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Esser TK, Böhning J, Önür A, Chinthapalli DK, Eriksson L, Grabarics M, Fremdling P, Konijnenberg A, Makarov A, Botman A, Peter C, Benesch JLP, Robinson CV, Gault J, Baker L, Bharat TAM, Rauschenbach S. Cryo-EM of soft-landed β-galactosidase: Gas-phase and native structures are remarkably similar. Sci Adv 2024; 10:eadl4628. [PMID: 38354247 PMCID: PMC10866560 DOI: 10.1126/sciadv.adl4628] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/11/2024] [Indexed: 02/16/2024]
Abstract
Native mass spectrometry (MS) has become widely accepted in structural biology, providing information on stoichiometry, interactions, homogeneity, and shape of protein complexes. Yet, the fundamental assumption that proteins inside the mass spectrometer retain a structure faithful to native proteins in solution remains a matter of intense debate. Here, we reveal the gas-phase structure of β-galactosidase using single-particle cryo-electron microscopy (cryo-EM) down to 2.6-Å resolution, enabled by soft landing of mass-selected protein complexes onto cold transmission electron microscopy (TEM) grids followed by in situ ice coating. We find that large parts of the secondary and tertiary structure are retained from the solution. Dehydration-driven subunit reorientation leads to consistent compaction in the gas phase. By providing a direct link between high-resolution imaging and the capability to handle and select protein complexes that behave problematically in conventional sample preparation, the approach has the potential to expand the scope of both native mass spectrometry and cryo-EM.
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Affiliation(s)
- Tim K. Esser
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
- Thermo Fisher Scientific, 1 Boundary Park, Hemel Hempstead, Hertfordshire HP2 7GE, UK
| | - Jan Böhning
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Alpcan Önür
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Dinesh K. Chinthapalli
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Lukas Eriksson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Marko Grabarics
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Paul Fremdling
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | - Alexander Makarov
- Thermo Fisher Scientific, Bremen 28199, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Aurelien Botman
- Thermo Fisher Scientific, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124, USA
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Justin L. P. Benesch
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Joseph Gault
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Lindsay Baker
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Tanmay A. M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stephan Rauschenbach
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
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Schneider T, Sawade K, Berner F, Peter C, Kovermann M. Specifying conformational heterogeneity of multi-domain proteins at atomic resolution. Structure 2023; 31:1259-1274.e10. [PMID: 37557171 DOI: 10.1016/j.str.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/02/2023] [Accepted: 07/14/2023] [Indexed: 08/11/2023]
Abstract
The conformational landscape of multi-domain proteins is inherently linked to their specific functions. This also holds for polyubiquitin chains that are assembled by two or more ubiquitin domains connected by a flexible linker thus showing a large interdomain mobility. However, molecular recognition and signal transduction are associated with particular conformational substates that are populated in solution. Here, we apply high-resolution NMR spectroscopy in combination with dual-scale MD simulations to explore the conformational space of K6-, K29-, and K33-linked diubiquitin molecules. The conformational ensembles are evaluated utilizing a paramagnetic cosolute reporting on solvent exposure plus a set of complementary NMR parameters. This approach unravels a conformational heterogeneity of diubiquitins and explains the diversity of structural models that have been determined for K6-, K29-, and K33-linked diubiquitins in free and ligand-bound states so far. We propose a general application of the approach developed here to demystify multi-domain proteins occurring in nature.
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Affiliation(s)
- Tobias Schneider
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Kevin Sawade
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Graduate School Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Frederic Berner
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany.
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3
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Sawade K, Marx A, Peter C, Kukharenko O. Combining molecular dynamics simulations and scoring method to computationally model ubiquitylated linker histones in chromatosomes. PLoS Comput Biol 2023; 19:e1010531. [PMID: 37527265 PMCID: PMC10442151 DOI: 10.1371/journal.pcbi.1010531] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 08/21/2023] [Accepted: 06/15/2023] [Indexed: 08/03/2023] Open
Abstract
The chromatin in eukaryotic cells plays a fundamental role in all processes during a cell's life cycle. This nucleoprotein is normally tightly packed but needs to be unpacked for expression and division. The linker histones are critical for such packaging processes and while most experimental and simulation works recognize their crucial importance, the focus is nearly always set on the nucleosome as the basic chromatin building block. Linker histones can undergo several modifications, but only few studies on their ubiquitylation have been conducted. Mono-ubiquitylated linker histones (HUb), while poorly understood, are expected to influence DNA compaction. The size of ubiquitin and the globular domain of the linker histone are comparable and one would expect an increased disorder upon ubiquitylation of the linker histone. However, the formation of higher order chromatin is not hindered and ubiquitylation of the linker histone may even promote gene expression. Structural data on chromatosomes is rare and HUb has never been modeled in a chromatosome so far. Descriptions of the chromatin complex with HUb would greatly benefit from computational structural data. In this study we generate molecular dynamics simulation data for six differently linked HUb variants with the help of a sampling scheme tailored to drive the exploration of phase space. We identify conformational sub-states of the six HUb variants using the sketch-map algorithm for dimensionality reduction and iterative HDBSCAN for clustering on the excessively sampled, shallow free energy landscapes. We present a highly efficient geometric scoring method to identify sub-states of HUb that fit into the nucleosome. We predict HUb conformations inside a nucleosome using on-dyad and off-dyad chromatosome structures as reference and show that unbiased simulations of HUb produce significantly more fitting than non-fitting HUb conformations. A tetranucleosome array is used to show that ubiquitylation can even occur in chromatin without too much steric clashes.
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Affiliation(s)
- Kevin Sawade
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Oleksandra Kukharenko
- Department of Chemistry, University of Konstanz, Konstanz, Germany
- Theory Department, Max-Planck Institute for Polymer Research, Mainz, Germany
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4
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Franke L, Peter C. Visualizing the Residue Interaction Landscape of Proteins by Temporal Network Embedding. J Chem Theory Comput 2023; 19:2985-2995. [PMID: 37122117 DOI: 10.1021/acs.jctc.2c01228] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Characterizing the structural dynamics of proteins with heterogeneous conformational landscapes is crucial to understanding complex biomolecular processes. To this end, dimensionality reduction algorithms are used to produce low-dimensional embeddings of the high-dimensional conformational phase space. However, identifying a compact and informative set of input features for the embedding remains an ongoing challenge. Here, we propose to harness the power of Residue Interaction Networks (RINs) and their centrality measures, established tools to provide a graph theoretical view on molecular structure. Specifically, we combine the closeness centrality, which captures global features of the protein conformation at residue-wise resolution, with EncoderMap, a hybrid neural-network autoencoder/multidimensional-scaling like dimensionality reduction algorithm. We find that the resulting low-dimensional embedding is a meaningful visualization of the residue interaction landscape that resolves structural details of the protein behavior while retaining global interpretability. This feature-based graph embedding of temporal protein graphs makes it possible to apply the general descriptive power of RIN formalisms to the analysis of protein simulations of complex processes such as protein folding and multidomain interactions requiring no protein-specific input. We demonstrate this on simulations of the fast folding protein Trp-Cage and the multidomain signaling protein FAT10. Due to its generality and modularity, the presented approach can easily be transferred to other protein systems.
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Affiliation(s)
- Leon Franke
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
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5
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Hunkler S, Diederichs K, Kukharenko O, Peter C. Fast conformational clustering of extensive molecular dynamics simulation data. J Chem Phys 2023; 158:144109. [PMID: 37061476 DOI: 10.1063/5.0142797] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
We present an unsupervised data processing workflow that is specifically designed to obtain a fast conformational clustering of long molecular dynamics simulation trajectories. In this approach, we combine two dimensionality reduction algorithms (cc_analysis and encodermap) with a density-based spatial clustering algorithm (hierarchical density-based spatial clustering of applications with noise). The proposed scheme benefits from the strengths of the three algorithms while avoiding most of the drawbacks of the individual methods. Here, the cc_analysis algorithm is applied for the first time to molecular simulation data. The encodermap algorithm complements cc_analysis by providing an efficient way to process and assign large amounts of data to clusters. The main goal of the procedure is to maximize the number of assigned frames of a given trajectory while keeping a clear conformational identity of the clusters that are found. In practice, we achieve this by using an iterative clustering approach and a tunable root-mean-square-deviation-based criterion in the final cluster assignment. This allows us to find clusters of different densities and different degrees of structural identity. With the help of four protein systems, we illustrate the capability and performance of this clustering workflow: wild-type and thermostable mutant of the Trp-cage protein (TC5b and TC10b), NTL9, and Protein B. Each of these test systems poses their individual challenges to the scheme, which, in total, give a nice overview of the advantages and potential difficulties that can arise when using the proposed method.
