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Article ; Online: Conformational variability in proteins bound to single-stranded DNA: A new benchmark for new docking perspectives.

Mias-Lucquin, Dominique / Chauvot de Beauchene, Isaure

2021 Volume 90, Issue 3, Page(s) 625–631

Abstract: We explored the Protein Data Bank (PDB) to collect protein-ssDNA structures and create a multi-conformational docking benchmark including both bound and unbound protein structures. Due to ssDNA high flexibility when not bound, no ssDNA unbound structure ... ...

Abstract	We explored the Protein Data Bank (PDB) to collect protein-ssDNA structures and create a multi-conformational docking benchmark including both bound and unbound protein structures. Due to ssDNA high flexibility when not bound, no ssDNA unbound structure is included in the benchmark. For the 91 sequence-identity groups identified as bound-unbound structures of the same protein, we studied the conformational changes in the protein induced by the ssDNA binding. Moreover, based on several bound or unbound protein structures in some groups, we also assessed the intrinsic conformational variability in either bound or unbound conditions and compared it to the supposedly binding-induced modifications. To illustrate a use case of this benchmark, we performed docking experiments using ATTRACT docking software. This benchmark is, to our knowledge, the first one made to peruse available structures of ssDNA-protein interactions to such an extent, aiming to improve computational docking tools dedicated to this kind of molecular interactions.
MeSH term(s)	Benchmarking ; Computational Biology ; DNA, Single-Stranded/chemistry ; Databases, Protein ; Molecular Conformation ; Molecular Docking Simulation ; Protein Binding ; Protein Conformation ; Proteins/chemistry ; Software
Chemical Substances	DNA, Single-Stranded ; Proteins
Language	English
Publishing date	2021-10-14
Publishing country	United States
Document type	Journal Article ; 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.26258
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Zs.A 2291: Show issues

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Article ; Online: Interactions of organophosphorus pesticides with ATP-binding cassette (ABC) drug transporters.

Chedik, Lisa / Mias-Lucquin, Dominique / Fardel, Olivier / Delalande, Olivier / Bruyere, Arnaud

Xenobiotica; the fate of foreign compounds in biological systems

2022 Volume 52, Issue 6, Page(s) 644–652

Abstract: Although pharmaceutical companies have to study drug-transporter interaction, environmental contaminant interactions with these transporters are not well characterised. In this study, we demonstrated ... ...

Abstract	Although pharmaceutical companies have to study drug-transporter interaction, environmental contaminant interactions with these transporters are not well characterised. In this study, we demonstrated using
MeSH term(s)	ATP Binding Cassette Transporter, Subfamily B/metabolism ; ATP Binding Cassette Transporter, Subfamily G, Member 2/metabolism ; ATP-Binding Cassette Transporters/metabolism ; Adenosine Triphosphate ; Drug Interactions ; Membrane Transport Proteins ; Naled ; Neoplasm Proteins/metabolism ; Organophosphorus Compounds ; Pesticides/pharmacology ; Pharmaceutical Preparations ; Phosmet
Chemical Substances	ATP Binding Cassette Transporter, Subfamily B ; ATP Binding Cassette Transporter, Subfamily G, Member 2 ; ATP-Binding Cassette Transporters ; Membrane Transport Proteins ; Neoplasm Proteins ; Organophosphorus Compounds ; Pesticides ; Pharmaceutical Preparations ; Adenosine Triphosphate (8L70Q75FXE) ; Naled (PAM1AI9KU1) ; Phosmet (VN04LI540Y)
Language	English
Publishing date	2022-10-05
Publishing country	England
Document type	Journal Article
ZDB-ID	120287-x
ISSN	1366-5928 ; 0049-8254
ISSN (online)	1366-5928
ISSN	0049-8254
DOI	10.1080/00498254.2022.2128467
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Zs.A 782: Show issues

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Article ; Online: Fine mapping of hydrophobic contacts reassesses the organization of the first three dystrophin coiled-coil repeats.

Mias-Lucquin, Dominique / Chéron, Angélique / Le Rumeur, Elisabeth / Hubert, Jean-François / Delalande, Olivier

Protein science : a publication of the Protein Society

2019 Volume 28, Issue 3, Page(s) 561–570

Abstract: Coiled-coil domain is a structural motif found in proteins crucial for achievement of central biological processes, such as cellular cohesion or neuro-transmission. The coiled-coil fold consists of alpha-helices bundle that can be repeated to form larger ...

