1
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Ghiringhelli LM, Baldauf C, Bereau T, Brockhauser S, Carbogno C, Chamanara J, Cozzini S, Curtarolo S, Draxl C, Dwaraknath S, Fekete Á, Kermode J, Koch CT, Kühbach M, Ladines AN, Lambrix P, Himmer MO, Levchenko SV, Oliveira M, Michalchuk A, Miller RE, Onat B, Pavone P, Pizzi G, Regler B, Rignanese GM, Schaarschmidt J, Scheidgen M, Schneidewind A, Sheveleva T, Su C, Usvyat D, Valsson O, Wöll C, Scheffler M. Shared metadata for data-centric materials science. Sci Data 2023; 10:626. [PMID: 37709811 PMCID: PMC10502089 DOI: 10.1038/s41597-023-02501-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/23/2023] [Indexed: 09/16/2023] Open
Affiliation(s)
- Luca M Ghiringhelli
- Physics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, Berlin, Germany.
- The NOMAD Laboratory at the Fritz-Haber-Institut of the Max-Planck-Gesellschaft and IRIS-Adlershof of the Humboldt-Universität zu Berlin, Berlin, Germany.
- Department of Materials Science and Engineering, Friedrich-Alexander Universität, Erlangen-Nürnberg, Germany.
| | - Carsten Baldauf
- Fritz-Haber-Institut of the Max-Planck-Gesellschaft, Berlin, Germany
| | - Tristan Bereau
- Van't Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam, Amsterdam, 1098 XH, The Netherlands
| | - Sandor Brockhauser
- Physics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christian Carbogno
- The NOMAD Laboratory at the Fritz-Haber-Institut of the Max-Planck-Gesellschaft and IRIS-Adlershof of the Humboldt-Universität zu Berlin, Berlin, Germany
| | - Javad Chamanara
- TIB - Leibniz Information Centre for Science and Technology and University Library, 30167, Hanover, Germany
| | - Stefano Cozzini
- AREA Science Park, località Padriciano, 34149, Trieste, Italy
| | - Stefano Curtarolo
- Center for Autonomous Materials Design and Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27708, USA
| | - Claudia Draxl
- Physics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, Berlin, Germany
- The NOMAD Laboratory at the Fritz-Haber-Institut of the Max-Planck-Gesellschaft and IRIS-Adlershof of the Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Ádám Fekete
- Physics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, Berlin, Germany
| | - James Kermode
- Warwick Centre for Predictive Modelling, School of Engineering, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Christoph T Koch
- Physics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Markus Kühbach
- Physics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Alvin Noe Ladines
- Physics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Patrick Lambrix
- Department of Computer and Information Science and The Swedish e-Science Research Centre, Linköping University, Linköping, Sweden
| | - Maja-Olivia Himmer
- The NOMAD Laboratory at the Fritz-Haber-Institut of the Max-Planck-Gesellschaft and IRIS-Adlershof of the Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sergey V Levchenko
- Center for Energy Science and Technology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Micael Oliveira
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Adam Michalchuk
- Federal Institute for Materials Research and Testing (BAM), 12489, Berlin, Germany
- School of Chemistry, University of Birmingham, B15 2TT, Edgbaston, Birmingham, UK
| | - Ronald E Miller
- Department of Mechanical and Aerospace Engineering, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Berk Onat
- Warwick Centre for Predictive Modelling, School of Engineering, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Pasquale Pavone
- Physics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Giovanni Pizzi
- Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
- Laboratory for Materials Simulations (LMS), Paul Scherrer Institut (PSI), CH-5232, Villigen, Switzerland
| | - Benjamin Regler
- The NOMAD Laboratory at the Fritz-Haber-Institut of the Max-Planck-Gesellschaft and IRIS-Adlershof of the Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gian-Marco Rignanese
- Institute of Condensed Matter and Nanosciences (IMCN), UCLouvain, Chemin des Étoiles 8, B-1348, Louvain-la-Neuve, Belgium
| | - Jörg Schaarschmidt
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Karlsruhe, Germany
| | - Markus Scheidgen
- Physics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Astrid Schneidewind
- Jülich Center for Neutron Science at MLZ, Forschungszentrum Jülich GmbH, Lichtenbergstrase 1, 85748, Garching, Germany
| | - Tatyana Sheveleva
- TIB - Leibniz Information Centre for Science and Technology and University Library, 30167, Hanover, Germany
| | - Chuanxun Su
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei, 230026, People's Republic of China
| | - Denis Usvyat
- Chemistry Department, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Omar Valsson
- Department of Chemistry, University of North Texas, Denton, TX, 76201, USA
| | - Christof Wöll
- Institute of Functional Interfaces, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Karlsruhe, Germany
| | - Matthias Scheffler
- Physics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, Berlin, Germany
- The NOMAD Laboratory at the Fritz-Haber-Institut of the Max-Planck-Gesellschaft and IRIS-Adlershof of the Humboldt-Universität zu Berlin, Berlin, Germany
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Kaygisiz K, Rauch-Wirth L, Dutta A, Yu X, Nagata Y, Bereau T, Münch J, Synatschke CV, Weil T. Data-mining unveils structure-property-activity correlation of viral infectivity enhancing self-assembling peptides. Nat Commun 2023; 14:5121. [PMID: 37612273 PMCID: PMC10447463 DOI: 10.1038/s41467-023-40663-6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/01/2023] [Indexed: 08/25/2023] Open
Abstract
Gene therapy via retroviral vectors holds great promise for treating a variety of serious diseases. It requires the use of additives to boost infectivity. Amyloid-like peptide nanofibers (PNFs) were shown to efficiently enhance retroviral gene transfer. However, the underlying mode of action of these peptides remains largely unknown. Data-mining is an efficient method to systematically study structure-function relationship and unveil patterns in a database. This data-mining study elucidates the multi-scale structure-property-activity relationship of transduction enhancing peptides for retroviral gene transfer. In contrast to previous reports, we find that not the amyloid fibrils themselves, but rather µm-sized β-sheet rich aggregates enhance infectivity. Specifically, microscopic aggregation of β-sheet rich amyloid structures with a hydrophobic surface pattern and positive surface charge are identified as key material properties. We validate the reliability of the amphiphilic sequence pattern and the general applicability of the key properties by rationally creating new active sequences and identifying short amyloidal peptides from various pathogenic and functional origin. Data-mining-even for small datasets-enables the development of new efficient retroviral transduction enhancers and provides important insights into the diverse bioactivity of the functional material class of amyloids.
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Affiliation(s)
- Kübra Kaygisiz
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Lena Rauch-Wirth
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstraße 1, 89081, Ulm, Germany
| | - Arghya Dutta
- Department Polymer Theory, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Xiaoqing Yu
- Department Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Yuki Nagata
- Department Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tristan Bereau
- Department Polymer Theory, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
- Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120, Heidelberg, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstraße 1, 89081, Ulm, Germany
| | - Christopher V Synatschke
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.
| | - Tanja Weil
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.
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Mohr B, van der Mast D, Bereau T. Condensed-Phase Molecular Representation to Link Structure and Thermodynamics in Molecular Dynamics. J Chem Theory Comput 2023. [PMID: 37395557 PMCID: PMC10373487 DOI: 10.1021/acs.jctc.3c00201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Molecular design requires systematic and broadly applicable methods to extract structure-property relationships. The focus of this study is on learning thermodynamic properties from molecular-liquid simulations. The methodology relies on an atomic representation originally developed for electronic properties: the Spectrum of London and Axilrod-Teller-Muto representation (SLATM). SLATM's expansion in one-, two-, and three-body interactions makes it amenable to probing structural ordering in molecular liquids. We show that such representation encodes enough critical information to permit the learning of thermodynamic properties via linear methods. We demonstrate our approach on the preferential insertion of small solute molecules toward cardiolipin membranes and monitor selectivity against a similar lipid. Our analysis reveals simple, interpretable relationships between two- and three-body interactions and selectivity, identifies key interactions to build optimal prototypical solutes, and charts a two-dimensional projection that displays clearly separated basins. The methodology is generally applicable to a variety of thermodynamic properties.