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Affiliation(s)
- Simon Hunkler
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Kay Diederichs
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | | | - Christine Peter
- Department of Chemistry, University of Konstanz, Konstanz, Germany
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6
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Hunkler S, Buhl T, Kukharenko O, Peter C. Generating a conformational landscape of ubiquitin chains at atomistic resolution by back-mapping based sampling. Front Chem 2023; 10:1087963. [PMID: 36704619 PMCID: PMC9871295 DOI: 10.3389/fchem.2022.1087963] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023] Open
Abstract
Ubiquitin chains are flexible multidomain proteins that have important biological functions in cellular signalling. Computational studies with all-atom molecular dynamics simulations of the conformational spaces of polyubiquitins can be challenging due to the system size and a multitude of long-lived meta-stable states. Coarse graining is an efficient approach to overcome this problem-at the cost of losing high-resolution details. Recently, we proposed the back-mapping based sampling (BMBS) approach that reintroduces atomistic information into a given coarse grained (CG) sampling based on a two-dimensional (2D) projection of the conformational landscape, produces an atomistic ensemble and allows to systematically compare the ensembles at the two levels of resolution. Here, we apply BMBS to K48-linked tri-ubiquitin, showing its applicability to larger systems than those it was originally introduced on and demonstrating that the algorithm scales very well with system size. In an extension of the original BMBS we test three different seeding strategies, i.e. different approaches from where in the CG landscape atomistic trajectories are initiated. Furthermore, we apply a recently introduced conformational clustering algorithm to the back-mapped atomistic ensemble. Thus, we obtain insight into the structural composition of the 2D landscape and illustrate that the dimensionality reduction algorithm separates different conformational characteristics very well into different regions of the map. This cluster analysis allows us to show how atomistic trajectories sample conformational states, move through the projection space and in sum converge to an atomistic conformational landscape that slightly differs from the original CG map, indicating a correction of flaws in the CG template.
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Affiliation(s)
- Simon Hunkler
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Teresa Buhl
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | | | - Christine Peter
- Department of Chemistry, University of Konstanz, Konstanz, Germany,*Correspondence: Christine Peter,
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7
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Gindele MB, Malaszuk KK, Peter C, Gebauer D. On the Binding Mechanisms of Calcium Ions to Polycarboxylates: Effects of Molecular Weight, Side Chain, and Backbone Chemistry. Langmuir 2022; 38:14409-14421. [PMID: 36367750 DOI: 10.1021/acs.langmuir.2c01662] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
We experimentally determined the characteristics and Langmuir parameters of the binding of calcium ions to different polycarboxylates. By using potentiometric titrations and isothermal titration calorimetry, the effects of side chain chemistry, pH value, and chain length were systematically investigated using the linear polymers poly(aspartic acid), poly(glutamic acid), and poly(acrylic acid). We demonstrate that for polymers with high polymerization degrees, the binding process is governed by higher-order effects, such as the change of apparent pKa of carboxyl groups, and contributions arising from the whole polymer chain while the chemistry of the monomer unit constituting the polymer plays a subordinate role. In addition, primary binding sites need to be present in the polymer, thus rendering the abundance and sequential arrangement of protonated and deprotonated groups important. The detection of higher-order effects contradicts the assumptions posed by the Langmuir model of noninteracting binding sites and puts a question mark on whether ion binding to polycarboxylates can be described using solely a Langmuir binding model. No single uniform mechanism fits all investigated systems, and the whole polymer chain, including terminal groups, needs to be considered for the interpretation of binding data. Therefore, one needs to be careful when explaining ion binding to polymers solely based on studies on monomers or oligomers.
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Affiliation(s)
- Maxim B Gindele
- Leibniz University Hannover, Institute of Inorganic Chemistry, Callinstr. 9, 30167Hannover, Germany
| | - Krzysztof K Malaszuk
- Leibniz University Hannover, Institute of Inorganic Chemistry, Callinstr. 9, 30167Hannover, Germany
| | - Christine Peter
- Theoretical Chemistry, University of Konstanz, Universitätsstr. 10, 78457Konstanz, Germany
| | - Denis Gebauer
- Leibniz University Hannover, Institute of Inorganic Chemistry, Callinstr. 9, 30167Hannover, Germany
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8
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Vogel K, Bläske T, Nagel MK, Globisch C, Maguire S, Mattes L, Gude C, Kovermann M, Hauser K, Peter C, Isono E. Lipid-mediated activation of plasma membrane-localized deubiquitylating enzymes modulate endosomal trafficking. Nat Commun 2022; 13:6897. [PMID: 36371501 PMCID: PMC9653390 DOI: 10.1038/s41467-022-34637-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
The abundance of plasma membrane-resident receptors and transporters has to be tightly regulated by ubiquitin-mediated endosomal degradation for the proper coordination of environmental stimuli and intracellular signaling. Arabidopsis OVARIAN TUMOR PROTEASE (OTU) 11 and OTU12 are plasma membrane-localized deubiquitylating enzymes (DUBs) that bind to phospholipids through a polybasic motif in the OTU domain. Here we show that the DUB activity of OTU11 and OTU12 towards K63-linked ubiquitin is stimulated by binding to lipid membranes containing anionic lipids. In addition, we show that the DUB activity of OTU11 against K6- and K11-linkages is also stimulated by anionic lipids, and that OTU11 and OTU12 can modulate the endosomal degradation of a model cargo and the auxin efflux transporter PIN2-GFP in vivo. Our results suggest that the catalytic activity of OTU11 and OTU12 is tightly connected to their ability to bind membranes and that OTU11 and OTU12 are involved in the fine-tuning of plasma membrane proteins in Arabidopsis.
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Affiliation(s)
- Karin Vogel
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Tobias Bläske
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Marie-Kristin Nagel
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Christoph Globisch
- grid.9811.10000 0001 0658 7699Computational and Theoretical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Shane Maguire
- grid.9811.10000 0001 0658 7699Biophysical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
| | - Lorenz Mattes
- grid.9811.10000 0001 0658 7699Biophysical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
| | - Christian Gude
- grid.6936.a0000000123222966School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Michael Kovermann
- grid.9811.10000 0001 0658 7699NMR, Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Karin Hauser
- grid.9811.10000 0001 0658 7699Biophysical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
| | - Christine Peter
- grid.9811.10000 0001 0658 7699Computational and Theoretical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Erika Isono
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
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9
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King M, Avaro JT, Peter C, Hauser K, Gebauer D. Solvent-mediated isotope effects strongly influence the early stages of calcium carbonate formation: exploring D 2O vs. H 2O in a combined computational and experimental approach. Faraday Discuss 2022; 235:36-55. [PMID: 35388817 DOI: 10.1039/d1fd00078k] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In experimental studies, heavy water (D2O) is employed, e.g., so as to shift the spectroscopic solvent background, but any potential effects of this solvent exchange on reaction pathways are often neglected. While the important role of light water (H2O) during the early stages of calcium carbonate formation has been realized, studies into the actual effects of aqueous solvent exchanges are scarce. Here, we present a combined computational and experimental approach to start to fill this gap. We extended a suitable force field for molecular dynamics (MD) simulations. Experimentally, we utilised advanced titration assays and time-resolved attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy. We find distinct effects in various mixtures of the two aqueous solvents, and in pure H2O or D2O. Disagreements between the computational results and experimental data regarding the stabilities of ion associates might be due to the unexplored role of HDO, or an unprobed complex phase behaviour of the solvent mixtures in the simulations. Altogether, however, our data suggest that calcium carbonate formation might proceed "more classically" in D2O. Also, there are indications for the formation of new structures in amorphous and crystalline calcium carbonates. There is huge potential towards further improving the understanding of mineralization mechanisms by studying solvent-mediated isotope effects, also beyond calcium carbonate. Last, it must be appreciated that H2O and D2O have significant, distinct effects on mineralization mechanisms, and that care has to be taken when experimental data from D2O studies are used, e.g., for the development of H2O-based computer models.
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Affiliation(s)
- Michael King
- Department of Chemistry, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Jonathan T Avaro
- Department of Chemistry, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany.,Empa, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Karin Hauser
- Department of Chemistry, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Denis Gebauer
- Institute of Inorganic Chemistry, Leibniz University of Hannover, Callinstr. 9, 30167 Hannover, Germany.
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10
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Sawade K, Peter C. Multiscale simulations of protein and membrane systems. Curr Opin Struct Biol 2021; 72:203-208. [PMID: 34953308 DOI: 10.1016/j.sbi.2021.11.010] [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: 08/28/2021] [Revised: 11/01/2021] [Accepted: 11/10/2021] [Indexed: 02/07/2023]
Abstract
Classical multiscale simulations are perfectly suited to investigate biological soft matter systems. Owing to the bridging between microscopically realistic and lower-resolution models or the integration of a hierarchy of subsystems, one gets access to biologically relevant system sizes and timescales. In recent years, increasingly complex systems and processes have come into focus such as multidomain proteins, phase separation processes in biopolymer solutions, multicomponent biomembranes, or multiprotein complexes up to entire viruses. The review shows factors that have contributed to this progress - from improved models to machine-learning-based analysis and scale-bridging methods.
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Affiliation(s)
- Kevin Sawade
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78 457, Konstanz, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78 457, Konstanz, Germany.
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11
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Bogomolovas J, Fleming JR, Franke B, Manso B, Simon B, Gasch A, Markovic M, Brunner T, Knöll R, Chen J, Labeit S, Scheffner M, Peter C, Mayans O. Titin kinase ubiquitination aligns autophagy receptors with mechanical signals in the sarcomere. EMBO Rep 2021; 22:e48018. [PMID: 34402565 PMCID: PMC8490993 DOI: 10.15252/embr.201948018] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/07/2021] [Accepted: 07/19/2021] [Indexed: 12/13/2022] Open
Abstract
Striated muscle undergoes remodelling in response to mechanical and physiological stress, but little is known about the integration of such varied signals in the myofibril. The interaction of the elastic kinase region from sarcomeric titin (A168-M1) with the autophagy receptors Nbr1/p62 and MuRF E3 ubiquitin ligases is well suited to link mechanosensing with the trophic response of the myofibril. To investigate the mechanisms of signal cross-talk at this titin node, we elucidated its 3D structure, analysed its response to stretch using steered molecular dynamics simulations and explored its functional relation to MuRF1 and Nbr1/p62 using cellular assays. We found that MuRF1-mediated ubiquitination of titin kinase promotes its scaffolding of Nbr1/p62 and that the process can be dynamically down-regulated by the mechanical unfolding of a linker sequence joining titin kinase with the MuRF1 receptor site in titin. We propose that titin ubiquitination is sensitive to the mechanical state of the sarcomere, the regulation of sarcomere targeting by Nbr1/p62 being a functional outcome. We conclude that MuRF1/Titin Kinase/Nbr1/p62 constitutes a distinct assembly that predictably promotes sarcomere breakdown in inactive muscle.
