbon nanotubes, MWCNTs) procured from the nanomaterial repository at the Joint Research Centre of the European Commission. Having established a sub-lethal concentration of these materials using two human cell lines representative of the immune system and the lungs, respectively, we performed RNA sequencing of the macrophage-like cell line after exposure for 6, 12, and 24 h. Downstream analysis of the transcriptomics data revealed significant effects on chemokine signaling pathways. CCR2 was identified as the most significantly upregulated gene in MWCNT-exposed cells. Using multiplex assays to evaluate cytokine and chemokine secretion, we could show significant effects of MWCNTs on several chemokines, including CCL2, a ligand of CCR2. The results demonstrate the importance of evaluating sub-lethal concentrations of nanomaterials in relevant target cells.

scholarly journals De novo design of a reversible phosphorylation-dependent switch for membrane targeting

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Leon Harrington ◽  
Jordan M. Fletcher ◽  
Tamara Heermann ◽  
Derek N. Woolfson ◽  
Petra Schwille
Keyword(s):  
Protein Interactions ◽  
Lipid Membrane ◽  
De Novo ◽  
Protein Localization ◽  
Protein Structures ◽  
Spatiotemporal Pattern ◽  
Membrane Targeting ◽  
Protein Protein Interactions ◽  
Reversible Phosphorylation ◽  
Potential Applications

AbstractModules that switch protein-protein interactions on and off are essential to develop synthetic biology; for example, to construct orthogonal signaling pathways, to control artificial protein structures dynamically, and for protein localization in cells or protocells. In nature, the E. coli MinCDE system couples nucleotide-dependent switching of MinD dimerization to membrane targeting to trigger spatiotemporal pattern formation. Here we present a de novo peptide-based molecular switch that toggles reversibly between monomer and dimer in response to phosphorylation and dephosphorylation. In combination with other modules, we construct fusion proteins that couple switching to lipid-membrane targeting by: (i) tethering a ‘cargo’ molecule reversibly to a permanent membrane ‘anchor’; and (ii) creating a ‘membrane-avidity switch’ that mimics the MinD system but operates by reversible phosphorylation. These minimal, de novo molecular switches have potential applications for introducing dynamic processes into designed and engineered proteins to augment functions in living cells and add functionality to protocells.

scholarly journals Optimization in S-SAD phasing - difference between solved and unsolved structure

2014 ◽  
Vol 70 (a1) ◽  
pp. C613-C613
Author(s):  
Jan Stránský ◽  
Tomáš Kovaľ ◽  
Lars Østergaard ◽  
Jarmila Dušková ◽  
Tereza Skálová ◽  
...  
Keyword(s):  
Data Processing ◽  
De Novo ◽  
Protein Structures ◽  
X Ray Diffraction ◽  
X Ray ◽  
Structure Solution ◽  
Sad Phasing ◽  
Optimal Values ◽  
Grant Agency ◽  
Intensity Reading

Development of X-ray diffraction technologies have made de novo phasing of protein structures by single-wavelength anomalous dispersion by sulphur (S-SAD) more common. As anomalous differences in the sulphur atomic factors are in the order of errors of measurement, careful intensity reading and data processing are crucial. S-SAD was used for de novo phasing of a small 12 kDa protein with 4 sulphur atoms per molecule at 2.3 Å, where the data did not enable a straightforward structure solution. Data processing was performed using XDS [1] and scaling using XSCALE. The sulphur substructure was determined by SHELXD [2] and phases were obtained from SHELXE [2]. Both algorithms strongly depend on input parameters and default values did not lead to the correct phases. Therefore a systematic search of optimal values of several parameters was used to find a solution. This method helped to confirm sulphur substructure and to differentiate the handedness of the solutions. Moreover, a script for comfortable conversion of SHELX outputs to MTZ format was developed, using programmes included in the CCP4 package [3]. The previously unsolvable protein structure was successfully resolved with the described procedure. This work was supported by the Grant Agency of the Czech Technical University in Prague, (SGS13/219/OHK4/3T/14), the Czech Science Foundation (P302/11/0855), project BIOCEV CZ.1.05/1.1.00/02.0109 from the ERDF.

scholarly journals Get Phases from Arsenic Anomalous Scattering: de novo SAD Phasing of Two Protein Structures Crystallized in Cacodylate Buffer