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Affiliation(s)
- Bernadette Mohr
- Van 't Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam, Amsterdam 1098 XH, The Netherlands
| | - Diego van der Mast
- Van 't Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam, Amsterdam 1098 XH, The Netherlands
| | - Tristan Bereau
- Van 't Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam, Amsterdam 1098 XH, The Netherlands
- Max Planck Institute for Polymer Research, Mainz 55128, Germany
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4
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Kaygisiz K, Dutta A, Rauch-Wirth L, Synatschke CV, Münch J, Bereau T, Weil T. Inverse design of viral infectivity-enhancing peptide fibrils from continuous protein-vector embeddings. Biomater Sci 2023. [PMID: 37341479 DOI: 10.1039/d3bm00412k] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Amyloid-like nanofibers from self-assembling peptides can promote viral gene transfer for therapeutic applications. Traditionally, new sequences are discovered either from screening large libraries or by creating derivatives of known active peptides. However, the discovery of de novo peptides, which are sequence-wise not related to any known active peptides, is limited by the difficulty to rationally predict structure-activity relationships because their activities typically have multi-scale and multi-parameter dependencies. Here, we used a small library of 163 peptides as a training set to predict de novo sequences for viral infectivity enhancement using a machine learning (ML) approach based on natural language processing. Specifically, we trained an ML model using continuous vector representations of the peptides, which were previously shown to retain relevant information embedded in the sequences. We used the trained ML model to sample the sequence space of peptides with 6 amino acids to identify promising candidates. These 6-mers were then further screened for charge and aggregation propensity. The resulting 16 new 6-mers were tested and found to be active with a 25% hit rate. Strikingly, these de novo sequences are the shortest active peptides for infectivity enhancement reported so far and show no sequence relation to the training set. Moreover, by screening the sequence space, we discovered the first hydrophobic peptide fibrils with a moderately negative surface charge that can enhance infectivity. Hence, this ML strategy is a time- and cost-efficient way for expanding the sequence space of short functional self-assembling peptides exemplified for therapeutic viral gene delivery.
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Affiliation(s)
- Kübra Kaygisiz
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Arghya Dutta
- Polymer Theory, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Lena Rauch-Wirth
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstraße 1, 89081 Ulm, Germany
| | - Christopher V Synatschke
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstraße 1, 89081 Ulm, Germany
| | - Tristan Bereau
- Polymer Theory, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Tanja Weil
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
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5
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Stieffenhofer M, Scherer C, May F, Bereau T, Andrienko D. Benchmarking coarse-grained models of organic semiconductors via deep backmapping. Front Chem 2022; 10:982757. [PMID: 36157043 PMCID: PMC9500322 DOI: 10.3389/fchem.2022.982757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
The potential of mean force is an effective coarse-grained potential, which is often approximated by pairwise potentials. While the approximated potential reproduces certain distributions of the reference all-atom model with remarkable accuracy, important cross-correlations are typically not captured. In general, the quality of coarse-grained models is evaluated at the coarse-grained resolution, hindering the detection of important discrepancies between the all-atom and coarse-grained ensembles. In this work, the quality of different coarse-grained models is assessed at the atomistic resolution deploying reverse-mapping strategies. In particular, coarse-grained structures for Tris-Meta-Biphenyl-Triazine are reverse-mapped from two different sources: 1) All-atom configurations projected onto the coarse-grained resolution and 2) snapshots obtained by molecular dynamics simulations based on the coarse-grained force fields. To assess the quality of the coarse-grained models, reverse-mapped structures of both sources are compared revealing significant discrepancies between the all-atom and the coarse-grained ensembles. Specifically, the reintroduced details enable force computations based on the all-atom force field that yield a clear ranking for the quality of the different coarse-grained models.
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Affiliation(s)
| | | | | | - Tristan Bereau
- Van ‘t Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam, Amsterdam, Netherlands
| | - Denis Andrienko
- Max Planck Institute for Polymer Research, Mainz, Germany
- *Correspondence: Denis Andrienko,
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Anelli A, Dietrich H, Ectors P, Stowasser F, Bereau T, Neumann M, Van Den Ende J. Integrating machine learning in crystal structure prediction for pharmaceutical compounds. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322091045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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Abstract
Compared to top-down coarse-grained (CG) models, bottom-up approaches are capable of offering higher structural fidelity. This fidelity results from the tight link to a higher-resolution reference, making the CG model chemically specific. Unfortunately, chemical specificity can be at odds with compound-screening strategies, which call for transferable parametrizations. Here we present an approach to reconcile bottom-up, structure-preserving CG models with chemical transferability. We consider the bottom-up CG parametrization of 3,441 C7O2 small-molecule isomers. Our approach combines atomic representations, unsupervised learning, and a large-scale extended-ensemble force-matching parametrization. We first identify a subset of 19 representative molecules, which maximally encode the local environment of all gas-phase conformers. Reference interactions between the 19 representative molecules were obtained from both homogeneous bulk liquids and various binary mixtures. An extended-ensemble parametrization over all 703 state points leads to a CG model that is both structure-based and chemically transferable. Remarkably, the resulting force field is on average more structurally accurate than single-state-point equivalents. Averaging over the extended ensemble acts as a mean-force regularizer, smoothing out both force and structural correlations that are overly specific to a single state point. Our approach aims at transferability through a set of CG bead types that can be used to easily construct new molecules, while retaining the benefits of a structure-based parametrization.
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Affiliation(s)
- Kiran H. Kanekal
- AK Kremer - Theory Group, Max Planck Institute for Polymer Research, Germany
| | | | - Tristan Bereau
- Van 't Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam, Netherlands
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8
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Kleinwächter I, Mohr B, Joppe A, Hellmann N, Bereau T, Osiewacz HD, Schneider D. CLiB - a novel cardiolipin-binder isolated via data-driven and in vitro screening. RSC Chem Biol 2022; 3:941-954. [PMID: 35866160 PMCID: PMC9257654 DOI: 10.1039/d2cb00125j] [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: 03/03/2022] [Accepted: 06/01/2022] [Indexed: 11/21/2022] Open
Abstract
Cardiolipin, the mitochondria marker lipid, is crucially involved in stabilizing the inner mitochondrial membrane and is vital for the activity of mitochondrial proteins and protein complexes. Directly targeting cardiolipin by a chemical-biology approach and thereby altering the cellular concentration of "available" cardiolipin eventually allows to systematically study the dependence of cellular processes on cardiolipin availability. In the present study, physics-based coarse-grained free energy calculations allowed us to identify the physical and chemical properties indicative of cardiolipin selectivity and to apply these to screen a compound database for putative cardiolipin-binders. The membrane binding properties of the 22 most promising molecules identified in the in silico approach were screened in vitro, using model membrane systems finally resulting in the identification of a single molecule, CLiB (CardioLipin-Binder). CLiB clearly affects respiration of cardiolipin-containing intact bacterial cells as well as of isolated mitochondria. Thus, the structure and function of mitochondrial membranes and membrane proteins might be (indirectly) targeted and controlled by CLiB for basic research and, potentially, also for therapeutic purposes.