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Affiliation(s)
- Julius Bogomolovas
- Department of MedicineSchool of MedicineUniversity of CaliforniaSan Diego, La JollaCAUSA
- Department of Cognitive and Clinical NeuroscienceCentral Institute of Mental HealthMedical Faculty MannheimHeidelberg UniversityMannheimGermany
- Department of Integrative PathophysiologyMedical Faculty MannheimUniversity of HeidelbergMannheimGermany
| | | | - Barbara Franke
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | - Bruno Manso
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | - Bernd Simon
- Structural and Computational Biology UnitEMBLHeidelbergGermany
| | - Alexander Gasch
- Department of Integrative PathophysiologyMedical Faculty MannheimUniversity of HeidelbergMannheimGermany
| | | | - Thomas Brunner
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | - Ralph Knöll
- Integrated Cardio Metabolic Centre (ICMC)Heart and Vascular ThemeUniversity Hospital, MedHKarolinska InstitutetHuddingeSweden
- Bioscience, CardiovascularRenal & MetabolismBioPharmaceuticalsR&D, AstraZenecaGothenburgSweden
| | - Ju Chen
- Department of MedicineSchool of MedicineUniversity of CaliforniaSan Diego, La JollaCAUSA
| | - Siegfried Labeit
- Department of Integrative PathophysiologyMedical Faculty MannheimUniversity of HeidelbergMannheimGermany
| | | | - Christine Peter
- Department of ChemistryUniversity of KonstanzKonstanzGermany
| | - Olga Mayans
- Department of BiologyUniversity of KonstanzKonstanzGermany
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12
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Lemke T, Edte M, Gebauer D, Peter C. Three Reasons Why Aspartic Acid and Glutamic Acid Sequences Have a Surprisingly Different Influence on Mineralization. J Phys Chem B 2021; 125:10335-10343. [PMID: 34473925 DOI: 10.1021/acs.jpcb.1c04467] [Citation(s) in RCA: 12] [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: 11/28/2022]
Abstract
Understanding the role of polymers rich in aspartic acid (Asp) and glutamic acid (Glu) is the key to gaining precise control over mineralization processes. Despite their chemical similarity, experiments revealed a surprisingly different influence of Asp and Glu sequences. We conducted molecular dynamics simulations of Asp and Glu peptides in the presence of calcium and chloride ions to elucidate the underlying phenomena. In line with experimental differences, in our simulations, we indeed find strong differences in the way the peptides interact with ions in solution. The investigated Asp pentapeptide tends to pull a lot of ions into its vicinity, and many structures with clusters of calcium and chloride ions on the surface of the peptide can be observed. Under the same conditions, comparatively fewer ions can be found in proximity of the investigated Glu pentapeptide, and the structures are characterized by single calcium ions bound to multiple carboxylate groups. Based on our simulation data, we identified three reasons contributing to these differences, leading to a new level of understanding additive-ion interactions.
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Affiliation(s)
- Tobias Lemke
- Theoretical Chemistry, University of Konstanz, 78547 Konstanz, Germany
| | - Moritz Edte
- Theoretical Chemistry, University of Konstanz, 78547 Konstanz, Germany
| | - Denis Gebauer
- Institute of Inorganic Chemistry, Leibniz University Hannover, 30167 Hannover, Germany
| | - Christine Peter
- Theoretical Chemistry, University of Konstanz, 78547 Konstanz, Germany
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13
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Schettler V, Peter C, Zimmermann T, Julius U, Roeseler E, Schlieper G, Heigl F, Grützmacher P, Löhlein I, Klingel R, Hohenstein B, Vogt A. The German Lipoprotein Apheresis Registry (GLAR) – more than 7 years on. Atherosclerosis 2021. [DOI: 10.1016/j.atherosclerosis.2021.06.067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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14
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Steuer J, Kukharenko O, Riedmiller K, Hartig JS, Peter C. Guanidine-II aptamer conformations and ligand binding modes through the lens of molecular simulation. Nucleic Acids Res 2021; 49:7954-7965. [PMID: 34233001 PMCID: PMC8373139 DOI: 10.1093/nar/gkab592] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 12/01/2022] Open
Abstract
Regulation of gene expression via riboswitches is a widespread mechanism in bacteria. Here, we investigate ligand binding of a member of the guanidine sensing riboswitch family, the guanidine-II riboswitch (Gd-II). It consists of two stem–loops forming a dimer upon ligand binding. Using extensive molecular dynamics simulations we have identified conformational states corresponding to ligand-bound and unbound states in a monomeric stem–loop of Gd-II and studied the selectivity of this binding. To characterize these states and ligand-dependent conformational changes we applied a combination of dimensionality reduction, clustering, and feature selection methods. In absence of a ligand, the shape of the binding pocket alternates between the conformation observed in presence of guanidinium and a collapsed conformation, which is associated with a deformation of the dimerization interface. Furthermore, the structural features responsible for the ability to discriminate against closely related analogs of guanidine are resolved. Based on these insights, we propose a mechanism that couples ligand binding to aptamer dimerization in the Gd-II system, demonstrating the value of computational methods in the field of nucleic acids research.
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Affiliation(s)
- Jakob Steuer
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457 Konstanz, Germany
| | - Oleksandra Kukharenko
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany.,Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Kai Riedmiller
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Jörg S Hartig
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457 Konstanz, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457 Konstanz, Germany
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15
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Dürr SL, Bohuszewicz O, Berta D, Suardiaz R, Jambrina PG, Peter C, Shao Y, Rosta E. The Role of Conserved Residues in the DEDDh Motif: the Proton-Transfer Mechanism of HIV-1 RNase H. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Simon L. Dürr
- Department of Chemistry, King’s College London, London SE1 1DB, U.K
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Olga Bohuszewicz
- Department of Chemistry, King’s College London, London SE1 1DB, U.K
| | - Dénes Berta
- Department of Physics and Astronomy, University College London; London WC1E 6BT, U.K
| | - Reynier Suardiaz
- Department of Chemistry, King’s College London, London SE1 1DB, U.K
| | | | - Christine Peter
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019-5251, United States
| | - Edina Rosta
- Department of Chemistry, King’s College London, London SE1 1DB, U.K
- Department of Physics and Astronomy, University College London; London WC1E 6BT, U.K
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16
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Flachmüller A, Mecking S, Peter C. Coarse grained simulation of the aggregation and structure control of polyethylene nanocrystals. J Phys Condens Matter 2021; 33:264001. [PMID: 33857931 DOI: 10.1088/1361-648x/abf881] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
Polyethylene (PE) telechelics with carboxylate functional groups at both ends have been shown to assemble into hexagonal nanocrystal platelets with a height defined by their chain length in basic CsOH-solution. In this coarse grained (CG) simulation study we show how properties of the functional groups alter the aggregation and crystallization behavior of those telechelics. Systematic variation of the parameters of the CG model showed that important factors which control nanoparticle stability and structure are the PE chain length and the hydrophilicity and the steric demand of the head groups. To characterize the aggregation process we analyzed the number and size of the obtained aggregates as well as intramolecular order and intermolecular alignment of the polymer chains. By comparison of CG and atomistic simulation data, it could be shown that atomistic simulations representing different chemical systems can be emulated with specific, different CG parameter sets. Thus, the results from the (generic) CG simulation models can be used to explain the effect of different head groups and different counterions on the aggregation of PE telechelics and the order of the obtained nanocrystals.
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Affiliation(s)
| | - Stefan Mecking
- Department of Chemistry, Universität Konstanz, Konstanz, Germany
| | - Christine Peter
- Department of Chemistry, Universität Konstanz, Konstanz, Germany
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17
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Fries SJ, Braun TS, Globisch C, Peter C, Drescher M, Deuerling E. Deciphering molecular details of the RAC-ribosome interaction by EPR spectroscopy. Sci Rep 2021; 11:8681. [PMID: 33883604 PMCID: PMC8060413 DOI: 10.1038/s41598-021-87847-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 11/27/2020] [Accepted: 03/25/2021] [Indexed: 11/09/2022] Open
Abstract
The eukaryotic ribosome-associated complex (RAC) plays a significant role in de novo protein folding. Its unique interaction with the ribosome, comprising contacts to both ribosomal subunits, suggests a RAC-mediated coordination between translation elongation and co-translational protein folding. Here, we apply electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin labeling (SDSL) to gain deeper insights into a RAC-ribosome contact affecting translational accuracy. We identified a local contact point of RAC to the ribosome. The data provide the first experimental evidence for the existence of a four-helix bundle as well as a long α-helix in full-length RAC, in solution as well as on the ribosome. Additionally, we complemented the structural picture of the region mediating this functionally important contact on the 40S ribosomal subunit. In sum, this study constitutes the first application of SDSL-EPR spectroscopy to elucidate the molecular details of the interaction between the 3.3 MDa translation machinery and a chaperone complex.
