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Depenveiller C, Wong H, Crowet JM, Debelle L, Baud S, Dauchez M, Belloy N. Challenging level of rigid-body approach involving numerical elements (CHLORAINE) applied to repeated elastin peptides. J Struct Biol 2023; 215:107986. [PMID: 37343710 DOI: 10.1016/j.jsb.2023.107986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/10/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
Elastic proteins and derived biomaterials contain numerous tandemly repeated peptides along their sequences, ranging from a few copies to hundreds. These repetitions are responsible for their biochemical, biological and biomechanical properties. These sequences are considered to be intrinsically disordered, and the variations in their behavior are actually mainly due to their high flexibility and lack of stable secondary structures originating from their unique amino acid sequences. Consequently, the simulation of elastic proteins and large elastomeric biomaterials using classical molecular dynamics is an important challenge. Here, we propose a novel approach that allows the application of the DURABIN protocol to repeated elastin-like peptides (r-ELPs) in a simple way. Four large r-ELPs were studied to evaluate our method, which was developed for simulating extracellular matrix proteins at the mesoscopic scale. After structure clustering applied on molecular dynamic trajectories of constitutive peptides (5-mers and 6-mers), the main conformations were used as starting points to define the corresponding primitives, further used as rigid body fragments in our program. Contributions derived from electrostatic and molecular hydrophobicity potentials were tested to evaluate their influence on the interactions during simple mesoscopic simulations. The CHLORAINE approach, despite the thinner granularity due to the size of the patterns used, was included in the DURABIN protocol and emerges as a promising way to simulate elastic macromolecular systems.
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Affiliation(s)
- C Depenveiller
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France; Université de Picardie Jules Verne, CNRS, GEC UMR 7025, 80039 Amiens, France
| | - H Wong
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France; Université de Reims Champagne Ardenne, Plateau de Modélisation Moléculaire Multi-Echelle (P3M), Maison de la simulation de Champagne Ardenne (MaSCA), 51097 Reims, France
| | - J M Crowet
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France; Université de Reims Champagne Ardenne, Plateau de Modélisation Moléculaire Multi-Echelle (P3M), Maison de la simulation de Champagne Ardenne (MaSCA), 51097 Reims, France
| | - L Debelle
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France
| | - S Baud
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France; Université de Reims Champagne Ardenne, Plateau de Modélisation Moléculaire Multi-Echelle (P3M), Maison de la simulation de Champagne Ardenne (MaSCA), 51097 Reims, France
| | - M Dauchez
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France; Université de Reims Champagne Ardenne, Plateau de Modélisation Moléculaire Multi-Echelle (P3M), Maison de la simulation de Champagne Ardenne (MaSCA), 51097 Reims, France
| | - N Belloy
- Université de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, 51097 Reims, France; Université de Reims Champagne Ardenne, Plateau de Modélisation Moléculaire Multi-Echelle (P3M), Maison de la simulation de Champagne Ardenne (MaSCA), 51097 Reims, France.
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Rondelli V, Koutsioubas A, Pršić J, Deboever E, Crowet JM, Lins L, Deleu M. Sitosterol and glucosylceramide cooperative transversal and lateral uneven distribution in plant membranes. Sci Rep 2021; 11:21618. [PMID: 34732753 PMCID: PMC8566578 DOI: 10.1038/s41598-021-00696-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/05/2021] [Indexed: 11/13/2022] Open
Abstract
The properties of biomembranes depend on the presence, local structure and relative distribution assumed by the thousands of components it is made of. As for animal cells, plant membranes have been demonstrated to be organized in subdomains with different persistence lengths and times. In plant cells, sitosterol has been demonstrated to confer to phospholipid membranes a more ordered structure while among lipids, glycosphingolipids are claimed to form rafts where they tightly pack with sterols. Glucosylceramides are glycosphingolipids involved in plant signalling and are essential for viability of cells and whole plant. The glucosylceramide-sitosterol structural coupling within PLPC membranes is here investigated by Langmuir films, in silico simulations and neutron reflectometry, unveiling that a strong direct interaction between the two molecules exists and governs their lateral and transversal distribution within membrane leaflets. The understanding of the driving forces governing specific molecules clustering and segregation in subdomains, such as glucosylceramide and sitosterol, have an impact on the mechanical properties of biomembranes and could reflect in the other membrane molecules partitioning and activity.
