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Article ; Online: Effects of Immunoglobulins G From Systemic Sclerosis Patients in Normal Dermal Fibroblasts: A Multi-Omics Study.

Chepy, Aurélien / Vivier, Solange / Bray, Fabrice / Ternynck, Camille / Meneboo, Jean-Pascal / Figeac, Martin / Filiot, Alexandre / Guilbert, Lucile / Jendoubi, Manel / Rolando, Christian / Launay, David / Dubucquoi, Sylvain / Marot, Guillemette / Sobanski, Vincent

Frontiers in immunology

2022 Volume 13, Page(s) 904631

Abstract: ... biomarkers, their pathogenic role is debated. This study explored the effect of purified immunoglobulin G ...

Abstract	Autoantibodies (Aabs) are frequent in systemic sclerosis (SSc). Although recognized as potent biomarkers, their pathogenic role is debated. This study explored the effect of purified immunoglobulin G (IgG) from SSc patients on protein and mRNA expression of dermal fibroblasts (FBs) using an innovative multi-omics approach. Dermal FBs were cultured in the presence of sera or purified IgG from patients with diffuse cutaneous SSc (dcSSc), limited cutaneous SSc or healthy controls (HCs). The FB proteome and transcriptome were explored using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) and microarray assays, respectively. Proteomic analysis identified 3,310 proteins. SSc sera and purified IgG induced singular protein profile patterns. These FB proteome changes depended on the Aab serotype, with a singular effect observed with purified IgG from anti-topoisomerase-I autoantibody (ATA) positive patients compared to HC or other SSc serotypes. IgG from ATA positive SSc patients induced enrichment in proteins involved in focal adhesion, cadherin binding, cytosolic part, or lytic vacuole. Multi-omics analysis was performed in two ways: first by restricting the analysis of the transcriptomic data to differentially expressed proteins; and secondly, by performing a global statistical analysis integrating proteomics and transcriptomics. Transcriptomic analysis distinguished 764 differentially expressed genes and revealed that IgG from dcSSc can induce extracellular matrix (ECM) remodeling changes in gene expression profiles in FB. Global statistical analysis integrating proteomics and transcriptomics confirmed that IgG from SSc can induce ECM remodeling and activate FB profiles. This effect depended on the serotype of the patient, suggesting that SSc Aab might play a pathogenic role in some SSc subsets.
MeSH term(s)	Autoantibodies ; Chromatography, Liquid ; Fibroblasts/metabolism ; Humans ; Immunoglobulin G ; Proteome/metabolism ; Proteomics ; Scleroderma, Systemic ; Tandem Mass Spectrometry
Chemical Substances	Autoantibodies ; Immunoglobulin G ; Proteome
Language	English
Publishing date	2022-06-29
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2022.904631
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Article ; Online: Regulating G protein-coupled receptors by topological inversion.

Denard, Bray / Han, Sungwon / Kim, JungYeon / Ross, Elliott M / Ye, Jin

eLife

2019 Volume 8

Abstract: G protein-coupled receptors (GPCRs) are a family of proteins containing seven transmembrane helices ...

Abstract	G protein-coupled receptors (GPCRs) are a family of proteins containing seven transmembrane helices, with the N- and C-terminus of the protein located at the extracellular space and cytosol, respectively. Here, we report that ceramide or related sphingolipids might invert the topology of many GPCRs that contain a GXXXN motif in their first transmembrane helix. The functional significance of this topological regulation is illustrated by the CCR5 chemokine receptor. In the absence of lipopolysaccharide (LPS), CCR5 adopts a topology consistent with that of GPCR, allowing mouse peritoneal macrophages to migrate toward its ligand CCL5. LPS stimulation results in increased production of dihydroceramide, which inverts the topology of CCR5, preventing macrophages from migrating toward CCL5. These results suggest that GPCRs may not always adopt the same topology and can be regulated through topological inversion. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that major issues remain unresolved (see decision letter).
MeSH term(s)	Allosteric Regulation ; Animals ; Cell Movement ; Cells, Cultured ; Ceramides/metabolism ; Lipopolysaccharides/metabolism ; Macrophages, Peritoneal/drug effects ; Macrophages, Peritoneal/physiology ; Mice, Inbred C57BL ; Protein Conformation ; Receptors, CCR5/chemistry ; Receptors, CCR5/metabolism ; Receptors, G-Protein-Coupled/chemistry ; Receptors, G-Protein-Coupled/metabolism
Chemical Substances	CCR5 protein, mouse ; Ceramides ; Lipopolysaccharides ; Receptors, CCR5 ; Receptors, G-Protein-Coupled ; dihydroceramide
Language	English
Publishing date	2019-03-05
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.40234
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Article ; Online: Neutrophil cathepsin G proteolysis of protease-activated receptor 4 generates a novel, functional tethered ligand.