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Affiliation(s)
- Sandra J Fries
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457, Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457, Konstanz, Germany
| | - Theresa S Braun
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457, Konstanz, Germany.,Department of Chemistry, Physical and Biophysical Chemistry, University of Konstanz, 78457, Konstanz, Germany
| | - Christoph Globisch
- Department of Chemistry, Computational and Theoretical Chemistry, University of Konstanz, 78457, Konstanz, Germany
| | - Christine Peter
- Department of Chemistry, Computational and Theoretical Chemistry, University of Konstanz, 78457, Konstanz, Germany
| | - Malte Drescher
- Department of Chemistry, Physical and Biophysical Chemistry, University of Konstanz, 78457, Konstanz, Germany.
| | - Elke Deuerling
- Department of Biology, Molecular Microbiology, University of Konstanz, 78457, Konstanz, Germany.
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18
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Peñalver L, Schmid P, Szamosvári D, Schildknecht S, Globisch C, Sawade K, Peter C, Böttcher T. A Ligand Selection Strategy Identifies Chemical Probes Targeting the Proteases of SARS-CoV-2. Angew Chem Int Ed Engl 2021; 60:6799-6806. [PMID: 33350010 PMCID: PMC7986205 DOI: 10.1002/anie.202016113] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Indexed: 01/05/2023]
Abstract
Activity-based probes are valuable tools for chemical biology. However, finding probes that specifically target the active site of an enzyme remains a challenging task. Herein, we present a ligand selection strategy that allows to rapidly tailor electrophilic probes to a target of choice and showcase its application for the two cysteine proteases of SARS-CoV-2 as proof of concept. The resulting probes were specific for the active site labeling of 3CLpro and PLpro with sufficient selectivity in a live cell model as well as in the background of a native human proteome. Exploiting the probes as tools for competitive profiling of a natural product library identified salvianolic acid derivatives as promising 3CLpro inhibitors. We anticipate that our ligand selection strategy will be useful to rapidly develop customized probes and discover inhibitors for a wide range of target proteins also beyond corona virus proteases.
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Affiliation(s)
- Lilian Peñalver
- Department of ChemistryKonstanz Research School Chemical BiologyZukunftskollegUniversity of KonstanzKonstanzGermany
| | - Philipp Schmid
- Department of ChemistryKonstanz Research School Chemical BiologyZukunftskollegUniversity of KonstanzKonstanzGermany
- Faculty of ChemistryDepartment of Biological Chemistry & Centre for Microbiology and Environmental Systems ScienceDivision of Microbial EcologyUniversity of ViennaViennaAustria
| | - Dávid Szamosvári
- Department of ChemistryKonstanz Research School Chemical BiologyZukunftskollegUniversity of KonstanzKonstanzGermany
| | - Stefan Schildknecht
- In Vitro Toxicology and BiomedicineDepartment of BiologyUniversity of KonstanzKonstanzGermany
- Albstadt-Sigmaringen UniversitySigmaringenGermany
| | | | - Kevin Sawade
- Department of ChemistryUniversity of KonstanzKonstanzGermany
| | - Christine Peter
- Department of ChemistryUniversity of KonstanzKonstanzGermany
| | - Thomas Böttcher
- Department of ChemistryKonstanz Research School Chemical BiologyZukunftskollegUniversity of KonstanzKonstanzGermany
- Faculty of ChemistryDepartment of Biological Chemistry & Centre for Microbiology and Environmental Systems ScienceDivision of Microbial EcologyUniversity of ViennaViennaAustria
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19
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Peñalver L, Schmid P, Szamosvári D, Schildknecht S, Globisch C, Sawade K, Peter C, Böttcher T. Eine Strategie zur Ligandenselektion identifiziert chemische Sonden für die Markierung von SARS‐CoV‐2‐Proteasen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Lilian Peñalver
- Fachbereich Chemie Konstanz Research School Chemical Biology Zukunftskolleg Universität Konstanz Konstanz Deutschland
| | - Philipp Schmid
- Fachbereich Chemie Konstanz Research School Chemical Biology Zukunftskolleg Universität Konstanz Konstanz Deutschland
- Fakultät für Chemie Institut für Biologische Chemie & Centre for Microbiology and Environmental Systems Science Division of Microbial Ecology Universität Wien Wien Österreich
| | - Dávid Szamosvári
- Fachbereich Chemie Konstanz Research School Chemical Biology Zukunftskolleg Universität Konstanz Konstanz Deutschland
| | - Stefan Schildknecht
- In Vitro Toxicology and Biomedicine Fachbereich Biologie Universität Konstanz Konstanz Deutschland
- Hochschule Albstadt-Sigmaringen Sigmaringen Deutschland
| | | | - Kevin Sawade
- Fachbereich Chemie Universität Konstanz Konstanz Deutschland
| | - Christine Peter
- Fachbereich Chemie Universität Konstanz Konstanz Deutschland
| | - Thomas Böttcher
- Fachbereich Chemie Konstanz Research School Chemical Biology Zukunftskolleg Universität Konstanz Konstanz Deutschland
- Fakultät für Chemie Institut für Biologische Chemie & Centre for Microbiology and Environmental Systems Science Division of Microbial Ecology Universität Wien Wien Österreich
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20
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Ripani G, Flachmüller A, Peter C, Palleschi A. Coarse-Grained Simulation of the Adsorption of Water on Au(111) Surfaces Using a Modified Stillinger-Weber Potential. ACS Omega 2020; 5:31055-31059. [PMID: 33324813 PMCID: PMC7726742 DOI: 10.1021/acsomega.0c04071] [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] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 10/22/2020] [Indexed: 06/12/2023]
Abstract
For reproducing the behavior of water molecules adsorbed on gold surfaces in terms of density of both bulk and interfacial water and in terms of structuring of water on top of gold atoms, the implementation of a multibody potential is necessary, thus the Stillinger-Weber potential was tested. The goal is using a single nonbonded potential for coarse-grained models, without the usage of explicit charges. In order to modify the angular part of the Stillinger-Weber potential from a single cosine to a piecewise function accounting for multiple equilibrium angles, employed for Au-Au-Au and Au-Au-water triplets, it is necessary to create a version of the simulation package LAMMPS that supports the assignment of multiple favored angles. This novel approach is able to reproduce the data obtained using quantum mechanical calculations and density profiles of both bulk and adsorbed water molecules obtained using classical polarizable force fields.
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Affiliation(s)
- Giorgio Ripani
- Department
of Chemical Science and Technologies, University
of Rome “Tor Vergata”, Via della Ricerca Scientifica, Rome 00133, Italy
| | - Alexander Flachmüller
- Theoretical
Chemistry, University of Konstanz, Konstanz 78547, Baden-Württemberg, Germany
| | - Christine Peter
- Theoretical
Chemistry, University of Konstanz, Konstanz 78547, Baden-Württemberg, Germany
| | - Antonio Palleschi
- Department
of Chemical Science and Technologies, University
of Rome “Tor Vergata”, Via della Ricerca Scientifica, Rome 00133, Italy
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21
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Berg A, Franke L, Scheffner M, Peter C. Correction to Machine Learning Driven Analysis of Large Scale Simulations Reveals Conformational Characteristics of Ubiquitin Chains. J Chem Theory Comput 2020; 16:7219. [DOI: 10.1021/acs.jctc.0c00992] [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: 11/28/2022]
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22
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Gkeka P, Stoltz G, Barati Farimani A, Belkacemi Z, Ceriotti M, Chodera JD, Dinner AR, Ferguson AL, Maillet JB, Minoux H, Peter C, Pietrucci F, Silveira A, Tkatchenko A, Trstanova Z, Wiewiora R, Lelièvre T. Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems. J Chem Theory Comput 2020; 16:4757-4775. [PMID: 32559068 PMCID: PMC8312194 DOI: 10.1021/acs.jctc.0c00355] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [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] [Indexed: 12/21/2022]
Abstract
Machine learning encompasses tools and algorithms that are now becoming popular in almost all scientific and technological fields. This is true for molecular dynamics as well, where machine learning offers promises of extracting valuable information from the enormous amounts of data generated by simulation of complex systems. We provide here a review of our current understanding of goals, benefits, and limitations of machine learning techniques for computational studies on atomistic systems, focusing on the construction of empirical force fields from ab initio databases and the determination of reaction coordinates for free energy computation and enhanced sampling.