PLoS ONE ◽  
2011 ◽  
Vol 6 (9) ◽  
pp. e24227 ◽  
Author(s):  
Xiang Liu ◽  
Heng Zhang ◽  
Xiao-Jun Wang ◽  
Lan-Fen Li ◽  
Xiao-Dong Su
Keyword(s):  
De Novo ◽  
Protein Structures ◽  
Anomalous Scattering ◽  
Cacodylate Buffer ◽  
Sad Phasing

scholarly journals De Novo Protein Design of Photochemical Reaction Centers

2021 ◽  
Author(s):  
Nathan Ennist ◽  
Zhenyu Zhao ◽  
Steven Stayrook ◽  
Bohdana Discher ◽  
P Leslie 'Les' Dutton ◽  
...  
Keyword(s):  
Reaction Center ◽  
Charge Separation ◽  
Rational Design ◽  
De Novo ◽  
Metal Cluster ◽  
Protein Structures ◽  
Essential Elements ◽  
Reaction Centers ◽  
Transient Absorption Spectroscopy

Abstract Natural photosynthetic protein complexes capture sunlight to power the energetic catalysis that supports life on Earth. Yet these natural protein structures carry an evolutionary legacy of complexity and fragility that encumbers protein reengineering efforts and obfuscates the underlying design rules for light-driven charge separation. De novo development of a simplified photosynthetic reaction center protein can clarify practical engineering principles needed to build new enzymes for efficient solar-to-fuel energy conversion. Here we report the rational design, X-ray crystal structure, and electron transfer activity of a multi-cofactor protein that incorporates essential elements of photosynthetic reaction centers. This highly stable, modular artificial protein framework can be reconstituted in vitro with interchangeable redox centers for nanometer-scale photochemical charge separation. Transient absorption spectroscopy demonstrates Photosystem II-like tyrosine and metal cluster oxidation, and we measure charge separation lifetimes exceeding 100 ms, ideal for light-activated catalysis. This de novo-designed reaction center builds upon engineering guidelines established for charge separation in earlier synthetic photochemical triads and modified natural proteins, and it shows how synthetic biology may lead to a new generation of genetically encoded, light-powered catalysts for solar fuel production.

Identification of a Putative Intracellular Allosteric Antagonist Binding-Site in the CXC Chemokine Receptors 1 and 2

2008 ◽  
Vol 74 (5) ◽  
pp. 1193-1202 ◽  
Author(s):  
David J. Nicholls ◽  
Nick P. Tomkinson ◽  
Katherine E. Wiley ◽  
Anne Brammall ◽  
Lorna Bowers ◽  
...  
Keyword(s):  
Binding Site ◽  
Chemokine Receptors ◽  
Cxc Chemokine ◽  
Antagonist Binding

scholarly journals Protein designer David Baker: I like doing things that seem like magic

2020 ◽  
Vol 7 (8) ◽  
pp. 1410-1412
Author(s):  
Weijie Zhao ◽  
Chu Wang
Keyword(s):  
Protein Design ◽  
De Novo ◽  
Protein Structures ◽  
Computational Prediction ◽  
Biological Functions ◽  
Personal Experiences ◽  
De Novo Protein Design ◽  
And Function ◽  
The University ◽  
Opening Up

Abstract Search ‘de novo protein design’ on Google and you will find the name David Baker in all results of the first page. Professor David Baker at the University of Washington and other scientists are opening up a new world of fantastic proteins. Protein is the direct executor of most biological functions and its structure and function are fully determined by its primary sequence. Baker's group developed the Rosetta software suite that enabled the computational prediction and design of protein structures. Being able to design proteins from scratch means being able to design executors for diverse purposes and benefit society in multiple ways. Recently, NSR interviewed Prof. Baker on this fast-developing field and his personal experiences.

scholarly journals Prediction and Characterization of RXLR Effectors in Pythium Species

2020 ◽  
Vol 33 (8) ◽  
pp. 1046-1058 ◽  
Author(s):  
Gan Ai ◽  
Kun Yang ◽  
Wenwu Ye ◽  
Yuee Tian ◽  
Yaxin Du ◽  
...  
Keyword(s):  
Genome Rearrangement ◽  
De Novo ◽  
Biological Control Agent ◽  
Protein Structures ◽  
Control Agent ◽  
Phytophthora Species ◽  
Host Cells ◽  
Pythium Species ◽  
Origin And Evolution ◽  
Rxlr Effectors

