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Floch A, Galochkina T, Pirenne F, Tournamille C, de Brevern AG. Molecular dynamics of the human RhD and RhAG blood group proteins. Front Chem 2024; 12:1360392. [PMID: 38566898 PMCID: PMC10985258 DOI: 10.3389/fchem.2024.1360392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction: Blood group antigens of the RH system (formerly known as "Rhesus") play an important role in transfusion medicine because of the severe haemolytic consequences of antibodies to these antigens. No crystal structure is available for RhD proteins with its partner RhAG, and the precise stoichiometry of the trimer complex remains unknown. Methods: To analyse their structural properties, the trimers formed by RhD and/or RhAG subunits were generated by protein modelling and molecular dynamics simulations were performed. Results: No major differences in structural behaviour were found between trimers of different compositions. The conformation of the subunits is relatively constant during molecular dynamics simulations, except for three large disordered loops. Discussion: This work makes it possible to propose a reasonable stoichiometry and demonstrates the potential of studying the structural behaviour of these proteins to investigate the hundreds of genetic variants relevant to transfusion medicine.
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Affiliation(s)
- Aline Floch
- University Paris Est Créteil, INSERM U955 Equipe Transfusion et Maladies du Globule Rouge, IMRB, Créteil, France
- Laboratoire de Biologie Médicale de Référence en Immuno-Hématologie Moléculaire, Etablissement Français du Sang Ile-de-France, Créteil, France
| | - Tatiana Galochkina
- Université Paris Cité and Université des Antilles and Université de la Réunion, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, DSIMB Bioinformatics team, Paris, France
| | - France Pirenne
- University Paris Est Créteil, INSERM U955 Equipe Transfusion et Maladies du Globule Rouge, IMRB, Créteil, France
- Laboratoire de Biologie Médicale de Référence en Immuno-Hématologie Moléculaire, Etablissement Français du Sang Ile-de-France, Créteil, France
| | - Christophe Tournamille
- University Paris Est Créteil, INSERM U955 Equipe Transfusion et Maladies du Globule Rouge, IMRB, Créteil, France
- Laboratoire de Biologie Médicale de Référence en Immuno-Hématologie Moléculaire, Etablissement Français du Sang Ile-de-France, Créteil, France
| | - Alexandre G. de Brevern
- Université Paris Cité and Université des Antilles and Université de la Réunion, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, DSIMB Bioinformatics team, Paris, France
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2
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Téletchéa S, Santuz H, Léonard S, Etchebest C. Repository of Enriched Structures of Proteins Involved in the Red Blood Cell Environment (RESPIRE). PLoS One 2019; 14:e0211043. [PMID: 30794542 PMCID: PMC6386447 DOI: 10.1371/journal.pone.0211043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 01/07/2019] [Indexed: 12/25/2022] Open
Abstract
The Red Blood Cell (RBC) is a metabolically-driven cell vital for processes such a gas transport and homeostasis. RBC possesses at its surface exposing antigens proteins that are critical in blood transfusion. Due to their importance, numerous studies address the cell function as a whole but more and more details of RBC structure and protein content are now studied using massive state-of-the art characterisation techniques. Yet, the resulting information is frequently scattered in many scientific articles, in many databases and specialized web servers. To provide a more compendious view of erythrocytes and of their protein content, we developed a dedicated database called RESPIRE that aims at gathering a comprehensive and coherent ensemble of information and data about proteins in RBC. This cell-driven database lists proteins found in erythrocytes. For a given protein entry, initial data are processed from external portals and enriched by using state-of-the-art bioinformatics methods. As structural information is extremely useful to understand protein function and predict the impact of mutations, a strong effort has been put on the prediction of protein structures with a special treatment for membrane proteins. Browsing the database is available through text search for reference gene names or protein identifiers, through pre-defined queries or via hyperlinks. The RESPIRE database provides valuable information and unique annotations that should be useful to a wide audience of biologists, clinicians and structural biologists. Database URL:http://www.dsimb.inserm.fr/respire