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Affiliation(s)
- Paraskevi Gkeka
- Integrated Drug Discovery, Sanofi R&D, 91385 Chilly-Mazarin, France
| | - Gabriel Stoltz
- CERMICS, Ecole des Ponts, Marne-la-Vallée, France
- Matherials Project-Team, Inria Paris, 75012 Paris, France
| | | | - Zineb Belkacemi
- Integrated Drug Discovery, Sanofi R&D, 91385 Chilly-Mazarin, France
- CERMICS, Ecole des Ponts, Marne-la-Vallée, France
| | - Michele Ceriotti
- Laboratory of Computational Science and Modelling, Institute of Materials, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Aaron R Dinner
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | | | - Hervé Minoux
- Integrated Drug Discovery, Sanofi R&D, 94403 Vitry-sur-Seine, France
| | | | - Fabio Pietrucci
- UMR CNRS 7590, MNHN, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, 75005 Paris, France
| | - Ana Silveira
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Zofia Trstanova
- School of Mathematics, The University of Edinburgh, Edinburgh EH9 3FD, U.K
| | - Rafal Wiewiora
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Tony Lelièvre
- CERMICS, Ecole des Ponts, Marne-la-Vallée, France
- Matherials Project-Team, Inria Paris, 75012 Paris, France
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23
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Hines E, Ponnampalam LS, Junchompoo C, Peter C, Vu L, Huynh T, Caillat M, Johnson AF, Minton G, Lewison RL, Verutes GM. Getting to the bottom of bycatch: a GIS-based toolbox to assess the risk of marine mammal bycatch. ENDANGER SPECIES RES 2020. [DOI: 10.3354/esr01037] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Marine mammal bycatch poses a particular challenge in developing countries, where data to document bycatch and its effects are often lacking. Using the Bycatch Risk Assessment (ByRA) toolkit, based on InVEST open-source models, we chose 4 field sites in Southeast Asia with varying amounts of data on marine mammals and fishing occurrence: Trat province in the eastern Gulf of Thailand, the Sibu-Tinggi Islands and Kuching Bay, Malaysia, and Kien Giang Biosphere Reserve in southwestern Vietnam. These field sites have similar species of coastal marine mammals, small-scale and commercial fisheries, and support for research from universities and/or management. In Thailand and Kuching, results showed changing patterns of fishing and Irrawaddy dolphin Orcaella brevirostris habitat use across seasons, showing how bycatch risk could change throughout the year. Risk maps for dugongs Dugong dugon in peninsular Malaysia highlighted patterns of bycatch risk concentrated around a mainland fishing pier, and revealed high risk in a northern subregion. In Vietnam, first maps of bycatch risk for the Irrawaddy dolphin showed the highest risk driven by intensive use of gillnets and trawling gear. ByRA pinpointed areas of spatial and seasonal bycatch exposure, and estimated the consequence of bycatch on local species, providing managers with critical information on where to focus bycatch mitigation and meet new global standards for US Marine Mammal Protection Act and other international regulation (e.g. Official Journal of the European Union 2019; Regulation 2019/1241) compliance. The toolbox, a transferable open-source tool, can be used to guide fisheries management, marine mammal conservation, spatial planning, and further research.
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Affiliation(s)
- E Hines
- Estuary & Ocean Science Center, and Department of Geography & Environment, San Francisco State University, Tiburon, CA 94920, USA
| | - LS Ponnampalam
- The MareCet Research Organization, 5, Jalan USJ 12/1B 47630 Subang Jaya, Selangor, Malaysia
| | - C Junchompoo
- Department of Marine and Coastal Resources, Ministry of Natural Resources and Environment, Chaeng Watthana Road, Lak Si District, Bangkok 10210, Thailand
| | - C Peter
- Universiti Malaysia Sarawak, Jalan Datuk Mohammad Musa, 94300 Kota Samarahan, Sarawak, Malaysia
| | - L Vu
- Vietnam Marine Megafauna Network, Center for Biodiversity Conservation and Endangered Species, 24, Street No 13, Lakeview City, Ho Chi Minh City, Vietnam
| | - T Huynh
- Southern Institute of Ecology, Vietnam Academy of Science and Technology, 01 Mac Dinh Chi, Ben Nghe, District 1, Ho Chi Minh City, Vietnam
- Graduate School of Natural Science and Technology, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1164, Japan
| | - M Caillat
- Environmental Defense Fund, San Francisco, CA 94105, USA
| | - AF Johnson
- MarFishEco Fisheries Consultants, 67/6 Brunswick Street, Edinburgh EH7 5HT, UK
- The Lyell Centre, Institute of Life and Earth Sciences, School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - G Minton
- Megaptera Marine Conservation, Laan van Rhemen van Rhemenshuizen 14, 2242 PT Wassenaar, The Netherlands
| | - RL Lewison
- Department of Biology, San Diego State University, CA 92182, USA
| | - GM Verutes
- Faculty of Political and Social Sciences, Universidade de Santiago de Compostela, Praza do Obradoiro, 0, 15705 Santiago de Compostela, A Coruña, Spain
- Campus Do*Mar, International Campus of Excellence, 36310 Vigo, Spain
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24
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Berg A, Franke L, Scheffner M, Peter C. Machine Learning Driven Analysis of Large Scale Simulations Reveals Conformational Characteristics of Ubiquitin Chains. J Chem Theory Comput 2020; 16:3205-3220. [PMID: 32196332 DOI: 10.1021/acs.jctc.0c00045] [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] [Indexed: 11/29/2022]
Abstract
Understanding the conformational characteristics of protein complexes in solution is crucial for a deeper insight in their biological function. Molecular dynamics simulations performed on high performance computing plants and with modern simulation techniques can be used to obtain large data sets that contain conformational and thermodynamic information about biomolecular systems. While this can in principle give a detailed picture of protein-protein interactions in solution and therefore complement experimental data, it also raises the challenge of processing exceedingly large high-dimensional data sets with several million samples. Here we present a novel method for the characterization of protein-protein interactions, which combines a neural network based dimensionality reduction technique to obtain a two-dimensional representation of the conformational space with a density based clustering algorithm for state detection and a metric which assesses the (dis)similarity between different conformational spaces. This method is highly scalable and therefore makes the analysis of massive data sets computationally tractable. We demonstrate the power of this approach to large scale data analysis by characterizing highly dynamic conformational phase spaces of differently linked ubiquitin (Ub) oligomers from coarse-grained simulations. We are able to extract a protein-protein interaction model for two unlinked Ub proteins which is then used to determine how the Ub-Ub interaction pattern is altered in Ub oligomers by the introduction of a covalent linkage. We find that the Ub chain conformational ensemble depends highly on the linkage type and for some cases also on the Ub chain length. By this, we obtain insight into the conformational characteristics of different Ub chains and how this may contribute to linkage type and chain length specific recognition.
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Affiliation(s)
- Andrej Berg
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
| | - Leon Franke
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
| | - Martin Scheffner
- Department of Biology, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
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25
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Mark AE, Peter C. Editorial overview: Theory and simulation: Progress, yes; revolutions, no. Curr Opin Struct Biol 2020; 61:iii-v. [DOI: 10.1016/j.sbi.2020.02.001] [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: 10/24/2022]
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Schneider T, Berg A, Peter C, Kovermann M. Exploring Artificially Conjugated Ubiquitin Dimers by Means of NMR Spectroscopy and MD Simulations. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.2783] [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: 10/25/2022] Open
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27
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Schettler VJJ, Neumann CL, Peter C, Zimmermann T, Julius U, Hohenstein B, Roeseler E, Heigl F, Grützmacher P, Blume H, Klingel R, Vogt A. Lipoprotein apheresis is an optimal therapeutic option to reduce increased Lp(a) levels. Clin Res Cardiol Suppl 2019; 14:33-38. [PMID: 30838552 DOI: 10.1007/s11789-019-00094-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Lipoprotein(a) (Lp(a)) is a genetic risk factor for cardiovascular disease (CVD) and is associated with the induction and sustaining of atherosclerotic cardiovascular diseases (ASCVD). Since 2008 Lp(a) along with progressive CVD has been approved as an indication for regular lipoprotein apheresis (LA) in Germany. The German Lipoprotein Apheresis Registry (GLAR) has been initiated to provide statistical evidence for the assessment of extracorporeal procedures to treat dyslipidemia for both LDL-cholesterol (LDL-C) and Lp(a). The GLAR now allows prospective investigations over a 5-year period about annual incidence rates of cardiovascular events. Here Lp(a) patients (LDL-C < 100 mg/dl; Lp(a) > 60 mg/dl or >120 nmol/l) showed the same reduction of major coronary (83%) and non-coronary events (63%) as had been formerly shown in the Pro(a)LiFe study. However, Lp(a) is not only an apolipoprotein(a) (apo(a)) and LDL-C containing particle, which is covalently bound to a LDL-C core by a disulphide bridge. The composition of this particle, inter alia containing oxidized phospholipids, gives pro-atherosclerotic, pro-inflammatory, and pro-thrombotic properties, inducing atherosclerotic processes mainly in the arterial wall. However, recent investigations have shown that a reduction of inflammatory settings without LDL-C or Lp(a) reduction may reduce ASCVD events. Lipoprotein apheresis (LA) could not only reduce LDL-C and Lp(a) in parallel, but also different inflammatory and coagulation parameters. In summary lipoprotein apheresis is not only anti-atherosclerotic, but also anti-inflammatory and anti-thrombotic and therefore an ideal treatment option with respect to the shown reduction of major adverse coronary events (MACE) and major adverse non-coronary events (MANCE) by reducing Lp(a) levels.