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Affiliation(s)
- Isabel Kleinwächter
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz Hanns-Dieter-Hüsch-Weg 17 55128 Mainz Germany
| | - Bernadette Mohr
- Van 't Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam Amsterdam The Netherlands
| | - Aljoscha Joppe
- Institute for Molecular Biosciences, J. W. Goethe University Frankfurt am Main Germany
| | - Nadja Hellmann
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz Hanns-Dieter-Hüsch-Weg 17 55128 Mainz Germany
| | - Tristan Bereau
- Van 't Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam Amsterdam The Netherlands
| | - Heinz D Osiewacz
- Institute for Molecular Biosciences, J. W. Goethe University Frankfurt am Main Germany
| | - Dirk Schneider
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz Hanns-Dieter-Hüsch-Weg 17 55128 Mainz Germany
- Institute of Molecular Physiology, Johannes Gutenberg University Mainz Hanns-Dieter-Hüsch-Weg 17 55128 Mainz Germany
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Mohr B, Shmilovich K, Kleinwächter IS, Schneider D, Ferguson AL, Bereau T. Data-driven discovery of cardiolipin-selective small molecules by computational active learning. Chem Sci 2022; 13:4498-4511. [PMID: 35656132 PMCID: PMC9019913 DOI: 10.1039/d2sc00116k] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/24/2022] [Indexed: 12/23/2022] Open
Abstract
Subtle variations in the lipid composition of mitochondrial membranes can have a profound impact on mitochondrial function. The inner mitochondrial membrane contains the phospholipid cardiolipin, which has been demonstrated to act as a biomarker for a number of diverse pathologies. Small molecule dyes capable of selectively partitioning into cardiolipin membranes enable visualization and quantification of the cardiolipin content. Here we present a data-driven approach that combines a deep learning-enabled active learning workflow with coarse-grained molecular dynamics simulations and alchemical free energy calculations to discover small organic compounds able to selectively permeate cardiolipin-containing membranes. By employing transferable coarse-grained models we efficiently navigate the all-atom design space corresponding to small organic molecules with molecular weight less than ≈500 Da. After direct simulation of only 0.42% of our coarse-grained search space we identify molecules with considerably increased levels of cardiolipin selectivity compared to a widely used cardiolipin probe 10-N-nonyl acridine orange. Our accumulated simulation data enables us to derive interpretable design rules linking coarse-grained structure to cardiolipin selectivity. The findings are corroborated by fluorescence anisotropy measurements of two compounds conforming to our defined design rules. Our findings highlight the potential of coarse-grained representations and multiscale modelling for materials discovery and design.
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Affiliation(s)
- Bernadette Mohr
- Van't Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam Amsterdam 1098 XH The Netherlands
| | - Kirill Shmilovich
- Pritzker School of Molecular Engineering, University of Chicago Chicago Illinois 60637 USA
| | - Isabel S Kleinwächter
- Department of Chemistry - Biochemistry, Johannes Gutenberg University Mainz 55128 Mainz Germany
| | - Dirk Schneider
- Department of Chemistry - Biochemistry, Johannes Gutenberg University Mainz 55128 Mainz Germany
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago Chicago Illinois 60637 USA
| | - Tristan Bereau
- Van't Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam Amsterdam 1098 XH The Netherlands .,Max Planck Institute for Polymer Research 55128 Mainz Germany
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Scheffler M, Aeschlimann M, Albrecht M, Bereau T, Bungartz HJ, Felser C, Greiner M, Groß A, Koch CT, Kremer K, Nagel WE, Scheidgen M, Wöll C, Draxl C. FAIR data enabling new horizons for materials research. Nature 2022; 604:635-642. [PMID: 35478233 DOI: 10.1038/s41586-022-04501-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 01/28/2022] [Indexed: 12/30/2022]
Abstract
The prosperity and lifestyle of our society are very much governed by achievements in condensed matter physics, chemistry and materials science, because new products for sectors such as energy, the environment, health, mobility and information technology (IT) rely largely on improved or even new materials. Examples include solid-state lighting, touchscreens, batteries, implants, drug delivery and many more. The enormous amount of research data produced every day in these fields represents a gold mine of the twenty-first century. This gold mine is, however, of little value if these data are not comprehensively characterized and made available. How can we refine this feedstock; that is, turn data into knowledge and value? For this, a FAIR (findable, accessible, interoperable and reusable) data infrastructure is a must. Only then can data be readily shared and explored using data analytics and artificial intelligence (AI) methods. Making data 'findable and AI ready' (a forward-looking interpretation of the acronym) will change the way in which science is carried out today. In this Perspective, we discuss how we can prepare to make this happen for the field of materials science.
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Affiliation(s)
- Matthias Scheffler
- Physics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, Berlin, Germany.,The NOMAD Laboratory at the Fritz Haber Institute of the Max Planck Society, Berlin, Germany
| | - Martin Aeschlimann
- Department of Physics and Research Center OPTIMAS, University of Kaiserslautern, Kaiserslautern, Germany
| | | | - Tristan Bereau
- Max-Planck-Institut für Polymerforschung, Mainz, Germany
| | | | - Claudia Felser
- Max Planck Institute for Chemical Physics of Solids, Dresden, Germany
| | - Mark Greiner
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Axel Groß
- Institute of Theoretical Chemistry, Ulm University and Helmholtz-Institute Ulm, Ulm, Germany
| | - Christoph T Koch
- Physics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Kurt Kremer
- Max-Planck-Institut für Polymerforschung, Mainz, Germany
| | - Wolfgang E Nagel
- Computer Science Department, Technical University Dresden, Dresden, Germany
| | - Markus Scheidgen
- Physics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christof Wöll
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Claudia Draxl
- Physics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, Berlin, Germany. .,The NOMAD Laboratory at the Fritz Haber Institute of the Max Planck Society, Berlin, Germany.
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Girard M, Bereau T. Imposed and induced asymmetries in membranes. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1653] [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: 11/15/2022] Open
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12
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Mondal P, Cazade PA, Das AK, Bereau T, Meuwly M. Multipolar Force Fields for Amide-I Spectroscopy from Conformational Dynamics of the Alanine Trimer. J Phys Chem B 2021; 125:10928-10938. [PMID: 34559531 DOI: 10.1021/acs.jpcb.1c05423] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dynamics and spectroscopy of N-methyl-acetamide (NMA) and trialanine in solution are characterized from molecular dynamics simulations using different energy functions, including a conventional point charge (PC)-based force field, one based on a multipolar (MTP) representation of the electrostatics, and a semiempirical DFT method. For the 1D infrared spectra, the frequency splitting between the two amide-I groups is 10 cm-1 from the PC, 13 cm-1 from the MTP, and 47 cm-1 from self-consistent charge density functional tight-binding (SCC-DFTB) simulations, compared with 25 cm-1 from experiment. The frequency trajectory required for the frequency fluctuation correlation function (FFCF) is determined from individual normal mode (INM) and full normal mode (FNM) analyses of the amide-I vibrations. The spectroscopy, time-zero magnitude of the FFCF C(t = 0), and the static component Δ02 from simulations using MTP and analysis based on FNM are all consistent with experiments for (Ala)3. Contrary to this, for the analysis excluding mode-mode coupling (INM), the FFCF decays to zero too rapidly and for simulations with a PC-based force field, the Δ02 is too small by a factor of two compared with experiments. Simulations with SCC-DFTB agree better with experiment for these observables than those from PC-based simulations. The conformational ensemble sampled from simulations using PCs is consistent with the literature (including PII, β, αR, and αL), whereas that covered by the MTP-based simulations is dominated by PII with some contributions from β and αR. This agrees with and confirms recently reported Bayesian-refined populations based on 1D infrared experiments. FNM analysis together with a MTP representation provides a meaningful model to correctly describe the dynamics of hydrated trialanine.