Stoller, Michelle L / Basak, Indranil / Denorme, Frederik / Rowley, Jesse W / Alsobrooks, James / Parsawar, Krishna / Nieman, Marvin T / Yost, Christian Con / Hamilton, Justin R / Bray, Paul F / Campbell, Robert A

Blood advances

2021 Volume 6, Issue 7, Page(s) 2303–2308

Abstract: ... ligand. Neutrophils release cathepsin G (CatG) at sites of injury and inflammation, which activates PAR4 ...

Abstract	Platelet-neutrophil interactions regulate ischemic vascular injury. Platelets are activated by serine proteases that cleave protease-activated receptor (PAR) amino termini, resulting in an activating tethered ligand. Neutrophils release cathepsin G (CatG) at sites of injury and inflammation, which activates PAR4 but not PAR1, although the molecular mechanism of CatG-induced PAR4 activation is unknown. We show that blockade of the canonical PAR4 thrombin cleavage site did not alter CatG-induced platelet aggregation, suggesting CatG cleaves a different site than thrombin. Mass spectrometry analysis using PAR4 N-terminus peptides revealed CatG cleavage at Ser67-Arg68. A synthetic peptide, RALLLGWVPTR, representing the tethered ligand resulting from CatG proteolyzed PAR4, induced PAR4-dependent calcium flux and greater platelet aggregation than the thrombin-generated GYPGQV peptide. Mutating PAR4 Ser67or Arg68 reduced CatG-induced calcium flux without affecting thrombin-induced calcium flux. Dog platelets, which contain a conserved CatG PAR4 Ser-Arg cleavage site, aggregated in response to human CatG and RALLLGWVPTR, while mouse (Ser-Gln) and rat (Ser-Glu) platelets were unresponsive. Thus, CatG amputates the PAR4 thrombin cleavage site by cleavage at Ser67-Arg68 and activates PAR4 by generating a new functional tethered ligand. These findings support PAR4 as an important CatG signaling receptor and suggest a novel therapeutic approach for blocking platelet-neutrophil-mediated pathophysiologies.
MeSH term(s)	Animals ; Cathepsin G ; Dogs ; Ligands ; Mice ; Neutrophils/metabolism ; Proteolysis ; Rats ; Receptors, Thrombin/metabolism
Chemical Substances	Ligands ; Receptors, Thrombin ; Cathepsin G (EC 3.4.21.20) ; protease-activated receptor 4 (JWE1M73YZN)
Language	English
Publishing date	2021-12-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2915908-8
ISSN	2473-9537 ; 2473-9529
ISSN (online)	2473-9537
ISSN	2473-9529
DOI	10.1182/bloodadvances.2021006133
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Article ; Online: Regulating G protein-coupled receptors by topological inversion

Bray Denard / Sungwon Han / JungYeon Kim / Elliott M Ross / Jin Ye

eLife, Vol

2019 Volume 8

Abstract: G protein-coupled receptors (GPCRs) are a family of proteins containing seven transmembrane helices ...

Abstract	G protein-coupled receptors (GPCRs) are a family of proteins containing seven transmembrane helices, with the N- and C-terminus of the protein located at the extracellular space and cytosol, respectively. Here, we report that ceramide or related sphingolipids might invert the topology of many GPCRs that contain a GXXXN motif in their first transmembrane helix. The functional significance of this topological regulation is illustrated by the CCR5 chemokine receptor. In the absence of lipopolysaccharide (LPS), CCR5 adopts a topology consistent with that of GPCR, allowing mouse peritoneal macrophages to migrate toward its ligand CCL5. LPS stimulation results in increased production of dihydroceramide, which inverts the topology of CCR5, preventing macrophages from migrating toward CCL5. These results suggest that GPCRs may not always adopt the same topology and can be regulated through topological inversion.Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that major issues remain unresolved (see decision letter).
Keywords	topology ; G protein-coupled receptor ; chemotaxis ; ceramide ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2019-03-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
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Article ; Online: SuperBiHelix method for predicting the pleiotropic ensemble of G-protein-coupled receptor conformations.

Bray, Jenelle K / Abrol, Ravinder / Goddard, William A / Trzaskowski, Bartosz / Scott, Caitlin E

Proceedings of the National Academy of Sciences of the United States of America

2013 Volume 111, Issue 1, Page(s) E72–8

Abstract: There is overwhelming evidence that G-protein-coupled receptors (GPCRs) exhibit several distinct ...

