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Hilpert C, Beranger L, Souza PCT, Vainikka PA, Nieto V, Marrink SJ, Monticelli L, Launay G. Facilitating CG Simulations with MAD: The MArtini Database Server. J Chem Inf Model 2023; 63:702-710. [PMID: 36656159 DOI: 10.1021/acs.jcim.2c01375] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The MArtini Database (MAD - https://mad.ibcp.fr) is a web server designed for the sharing of structures and topologies of molecules parametrized with the Martini coarse-grained (CG) force field. MAD can also convert atomistic structures into CG structures and prepare complex systems (including proteins, lipids, etc.) for molecular dynamics (MD) simulations at the CG level. It is dedicated to the generation of input files for Martini 3, the most recent version of this popular CG force field. Specifically, the MAD server currently includes tools to submit or retrieve CG models of a wide range of molecules (lipids, carbohydrates, nanoparticles, etc.), transform atomistic protein structures into CG structures and topologies, with fine control on the process and assemble biomolecules into large systems, and deliver all files necessary to start simulations in the GROMACS MD engine.
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Affiliation(s)
- Cécile Hilpert
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Louis Beranger
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Paulo C T Souza
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Petteri A Vainikka
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Vincent Nieto
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Luca Monticelli
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Guillaume Launay
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
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Grünewald F, Punt MH, Jefferys EE, Vainikka PA, König M, Virtanen V, Meyer TA, Pezeshkian W, Gormley AJ, Karonen M, Sansom MSP, Souza PCT, Marrink SJ. Martini 3 Coarse-Grained Force Field for Carbohydrates. J Chem Theory Comput 2022; 18:7555-7569. [PMID: 36342474 DOI: 10.1021/acs.jctc.2c00757] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Martini 3 force field is a full reparametrization of the Martini coarse-grained model for biomolecular simulations. Due to the improved interaction balance, it allows for a more accurate description of condensed phase systems. In the present work, we develop a consistent strategy to parametrize carbohydrate molecules accurately within the framework of Martini 3. In particular, we develop a canonical mapping scheme which decomposes arbitrarily large carbohydrates into a limited number of fragments. Bead types for these fragments have been assigned by matching physicochemical properties of mono- and disaccharides. In addition, guidelines for assigning bonds, angles, and dihedrals were developed. These guidelines enable a more accurate description of carbohydrate conformations than in the Martini 2 force field. We show that models obtained with this approach are able to accurately reproduce osmotic pressures of carbohydrate water solutions. Furthermore, we provide evidence that the model differentiates correctly the solubility of the polyglucoses dextran (water-soluble) and cellulose (water insoluble but soluble in ionic liquids). Finally, we demonstrate that the new building blocks can be applied to glycolipids. We show they are able to reproduce membrane properties and induce binding of peripheral membrane proteins. These test cases demonstrate the validity and transferability of our approach.
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Affiliation(s)
- Fabian Grünewald
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Mats H Punt
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Elizabeth E Jefferys
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Petteri A Vainikka
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Melanie König
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Valtteri Virtanen
- Natural Chemistry Research Group, Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Travis A Meyer
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands.,The Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Copenhagen 2100, Denmark
| | - Adam J Gormley
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Maarit Karonen
- Natural Chemistry Research Group, Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS and University of Lyon, Lyon 69367, France
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
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Zhou Q, Chen J, Luan Y, Vainikka PA, Thallmair S, Marrink SJ, Feringa BL, van Rijn P. Unidirectional rotating molecular motors dynamically interact with adsorbed proteins to direct the fate of mesenchymal stem cells. Sci Adv 2020; 6:eaay2756. [PMID: 32064345 PMCID: PMC6989133 DOI: 10.1126/sciadv.aay2756] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 11/21/2019] [Indexed: 05/12/2023]
Abstract
Artificial rotary molecular motors convert energy into controlled motion and drive a system out of equilibrium with molecular precision. The molecular motion is harnessed to mediate the adsorbed protein layer and then ultimately to direct the fate of human bone marrow-derived mesenchymal stem cells (hBM-MSCs). When influenced by the rotary motion of light-driven molecular motors grafted on surfaces, the adsorbed protein layer primes hBM-MSCs to differentiate into osteoblasts, while without rotation, multipotency is better maintained. We have shown that the signaling effects of the molecular motion are mediated by the adsorbed cell-instructing protein layer, influencing the focal adhesion-cytoskeleton actin transduction pathway and regulating the protein and gene expression of hBM-MSCs. This unique molecular-based platform paves the way for implementation of dynamic interfaces for stem cell control and provides an opportunity for novel dynamic biomaterial engineering for clinical applications.