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Affiliation(s)
- Padmabati Mondal
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel 4056, Switzerland
| | - Pierre-André Cazade
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel 4056, Switzerland
| | - Akshaya K Das
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel 4056, Switzerland
| | - Tristan Bereau
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel 4056, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel 4056, Switzerland.,Department of Chemistry, Brown University, Providence/RI 02912, United States
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13
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Dutta A, Vreeken J, Ghiringhelli LM, Bereau T. Data-driven equation for drug-membrane permeability across drugs and membranes. J Chem Phys 2021; 154:244114. [PMID: 34241352 DOI: 10.1063/5.0053931] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Drug efficacy depends on its capacity to permeate across the cell membrane. We consider the prediction of passive drug-membrane permeability coefficients. Beyond the widely recognized correlation with hydrophobicity, we additionally consider the functional relationship between passive permeation and acidity. To discover easily interpretable equations that explain the data well, we use the recently proposed sure-independence screening and sparsifying operator (SISSO), an artificial-intelligence technique that combines symbolic regression with compressed sensing. Our study is based on a large in silico dataset of 0.4 × 106 small molecules extracted from coarse-grained simulations. We rationalize the equation suggested by SISSO via an analysis of the inhomogeneous solubility-diffusion model in several asymptotic acidity regimes. We further extend our analysis to the dependence on lipid-membrane composition. Lipid-tail unsaturation plays a key role but surprisingly contributes stepwise rather than proportionally. Our results are in line with previously observed changes in permeability, suggesting the distinction between liquid-disordered and liquid-ordered permeation. Together, compressed sensing with analytically derived asymptotes establish and validate an accurate, broadly applicable, and interpretable equation for passive permeability across both drug and lipid-tail chemistry.
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Affiliation(s)
- Arghya Dutta
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Jilles Vreeken
- CISPA Helmholtz Center for Information Security, Saarbrücken, Germany
| | - Luca M Ghiringhelli
- The NOMAD Laboratory at the Fritz Haber Institute of the Max Planck Society and Humboldt University, Berlin, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Mainz, Germany
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14
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Dutta A, Vreeken J, Ghiringhelli LM, Bereau T. Publisher's Note: "Data-driven equation for drug-membrane permeability across drugs and membranes" [J. Chem. Phys. 154, 244114 (2021)]. J Chem Phys 2021; 155:039901. [PMID: 34293893 DOI: 10.1063/5.0061875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Arghya Dutta
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Jilles Vreeken
- CISPA Helmholtz Center for Information Security, Saarbrücken, Germany
| | - Luca M Ghiringhelli
- The NOMAD Laboratory at the Fritz Haber Institute of the Max Planck Society and Humboldt University, Berlin, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Mainz, Germany
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15
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Girard M, Bereau T. Finite-size transitions in complex membranes. Biophys J 2021; 120:2436-2443. [PMID: 33961864 DOI: 10.1016/j.bpj.2021.03.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/04/2021] [Accepted: 03/23/2021] [Indexed: 11/15/2022] Open
Abstract
The lipid-raft hypothesis postulates that cell membranes possess some degree of lateral organization. The hypothesis has attracted much attention while remaining controversial, with an underlying mechanism that remains elusive. One idea that supports rafts relies on the membrane lying near a critical point. Although supported by experimental evidence, holding a many-component membrane at criticality requires a delicate tuning of all components-a daunting task. Here, we propose a coherent framework to reconcile critical behavior and lipid regulation. Using a lattice model, we show that lipid regulation of a complex membrane, i.e., allowing composition to fluctuate based on relative chemical potentials, can lead to critical behavior. The results are robust against specific values of the chemical potentials. Instead of a conventional transition point, criticality is observed over a large temperature range. This surprising behavior arises from finite-size effects, causing nonequivalent time and space averages. The instantaneous lipid distribution effectively develops a translational symmetry, which we relate to long-wavelength Goldstone modes. The framework is robust and reproduces important experimental trends; membrane-demixing temperature closely follows cell-growth temperature. It also ensures criticality of fixed-composition extracts, such as giant plasma membrane vesicles. Our clear picture provides a strong argument in favor of the critical-membrane hypothesis, without the need for specific sensing mechanisms.
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Affiliation(s)
- Martin Girard
- Max Planck Institute for Polymer Research, Mainz, Germany.
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Mainz, Germany; Van 't Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam, Amsterdam, the Netherlands
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16
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Rudzinski JF, Kloth S, Wörner S, Pal T, Kremer K, Bereau T, Vogel M. Dynamical properties across different coarse-grained models for ionic liquids. J Phys Condens Matter 2021; 33:224001. [PMID: 33592598 DOI: 10.1088/1361-648x/abe6e1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/16/2021] [Indexed: 06/12/2023]
Abstract
Room-temperature ionic liquids (RTILs) stand out among molecular liquids for their rich physicochemical characteristics, including structural and dynamic heterogeneity. The significance of electrostatic interactions in RTILs results in long characteristic length- and timescales, and has motivated the development of a number of coarse-grained (CG) simulation models. In this study, we aim to better understand the connection between certain CG parameterization strategies and the dynamical properties and transferability of the resulting models. We systematically compare five CG models: a model largely parameterized from experimental thermodynamic observables; a refinement of this model to increase its structural accuracy; and three models that reproduce a given set of structural distribution functions by construction, with varying intramolecular parameterizations and reference temperatures. All five CG models display limited structural transferability over temperature, and also result in various effective dynamical speedup factors, relative to a reference atomistic model. On the other hand, the structure-based CG models tend to result in more consistent cation-anion relative diffusion than the thermodynamic-based models, for a single thermodynamic state point. By linking short- and long-timescale dynamical behaviors, we demonstrate that the varying dynamical properties of the different CG models can be largely collapsed onto a single curve, which provides evidence for a route to constructing dynamically-consistent CG models of RTILs.
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Affiliation(s)
| | - Sebastian Kloth
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - Svenja Wörner
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Tamisra Pal
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
- Van 't Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam, Amsterdam 1098 XH, The Netherlands
| | - Michael Vogel
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
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17
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Girard M, Bereau T. Computer simulations of lipid regulation by molecular semigrand canonical ensembles. Biophys J 2021; 120:2370-2373. [PMID: 33940023 DOI: 10.1016/j.bpj.2021.04.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 10/30/2020] [Revised: 04/06/2021] [Accepted: 04/22/2021] [Indexed: 11/15/2022] Open
Abstract
The plasma membrane is the interface between cells and exterior media. Although its existence has been known for a long time, organization of its constituent lipids remain a challenge. Recently, we have proposed that lipid populations may be controlled by chemical potentials of different lipid species, resulting in semigrand canonical thermodynamic ensembles. However, the currently available molecular dynamics software packages do not facilitate the control of chemical potentials at the molecular level. Here, we propose a variation of existing algorithms that efficiently characterizes and controls the chemical nature of each lipid. Additionally, we allow coupling with collective variables and show that it can be used to dynamically create asymmetric membranes. This algorithm is openly available as a plugin for the HOOMD-Blue molecular dynamics engine.
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Affiliation(s)
- Martin Girard
- Max Planck Institute for Polymer Research, Mainz, Germany.