Abstract	Coiled-coil domain is a structural motif found in proteins crucial for achievement of central biological processes, such as cellular cohesion or neuro-transmission. The coiled-coil fold consists of alpha-helices bundle that can be repeated to form larger filament. Hydrophobic residues, distributed following a regular seven-residues' pattern, named heptad pattern, are commonly admitted to be essential for the formation and the stability of canonical coiled-coil repeats. Here we investigated the first three coiled-coil repeats (R1-R3) of the central domain of dystrophin, a scaffolding protein in muscle cells whose deficiency leads to Duchenne and Becker Muscular Dystrophies. By an atomic description of the hydrophobic interactions, we highlighted (i) that coiled-coil filament conformational changes are associated to specific patterns of inter-helices hydrophobic contacts, (ii) that inter-repeat hydrophobic interactions determine the behavior of linker regions including filament kinks, and (iii) that a non-strict conservation of the heptad patterns is leading to a relative plasticity of the dystrophin coiled-coil repeats. These structural features and modulations of the coiled-coil fold could better explain the mechanical properties of the central domain of dystrophin. This contribution to the understanding of the structure-function relationship of dystrophin, and especially of the R1-R3 fragment frequently used in the design of protein for gene therapies, should help in the improvement of the strategies for the cure of muscular dystrophies.
MeSH term(s)	Amino Acid Sequence ; Dystrophin/chemistry ; Dystrophin/metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Muscular Dystrophies/metabolism ; Protein Conformation, alpha-Helical ; Protein Domains
Chemical Substances	Dystrophin
Language	English
Publishing date	2019-01-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.3557
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Zs.A 3407: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: In Silico Prediction for Intestinal Absorption and Brain Penetration of Chemical Pesticides in Humans.

Chedik, Lisa / Mias-Lucquin, Dominique / Bruyere, Arnaud / Fardel, Olivier

International journal of environmental research and public health

2017 Volume 14, Issue 7

Abstract: Intestinal absorption and brain permeation constitute key parameters of toxicokinetics for pesticides, conditioning their toxicity, including neurotoxicity. However, they remain poorly characterized in humans. The present study was therefore designed to ... ...

Abstract	Intestinal absorption and brain permeation constitute key parameters of toxicokinetics for pesticides, conditioning their toxicity, including neurotoxicity. However, they remain poorly characterized in humans. The present study was therefore designed to evaluate human intestine and brain permeation for a large set of pesticides (
Language	English
Publishing date	2017-06-30
Publishing country	Switzerland
Document type	Journal Article
ISSN	1660-4601
ISSN (online)	1660-4601
DOI	10.3390/ijerph14070708
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Article ; Online: Exploration of DNA processing features unravels novel properties of ICE conjugation in Gram-positive bacteria.

Laroussi, Haifa / Aoudache, Yanis / Robert, Emilie / Libante, Virginie / Thiriet, Louise / Mias-Lucquin, Dominique / Douzi, Badreddine / Roussel, Yvonne / Chauvot de Beauchêne, Isaure / Soler, Nicolas / Leblond-Bourget, Nathalie

Nucleic acids research

2022 Volume 50, Issue 14, Page(s) 8127–8142

Abstract: Integrative and conjugative elements (ICEs) are important drivers of horizontal gene transfer in prokaryotes. They are responsible for antimicrobial resistance spread, a major current health concern. ICEs are initially processed by relaxases that ... ...

Abstract	Integrative and conjugative elements (ICEs) are important drivers of horizontal gene transfer in prokaryotes. They are responsible for antimicrobial resistance spread, a major current health concern. ICEs are initially processed by relaxases that recognize the binding site of oriT sequence and nick at a conserved nic site. The ICESt3/Tn916/ICEBs1 superfamily, which is widespread among Firmicutes, encodes uncanonical relaxases belonging to a recently identified family called MOBT. This family is related to the rolling circle replication initiators of the Rep_trans family. The nic site of these MOBT relaxases is conserved but their DNA binding site is still unknown. Here, we identified the bind site of RelSt3, the MOBT relaxase from ICESt3. Unexpectedly, we found this bind site distantly located from the nic site. We revealed that the binding of the RelSt3 N-terminal HTH domain is required for efficient nicking activity. We also deciphered the role of RelSt3 in the initial and final stages of DNA processing during conjugation. Especially, we demonstrated a strand transfer activity, and the formation of covalent DNA-relaxase intermediate for a MOBT relaxase.
MeSH term(s)	Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Binding Sites ; Conjugation, Genetic ; DNA Nucleotidyltransferases/genetics ; DNA Nucleotidyltransferases/metabolism ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; Gram-Positive Bacteria/genetics ; Interspersed Repetitive Sequences ; Plasmids/genetics
Chemical Substances	Bacterial Proteins ; DNA, Bacterial ; DNA Nucleotidyltransferases (EC 2.7.7.-) ; DNA relaxase (EC 2.7.7.-)
Language	English
Publishing date	2022-07-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkac607
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Zs.A 1067: Show issues

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Article ; Online: Singular Interface Dynamics of the SARS-CoV-2 Delta Variant Explained with Contact Perturbation Analysis.