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Affiliation(s)
- Qihui Zhou
- Institute for Translational Medicine, Department of Periodontology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266021, China
- University of Groningen, University Medical Center Groningen, Department of Biomedical Engineering—FB40, W.J. Kolff Institute for Biomedical Engineering and Materials Science—FB41, A. Deusinglaan 1, 9713 AV Groningen, Netherlands
| | - Jiawen Chen
- Center for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AG Groningen, Netherlands
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Yafei Luan
- University of Groningen, University Medical Center Groningen, Department of Biomedical Engineering—FB40, W.J. Kolff Institute for Biomedical Engineering and Materials Science—FB41, A. Deusinglaan 1, 9713 AV Groningen, Netherlands
| | - Petteri A. Vainikka
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Sebastian Thallmair
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Siewert J. Marrink
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
| | - Ben L. Feringa
- Center for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AG Groningen, Netherlands
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Patrick van Rijn
- University of Groningen, University Medical Center Groningen, Department of Biomedical Engineering—FB40, W.J. Kolff Institute for Biomedical Engineering and Materials Science—FB41, A. Deusinglaan 1, 9713 AV Groningen, Netherlands
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
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Thallmair S, Vainikka PA, Marrink SJ. Lipid Fingerprints and Cofactor Dynamics of Light-Harvesting Complex II in Different Membranes. Biophys J 2019; 116:1446-1455. [PMID: 30954210 PMCID: PMC6486485 DOI: 10.1016/j.bpj.2019.03.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 12/20/2018] [Revised: 02/22/2019] [Accepted: 03/12/2019] [Indexed: 11/29/2022] Open
Abstract
Plant light-harvesting complex II (LHCII) is the key antenna complex for plant photosynthesis. We present coarse-grained molecular dynamics simulations of monomeric and trimeric LHCII in a realistic thylakoid membrane environment based on the Martini force field. The coarse-grained protein model has been optimized with respect to atomistic reference simulations. Our simulations provide detailed insights in the thylakoid lipid fingerprint of LHCII which compares well with experimental data from membrane protein purification. Comparing the monomer and trimeric LHCII reveals a stabilizing effect of trimerization on the chromophores as well as the protein. Moreover, the average chromophore distance shortens in the trimer leading to stronger excitonic couplings. When changing the native thylakoid environment to a model membrane the protein flexibility remains constant, whereas the chromophore flexibility is reduced. Overall, the presented LHCII model lays the foundation to investigate the μs dynamics of this key antenna protein of plants.
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Affiliation(s)
- Sebastian Thallmair
- Groningen Biomolecular Sciences and Biotechnology Institute and The Zernike Institute for Advanced Material, University of Groningen, Groningen, The Netherlands.
| | - Petteri A Vainikka
- Groningen Biomolecular Sciences and Biotechnology Institute and The Zernike Institute for Advanced Material, University of Groningen, Groningen, The Netherlands; Department of Chemistry, University of Turku, Turku, Finland
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and The Zernike Institute for Advanced Material, University of Groningen, Groningen, The Netherlands.
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Thallmair S, Vainikka PA, Marrink SJ. Molecular Dynamcis of Light-Harvesting Complex II Embedded in the Thylakoid Membrane. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Affiliation(s)
- Maksim Misin
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow, Glasgow G4 0NG, United Kingdom
| | - Petteri A. Vainikka
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Maxim V. Fedorov
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow, Glasgow G4 0NG, United Kingdom
- Skolkovo Institute of Science and Technology, 3 Nobel Street, Moscow 143026, Russian Federation
| | - David S. Palmer
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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