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Affiliation(s)
- V Rondelli
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milano, Italy.
| | - A Koutsioubas
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, Garching, Germany.
| | - J Pršić
- Microbial Processes and Interactions Laboratory (MiPI), TERRA Research Center, Gembloux Agro-Bio Tech, Université de Liège, Gembloux, Belgium
| | - E Deboever
- Laboratoire de Biophysique Moléculaire aux Interfaces, Structure Fédérative de Recherche Condorcet, TERRA Research Center, Gembloux Agro-Bio Tech, Université de Liège, Gembloux, Belgium.,Laboratory of Natural Molecules Chemistry, Gembloux Agro-Bio Tech, University of Liège, 2, Passage des Déportés, 5030, Gembloux, Belgium.,FytoFend S.A., rue Georges Legrand, 6, 5032, Isnes, Belgium
| | - J M Crowet
- Université de Reims Champagne-Ardenne, UFR Sciences Exactes et Naturelles, Reims, France
| | - L Lins
- Laboratoire de Biophysique Moléculaire aux Interfaces, Structure Fédérative de Recherche Condorcet, TERRA Research Center, Gembloux Agro-Bio Tech, Université de Liège, Gembloux, Belgium
| | - M Deleu
- Laboratoire de Biophysique Moléculaire aux Interfaces, Structure Fédérative de Recherche Condorcet, TERRA Research Center, Gembloux Agro-Bio Tech, Université de Liège, Gembloux, Belgium.
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Crowet JM, Nasir MN, Dony N, Deschamps A, Stroobant V, Morsomme P, Deleu M, Soumillion P, Lins L. Insight into the Self-Assembling Properties of Peptergents: A Molecular Dynamics Simulation Study. Int J Mol Sci 2018; 19:ijms19092772. [PMID: 30223492 PMCID: PMC6163580 DOI: 10.3390/ijms19092772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 09/06/2018] [Accepted: 09/10/2018] [Indexed: 11/16/2022] Open
Abstract
By manipulating the various physicochemical properties of amino acids, the design of peptides with specific self-assembling properties has been emerging for more than a decade. In this context, short peptides possessing detergent properties (so-called "peptergents") have been developed to self-assemble into well-ordered nanostructures that can stabilize membrane proteins for crystallization. In this study, the peptide with "peptergency" properties, called ADA8 and extensively described by Tao et al., is studied by molecular dynamic simulations for its self-assembling properties in different conditions. In water, it spontaneously forms beta sheets with a β barrel-like structure. We next simulated the interaction of this peptide with a membrane protein, the bacteriorhodopsin, in the presence or absence of a micelle of dodecylphosphocholine. According to the literature, the peptergent ADA8 is thought to generate a belt of β structures around the hydrophobic helical domain that could help stabilize purified membrane proteins. Molecular dynamic simulations are here used to image this mechanism and provide further molecular details for the replacement of detergent molecules around the protein. In addition, we generalized this behavior by designing an amphipathic peptide with beta propensity, which was called ABZ12. Both peptides are able to surround the membrane protein and displace surfactant molecules. To our best knowledge, this is the first molecular mechanism proposed for "peptergency".
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Affiliation(s)
- Jean Marc Crowet
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, University of Liège, Passage des déportés 2, 5030 Gembloux, Belgium.
| | - Mehmet Nail Nasir
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, University of Liège, Passage des déportés 2, 5030 Gembloux, Belgium.
| | - Nicolas Dony
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, University of Liège, Passage des déportés 2, 5030 Gembloux, Belgium.
| | - Antoine Deschamps
- Institut des Sciences de la Vie, Université catholique de Louvain, 4-5 Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium.
| | - Vincent Stroobant
- Ludwig Institute for Cancer Research, de Duve Institute and Université Catholique de Louvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium.
| | - Pierre Morsomme
- Institut des Sciences de la Vie, Université catholique de Louvain, 4-5 Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium.
| | - Magali Deleu
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, University of Liège, Passage des déportés 2, 5030 Gembloux, Belgium.
| | - Patrice Soumillion
- Institut des Sciences de la Vie, Université catholique de Louvain, 4-5 Place Croix du Sud, 1348 Louvain-la-Neuve, Belgium.
| | - Laurence Lins
- Laboratoire de Biophysique Moléculaire aux Interfaces, Gembloux Agro-Bio Tech, University of Liège, Passage des déportés 2, 5030 Gembloux, Belgium.
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Dony N, Crowet JM, Joris B, Brasseur R, Lins L. SAHBNET, an accessible surface-based elastic network: an application to membrane protein. Int J Mol Sci 2013; 14:11510-26. [PMID: 23722660 PMCID: PMC3709745 DOI: 10.3390/ijms140611510] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 05/02/2013] [Accepted: 05/20/2013] [Indexed: 11/06/2022] Open
Abstract
Molecular Dynamics is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. Here, we present an elastic network, SAHBNET (Surface Accessibility Hydrogen-Bonds elastic NETwork), that will maintain the structure of soluble or membrane proteins based on the hydrogen bonds present in the atomistic structure and the proximity between buried residues. This network is applied on the coarse-grained beads defined by the MARTINI model, and was designed to be more physics-based than a simple elastic network. The SAHBNET model is evaluated against atomistic simulations, and compared with ELNEDYN models. The SAHBNET is then used to simulate two membrane proteins inserted in complex lipid bilayers. These bilayers are formed by self-assembly and the use of a modified version of the GROMACS tool genbox (which is accessible through the gcgs.gembloux.ulg.ac.be website). The results show that SAHBNET keeps the structure close to the atomistic one and is successfully used for the simulation of membrane proteins.