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Affiliation(s)
- V J J Schettler
- Center of Nephrology Göttingen GbR, An der Lutter 24, 37075, Göttingen, Germany.
| | - C L Neumann
- BRAVE-Benefit for Research on Arterial Hypertension, Dyslipidemia and Vascular Risk and Education e. V, Göttingen, Germany
| | - C Peter
- BioArtProducts GmbH (B.A.P.), Rostock, Germany
| | | | - U Julius
- Extracorporeal Treatment and Apheresis Center, Department of Internal Medicine III, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - B Hohenstein
- Extracorporeal Treatment and Apheresis Center, Department of Internal Medicine III, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - E Roeseler
- Center for Nephrology, Hypertension, and Metabolic Diseases, Hanover, Germany
| | - F Heigl
- Medical Care Centre Kempten-Allgäu, Kempten, Germany
| | - P Grützmacher
- Department of Medicine II for Nephrology, Hypertension and Vascular Risks, AGAPLESION Markus Hospital, Frankfurt, Germany
| | - H Blume
- Scientific Institute for Nephrology (WiNe), Düsseldorf, Germany
| | - R Klingel
- Apheresis Research Institute, Stadtwaldgürtel 77, 50935, Cologne, Germany
| | - A Vogt
- Medizinische Klinik und Poliklinik 4, Universität München, Munich, Germany
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Lemke T, Berg A, Jain A, Peter C. EncoderMap(II): Visualizing Important Molecular Motions with Improved Generation of Protein Conformations. J Chem Inf Model 2019; 59:4550-4560. [PMID: 31647645 DOI: 10.1021/acs.jcim.9b00675] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Dimensionality reduction can be used to project high-dimensional molecular data into a simplified, low-dimensional map. One feature of our recently introduced dimensionality reduction technique EncoderMap, which relies on the combination of an autoencoder with multidimensional scaling, is its ability to do the reverse. It is able to generate conformations for any selected points in the low-dimensional map. This transfers the simplified, low-dimensional map back into the high-dimensional conformational space. Although the output is again high-dimensional, certain aspects of the simplification are preserved. The generated conformations only mirror the most dominant conformational differences that determine the positions of conformational states in the low-dimensional map. This allows depicting such differences and-in consequence-visualizing molecular motions and gives a unique perspective on high-dimensional conformational data. In our previous work, protein conformations described in backbone dihedral angle space were used as the input for EncoderMap, and conformations were also generated in this space. For large proteins, however, the generation of conformations is inaccurate with this approach due to the local character of backbone dihedral angles. Here, we present an improved variant of EncoderMap which is able to generate large protein conformations that are accurate in short-range and long-range orders. This is achieved by differentiable reconstruction of Cartesian coordinates from the generated dihedrals, which allows adding a contribution to the cost function that monitors the accuracy of all pairwise distances between the Cα-atoms of the generated conformations. The improved capabilities to generate conformations of large, even multidomain, proteins are demonstrated for two examples: diubiquitin and a part of the Ssa1 Hsp70 yeast chaperone. We show that the improved variant of EncoderMap can nicely visualize motions of protein domains relative to each other but is also able to highlight important conformational changes within the individual domains.
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Affiliation(s)
- Tobias Lemke
- Theoretical Chemistry , University of Konstanz , 78547 Konstanz , Baden-Württemberg , Germany
| | - Andrej Berg
- Theoretical Chemistry , University of Konstanz , 78547 Konstanz , Baden-Württemberg , Germany
| | - Alok Jain
- Theoretical Chemistry , University of Konstanz , 78547 Konstanz , Baden-Württemberg , Germany.,Department of Biotechnology , National Institute of Pharmaceutical Education and Research Ahmedabad , Gandhinagar , Gujarat 382355 , India
| | - Christine Peter
- Theoretical Chemistry , University of Konstanz , 78547 Konstanz , Baden-Württemberg , Germany
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Hunkler S, Lemke T, Peter C, Kukharenko O. Back-mapping based sampling: Coarse grained free energy landscapes as a guideline for atomistic exploration. J Chem Phys 2019; 151:154102. [DOI: 10.1063/1.5115398] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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
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Abstract
Interacting proteins can form aggregates and protein-protein interfaces with multiple patterns and different stabilities. Using molecular simulation one would like to understand the formation of these aggregates and which of the observed states are relevant for protein function and recognition. To characterize the complex configurational ensemble of protein aggregates, one needs a quantitative measure for the similarity of structures. We present well-suited descriptors that capture the essential features of non-covalent protein contact formation and domain motion. This set of collective variables is used with a nonlinear multi-dimensional scaling-based dimensionality reduction technique to obtain a low-dimensional representation of the configurational landscape of two ubiquitin proteins from coarse-grained simulations. We show that this two-dimensional representation is a powerful basis to identify meaningful states in the ensemble of aggregated structures and to calculate distributions and free energy landscapes for different sets of simulations. By using a measure to quantitatively compare free energy landscapes we can show how the introduction of a covalent bond between two ubiquitin proteins at different positions alters the configurational states of these dimers.
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Affiliation(s)
- Andrej Berg
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
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32
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Bohnhorst B, Seidel K, Böhne C, Peter C, Pirr S. Heart rate, respiratory rate, apnoeas and peripheral arterial oxygen saturation in healthy term neonates during quiet sleep. Acta Paediatr 2019; 108:231-238. [PMID: 29926973 DOI: 10.1111/apa.14470] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 05/09/2018] [Accepted: 06/19/2018] [Indexed: 02/06/2023]
Abstract
AIM This study compiled percentiles for cardiorespiratory parameters in healthy term neonates during quiet sleep. METHODS We enrolled 215 healthy term neonates born at Hannover Medical School, Germany, between October 2011 and March 2013. They were prospectively observed on the maternity ward at a median age of two days using six-hour recordings of pulse oximeter plethysmography, oxygen saturation, thoracic breathing movements and electrocardiogram during sleep in a supine position. We examined their heart rate, respiratory rate and oxygen saturation during quiet sleep, plus bradycardias, apnoeas lasting at least four-seconds and desaturations below 85%. RESULTS The 3rd, 50th and 97th percentiles were calculated as follows: heart rate 87, 112 and 133 beats per minute, respiratory rate 32, 44 and 57 per minute and oxygen saturation 94, 98 and 100%. Desaturations, apnoeas and bradycardias below 80 beats per minute were common and recorded in 54%, 98% and 30% of participants. In contrast, only 7% experienced bradycardias of less than two-thirds of the baseline heart rate and 5% experienced apnoeas exceeding 15 seconds. CONCLUSION Our results will facilitate the evidence-based valuation of cardiorespiratory parameters in term neonates and help validate the significance of cardiorespiratory events in preterm infants at discharge.
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Affiliation(s)
- B Bohnhorst
- Department of Paediatric Pneumology, Allergology and Neonatology; Hannover Medical School; Hannover Germany
| | - K Seidel
- Medical Clinic 3; St. Bernward Hospital; Hildesheim Germany
| | - C Böhne
- Department of Paediatric Pneumology, Allergology and Neonatology; Hannover Medical School; Hannover Germany
| | - C Peter
- Department of Paediatric Pneumology, Allergology and Neonatology; Hannover Medical School; Hannover Germany
| | - S Pirr
- Department of Paediatric Pneumology, Allergology and Neonatology; Hannover Medical School; Hannover Germany
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Affiliation(s)
- Tobias Lemke
- Theoretical Chemistry, University of Konstanz, 78547 Konstanz, Germany
| | - Christine Peter
- Theoretical Chemistry, University of Konstanz, 78547 Konstanz, Germany
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Jain A, Globisch C, Verma S, Peter C. Coarse-Grained Simulations of Peptide Nanoparticle Formation: Role of Local Structure and Nonbonded Interactions. J Chem Theory Comput 2019; 15:1453-1462. [DOI: 10.1021/acs.jctc.8b01138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Alok Jain
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Ahmedabad, Gujarat 380054, India
- Department of Chemistry, University of Konstanz, Konstanz 78464, Germany
| | - Christoph Globisch
- Department of Chemistry, University of Konstanz, Konstanz 78464, Germany
| | - Sandeep Verma
- Department of Chemistry and Center for Nanoscience, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Konstanz 78464, Germany
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35
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Berg A, Kukharenko O, Scheffner M, Peter C. Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers. PLoS Comput Biol 2018; 14:e1006589. [PMID: 30444864 PMCID: PMC6268000 DOI: 10.1371/journal.pcbi.1006589] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 11/30/2018] [Accepted: 10/22/2018] [Indexed: 12/25/2022] Open
Abstract
Covalent modification of proteins by ubiquitin or ubiquitin chains is one of the most prevalent post-translational modifications in eukaryotes. Different types of ubiquitin chains are assumed to selectively signal respectively modified proteins for different fates. In support of this hypothesis, structural studies have shown that the eight possible ubiquitin dimers adopt different conformations. However, at least in some cases, these structures cannot sufficiently explain the molecular basis of the selective signaling mechanisms. This indicates that the available structures represent only a few distinct conformations within the entire conformational space adopted by a ubiquitin dimer. Here, molecular simulations on different levels of resolution can complement the structural information. We have combined exhaustive coarse grained and atomistic simulations of all eight possible ubiquitin dimers with a suitable dimensionality reduction technique and a new method to characterize protein-protein interfaces and the conformational landscape of protein conjugates. We found that ubiquitin dimers exhibit characteristic linkage type-dependent properties in solution, such as interface stability and the character of contacts between the subunits, which can be directly correlated with experimentally observed linkage-specific properties. Post-translational modification of proteins by covalent attachment of ubiquitin is a key cellular process, regulating for example the fate and recycling of proteins. We present a new method to combine multiscale simulation with advanced analysis methods to characterize the states of ubiquitin-ubiquitin conjugates. We found that the linkage position affects the conformational space of ubiquitin dimers, determining the number and stability of relevant states, the character of subunit contacts and the nature of the surface exposed to possible binding partners.
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Affiliation(s)
- Andrej Berg
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | | | - Martin Scheffner
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Konstanz, Germany
- * E-mail:
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36
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Aichem A, Anders S, Catone N, Rößler P, Stotz S, Berg A, Schwab R, Scheuermann S, Bialas J, Schütz-Stoffregen MC, Schmidtke G, Peter C, Groettrup M, Wiesner S. Author Correction: The structure of the ubiquitin-like modifier FAT10 reveals an alternative targeting mechanism for proteasomal degradation. Nat Commun 2018; 9:4646. [PMID: 30389928 PMCID: PMC6214955 DOI: 10.1038/s41467-018-07183-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The original version of the Supplementary Information associated with this Article inadvertently omitted Supplementary Table 3. The HTML version of the Article has been updated to include a corrected version of the Supplementary Information.