Abstract	There is overwhelming evidence that G-protein-coupled receptors (GPCRs) exhibit several distinct low-energy conformations, each of which might favor binding to different ligands and/or lead to different downstream functions. Understanding the function of such proteins requires knowledge of the ensemble of low-energy configurations that might play a role in this pleiotropic functionality. We earlier reported the BiHelix method for efficiently sampling the (12)(7) = 35 million conformations resulting from 30° rotations about the axis (η) of all seven transmembrane helices (TMHs), showing that the experimental structure is reliably selected as the best conformation from this ensemble. However, various GPCRs differ sufficiently in the tilts of the TMHs that this method need not predict the optimum conformation starting from any other template. In this paper, we introduce the SuperBiHelix method in which the tilt angles (θ, ϕ) are optimized simultaneously with rotations (η) efficiently enough that it is practical and sufficient to sample (5 × 3 × 5)(7) = 13 trillion configurations. This method can correctly identify the optimum structure of a GPCR starting with the template from a different GPCR. We have validated this method by predicting known crystal structure conformations starting from the template of a different protein structure. We find that the SuperBiHelix conformational ensemble includes the higher energy conformations associated with the active protein in addition to those associated with the more stable inactive protein. This methodology was then applied to design and experimentally confirm structures of three mutants of the CB1 cannabinoid receptor associated with different functions.
MeSH term(s)	Algorithms ; Binding Sites ; Computational Biology ; Crystallography, X-Ray ; Humans ; Ligands ; Molecular Docking Simulation/methods ; Mutation ; Protein Binding ; Protein Structure, Tertiary ; Receptor, Adenosine A2A/chemistry ; Receptor, Cannabinoid, CB1/chemistry ; Receptors, Adrenergic, beta-2/chemistry ; Receptors, G-Protein-Coupled/chemistry ; Software
Chemical Substances	Ligands ; Receptor, Adenosine A2A ; Receptor, Cannabinoid, CB1 ; Receptors, Adrenergic, beta-2 ; Receptors, G-Protein-Coupled
Language	English
Publishing date	2013-12-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1321233111
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Article ; Online: The sexual adult of Cercaria praecox Walker, 1971 (Digenea: Fellodistomidae), with the proposal of Oceroma n. g.

Cribb, Thomas H / Miller, Terrence L / Bray, Rodney A / Cutmore, Scott C

Systematic parasitology

2014 Volume 88, Issue 1, Page(s) 1–10

Abstract: ... n. g. Analysis of 28S rDNA sequences demonstrates that this species forms a clade with Coomera Dove ...

Abstract	A sexual adult trematode that is considered to be conspecific with the distinctive larval trematode Cercaria praecox Walker, 1971 is reported from the kyphosid fish Scorpis lineolata Kner in Moreton Bay, Queensland, Australia. The sexual adult is consistent with the cercarial body of Cercaria praecox in having a single caecum with an asymmetrical appendix, symmetrical testes immediately posterior to the ventral sucker, and the ovary and vitellarium both well posterior to the testes. This combination of characters is distinct within the Fellodistomidae Nicoll, 1909 and requires the proposal of a new genus, Oceroma n. g. Analysis of 28S rDNA sequences demonstrates that this species forms a clade with Coomera Dove & Cribb, 1995 within the Fellodistomidae. The life-cycle of the species is predicted to require two hosts and to involve the direct ingestion of the cercaria.
MeSH term(s)	Animals ; Cercaria/anatomy & histology ; Cercaria/classification ; Cercaria/genetics ; DNA, Ribosomal Spacer/genetics ; Fish Diseases/parasitology ; Fishes/parasitology ; Molecular Sequence Data ; Phylogeny ; Queensland ; RNA, Ribosomal, 28S/genetics ; Species Specificity ; Trematoda/anatomy & histology ; Trematoda/classification ; Trematoda/genetics ; Trematode Infections/parasitology ; Trematode Infections/veterinary
Chemical Substances	DNA, Ribosomal Spacer ; RNA, Ribosomal, 28S
Language	English
Publishing date	2014-04-08
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2018846-8
ISSN	1573-5192 ; 0165-5752
ISSN (online)	1573-5192
ISSN	0165-5752
DOI	10.1007/s11230-014-9478-3
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Article ; Online: Conformational ensemble view of G protein-coupled receptors and the effect of mutations and ligand binding.

Abrol, Ravinder / Kim, Soo-Kyung / Bray, Jenelle K / Trzaskowski, Bartosz / Goddard, William A

Methods in enzymology

2013 Volume 520, Page(s) 31–48

Abstract: G protein-coupled receptors (GPCRs) are integral membrane proteins that can convert ... inverse agonists, antagonists, and agonists), or binding to G proteins, etc. Structure determination ...