RXLR effectors, a class of secreted proteins that are transferred into host cells to manipulate host immunity, have been reported to widely exist in oomycetes, including those from genera Phytophthora, Hyaloperonospora, Albugo, and Saprolegnia. However, in Pythium species, no RXLR effector has yet been characterized, and the origin and evolution of such virulent effectors are still unknown. Here, we developed a modified regular expression method for de novo identification of RXLRs and characterized 359 putative RXLR effectors in nine Pythium species. Phylogenetic analysis revealed that all oomycetous RXLRs formed a single superfamily, suggesting that they might have a common ancestor. RXLR effectors from Pythium and Phytophthora species exhibited similar sequence features, protein structures, and genome locations. In particular, there were significantly more RXLR proteins in the mosquito biological control agent P. guiyangense than in the other eight Pythium species, and P. guiyangense RXLRs might be the result of gene duplication and genome rearrangement events, as indicated by synteny analysis. Expression pattern analysis of RXLR-encoding genes in the plant pathogen P. ultimum detected transcripts of the majority of the predicted RXLR genes, with some RXLR effectors induced in infection stages and one RXLR showing necrosis-inducing activity. Furthermore, all predicted RXLR genes were cloned from two biocontrol agents, P. oligandrum and P. periplocum, and three of the RXLR genes were found to induce a defense response in Nicotiana benthamiana. Taken together, our findings represent the first evidence of RXLR effectors in Pythium species, providing valuable information on their evolutionary patterns and the mechanisms of their interactions with diverse hosts.

Novel drug‐eluting soy‐protein structures for wound healing applications

2019 ◽  
Vol 30 (10) ◽  
pp. 2523-2538 ◽  
Author(s):  
Maya Baranes‐Zeevi ◽  
Daniella Goder ◽  
Meital Zilberman
Keyword(s):  
Wound Healing ◽  
Soy Protein ◽  
Protein Structures ◽  
Drug Eluting ◽  
Novel Drug

Down-regulation of neutrophil functions by the ELR+CXC chemokine platelet basic protein

Blood ◽  
2000 ◽  
Vol 96 (9) ◽  
pp. 2965-2972 ◽  
Author(s):  
Jan E. Ehlert ◽  
Andreas Ludwig ◽  
Tobias A. Grimm ◽  
Buko Lindner ◽  
Hans-Dieter Flad ◽  
...  
Keyword(s):  
Amino Acids ◽  
Binding Sites ◽  
Chemokine Receptors ◽  
Cell Activation ◽  
Basic Protein ◽  
Cathepsin G ◽  
Terminal Part ◽  
Down Regulation ◽  
Cxc Chemokine ◽  
Continuous Accumulation

Abstract The platelet-derived neutrophil-activating peptide 2 (NAP-2, 70 amino acids) belongs to the ELR+ CXC subfamily of chemokines. Similar to other members of this group, such as IL-8, NAP-2 activates chemotaxis and degranulation in neutrophils (polymorphonuclear [PMN]) through chemokine receptors CXCR-1 and CXCR-2. However, platelets do not secrete NAP-2 as an active chemokine but as the C-terminal part of several precursors that lack PMN-stimulating capacity. As we have previously shown, PMN themselves may liberate NAP-2 from the precursor connective tissue-activating peptide III (CTAP-III, 85 amino acids) by proteolysis. Instead of inducing cell activation, continuous accumulation of the chemokine in the surroundings of the processing cells results in the down-regulation of specific surface-expressed NAP-2 binding sites and in the desensitization of chemokine-induced PMN degranulation. Thus, NAP-2 precursors may be regarded as indirect mediators of functional desensitization in neutrophils. In the current study we investigated the biologic impact of another major NAP-2 precursor, the platelet basic protein (PBP, 94 amino acids). We show that PBP is considerably more potent than CTAP-III to desensitize degranulation and chemotaxis in neutrophils. We present data suggesting that the high desensitizing capacity of PBP is based on its enhanced proteolytic cleavage into NAP-2 by neutrophil-expressed cathepsin G and that it involves efficient down-regulation of surface-expressed CXCR-2 while CXCR-1 is hardly affected. Correspondingly, we found PBP and, less potently, CTAP-III to inhibit CXCR-2– but not CXCR-1– dependent chemotaxis of neutrophils toward NAP-2. Altogether our findings demonstrate that the anti-inflammatory capacity of NAP-2 is governed by the species of its precursors.

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