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Mainz, Germany; Van 't Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam, Amsterdam, the Netherlands
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18
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Abstract
Computer simulations generate microscopic trajectories of complex systems at a single thermodynamic state point. We recently introduced a Maximum Caliber (MaxCal) approach for dynamical reweighting. Our approach mapped these trajectories to a Markovian description on the configurational coordinates and reweighted path probabilities as a function of external forces. Trajectory probabilities can be dynamically reweighted both from and to equilibrium or non-equilibrium steady states. As the system's dimensionality increases, an exhaustive description of the microtrajectories becomes prohibitive-even with a Markovian assumption. Instead, we reduce the dimensionality of the configurational space to collective variables (CVs). Going from configurational to CV space, we define local entropy productions derived from configurationally averaged mean forces. The entropy production is shown to be a suitable constraint on MaxCal for non-equilibrium steady states expressed as a function of CVs. We test the reweighting procedure on two systems: a particle subject to a two-dimensional potential and a coarse-grained peptide. Our CV-based MaxCal approach expands dynamical reweighting to larger systems, for both static and dynamical properties, and across a large range of driving forces.
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Affiliation(s)
- Marius Bause
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
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19
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Kleinwächter IS, Pannwitt S, Centi A, Hellmann N, Thines E, Bereau T, Schneider D. The Bacteriostatic Activity of 2-Phenylethanol Derivatives Correlates with Membrane Binding Affinity. Membranes (Basel) 2021; 11:membranes11040254. [PMID: 33807437 PMCID: PMC8067230 DOI: 10.3390/membranes11040254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 11/16/2022]
Abstract
The hydrophobic tails of aliphatic primary alcohols do insert into the hydrophobic core of a lipid bilayer. Thereby, they disrupt hydrophobic interactions between the lipid molecules, resulting in a decreased lipid order, i.e., an increased membrane fluidity. While aromatic alcohols, such as 2-phenylethanol, also insert into lipid bilayers and disturb the membrane organization, the impact of aromatic alcohols on the structure of biological membranes, as well as the potential physiological implication of membrane incorporation has only been studied to a limited extent. Although diverse targets are discussed to be causing the bacteriostatic and bactericidal activity of 2-phenylethanol, it is clear that 2-phenylethanol severely affects the structure of biomembranes, which has been linked to its bacteriostatic activity. Yet, in fungi some 2-phenylethanol derivatives are also produced, some of which appear to also have bacteriostatic activities. We showed that the 2-phenylethanol derivatives phenylacetic acid, phenyllactic acid, and methyl phenylacetate, but not Tyrosol, were fully incorporated into model membranes and affected the membrane organization. Furthermore, we observed that the propensity of the herein-analyzed molecules to partition into biomembranes positively correlated with their respective bacteriostatic activity, which clearly linked the bacteriotoxic activity of the substances to biomembranes.
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Affiliation(s)
- Isabel S. Kleinwächter
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; (I.S.K.); (S.P.); (N.H.)
| | - Stefanie Pannwitt
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; (I.S.K.); (S.P.); (N.H.)
| | - Alessia Centi
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany; (A.C.); (T.B.)
| | - Nadja Hellmann
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; (I.S.K.); (S.P.); (N.H.)
| | - Eckhard Thines
- Institute of Molecular Physiology, Johannes Gutenberg University, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany;
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany; (A.C.); (T.B.)
- Van ‘t Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Dirk Schneider
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; (I.S.K.); (S.P.); (N.H.)
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany; (A.C.); (T.B.)
- Correspondence: ; Tel.: +49-6131-39-25833; Fax: +49-6131-39-25348
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20
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Bereau T. Inserting Small Molecules Across Membrane Mixtures: Insight from the Potential of Mean Force. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.326] [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: 11/29/2022] Open
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21
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Girard M, Bereau T. Insights into Regulation of Cell Membranes through Regulated Ensembles. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.266] [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: 10/22/2022] Open
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22
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Affiliation(s)
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
- Van ’t Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam, Amsterdam 1098 XH, The Netherlands
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23
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Stieffenhofer M, Wand M, Bereau T. Adversarial reverse mapping of equilibrated condensed-phase molecular structures. Mach Learn : Sci Technol 2020. [DOI: 10.1088/2632-2153/abb6d4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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24
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Abstract
Polymorphism rationalizes how processing can control the final structure of a material. The rugged free-energy landscape and exceedingly slow kinetics in the solid state have so far hampered computational investigations. We report for the first time the free-energy landscape of a polymorphic crystalline polymer, syndiotactic polystyrene. Coarse-grained metadynamics simulations allow us to efficiently sample the landscape at large. The free-energy difference between the two main polymorphs, α and β, is further investigated by quantum-chemical calculations. The results of the two methods are in line with experimental observations: they predict β as the more stable polymorph under standard conditions. Critically, the free-energy landscape suggests how the α polymorph may lead to experimentally observed kinetic traps. The combination of multiscale modeling, enhanced sampling, and quantum-chemical calculations offers an appealing strategy to uncover complex free-energy landscapes with polymorphic behavior.
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Affiliation(s)
- Chan Liu
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
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25
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Girard M, Bereau T. Regulating Lipid Composition Rationalizes Acyl Tail Saturation Homeostasis in Ectotherms. Biophys J 2020; 119:892-899. [PMID: 32814063 DOI: 10.1016/j.bpj.2020.07.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 06/16/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
Cell membranes mainly consist of lipid bilayers with an actively regulated composition. The underlying processes are still poorly understood, in particular, how the hundreds of components are controlled. Cholesterol has been found to correlate with phospholipid saturation for reasons that remain unclear. To better understand the link between cell membrane regulation and chemical composition, we establish a computational framework based on chemical reaction networks, resulting in multiple semigrand canonical ensembles. By running computer simulations, we show that regulating the chemical potential of lipid species is sufficient to reproduce the experimentally observed increase in acyl tail saturation with added cholesterol. Our model proposes a different picture of lipid regulation in which components can be regulated passively instead of actively. In this picture, phospholipid acyl tail composition naturally adapts to added molecules such as cholesterol or proteins. A comparison between regulated membranes with commonly studied ternary model membranes shows stark differences: for instance, correlation lengths and viscosities observed are independent of lipid chemical affinity.
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Affiliation(s)
- Martin Girard
- Max Planck Institute for Polymer Research, Mainz, Germany.
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Mainz, Germany; Van 't Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam, Amsterdam, the Netherlands
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26
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Affiliation(s)
- Clemens Rauer
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
- Van ’t Hoff Institute for Molecular Sciences and Informatics Institute, University of Amsterdam, Amsterdam 1098 XH, The Netherlands
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27
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Scherer C, Scheid R, Andrienko D, Bereau T. Kernel-Based Machine Learning for Efficient Simulations of Molecular Liquids. J Chem Theory Comput 2020; 16:3194-3204. [PMID: 32282206 PMCID: PMC7304872 DOI: 10.1021/acs.jctc.9b01256] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [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: 12/18/2019] [Indexed: 11/29/2022]
Abstract
Current machine learning (ML) models aimed at learning force fields are plagued by their high computational cost at every integration time step. We describe a number of practical and computationally efficient strategies to parametrize traditional force fields for molecular liquids from ML: the particle decomposition ansatz to two- and three-body force fields, the use of kernel-based ML models that incorporate physical symmetries, the incorporation of switching functions close to the cutoff, and the use of covariant meshing to boost the training set size. Results are presented for model molecular liquids: pairwise Lennard-Jones, three-body Stillinger-Weber, and bottom-up coarse-graining of water. Here, covariant meshing proves to be an efficient strategy to learn canonically averaged instantaneous forces. We show that molecular dynamics simulations with tabulated two- and three-body ML potentials are computationally efficient and recover two- and three-body distribution functions. Many-body representations, decomposition, and kernel regression schemes are all implemented in the open-source software package VOTCA.