Gheeraert, Aria / Vuillon, Laurent / Chaloin, Laurent / Moncorgé, Olivier / Very, Thibaut / Perez, Serge / Leroux, Vincent / Chauvot de Beauchêne, Isaure / Mias-Lucquin, Dominique / Devignes, Marie-Dominique / Rivalta, Ivan / Maigret, Bernard

Journal of chemical information and modeling

2022 Volume 62, Issue 12, Page(s) 3107–3122

Abstract: Emerging SARS-CoV-2 variants raise concerns about our ability to withstand the Covid-19 pandemic, and therefore, understanding mechanistic differences of those variants is crucial. In this study, we investigate disparities between the SARS-CoV-2 wild ... ...

Abstract	Emerging SARS-CoV-2 variants raise concerns about our ability to withstand the Covid-19 pandemic, and therefore, understanding mechanistic differences of those variants is crucial. In this study, we investigate disparities between the SARS-CoV-2 wild type and five variants that emerged in late 2020, focusing on the structure and dynamics of the spike protein interface with the human angiotensin-converting enzyme 2 (ACE2) receptor, by using crystallographic structures and extended analysis of microsecond molecular dynamics simulations. Dihedral angle principal component analysis (PCA) showed the strong similarities in the spike receptor binding domain (RBD) dynamics of the Alpha, Beta, Gamma, and Delta variants, in contrast with those of WT and Epsilon. Dynamical perturbation networks and contact PCA identified the peculiar interface dynamics of the Delta variant, which cannot be directly imputable to its specific L452R and T478K mutations since those residues are not in direct contact with the human ACE2 receptor. Our outcome shows that in the Delta variant the L452R and T478K mutations act synergistically on neighboring residues to provoke drastic changes in the spike/ACE2 interface; thus a singular mechanism of action eventually explains why it dominated over preceding variants.
MeSH term(s)	Angiotensin-Converting Enzyme 2/genetics ; COVID-19 ; Humans ; Molecular Dynamics Simulation ; Mutation ; Pandemics ; Protein Binding ; SARS-CoV-2/genetics
Chemical Substances	Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2022-06-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.2c00350
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Zs.A 1230: Show issues

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Article ; Online: How the central domain of dystrophin acts to bridge F-actin to sarcolemmal lipids.

Mias-Lucquin, Dominique / Dos Santos Morais, Raphael / Chéron, Angélique / Lagarrigue, Mélanie / Winder, Steve J / Chenuel, Thomas / Pérez, Javier / Appavou, Marie-Sousai / Martel, Anne / Alviset, Guillaume / Le Rumeur, Elisabeth / Combet, Sophie / Hubert, Jean-François / Delalande, Olivier

Journal of structural biology

2019 Volume 209, Issue 1, Page(s) 107411

Abstract: Dystrophin is a large intracellular protein that prevents sarcolemmal ruptures by providing a mechanical link between the intracellular actin cytoskeleton and the transmembrane dystroglycan complex. Dystrophin deficiency leads to the severe muscle ... ...