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Affiliation(s)
- Nicolas Dony
- Center of Protein Engineering, University of Liège, Institut de chimie B6a, B-4000 Liège, Belgium; E-Mails: (N.D.); (B.J.)
| | - Jean Marc Crowet
- Numerical Molecular Biophysics Unit, Gembloux Agro-Bio Tech, University of Liège, Passage des déportés, B-5030 Gembloux, Belgium; E-Mails: (J.M.C.); (R.B.)
| | - Bernard Joris
- Center of Protein Engineering, University of Liège, Institut de chimie B6a, B-4000 Liège, Belgium; E-Mails: (N.D.); (B.J.)
| | - Robert Brasseur
- Numerical Molecular Biophysics Unit, Gembloux Agro-Bio Tech, University of Liège, Passage des déportés, B-5030 Gembloux, Belgium; E-Mails: (J.M.C.); (R.B.)
| | - Laurence Lins
- Numerical Molecular Biophysics Unit, Gembloux Agro-Bio Tech, University of Liège, Passage des déportés, B-5030 Gembloux, Belgium; E-Mails: (J.M.C.); (R.B.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +32-81-622-521; Fax: +32-81-622-522
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Santini S, Crowet JM, Thomas A, Paquot M, Vandenbol M, Thonart P, Wathelet JP, Blecker C, Lognay G, Brasseur R, Lins L, Charloteaux B. Study of Thermomyces lanuginosa lipase in the presence of tributyrylglycerol and water. Biophys J 2009; 96:4814-25. [PMID: 19527641 DOI: 10.1016/j.bpj.2009.03.040] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2008] [Revised: 02/09/2009] [Accepted: 03/24/2009] [Indexed: 10/20/2022] Open
Abstract
The Thermomyces lanuginosa lipase has been extensively studied in industrial and biotechnological research because of its potential for triacylglycerol transformation. This protein is known to catalyze both hydrolysis at high water contents and transesterification in quasi-anhydrous conditions. Here, we investigated the Thermomyces lanuginosa lipase structure in solution in the presence of a tributyrin aggregate using 30 ns molecular-dynamics simulations. The water content of the active-site groove was modified between the runs to focus on the protein-water molecule interactions and their implications for protein structure and protein-lipid interactions. The simulations confirmed the high plasticity of the lid fragment and showed that lipid molecules also bind to a secondary pocket beside the lid. Together, these results strongly suggest that the lid plays a role in the anchoring of the protein to the aggregate. The simulations also revealed the existence of a polar channel that connects the active-site groove to the outside solvent. At the inner extremity of this channel, a tyrosine makes hydrogen bonds with residues interacting with the catalytic triad. This system could function as a pipe (polar channel) controlled by a valve (the tyrosine) that could regulate the water content of the active site.
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Affiliation(s)
- S Santini
- Center of Numerical Molecular Biophysics, Gembloux Agricultural University, Gembloux, Belgium
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Charloteaux B, Lorin A, Crowet JM, Stroobant V, Lins L, Thomas A, Brasseur R. The N-terminal 12 Residue Long Peptide of HIV gp41 is the Minimal Peptide Sufficient to Induce Significant T-cell-like Membrane Destabilization in Vitro. J Mol Biol 2006; 359:597-609. [PMID: 16677669 DOI: 10.1016/j.jmb.2006.04.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2006] [Accepted: 04/03/2006] [Indexed: 11/26/2022]
Abstract
Here, we predicted the minimal N-terminal fragment of gp41 required to induce significant membrane destabilization using IMPALA. This algorithm is dedicated to predict peptide interaction with a membrane. We based our prediction of the minimal fusion peptide on the tilted peptide theory. This theory proposes that some protein fragments having a peculiar distribution of hydrophobicity adopt a tilted orientation at a hydrophobic/hydrophilic interface. As a result of this orientation, tilted peptides should disrupt the interface. We analysed in silico the membrane-interacting properties of gp41 N-terminal peptides of different length derived from the isolate BRU and from an alignment of 710 HIV strains available on the Los Alamos National Laboratory. Molecular modelling results indicated that the 12 residue long peptide should be the minimal fusion peptide. We then assayed lipid-mixing and leakage of T-cell-like liposomes with N-terminal peptides of different length as first challenge of our predictions. Experimental results confirmed that the 12 residue long peptide is necessary and sufficient to induce membrane destabilization to the same extent as the 23 residue long fusion peptide. In silico analysis of some fusion-incompetent mutants presented in the literature further revealed that they cannot insert into a modelled membrane correctly tilted. According to this work, the tilted peptide model appears to explain at least partly the membrane destabilization properties of HIV fusion peptide.
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Affiliation(s)
- B Charloteaux
- Centre de Biophysique Moléculaire Numérique, Faculté Universitaire des Sciences Agronomiques, Passage des déportés, B-5030 Gembloux, Belgium.
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