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Affiliation(s)
- S. Téletchéa
- Institut National de la Transfusion Sanguine, Paris, France
- Inserm, UMR_S 1134, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- Laboratory of Excellence GR-Ex., Paris, France
- UFIP, University of Nantes, CNRS UMR 6286, Nantes, France
| | - H. Santuz
- Institut National de la Transfusion Sanguine, Paris, France
- Inserm, UMR_S 1134, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- Laboratory of Excellence GR-Ex., Paris, France
| | - S. Léonard
- Institut National de la Transfusion Sanguine, Paris, France
- Inserm, UMR_S 1134, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- Laboratory of Excellence GR-Ex., Paris, France
| | - C. Etchebest
- Institut National de la Transfusion Sanguine, Paris, France
- Inserm, UMR_S 1134, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- Laboratory of Excellence GR-Ex., Paris, France
- * E-mail:
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de Brevern AG, Floch A, Barrault A, Martret J, Bodivit G, Djoudi R, Pirenne F, Tournamille C. Alloimmunization risk associated with amino acid 223 substitution in the RhD protein: analysis in the light of molecular modeling. Transfusion 2018; 58:2683-2692. [DOI: 10.1111/trf.14809] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 04/09/2018] [Accepted: 04/21/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Alexandre G. de Brevern
- INSERM UMR_S 1134; Univ. Paris Diderot, Sorbonne Paris Cité, Univ. de la Réunion, Univ. Antilles; Paris
- Laboratory of Excellence GR-Ex; Paris
- Institut National de la Transfusion Sanguine (INTS); Paris
| | - Aline Floch
- Laboratory of Excellence GR-Ex; Paris
- Etablissement Français du Sang Ile de France; Créteil France
- IMRB-INSERM U955 Team 2 “Transfusion et Maladies du Globule Rouge”; Créteil France
- UPEC; Université Paris Est-Créteil; Créteil France
| | | | | | - Gwellaouen Bodivit
- Laboratory of Excellence GR-Ex; Paris
- Etablissement Français du Sang Ile de France; Créteil France
- IMRB-INSERM U955 Team 2 “Transfusion et Maladies du Globule Rouge”; Créteil France
| | - Rachid Djoudi
- Etablissement Français du Sang Ile de France; Créteil France
| | - France Pirenne
- Laboratory of Excellence GR-Ex; Paris
- Etablissement Français du Sang Ile de France; Créteil France
- IMRB-INSERM U955 Team 2 “Transfusion et Maladies du Globule Rouge”; Créteil France
- UPEC; Université Paris Est-Créteil; Créteil France
| | - Christophe Tournamille
- Laboratory of Excellence GR-Ex; Paris
- Etablissement Français du Sang Ile de France; Créteil France
- IMRB-INSERM U955 Team 2 “Transfusion et Maladies du Globule Rouge”; Créteil France
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Postic G, Hamelryck T, Chomilier J, Stratmann D. MyPMFs: a simple tool for creating statistical potentials to assess protein structural models. Biochimie 2018; 151:37-41. [PMID: 29857183 DOI: 10.1016/j.biochi.2018.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 05/25/2018] [Indexed: 01/18/2023]
Abstract
Evaluating the model quality of protein structures that evolve in environments with particular physicochemical properties requires scoring functions that are adapted to their specific residue compositions and/or structural characteristics. Thus, computational methods developed for structures from the cytosol cannot work properly on membrane or secreted proteins. Here, we present MyPMFs, an easy-to-use tool that allows users to train statistical potentials of mean force (PMFs) on the protein structures of their choice, with all parameters being adjustable. We demonstrate its use by creating an accurate statistical potential for transmembrane protein domains. We also show its usefulness to study the influence of the physical environment on residue interactions within protein structures. Our open-source software is freely available for download at https://github.com/bibip-impmc/mypmfs.
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Affiliation(s)
- Guillaume Postic
- Sorbonne Université, UMR 7590 CNRS, MNHN, IRD, Institut de Minéralogie de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France.