Abstract	Dystrophin is a large intracellular protein that prevents sarcolemmal ruptures by providing a mechanical link between the intracellular actin cytoskeleton and the transmembrane dystroglycan complex. Dystrophin deficiency leads to the severe muscle wasting disease Duchenne Muscular Dystrophy and the milder allelic variant, Becker Muscular Dystrophy (DMD and BMD). Previous work has shown that concomitant interaction of the actin binding domain 2 (ABD2) comprising spectrin like repeats 11 to 15 (R11-15) of the central domain of dystrophin, with both actin and membrane lipids, can greatly increase membrane stiffness. Based on a combination of SAXS and SANS measurements, mass spectrometry analysis of cross-linked complexes and interactive low-resolution simulations, we explored in vitro the molecular properties of dystrophin that allow the formation of ABD2-F-actin and ABD2-membrane model complexes. In dystrophin we identified two subdomains interacting with F-actin, one located in R11 and a neighbouring region in R12 and another one in R15, while a single lipid binding domain was identified at the C-terminal end of R12. Relative orientations of the dystrophin central domain with F-actin and a membrane model were obtained from docking simulation under experimental constraints. SAXS-based models were then built for an extended central subdomain from R4 to R19, including ABD2. Overall results are compatible with a potential F-actin/dystrophin/membrane lipids ternary complex. Our description of this selected part of the dystrophin associated complex bridging muscle cell membrane and cytoskeleton opens the way to a better understanding of how cell muscle scaffolding is maintained through this essential protein.
MeSH term(s)	Actin Cytoskeleton/genetics ; Actin Cytoskeleton/ultrastructure ; Actins/genetics ; Actins/ultrastructure ; Dystrophin/genetics ; Dystrophin/ultrastructure ; Humans ; Lipids/chemistry ; Lipids/genetics ; Muscular Dystrophy, Duchenne/genetics ; Muscular Dystrophy, Duchenne/pathology ; Protein Binding ; Sarcolemma/genetics ; Sarcolemma/ultrastructure ; Scattering, Small Angle ; Ternary Complex Factors/genetics ; Ternary Complex Factors/ultrastructure ; X-Ray Diffraction
Chemical Substances	Actins ; Dystrophin ; Lipids ; Ternary Complex Factors
Language	English
Publishing date	2019-11-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1032718-6
ISSN	1095-8657 ; 1047-8477
ISSN (online)	1095-8657
ISSN	1047-8477
DOI	10.1016/j.jsb.2019.107411
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Zs.A 1428: Show issues

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Article ; Online: Human Dystrophin Structural Changes upon Binding to Anionic Membrane Lipids.

Dos Santos Morais, Raphael / Delalande, Olivier / Pérez, Javier / Mias-Lucquin, Dominique / Lagarrigue, Mélanie / Martel, Anne / Molza, Anne-Elisabeth / Chéron, Angélique / Raguénès-Nicol, Céline / Chenuel, Thomas / Bondon, Arnaud / Appavou, Marie-Sousai / Le Rumeur, Elisabeth / Combet, Sophie / Hubert, Jean-François

Biophysical journal

2018 Volume 115, Issue 7, Page(s) 1231–1239

Abstract: Scaffolding proteins play important roles in supporting the plasma membrane (sarcolemma) of muscle cells. Among them, dystrophin strengthens the sarcolemma through protein-lipid interactions, and its absence due to gene mutations leads to the severe ... ...

Abstract	Scaffolding proteins play important roles in supporting the plasma membrane (sarcolemma) of muscle cells. Among them, dystrophin strengthens the sarcolemma through protein-lipid interactions, and its absence due to gene mutations leads to the severe Duchenne muscular dystrophy. Most of the dystrophin protein consists of a central domain made of 24 spectrin-like coiled-coil repeats (R). Using small angle neutron scattering (SANS) and the contrast variation technique, we specifically probed the structure of the three first consecutive repeats 1-3 (R1-3), a part of dystrophin known to physiologically interact with membrane lipids. R1-3 free in solution was compared to its structure adopted in the presence of phospholipid-based bicelles. SANS data for the protein/lipid complexes were obtained with contrast-matched bicelles under various phospholipid compositions to probe the role of electrostatic interactions. When bound to anionic bicelles, large modifications of the protein three-dimensional structure were detected, as revealed by a significant increase of the protein gyration radius from 42 ± 1 to 60 ± 4 Å. R1-3/anionic bicelle complexes were further analyzed by coarse-grained molecular dynamics simulations. From these studies, we report an all-atom model of R1-3 that highlights the opening of the R1 coiled-coil repeat when bound to the membrane lipids. This model is totally in agreement with SANS and click chemistry/mass spectrometry data. We conclude that the sarcolemma membrane anchoring that occurs during the contraction/elongation process of muscles could be ensured by this coiled-coil opening. Therefore, understanding these structural changes may help in the design of rationalized shortened dystrophins for gene therapy. Finally, our strategy opens up new possibilities for structure determination of peripheral and integral membrane proteins not compatible with different high-resolution structural methods.
MeSH term(s)	Dystrophin/chemistry ; Dystrophin/metabolism ; Humans ; Membrane Lipids/chemistry ; Membrane Lipids/metabolism ; Micelles ; Molecular Dynamics Simulation ; Protein Binding ; Protein Conformation, alpha-Helical
Chemical Substances	Dystrophin ; Membrane Lipids ; Micelles
Language	English
Publishing date	2018-08-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2018.07.039
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Zs.A 235: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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