1
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Ghysbrecht S, Keller BG. Thermal isomerization rates in retinal analogues using Ab-Initio molecular dynamics. J Comput Chem 2024; 45:1390-1403. [PMID: 38414274 DOI: 10.1002/jcc.27332] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/29/2024]
Abstract
For a detailed understanding of chemical processes in nature and industry, we need accurate models of chemical reactions in complex environments. While Eyring transition state theory is commonly used for modeling chemical reactions, it is most accurate for small molecules in the gas phase. A wide range of alternative rate theories exist that can better capture reactions involving complex molecules and environmental effects. However, they require that the chemical reaction is sampled by molecular dynamics simulations. This is a formidable challenge since the accessible simulation timescales are many orders of magnitude smaller than typical timescales of chemical reactions. To overcome these limitations, rare event methods involving enhanced molecular dynamics sampling are employed. In this work, thermal isomerization of retinal is studied using tight-binding density functional theory. Results from transition state theory are compared to those obtained from enhanced sampling. Rates obtained from dynamical reweighting using infrequent metadynamics simulations were in close agreement with those from transition state theory. Meanwhile, rates obtained from application of Kramers' rate equation to a sampled free energy profile along a torsional dihedral reaction coordinate were found to be up to three orders of magnitude higher. This discrepancy raises concerns about applying rate methods to one-dimensional reaction coordinates in chemical reactions.
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Affiliation(s)
- Simon Ghysbrecht
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Bettina G Keller
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
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2
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Proksch J, Dal Colle MCS, Heinz F, Schmidt RF, Gottwald J, Delbianco M, Keller BG, Gradzielski M, Alexiev U, Koksch B. Impact of glycan nature on structure and viscoelastic properties of glycopeptide hydrogels. J Pept Sci 2024:e3599. [PMID: 38567550 DOI: 10.1002/psc.3599] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 04/04/2024]
Abstract
Mucus is a complex biological hydrogel that acts as a barrier for almost everything entering or exiting the body. It is therefore of emerging interest for biomedical and pharmaceutical applications. Besides water, the most abundant components are the large and densely glycosylated mucins, glycoproteins of up to 20 MDa and carbohydrate content of up to 80 wt%. Here, we designed and explored a library of glycosylated peptides to deconstruct the complexity of mucus. Using the well-characterized hFF03 coiled-coil system as a hydrogel-forming peptide scaffold, we systematically probed the contribution of single glycans to the secondary structure as well as the formation and viscoelastic properties of the resulting hydrogels. We show that glycan-decoration does not affect α-helix and coiled-coil formation while it alters gel stiffness. By using oscillatory macrorheology, dynamic light scattering microrheology, and fluorescence lifetime-based nanorheology, we characterized the glycopeptide materials over several length scales. Molecular simulations revealed that the glycosylated linker may extend into the solvent, but more frequently interacts with the peptide, thereby likely modifying the stability of the self-assembled fibers. This systematic study highlights the interplay between glycan structure and hydrogel properties and may guide the development of synthetic mucus mimetics.
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Affiliation(s)
- Jonas Proksch
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Marlene C S Dal Colle
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Frederick Heinz
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Robert F Schmidt
- Stranski-Laboratorium für Physikalische und Theoretische Chemie, Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | | | - Martina Delbianco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Bettina G Keller
- Stranski-Laboratorium für Physikalische und Theoretische Chemie, Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Michael Gradzielski
- Stranski-Laboratorium für Physikalische und Theoretische Chemie, Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Ulrike Alexiev
- Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
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3
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Heinz F, Proksch J, Schmidt RF, Gradzielski M, Koksch B, Keller BG. How Chromophore Labels Shape the Structure and Dynamics of a Peptide Hydrogel. Biomacromolecules 2024; 25:1262-1273. [PMID: 38288602 PMCID: PMC10865361 DOI: 10.1021/acs.biomac.3c01225] [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: 11/07/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 02/13/2024]
Abstract
Biocompatible and functionalizable hydrogels have a wide range of (potential) medicinal applications. The hydrogelation process, particularly for systems with very low polymer weight percentages (<1 wt %), remains poorly understood, making it challenging to predict the self-assembly of a given molecular building block into a hydrogel. This severely hinders the rational design of self-assembled hydrogels. In this study, we demonstrate the impact of an N-terminal group on the self-assembly and rheology of the peptide hydrogel hFF03 (hydrogelating, fibril forming peptide 03) using molecular dynamics simulations, oscillatory shear rheology, and circular dichroism spectroscopy. We find that the chromophore and even its specific regioisomers have a significant influence on the microscopic structure and dynamics of the self-assembled fibril, and on the macroscopic mechanical properties. This is because the chromophore influences the possible salt bridges, which form and stabilize the fibril formation. Furthermore, we find that the solvation shell fibrils by itself cannot explain the viscoelasticity of hFF03 hydrogels. Our atomistic model of the hFF03 fibril formation enables a more rational design of these hydrogels. In particular, altering the N-terminal chromophore emerges as a design strategy to tune the mechanic properties of these self-assembled peptide hydrogels.