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Affiliation(s)
- Annette Aichem
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz D-78457, Germany.,Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen CH-8280, Switzerland
| | - Samira Anders
- Max Planck Institute for Developmental Biology, Tübingen D-72076, Germany
| | - Nicola Catone
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen CH-8280, Switzerland
| | - Philip Rößler
- Max Planck Institute for Developmental Biology, Tübingen D-72076, Germany
| | - Sophie Stotz
- Max Planck Institute for Developmental Biology, Tübingen D-72076, Germany
| | - Andrej Berg
- Computational and Theoretical Chemistry, Department of Chemistry, University of Konstanz, Konstanz D-78457, Germany
| | - Ricarda Schwab
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz D-78457, Germany.,Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen CH-8280, Switzerland
| | - Sophia Scheuermann
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz D-78457, Germany.,Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen CH-8280, Switzerland
| | - Johanna Bialas
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz D-78457, Germany.,Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen CH-8280, Switzerland
| | - Mira C Schütz-Stoffregen
- Max Planck Institute for Developmental Biology, Tübingen D-72076, Germany.,Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg D-93040, Germany
| | - Gunter Schmidtke
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz D-78457, Germany.,Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen CH-8280, Switzerland
| | - Christine Peter
- Computational and Theoretical Chemistry, Department of Chemistry, University of Konstanz, Konstanz D-78457, Germany
| | - Marcus Groettrup
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz D-78457, Germany. .,Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen CH-8280, Switzerland.
| | - Silke Wiesner
- Max Planck Institute for Developmental Biology, Tübingen D-72076, Germany. .,Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg D-93040, Germany.
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37
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Lemke T, Peter C, Kukharenko O. Efficient Sampling and Characterization of Free Energy Landscapes of Ion–Peptide Systems. J Chem Theory Comput 2018; 14:5476-5488. [DOI: 10.1021/acs.jctc.8b00560] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Tobias Lemke
- Theoretical Chemistry, University of Konstanz, 78547 Konstanz, Germany
| | - Christine Peter
- Theoretical Chemistry, University of Konstanz, 78547 Konstanz, Germany
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38
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Aichem A, Anders S, Catone N, Rößler P, Stotz S, Berg A, Schwab R, Scheuermann S, Bialas J, Schütz-Stoffregen MC, Schmidtke G, Peter C, Groettrup M, Wiesner S. The structure of the ubiquitin-like modifier FAT10 reveals an alternative targeting mechanism for proteasomal degradation. Nat Commun 2018; 9:3321. [PMID: 30127417 PMCID: PMC6102260 DOI: 10.1038/s41467-018-05776-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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: 04/17/2018] [Accepted: 07/27/2018] [Indexed: 01/06/2023] Open
Abstract
FAT10 is a ubiquitin-like modifier that directly targets proteins for proteasomal degradation. Here, we report the high-resolution structures of the two individual ubiquitin-like domains (UBD) of FAT10 that are joined by a flexible linker. While the UBDs of FAT10 show the typical ubiquitin-fold, their surfaces are entirely different from each other and from ubiquitin explaining their unique binding specificities. Deletion of the linker abrogates FAT10-conjugation while its mutation blocks auto-FAT10ylation of the FAT10-conjugating enzyme USE1 but not bulk conjugate formation. FAT10- but not ubiquitin-mediated degradation is independent of the segregase VCP/p97 in the presence but not the absence of FAT10’s unstructured N-terminal heptapeptide. Stabilization of the FAT10 UBDs strongly decelerates degradation suggesting that the intrinsic instability of FAT10 together with its disordered N-terminus enables the rapid, joint degradation of FAT10 and its substrates without the need for FAT10 de-conjugation and partial substrate unfolding. The ubiquitin-like modifier FAT10 is composed of two ubiquitin-like domains (UBDs). Here the authors present the FAT10 UBD structures and show that the unstructured FAT10 N-terminal heptapeptide together with the poor stability of FAT10 facilitate the rapid proteasomal targeting of FAT10 along with its substrates.
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Affiliation(s)
- Annette Aichem
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, D-78457, Germany.,Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, CH-8280, Switzerland
| | - Samira Anders
- Max Planck Institute for Developmental Biology, Tübingen, D-72076, Germany
| | - Nicola Catone
- Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, CH-8280, Switzerland
| | - Philip Rößler
- Max Planck Institute for Developmental Biology, Tübingen, D-72076, Germany
| | - Sophie Stotz
- Max Planck Institute for Developmental Biology, Tübingen, D-72076, Germany
| | - Andrej Berg
- Computational and Theoretical Chemistry, Department of Chemistry, University of Konstanz, Konstanz, D-78457, Germany
| | - Ricarda Schwab
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, D-78457, Germany.,Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, CH-8280, Switzerland
| | - Sophia Scheuermann
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, D-78457, Germany.,Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, CH-8280, Switzerland
| | - Johanna Bialas
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, D-78457, Germany.,Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, CH-8280, Switzerland
| | - Mira C Schütz-Stoffregen
- Max Planck Institute for Developmental Biology, Tübingen, D-72076, Germany.,Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, D-93040, Germany
| | - Gunter Schmidtke
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, D-78457, Germany.,Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, CH-8280, Switzerland
| | - Christine Peter
- Computational and Theoretical Chemistry, Department of Chemistry, University of Konstanz, Konstanz, D-78457, Germany
| | - Marcus Groettrup
- Division of Immunology, Department of Biology, University of Konstanz, Konstanz, D-78457, Germany. .,Biotechnology Institute Thurgau at the University of Konstanz, Kreuzlingen, CH-8280, Switzerland.
| | - Silke Wiesner
- Max Planck Institute for Developmental Biology, Tübingen, D-72076, Germany. .,Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, D-93040, Germany.
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Mukherjee B, Peter C, Kremer K. Single molecule translocation in smectics illustrates the challenge for time-mapping in simulations on multiple scales. J Chem Phys 2018; 147:114501. [PMID: 28938812 DOI: 10.1063/1.5001482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Understanding the connections between the characteristic dynamical time scales associated with a coarse-grained (CG) and a detailed representation is central to the applicability of the coarse-graining methods to understand molecular processes. The process of coarse graining leads to an accelerated dynamics, owing to the smoothening of the underlying free-energy landscapes. Often a single time-mapping factor is used to relate the time scales associated with the two representations. We critically examine this idea using a model system ideally suited for this purpose. Single molecular transport properties are studied via molecular dynamics simulations of the CG and atomistic representations of a liquid crystalline, azobenzene containing mesogen, simulated in the smectic and the isotropic phases. The out-of-plane dynamics in the smectic phase occurs via molecular hops from one smectic layer to the next. Hopping can occur via two mechanisms, with and without significant reorientation. The out-of-plane transport can be understood as a superposition of two (one associated with each mode of transport) independent continuous time random walks for which a single time-mapping factor would be rather inadequate. A comparison of the free-energy surfaces, relevant to the out-of-plane transport, qualitatively supports the above observations. Thus, this work underlines the need for building CG models that exhibit both structural and dynamical consistency to the underlying atomistic model.
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Affiliation(s)
| | - Christine Peter
- Department of Chemistry, University of Konstanz, 78547 Konstanz, Germany
| | - Kurt Kremer
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany
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40
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Matthäus V, Haiden N, Abou-Dakn M, Berns M, Eglin K, Flemmer A, Gebauer C, Glanzmann R, Graf-Rohrmeister K, Grunert J, Hattinger-Jürgenssen E, Herber-Jonat S, Hofstätter E, Klotz D, Kujawa M, Liegl Y, Malzacher A, Peter C, Radke M, Sams E, Mader S. Empfehlungen zur Förderung von Frauenmilchbanken in Deutschland, Österreich und der Schweiz (D-A-CH-Raum). Monatsschr Kinderheilkd 2018. [DOI: 10.1007/s00112-018-0447-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Poon GG, Lemke T, Peter C, Molinero V, Peters B. Soluble Oligomeric Nucleants: Simulations of Chain Length, Binding Strength, and Volume Fraction Effects. J Phys Chem Lett 2017; 8:5815-5820. [PMID: 29116791 DOI: 10.1021/acs.jpclett.7b02651] [Citation(s) in RCA: 3] [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: 06/07/2023]
Abstract
Recent theories and simulations suggest that molecular additives can bind to the surfaces of nuclei, lower the surface energy, and accelerate nucleation. Experiments have shown that oligomeric and polymeric additives can also modify nucleation rates of proteins, ice, and minerals; however, general design principles for oligomeric or polymeric promoters do not yet exist. Here we investigate oligomeric additives for which each segment of the oligomer can bind to surfaces of nuclei. We use semigrand canonical Monte Carlo simulations in a Potts lattice gas model to study the effects of oligomer chain length, volume fraction, and binding strength. We find that increasing each of those parameters lowers the nucleation barrier. At extremely low oligomer concentrations, the nucleation kinetics can be modeled as though each oligomer is a heterogeneous nucleation site in solution.