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Affiliation(s)
- Christoph Scherer
- Max Planck Institute for
Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - René Scheid
- Max Planck Institute for
Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Denis Andrienko
- Max Planck Institute for
Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Tristan Bereau
- Max Planck Institute for
Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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28
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Barnett JW, Bilchak CR, Wang Y, Benicewicz BC, Murdock LA, Bereau T, Kumar SK. Designing exceptional gas-separation polymer membranes using machine learning. Sci Adv 2020; 6:eaaz4301. [PMID: 32440545 PMCID: PMC7228755 DOI: 10.1126/sciadv.aaz4301] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 03/02/2020] [Indexed: 05/22/2023]
Abstract
The field of polymer membrane design is primarily based on empirical observation, which limits discovery of new materials optimized for separating a given gas pair. Instead of relying on exhaustive experimental investigations, we trained a machine learning (ML) algorithm, using a topological, path-based hash of the polymer repeating unit. We used a limited set of experimental gas permeability data for six different gases in ~700 polymeric constructs that have been measured to date to predict the gas-separation behavior of over 11,000 homopolymers not previously tested for these properties. To test the algorithm's accuracy, we synthesized two of the most promising polymer membranes predicted by this approach and found that they exceeded the upper bound for CO2/CH4 separation performance. This ML technique, which is trained using a relatively small body of experimental data (and no simulation data), evidently represents an innovative means of exploring the vast phase space available for polymer membrane design.
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Affiliation(s)
- J. Wesley Barnett
- Department of Chemical Engineering, Columbia University, New York, NY, USA
| | - Connor R. Bilchak
- Department of Chemical Engineering, Columbia University, New York, NY, USA
| | - Yiwen Wang
- Department of Chemical Engineering, Columbia University, New York, NY, USA
| | - Brian C. Benicewicz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Laura A. Murdock
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Sanat K. Kumar
- Department of Chemical Engineering, Columbia University, New York, NY, USA
- Corresponding author.
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29
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Bozkurt Varolgüneş Y, Bereau T, Rudzinski JF. Interpretable embeddings from molecular simulations using Gaussian mixture variational autoencoders. Mach Learn : Sci Technol 2020. [DOI: 10.1088/2632-2153/ab80b7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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30
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Centi A, Dutta A, Parekh SH, Bereau T. Inserting Small Molecules across Membrane Mixtures: Insight from the Potential of Mean Force. Biophys J 2020; 118:1321-1332. [PMID: 32075746 DOI: 10.1016/j.bpj.2020.01.039] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/05/2020] [Accepted: 01/27/2020] [Indexed: 11/29/2022] Open
Abstract
Small solutes have been shown to alter the lateral organization of cell membranes and reconstituted phospholipid bilayers; however, the mechanisms by which these changes happen are still largely unknown. Traditionally, both experiment and simulation studies have been restricted to testing only a few compounds at a time, failing to identify general molecular descriptors or chemical properties that would allow extrapolating beyond the subset of considered solutes. In this work, we probe the competing energetics of inserting a solute in different membrane environments by means of the potential of mean force. We show that these calculations can be used as a computationally efficient proxy to establish whether a solute will stabilize or destabilize domain phase separation. Combined with umbrella-sampling simulations and coarse-grained molecular dynamics simulations, we are able to screen solutes across a wide range of chemistries and polarities. Our results indicate that for the system under consideration, preferential partitioning and therefore effectiveness in altering membrane phase separation are strictly linked to the location of insertion in the bilayer (i.e., midplane or interface). Our approach represents a fast and simple tool for obtaining structural and thermodynamic insight into the partitioning of small molecules between lipid domains and its relation to phase separation, ultimately providing a platform for identifying the key determinants of this process.
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Affiliation(s)
- Alessia Centi
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Arghya Dutta
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Sapun H Parekh
- Max Planck Institute for Polymer Research, Mainz, Germany; Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Mainz, Germany.
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31
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Abstract
The permeation of small-molecule drugs across a phospholipid membrane bears much interest both in the pharmaceutical sciences and in physical chemistry. Connecting the chemistry of the drug and the lipids to the resulting thermodynamic properties remains of immediate importance. Here we report molecular dynamics (MD) simulation trajectories using the coarse-grained (CG) Martini force field. A wide, representative coverage of chemistry is provided: across solutes-exhaustively enumerating all 105 CG dimers-and across six phospholipids. For each combination, umbrella-sampling simulations provide detailed structural information of the solute at all depths from the bilayer midplane to bulk water, allowing a precise reconstruction of the potential of mean force. Overall, the present database contains trajectories from 15,120 MD simulations. This database may serve the further identification of structure-property relationships between compound chemistry and drug permeability.
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Affiliation(s)
| | - Alessia Centi
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | - Roberto Menichetti
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
- Physics Department, University of Trento, 38123, Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, 38123, Trento, Italy
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany.
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Koch AHR, Morsbach S, Bereau T, Lévêque G, Butt HJ, Deserno M, Landfester K, Fytas G. Probing Nanoparticle/Membrane Interactions by Combining Amphiphilic Diblock Copolymer Assembly and Plasmonics. J Phys Chem B 2020; 124:742-750. [PMID: 31951417 PMCID: PMC7008459 DOI: 10.1021/acs.jpcb.9b10469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Indexed: 11/29/2022]
Abstract
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Understanding the interactions between
nanoparticles (NPs) and boundaries of cells is crucial both for their
toxicity and therapeutic applications. Besides specific receptor-mediated
endocytosis of surface-functionalized NPs, passive internalization
is prompted by relatively unspecific parameters, such as particle
size and charge. Based on theoretical treatments, adhesion to and
bending of the cell membrane can induce NP wrapping. Experimentally,
powerful tools are needed to selectively probe possible membrane-NP
motifs at very dilute conditions and avoid dye labeling. In this work,
we employ surface resonance-enhanced dynamic light scattering, surface
plasmon resonance, electron microscopy, and simulations for sensing
interactions between plasmonic AuNPs and polymersomes. We distinguish
three different interaction scenarios at nanomolar concentrations
by tuning the surface charge of AuNPs and rationalize these events
by balancing vesicle bending and electrostatic/van der Waals AuNP
and vesicle adhesion. The clarification of the physical conditions
under which nanoparticles passively translocate across membranes can
aid in the rational design of drugs that cannot exploit specific modes
of cellular uptake and also elucidates physical properties that render
nanoparticles in the environment particularly toxic.