Abstract	G protein-coupled receptors (GPCRs) are integral membrane proteins that can convert an extracellular signal into multiple intracellular signaling processes. This pleiotropy of GPCRs is enabled by their structural flexibility manifested in thermally accessible multiple conformations, each of which may be capable of activating a different signaling cascade inside the cell (Kenakin & Miller, 2010). Different subsets of conformations can be potentially stabilized through mutations, or binding to various ligands (inverse agonists, antagonists, and agonists), or binding to G proteins, etc. Structure determination efforts have led to a small subset of these receptors being crystallized in one or two distinct conformations, but computational methods can predict an ensemble of conformations that characterize the full thermodynamic landscape of the receptor. Mutations in the receptor or binding of ligands can modulate this energy landscape, by stabilizing a unique set of conformations under different conditions, which may correspond to a specific downstream physiological function. These studies can provide testable hypotheses on the structural basis of GPCR activation and functional selectivity.
MeSH term(s)	Adenosine A3 Receptor Agonists ; Adenosine A3 Receptor Antagonists ; Humans ; Ligands ; Mutation ; Protein Binding ; Protein Conformation ; Receptor, Adenosine A3/metabolism ; Receptors, CCR5/genetics ; Receptors, CCR5/metabolism ; Receptors, G-Protein-Coupled/genetics ; Receptors, G-Protein-Coupled/metabolism
Chemical Substances	Adenosine A3 Receptor Agonists ; Adenosine A3 Receptor Antagonists ; Ligands ; Receptor, Adenosine A3 ; Receptors, CCR5 ; Receptors, G-Protein-Coupled
Language	English
Publishing date	2013
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1557-7988 ; 0076-6879
ISSN (online)	1557-7988
ISSN	0076-6879
DOI	10.1016/B978-0-12-391861-1.00002-2
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Article ; Online: Structure prediction of G protein-coupled receptors and their ensemble of functionally important conformations.

Abrol, Ravinder / Griffith, Adam R / Bray, Jenelle K / Goddard, William A

Methods in molecular biology (Clifton, N.J.)

2012 Volume 914, Page(s) 237–254

Abstract: G protein-coupled receptors (GPCRs) are integral membrane proteins whose "pleiotropic" nature ... enables transmembrane (TM) signal transduction, amplification, and diversification via G protein-coupled ...

Abstract	G protein-coupled receptors (GPCRs) are integral membrane proteins whose "pleiotropic" nature enables transmembrane (TM) signal transduction, amplification, and diversification via G protein-coupled and β arrestin-coupled pathways. GPCRs appear to enable this by being structurally flexible and by existing in different conformational states with potentially different signaling and functional consequences. We describe a method for the prediction of the three-dimensional structures of these different conformations of GPCRs starting from their amino acid sequence. It combines a unique protocol of computational methods that first predict the TM regions of these receptors and TM helix shapes based on those regions, which is followed by a locally complete sampling of TM helix packings and their scoring that results in a few (~10-20) lowest energy conformations likely to play a role in binding to different ligands and signaling events. Prediction of the structures for multiple conformations of a GPCR is starting to enable the testing of multiple hypotheses related to GPCR activation and binding to ligands with different signaling profiles.
MeSH term(s)	Amino Acid Sequence ; Computational Biology/methods ; Hydrophobic and Hydrophilic Interactions ; Molecular Sequence Data ; Protein Structure, Secondary ; Receptors, G-Protein-Coupled/chemistry ; Sequence Alignment
Chemical Substances	Receptors, G-Protein-Coupled
Language	English
Publishing date	2012
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-62703-023-6_14
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Article ; Online: Bihelix: Towards de novo structure prediction of an ensemble of G-protein coupled receptor conformations.

Abrol, Ravinder / Bray, Jenelle K / Goddard, William A

Proteins

2011 Volume 80, Issue 2, Page(s) 505–518

Abstract: G-Protein Coupled Receptors (GPCRs) play a critical role in cellular signal transduction pathways ...