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Affiliation(s)
- Geoffrey G Poon
- Department of Chemical Engineering, University of California , Santa Barbara, California 93106, United States
| | - Tobias Lemke
- Department of Chemistry, University of Konstanz , Konstanz 78457, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz , Konstanz 78457, Germany
| | - Valeria Molinero
- Department of Chemistry, The University of Utah , Salt Lake City, Utah 84112, United States
| | - Baron Peters
- Department of Chemical Engineering, University of California , Santa Barbara, California 93106, United States
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42
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Lemke T, Peter C. Neural Network Based Prediction of Conformational Free Energies - A New Route toward Coarse-Grained Simulation Models. J Chem Theory Comput 2017; 13:6213-6221. [DOI: 10.1021/acs.jctc.7b00864] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tobias Lemke
- Theoretical Chemistry, University of Konstanz, 78547 Konstanz, Germany
| | - Christine Peter
- Theoretical Chemistry, University of Konstanz, 78547 Konstanz, Germany
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43
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Affiliation(s)
- Andrej Berg
- Department
of Chemistry, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
| | - Christine Peter
- Department
of Chemistry, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
| | - Karen Johnston
- Department
of Chemical and Process Engineering, University of Strathclyde, James Weir Building, 75 Montrose Street, Glasgow G1 1XJ, United Kingdom
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Mishra NK, Jain A, Peter C, Verma S. Combining Experimental and Simulation Techniques to Understand Morphology Control in Pentapeptide Nanostructures. J Phys Chem B 2017; 121:8155-8161. [DOI: 10.1021/acs.jpcb.7b06005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Narendra Kumar Mishra
- Department
of Chemistry, Center for Nanoscience and Soft Nanotechnology, Indian Institute of Technology Kanpur, Kanpur, 208016 (UP), India
| | - Alok Jain
- Fachbereich
Chemie, Universität Konstanz, D-78457 Konstanz, Germany
| | - Christine Peter
- Fachbereich
Chemie, Universität Konstanz, D-78457 Konstanz, Germany
| | - Sandeep Verma
- Department
of Chemistry, Center for Nanoscience and Soft Nanotechnology, Indian Institute of Technology Kanpur, Kanpur, 208016 (UP), India
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45
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Schettler VJJ, Neumann CL, Peter C, Zimmermann T, Julius U, Roeseler E, Heigl F, Grützmacher P, Blume H, Vogt A. Erratum to: The German Lipoprotein Apheresis Registry (GLAR) - almost 5 years on. Clin Res Cardiol Suppl 2017:10.1007/s11789-017-0092-1. [PMID: 28717887 DOI: 10.1007/s11789-017-0092-1] [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: 10/19/2022]
Affiliation(s)
- V J J Schettler
- Center of Nephrology Göttingen GbR, An der Lutter 24, 37075, Göttingen, Germany.
| | - C L Neumann
- BRAVE e Benefit for Research on Arterial Hypertension, Dyslipidemia and Vascular Risk and Education e.V., Göttingen, Germany
| | - C Peter
- BioArtProducts GmbH (B.A.P.), Rostock, Germany
- Rostock Group (EXIM), Fraunhofer Institute for Cell Therapy and Immunology IZI, Rostock, Germany
| | | | - U Julius
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - E Roeseler
- Center for Nephrology, Hypertension, and Metabolic Diseases, Hannover, Germany
| | - F Heigl
- Medical Care Centre Kempten-Allgäu, Kempten, Germany
| | - P Grützmacher
- Department of Medicine II for Nephrology, Hypertension and Vascular Risks, AGAPLESION Markus Hospital, Frankfurt, Germany
| | - H Blume
- Scientific Institute for Nephrology (WiNe), Düsseldorf, Germany
| | - A Vogt
- Medizinische Klinik und Poliklinik 4, Universität München, Munich, Germany
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Schettler VJJ, Neumann CL, Peter C, Zimmermann T, Julius U, Roeseler E, Heigl F, Grützmacher P, Blume H. Current insights into the German Lipoprotein Apheresis Registry (GLAR) - Almost 5 years on. ATHEROSCLEROSIS SUPP 2017; 30:50-55. [PMID: 29096861 DOI: 10.1016/j.atherosclerosissup.2017.05.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
BACKGROUND In recent years the Federal Joint Committee (G-BA), a paramount decision-making body of the German health care system required a reassessment of the approval of chronic lipoprotein apheresis therapy for regular reimbursement. Since 2005 an interdisciplinary German apheresis working group has been established by members of both German Societies of Nephrology. In 2009 the working group completed the indication for lipoprotein apheresis with respect to current cardiovascular guidelines and current scientific knowledge for the registry. In 2011 the German Lipoprotein Apheresis Registry (GLAR) was launched and data acquired over nearly 5 years can now be reported. METHODS AND RESULTS All data were collected and analyzed during the time period 2012-2015. Over this time interval, 68 German apheresis centers collected retrospective and prospective observational data of 1.283 patients undergoing lipoprotein apheresis (LA) treatment of high LDL-cholesterol (LDL-C) levels and/or high lipoprotein(a) (Lp(a)) levels suffering from progressive cardiovascular disease (CVD). A total of 15,167 documented LA treatments were investigated. All patients treated by LA exhibited a median LDL-C reduction rate of 68.6%, and a median Lp(a) reduction rate of 70.4%. Analogue to the Pro(a)LiFe pattern, patient data were analyzed and compared with respect to the incidence rate of coronary events (MACE) 1 and 2 years before the start of LA treatment (y-2 and y-1) and prospectively one year on LA treatment (y+1). During the first year of LA treatment a MACE reduction of 97% was be observed. In the years considered, LA treatment side effects occurred at a low rate (ca. 5%) and mainly comprised puncture problems. CONCLUSIONS For the first time data generated by the GLAR shows that LA lowers the incidence rate of cardiovascular events in patients with high LDL-C and/or high Lp(a) levels, progressive CVD and maximally tolerated lipid lowering medication. In addition LA treatments were found to be safe, exhibiting a low rate of side effects.
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Affiliation(s)
| | - C L Neumann
- BRAVE e Benefit for Research on Arterial Hypertension, Dyslipidemia and Vascular Risk and Education e.V., Göttingen, Germany
| | - C Peter
- BioArtProducts GmbH (B.A.P.), Rostock, Germany; Fraunhofer Institute for Cell Therapy and Immunology IZI, Rostock Group (EXIM), Germany
| | | | - U Julius
- Department of Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - E Roeseler
- Center for Nephrology, Hypertension, and Metabolic Diseases, Hannover, Germany
| | - F Heigl
- Medical Care Centre Kempten-Allgäu, Kempten, Germany
| | - P Grützmacher
- Department of Medicine II for Nephrology, Hypertension and Vascular Risks, AGAPLESION Markus Hospital, Frankfurt, Germany
| | - H Blume
- Scientific Institute for Nephrology (WiNe), Düsseldorf, Germany
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Peter C, Derible A, Parmentier J, Le Drian C, Becht JM. A green direct preparation of a magnetic ordered mesoporous carbon catalyst containing Fe–Pd alloys: application to Suzuki–Miyaura reactions in propane-1,2-diol. NEW J CHEM 2017. [DOI: 10.1039/c7nj00030h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A mesoporous carbon containing Fe–Pd alloys showed excellent activity for Suzuki–Miyaura couplings using tiny amounts of Pd and afforded Pd-free products after reaction.
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Affiliation(s)
- C. Peter
- Institut de Science des Matériaux de Mulhouse (UMR-CNRS 7361)
- Université de Haute Alsace
- 68057 Mulhouse cedex
- France
| | - A. Derible
- Institut de Science des Matériaux de Mulhouse (UMR-CNRS 7361)
- Université de Haute Alsace
- 68057 Mulhouse cedex
- France
| | - J. Parmentier
- Institut de Science des Matériaux de Mulhouse (UMR-CNRS 7361)
- Université de Haute Alsace
- 68057 Mulhouse cedex
- France
| | - C. Le Drian
- Institut de Science des Matériaux de Mulhouse (UMR-CNRS 7361)
- Université de Haute Alsace
- 68057 Mulhouse cedex
- France
| | - J.-M. Becht
- Institut de Science des Matériaux de Mulhouse (UMR-CNRS 7361)
- Université de Haute Alsace
- 68057 Mulhouse cedex
- France
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Au L, Grant M, Haydon A, Oliva K, Wilkins S, Segelov E, Antill Y, Peter C, Ranchod P, Polglase A, Chin M, Chip F, Skinner S, Roger W, McMurrick P, Shapiro J. 198P Use of chemotherapy and mismatch repair deficiency testing in resected stage II colon cancer. Ann Oncol 2016. [DOI: 10.1016/s0923-7534(21)00356-2] [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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49
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Au L, Grant M, Haydon A, Oliva K, Wilkins S, Segelov E, Antill Y, Peter C, Ranchod P, Polglase A, Chin M, Chip F, Skinner S, Roger W, McMurrick P, Shapiro J. 198P Use of chemotherapy and mismatch repair deficiency testing in resected stage II colon cancer. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw581.031] [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: 11/13/2022] Open
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50
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Abstract
Polymer nanocomposites render a range of outstanding materials from natural products such as silk, sea shells and bones, to synthesized nanoclay or carbon nanotube reinforced polymer systems. In contrast to the fast expanding interest in this type of material, the fundamental mechanisms of their mixing, phase behavior and reinforcement, especially for higher nanoparticle content as relevant for bio-inorganic composites, are still not fully understood. Although polymer nanocomposites exhibit diverse morphologies, qualitatively their mechanical properties are believed to be governed by a few parameters, namely their internal polymer network topology, nanoparticle volume fraction, particle surface properties and so on. Relating material mechanics to such elementary parameters is the purpose of this work. By taking a coarse-grained molecular modeling approach, we study an range of different polymer nanocomposites. We vary polymer nanoparticle connectivity, surface geometry and volume fraction to systematically study rheological/mechanical properties. Our models cover different materials, and reproduce key characteristics of real nanocomposites, such as phase separation, mechanical reinforcement. The results shed light on establishing elementary structure, property and function relationship of polymer nanocomposites.
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Affiliation(s)
- Senbo Xiao
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, D-55128 Mainz, Germany
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