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Affiliation(s)
- Amelie H R Koch
- Max Planck Institute for Polymer Research , Ackermannweg 10 , 55128 Mainz , Germany
| | - Svenja Morsbach
- Max Planck Institute for Polymer Research , Ackermannweg 10 , 55128 Mainz , Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research , Ackermannweg 10 , 55128 Mainz , Germany
| | - Gaëtan Lévêque
- Institut d'Électronique, de Microélectronique et de Nanotechnologie (IEMN), UMR-CNRS 8520, Faculté de Sciences et Technologies , Université de Lille , 59655 Villeneuve d'Ascq , France
| | - Hans-Jürgen Butt
- Max Planck Institute for Polymer Research , Ackermannweg 10 , 55128 Mainz , Germany
| | - Markus Deserno
- Department of Physics , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Katharina Landfester
- Max Planck Institute for Polymer Research , Ackermannweg 10 , 55128 Mainz , Germany
| | - George Fytas
- Max Planck Institute for Polymer Research , Ackermannweg 10 , 55128 Mainz , Germany.,IESL-FORTH , P.O. Box 1527, 71110 Heraklion , Greece
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33
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Wörner SJ, Bereau T, Kremer K, Rudzinski JF. Direct route to reproducing pair distribution functions with coarse-grained models via transformed atomistic cross correlations. J Chem Phys 2020; 151:244110. [PMID: 31893905 DOI: 10.1063/1.5131105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Coarse-grained (CG) models are often parameterized to reproduce one-dimensional structural correlation functions of an atomically detailed model along the degrees of freedom governing each interaction potential. While cross correlations between these degrees of freedom inform the optimal set of interaction parameters, the correlations generated from the higher-resolution simulations are often too complex to act as an accurate proxy for the CG correlations. Instead, the most popular methods determine the interaction parameters iteratively while assuming that individual interactions are uncorrelated. While these iterative methods have been validated for a wide range of systems, they also have disadvantages when parameterizing models for multicomponent systems or when refining previously established models to better reproduce particular structural features. In this work, we propose two distinct approaches for the direct (i.e., noniterative) parameterization of a CG model by adjusting the high-resolution cross correlations of an atomistic model in order to more accurately reflect correlations that will be generated by the resulting CG model. The derived models more accurately describe the low-order structural features of the underlying AA model while necessarily generating inherently distinct cross correlations compared with the atomically detailed reference model. We demonstrate the proposed methods for a one-site-per-molecule representation of liquid water, where pairwise interactions are incapable of reproducing the true tetrahedral solvation structure. We then investigate the precise role that distinct cross-correlation features play in determining the correct pair correlation functions, evaluating the importance of the placement of correlation features as well as the balance between features appearing in different solvation shells.
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Affiliation(s)
- Svenja J Wörner
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
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34
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Abstract
Computer simulations generate trajectories at a single, well-defined thermodynamic state point. Statistical reweighting offers the means to reweight static and dynamical properties to different equilibrium state points by means of analytic relations. We extend these ideas to nonequilibrium steady states by relying on a maximum path entropy formalism subject to physical constraints. Stochastic thermodynamics analytically relates the forward and backward probabilities of any pathway through the external nonconservative force, enabling reweighting both in and out of equilibrium. We avoid the combinatorial explosion of microtrajectories by systematically constructing pathways through Markovian transitions. We further identify a quantity that is invariant to dynamical reweighting, analogous to the density of states in equilibrium reweighting.
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Affiliation(s)
- Marius Bause
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | | | - Kurt Kremer
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
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35
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Hoffmann C, Menichetti R, Kanekal KH, Bereau T. Controlled exploration of chemical space by machine learning of coarse-grained representations. Phys Rev E 2019; 100:033302. [PMID: 31639967 DOI: 10.1103/physreve.100.033302] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Indexed: 11/07/2022]
Abstract
The size of chemical compound space is too large to be probed exhaustively. This leads high-throughput protocols to drastically subsample and results in sparse and nonuniform datasets. Rather than arbitrarily selecting compounds, we systematically explore chemical space according to the target property of interest. We first perform importance sampling by introducing a Markov chain Monte Carlo scheme across compounds. We then train a machine learning (ML) model on the sampled data to expand the region of chemical space probed. Our boosting procedure enhances the number of compounds by a factor 2 to 10, enabled by the ML model's coarse-grained representation, which both simplifies the structure-property relationship and reduces the size of chemical space. The ML model correctly recovers linear relationships between transfer free energies. These linear relationships correspond to features that are global to the dataset, marking the region of chemical space up to which predictions are reliable; this is a more robust alternative to the predictive variance. Bridging coarse-grained simulations with ML gives rise to an unprecedented database of drug-membrane insertion free energies for 1.3 million compounds.
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Affiliation(s)
| | | | - Kiran H Kanekal
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
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36
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Affiliation(s)
- Kiran H. Kanekal
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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37
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Affiliation(s)
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Mainz, Germany
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38
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Abstract
Unraveling the relation between the chemical structure of small druglike compounds and their rate of passive permeation across lipid membranes is of fundamental importance for pharmaceutical applications. The elucidation of a comprehensive structure-permeability relationship expressed in terms of a few molecular descriptors is unfortunately hampered by the overwhelming number of possible compounds. In this work, we reduce a priori the size and diversity of chemical space to solve an analogous-but smoothed out-structure-property relationship problem. This is achieved by relying on a physics-based coarse-grained model that reduces the size of chemical space, enabling a comprehensive exploration of this space with greatly reduced computational cost. We perform high-throughput coarse-grained (HTCG) simulations to derive a permeability surface in terms of two simple molecular descriptors-bulk partitioning free energy and pK a. The surface is constructed by exhaustively simulating all coarse-grained compounds that are representative of small organic molecules (ranging from 30 to 160 Da) in a high-throughput scheme. We provide results for acidic, basic, and zwitterionic compounds. Connecting back to the atomic resolution, the HTCG predictions for more than 500 000 compounds allow us to establish a clear connection between specific chemical groups and the resulting permeability coefficient, enabling for the first time an inverse design procedure. Our results have profound implications for drug synthesis: the predominance of commonly employed chemical moieties narrows down the range of permeabilities.
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Affiliation(s)
| | | | - Tristan Bereau
- Max Planck Institute for
Polymer Research, 55128 Mainz, Germany
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39
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Bereau T, Rudzinski JF. Conformationally-Dependent Surface Hopping for Reproducing Structural Cross-Correlations with Coarse-Grained Models. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1647] [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: 11/24/2022] Open
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40
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Menichetti R, Kanekal KH, Bereau T. Investigating Drug-Membrane Permeability across Chemical Compound Space using High-Throughput Coarse-Grained Simulations. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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41
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Rudzinski JF, Radu M, Bereau T. Automated detection of many-particle solvation states for accurate characterizations of diffusion kinetics. J Chem Phys 2019; 150:024102. [PMID: 30646696 DOI: 10.1063/1.5064808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Discrete-space kinetic models, i.e., Markov state models, have emerged as powerful tools for reducing the complexity of trajectories generated from molecular dynamics simulations. These models require configuration-space representations that accurately characterize the relevant dynamics. Well-established, low-dimensional order parameters for constructing this representation have led to widespread application of Markov state models to study conformational dynamics in biomolecular systems. On the contrary, applications to characterize single-molecule diffusion processes have been scarce and typically employ system-specific, higher-dimensional order parameters to characterize the local solvation state of the molecule. In this work, we propose an automated method for generating a coarse configuration-space representation, using generic features of the solvation structure-the coordination numbers about each particle. To overcome the inherent noisy behavior of these low-dimensional observables, we treat the features as indicators of an underlying, latent Markov process. The resulting hidden Markov models filter the trajectories of each feature into the most likely latent solvation state at each time step. The filtered trajectories are then used to construct a configuration-space discretization, which accurately describes the diffusion kinetics. The method is validated on a standard model for glassy liquids, where particle jumps between local cages determine the diffusion properties of the system. Not only do the resulting models provide quantitatively accurate characterizations of the diffusion constant, but they also reveal a mechanistic description of diffusive jumps, quantifying the heterogeneity of local diffusion.
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Affiliation(s)
| | - Marc Radu
- Max Planck Institute for Polymer Research, Mainz 55128, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Mainz 55128, Germany
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42
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Bereau T, Rudzinski JF. Accurate Structure-Based Coarse Graining Leads to Consistent Barrier-Crossing Dynamics. Phys Rev Lett 2018; 121:256002. [PMID: 30608819 DOI: 10.1103/physrevlett.121.256002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/09/2018] [Indexed: 06/09/2023]
Abstract
Structure-based coarse graining of molecular systems offers a systematic route to reproduce the many-body potential of mean force. Unfortunately, common strategies are inherently limited by the molecular mechanics force field employed. Here, we extend the concept of multisurface dynamics, initially developed to describe electronic transitions in chemical reactions, to accurately sample the conformational ensemble of a classical system in equilibrium. In analogy to describing different electronic configurations, a surface-hopping scheme couples distinct conformational basins beyond the additivity of the Hamiltonian. The incorporation of more surfaces leads systematically toward improved cross-correlations. The resulting models naturally achieve consistent long-time dynamics for systems governed by barrier-crossing events.