| | - Thomas Hamelryck
- Bioinformatics Centre, Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Image Section, Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Jacques Chomilier
- Sorbonne Université, UMR 7590 CNRS, MNHN, IRD, Institut de Minéralogie de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Dirk Stratmann
- Sorbonne Université, UMR 7590 CNRS, MNHN, IRD, Institut de Minéralogie de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
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Postic G, Ghouzam Y, Etchebest C, Gelly JC. TMPL: a database of experimental and theoretical transmembrane protein models positioned in the lipid bilayer. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:3084696. [PMID: 28365741 PMCID: PMC5467549 DOI: 10.1093/database/bax022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/23/2017] [Indexed: 01/13/2023]
Abstract
Knowing the position of protein structures within the membrane is crucial for fundamental and applied research in the field of molecular biology. Only few web resources propose coordinate files of oriented transmembrane proteins, and these exclude predicted structures, although they represent the largest part of the available models. In this article, we present TMPL (http://www.dsimb.inserm.fr/TMPL/), a database of transmembrane protein structures (α-helical and β-sheet) positioned in the lipid bilayer. It is the first database to include theoretical models of transmembrane protein structures, making it a large repository with more than 11 000 entries. The TMPL database also contains experimentally solved protein structures, which are available as either atomistic or coarse-grained models. A unique feature of TMPL is the possibility for users to update the database by uploading, through an intuitive web interface, the membrane assignments they can obtain with our recent OREMPRO web server.
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Affiliation(s)
- Guillaume Postic
- Inserm U1134, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, Paris, France.,Institut National de la Transfusion Sanguine, Paris, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Yassine Ghouzam
- Inserm U1134, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, Paris, France.,Institut National de la Transfusion Sanguine, Paris, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Catherine Etchebest
- Inserm U1134, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, Paris, France.,Institut National de la Transfusion Sanguine, Paris, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Jean-Christophe Gelly
- Inserm U1134, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, Paris, France.,Institut National de la Transfusion Sanguine, Paris, France.,Laboratory of Excellence GR-Ex, Paris, France
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6
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Extension of the classical classification of β-turns. Sci Rep 2016; 6:33191. [PMID: 27627963 PMCID: PMC5024104 DOI: 10.1038/srep33191] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/22/2016] [Indexed: 11/29/2022] Open
Abstract
The functional properties of a protein primarily depend on its three-dimensional (3D) structure. These properties have classically been assigned, visualized and analysed on the basis of protein secondary structures. The β-turn is the third most important secondary structure after helices and β-strands. β-turns have been classified according to the values of the dihedral angles φ and ψ of the central residue. Conventionally, eight different types of β-turns have been defined, whereas those that cannot be defined are classified as type IV β-turns. This classification remains the most widely used. Nonetheless, the miscellaneous type IV β-turns represent 1/3rd of β-turn residues. An unsupervised specific clustering approach was designed to search for recurrent new turns in the type IV category. The classical rules of β-turn type assignment were central to the approach. The four most frequently occurring clusters defined the new β-turn types. Unexpectedly, these types, designated IV1, IV2, IV3 and IV4, represent half of the type IV β-turns and occur more frequently than many of the previously established types. These types show convincing particularities, in terms of both structures and sequences that allow for the classical β-turn classification to be extended for the first time in 25 years.
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Postic G, Ghouzam Y, Guiraud V, Gelly JC. Membrane positioning for high- and low-resolution protein structures through a binary classification approach. Protein Eng Des Sel 2015; 29:87-91. [PMID: 26685702 DOI: 10.1093/protein/gzv063] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/08/2015] [Indexed: 11/13/2022] Open
Abstract
The critical importance of algorithms for orienting proteins in the lipid bilayer stems from the extreme difficulty in obtaining experimental data about the membrane boundaries. Here, we present a computational method for positioning protein structures in the membrane, based on the sole alpha carbon coordinates and, therefore, compatible with both high and low structural resolutions. Our algorithm follows a new and simple approach, by treating the membrane assignment problem as a binary classification. Compared with the state-of-the-art algorithms, our method achieves similar accuracy, while being faster. Finally, our open-source software is also capable of processing coarse-grained models of protein structures.
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Affiliation(s)
- Guillaume Postic
- Inserm U1134, Paris, France Univ. Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, Paris, France Institut National de la Transfusion Sanguine, Paris, France Laboratory of Excellence GR-Ex, Paris, France
| | - Yassine Ghouzam
- Inserm U1134, Paris, France Univ. Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, Paris, France Institut National de la Transfusion Sanguine, Paris, France Laboratory of Excellence GR-Ex, Paris, France
| | - Vincent Guiraud
- Inserm U1134, Paris, France Univ. Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, Paris, France Institut National de la Transfusion Sanguine, Paris, France Laboratory of Excellence GR-Ex, Paris, France
| | - Jean-Christophe Gelly
- Inserm U1134, Paris, France Univ. Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, Paris, France Institut National de la Transfusion Sanguine, Paris, France Laboratory of Excellence GR-Ex, Paris, France
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