Abstract	G-Protein Coupled Receptors (GPCRs) play a critical role in cellular signal transduction pathways and are prominent therapeutic targets. Recently there has been major progress in obtaining experimental structures for a few GPCRs. Each GPCR, however, exhibits multiple conformations that play a role in their function and we have been developing methods aimed at predicting structures for all these conformations. Analysis of available structures shows that these conformations differ in relative helix tilts and rotations. The essential issue is, determining how to orient each of the seven helices about its axis since this determines how it interacts with the other six helices. Considering all possible helix rotations to ensure that no important packings are overlooked, and using rotation angle increments of 30° about the helical axis would still lead to 12(7) or 35 million possible conformations each with optimal residue positions. We show in this paper how to accomplish this. The fundamental idea is to optimize the interactions between each pair of contacting helices while ignoring the other 5 and then to estimate the energies of all 35 million combinations using these pair-wise interactions. This BiHelix approach dramatically reduces the effort to examine the complete set of conformations and correctly identifies the crystal packing for the experimental structures plus other near-native packings we believe may play an important role in activation. This approach also enables a detailed structural analysis of functionally distinct conformations using helix-helix interaction energy landscapes and should be useful for other helical transmembrane proteins as well.
MeSH term(s)	Algorithms ; Membrane Proteins/chemistry ; Models, Molecular ; Protein Conformation ; Receptors, G-Protein-Coupled/chemistry ; Reproducibility of Results
Chemical Substances	Membrane Proteins ; Receptors, G-Protein-Coupled
Language	English
Publishing date	2011-12-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	806683-8
ISSN	1097-0134 ; 0887-3585
ISSN (online)	1097-0134
ISSN	0887-3585
DOI	10.1002/prot.23216
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Zs.A 2291: Show issues

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Article ; Online: Cryptic species of Euryakaina n. g. (Digenea: Cryptogonimidae) from sympatric lutjanids in the Indo-West Pacific.

Miller, Terrence L / Adlard, Robert D / Bray, Rodney A / Justine, Jean-Lou / Cribb, Thomas H

Systematic parasitology

2010 Volume 77, Issue 3, Page(s) 185–204

Abstract: ... g., as E. manilensis n. comb. and E. marina n. comb., based on comparative analysis ... with other cryptogonimid taxa. Euryakaina n. g. is distinguished from all other cryptogonimid genera by the combination ...

Abstract	A survey of the endohelminth fauna of Indo-West Pacific Lutjanidae (Perciformes) revealed the presence of the species Siphoderina manilensis (Velasquez, 1961) Miller & Cribb, 2008 and S. marina (Hafeezullah & Siddiqi, 1970) Miller & Cribb, 2008 in seven Lutjanus spp. from sites off the Great Barrier Reef, the Maldives, New Caledonia and Ningaloo Reef, Western Australia. A combination of morphological and ribosomal DNA analyses of these cryptogonimids prompted the transfer of these taxa to a new genus, Euryakaina n. g., as E. manilensis n. comb. and E. marina n. comb., based on comparative analysis with other cryptogonimid taxa. Euryakaina n. g. is distinguished from all other cryptogonimid genera by the combination of a fusiform body, the few relatively small, widely spaced oral spines (sometimes absent), a highly lobed ovary, opposite to slightly oblique testes, vitelline follicles that extend from the anterior margin of the testes to slightly posterior to the intestinal bifurcation, and an excretory vesicle that bifurcates dorsal to the ovary and reunites briefly slightly posterior to the intestinal bifurcation. Morphometric analysis of these taxa alone suggests they should be reduced to synonymy, but DNA sequence analyses and ecological niche partitioning provide evidence that they form a cryptic species complex in sympatric lutjanids in the Indo-West Pacific. The secondary structure of the ITS2 rDNA for species of Euryakaina was also modelled and analysed for the presences of compensatory base changes (CBCs) or hemi-CBCs in order to explore the usefulness of these changes as a tool to help elucidate the taxonomy of this complex system. We also report what we interpret here as intraspecific variation in the ITS2 rDNA between individuals of E. manilensis from Lutjanus vitta recovered off the Great Barrier Reef and New Caledonia.
MeSH term(s)	Animals ; Base Sequence ; DNA, Helminth/genetics ; DNA, Ribosomal Spacer ; Female ; Intestines/parasitology ; Molecular Sequence Data ; Nucleic Acid Conformation ; Perciformes/parasitology ; Phylogeny ; Principal Component Analysis ; RNA, Helminth/chemistry ; RNA, Helminth/genetics ; RNA, Ribosomal/chemistry ; Trematoda/anatomy & histology ; Trematoda/classification ; Trematoda/genetics ; Western Australia
Chemical Substances	DNA, Helminth ; DNA, Ribosomal Spacer ; RNA, Helminth ; RNA, Ribosomal
Language	English
Publishing date	2010-10-20
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2018846-8
ISSN	1573-5192 ; 0165-5752
ISSN (online)	1573-5192
ISSN	0165-5752
DOI	10.1007/s11230-010-9266-7
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