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Affiliation(s)
- Tristan Bereau
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
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43
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Morsbach S, Gonella G, Mailänder V, Wegner S, Wu S, Weidner T, Berger R, Koynov K, Vollmer D, Encinas N, Kuan SL, Bereau T, Kremer K, Weil T, Bonn M, Butt HJ, Landfester K. Engineering von Proteinen an Oberflächen: Von komplementärer Charakterisierung zu Materialoberflächen mit maßgeschneiderten Funktionen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Svenja Morsbach
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Grazia Gonella
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Volker Mailänder
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
- Abteilung für Dermatologie; Universitätsmedizin der Johannes Gutenberg-Universität Mainz; Langenbeckstraße 1 55131 Mainz Deutschland
| | - Seraphine Wegner
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Si Wu
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Tobias Weidner
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
- Abteilung für Chemie; Universität Aarhus; Langelandsgade 140 8000 Aarhus C Dänemark
| | - Rüdiger Berger
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Kaloian Koynov
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Doris Vollmer
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Noemí Encinas
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Seah Ling Kuan
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Tristan Bereau
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Kurt Kremer
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Tanja Weil
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Mischa Bonn
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Hans-Jürgen Butt
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Katharina Landfester
- Max Planck-Institut für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
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44
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Morsbach S, Gonella G, Mailänder V, Wegner S, Wu S, Weidner T, Berger R, Koynov K, Vollmer D, Encinas N, Kuan SL, Bereau T, Kremer K, Weil T, Bonn M, Butt HJ, Landfester K. Engineering Proteins at Interfaces: From Complementary Characterization to Material Surfaces with Designed Functions. Angew Chem Int Ed Engl 2018; 57:12626-12648. [PMID: 29663610 PMCID: PMC6391961 DOI: 10.1002/anie.201712448] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/13/2018] [Indexed: 01/17/2023]
Abstract
Once materials come into contact with a biological fluid containing proteins, proteins are generally—whether desired or not—attracted by the material's surface and adsorb onto it. The aim of this Review is to give an overview of the most commonly used characterization methods employed to gain a better understanding of the adsorption processes on either planar or curved surfaces. We continue to illustrate the benefit of combining different methods to different surface geometries of the material. The thus obtained insight ideally paves the way for engineering functional materials that interact with proteins in a predetermined manner.
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Affiliation(s)
- Svenja Morsbach
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Grazia Gonella
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Volker Mailänder
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.,Department of Dermatology, University Medical Center Johannes Gutenberg-University Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Seraphine Wegner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Si Wu
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tobias Weidner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.,Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Rüdiger Berger
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Kaloian Koynov
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Doris Vollmer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Noemí Encinas
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Seah Ling Kuan
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Hans-Jürgen Butt
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Katharina Landfester
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
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45
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Menichetti R, Kanekal KH, Kremer K, Bereau T. In silico screening of drug-membrane thermodynamics reveals linear relations between bulk partitioning and the potential of mean force. J Chem Phys 2018; 147:125101. [PMID: 28964031 DOI: 10.1063/1.4987012] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The partitioning of small molecules in cell membranes-a key parameter for pharmaceutical applications-typically relies on experimentally available bulk partitioning coefficients. Computer simulations provide a structural resolution of the insertion thermodynamics via the potential of mean force but require significant sampling at the atomistic level. Here, we introduce high-throughput coarse-grained molecular dynamics simulations to screen thermodynamic properties. This application of physics-based models in a large-scale study of small molecules establishes linear relationships between partitioning coefficients and key features of the potential of mean force. This allows us to predict the structure of the insertion from bulk experimental measurements for more than 400 000 compounds. The potential of mean force hereby becomes an easily accessible quantity-already recognized for its high predictability of certain properties, e.g., passive permeation. Further, we demonstrate how coarse graining helps reduce the size of chemical space, enabling a hierarchical approach to screening small molecules.
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Affiliation(s)
- Roberto Menichetti
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kiran H Kanekal
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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46
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Bereau T, DiStasio RA, Tkatchenko A, von Lilienfeld OA. Non-covalent interactions across organic and biological subsets of chemical space: Physics-based potentials parametrized from machine learning. J Chem Phys 2018; 148:241706. [DOI: 10.1063/1.5009502] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Tristan Bereau
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Robert A. DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Alexandre Tkatchenko
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg,
Luxembourg
| | - O. Anatole von Lilienfeld
- Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials (MARVEL), Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel,
Switzerland
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47
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Rudzinski JF, Bereau T. Structural-kinetic-thermodynamic relationships identified from physics-based molecular simulation models. J Chem Phys 2018; 148:204111. [PMID: 29865838 DOI: 10.1063/1.5025125] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Coarse-grained molecular simulation models have provided immense, often general, insight into the complex behavior of condensed-phase systems but suffer from a lost connection to the true dynamical properties of the underlying system. In general, the physics that is built into a model shapes the free-energy landscape, restricting the attainable static and kinetic properties. In this work, we perform a detailed investigation into the property interrelationships resulting from these restrictions, for a representative system of the helix-coil transition. Inspired by high-throughput studies, we systematically vary force-field parameters and monitor their structural, kinetic, and thermodynamic properties. The focus of our investigation is a simple coarse-grained model, which accurately represents the underlying structural ensemble, i.e., effectively avoids sterically-forbidden configurations. As a result of this built-in physics, we observe a rather large restriction in the topology of the networks characterizing the simulation kinetics. When screening across force-field parameters, we find that structurally accurate models also best reproduce the kinetics, suggesting structural-kinetic relationships for these models. Additionally, an investigation into thermodynamic properties reveals a link between the cooperativity of the transition and the network topology at a single reference temperature.
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Affiliation(s)
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Mainz 55128, Germany
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48
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Affiliation(s)
- Chan Liu
- Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
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49
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Bereau T. Computational High-throughput Screening of Drug-Membrane Thermodynamics. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.3044] [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: 10/18/2022] Open
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50
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Menichetti R, Kremer K, Bereau T. Efficient potential of mean force calculation from multiscale simulations: Solute insertion in a lipid membrane. Biochem Biophys Res Commun 2017; 498:282-287. [PMID: 28870809 DOI: 10.1016/j.bbrc.2017.08.095] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 07/21/2017] [Accepted: 08/24/2017] [Indexed: 10/18/2022]
Abstract
The determination of potentials of mean force for solute insertion in a lipid membrane by means of all-atom molecular dynamics simulations is often hampered by sampling issues. Recently, a multiscale method has been proposed to leverage the conformational ensemble of a lower-resolution model as starting point for higher resolution simulations. In this work, we analyze the efficiency of this method by comparing its predictions for propanol insertion into a lipid membrane against conventional atomistic umbrella sampling simulation results. The multiscale approach is confirmed to provide accurate results with a gain of one order of magnitude in computational time. We then investigate the role of the coarse-grained representation. We find that the accuracy of the results is tightly connected to the presence of a good configurational overlap between the coarse-grained and atomistic models-a general requirement when developing multiscale simulation methods.
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Affiliation(s)
- Roberto Menichetti
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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