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Affiliation(s)
- Frederick Heinz
- Department
of Biology, Chemistry and Pharmacy, Freie
Universität Berlin, Arnimallee 22, Berlin 14195, Germany
| | - Jonas Proksch
- Department
of Biology, Chemistry and Pharmacy, Freie
Universität Berlin, Arnimallee 22, Berlin 14195, Germany
| | - Robert F. Schmidt
- Stranski-Laboratorium
für Physikalische und Theoretische Chemie, Institut für
Chemie, Technische Universität Berlin, Straße des 17. Juni 124, Berlin 10623, Germany
| | - Michael Gradzielski
- Stranski-Laboratorium
für Physikalische und Theoretische Chemie, Institut für
Chemie, Technische Universität Berlin, Straße des 17. Juni 124, Berlin 10623, Germany
| | - Beate Koksch
- Department
of Biology, Chemistry and Pharmacy, Freie
Universität Berlin, Arnimallee 22, Berlin 14195, Germany
| | - Bettina G. Keller
- Department
of Biology, Chemistry and Pharmacy, Freie
Universität Berlin, Arnimallee 22, Berlin 14195, Germany
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4
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Müll M, Pourmasoumi F, Wehrhan L, Nosovska O, Stephan P, Zeihe H, Vilotijevic I, Keller BG, Kries H. Biosynthetic incorporation of fluorinated amino acids into the nonribosomal peptide gramicidin S. RSC Chem Biol 2023; 4:692-697. [PMID: 37654511 PMCID: PMC10467612 DOI: 10.1039/d3cb00061c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/24/2023] [Indexed: 09/02/2023] Open
Abstract
Fluorine is a key element in medicinal chemistry, as it can significantly enhance the pharmacological properties of drugs. In this study, we aimed to biosynthetically produce fluorinated analogues of the antimicrobial cyclic decapeptide gramicidin S (GS). However, our results show that the A-domain of the NRPS module GrsA rejects 4-fluorinated analogues of its native substrate Phe due to an interrupted T-shaped aromatic interaction in the binding pocket. We demonstrate that GrsA mutant W239S improves the incorporation of 4-fluorinated Phe into GS both in vitro and in vivo. Our findings provide new insights into the behavior of NRPSs towards fluorinated amino acids and strategies for the engineered biosynthesis of fluorinated peptides.
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Affiliation(s)
- Maximilian Müll
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI Jena) Jena 07745 Germany
| | - Farzaneh Pourmasoumi
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI Jena) Jena 07745 Germany
| | - Leon Wehrhan
- Freie Universität Berlin, Department of Biology, Chemistry, and Pharmacy, Institute of Chemistry and Biochemistry Arnimallee 20 Berlin 14195 Germany
| | - Olena Nosovska
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena Humboldtstr. 10 Jena 07743 Germany
| | - Philipp Stephan
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI Jena) Jena 07745 Germany
| | - Hannah Zeihe
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI Jena) Jena 07745 Germany
| | - Ivan Vilotijevic
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena Humboldtstr. 10 Jena 07743 Germany
| | - Bettina G Keller
- Freie Universität Berlin, Department of Biology, Chemistry, and Pharmacy, Institute of Chemistry and Biochemistry Arnimallee 20 Berlin 14195 Germany
| | - Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI Jena) Jena 07745 Germany
- University of Bayreuth, Organic Chemistry I Bayreuth 95440 Germany
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5
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Bolhuis PG, Brotzakis ZF, Keller BG. Optimizing molecular potential models by imposing kinetic constraints with path reweighting. J Chem Phys 2023; 159:074102. [PMID: 37581416 DOI: 10.1063/5.0151166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 06/19/2023] [Indexed: 08/16/2023] Open
Abstract
Empirical force fields employed in molecular dynamics simulations of complex systems are often optimized to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the interconversion rates between metastable states in such systems is hardly ever incorporated in a force field due to a lack of an efficient approach. Here, we introduce such a framework based on the relationship between dynamical observables, such as rate constants, and the underlying molecular model parameters using the statistical mechanics of trajectories. Given a prior ensemble of molecular dynamics trajectories produced with imperfect force field parameters, the approach allows for the optimal adaption of these parameters such that the imposed constraint of equally predicted and experimental rate constant is obeyed. To do so, the method combines the continuum path ensemble maximum caliber approach with path reweighting methods for stochastic dynamics. When multiple solutions are found, the method selects automatically the combination that corresponds to the smallest perturbation of the entire path ensemble, as required by the maximum entropy principle. To show the validity of the approach, we illustrate the method on simple test systems undergoing rare event dynamics. Next to simple 2D potentials, we explore particle models representing molecular isomerization reactions and protein-ligand unbinding. Besides optimal interaction parameters, the methodology gives physical insights into what parts of the model are most sensitive to the kinetics. We discuss the generality and broad implications of the methodology.
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Affiliation(s)
- Peter G Bolhuis
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Z Faidon Brotzakis
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Bettina G Keller
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Arnimallee 22, D-14195 Berlin, Germany
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6
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Zupan H, Heinz F, Keller BG. Grid-based state space exploration for molecular binding. CAN J CHEM 2023. [DOI: 10.1139/cjc-2022-0282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Binding processes are difficult to sample with molecular-dynamics (MD) simulations. In particular, the state space exploration is often incomplete. Evaluating the molecular interaction energy on a grid circumvents this problem but is heavily limited by state space dimensionality. Here, we make the first steps towards a low-dimensional grid-based model of molecular binding. We discretise the state space of relative positions and orientations of the two molecules under the rigid body assumption. The corresponding program is published as the Python package molgri. For the rotational component of the grids, we test algorithms based on Euler angles, polyhedra and quaternions, of which the polyhedra-based are the most uniform. The program outputs a sequence of molecular structures that can be easily processed by standard MD programs to calculate grid point energies. We demonstrate the grid-based approach on two molecular systems: a water dimer and a coiled-coil protein interacting with a chloride anion. For the second system we relax the rigid-body assumption and improve the accuracy of the grid point energies by an energy minimisation. In both cases, oriented bonding patterns and energies confirm expectations from chemical intuition and MD simulations. We also demonstrate how analysis of energy contributions on a grid can be performed and demonstrate that electrostatically-driven association is sufficiently resolved by point-energy calculations. Overall, grid-based models of molecular binding are potentially a powerful complement to molecular sampling approaches, and we see the potential to expand the method to quantum chemistry and flexible docking applications.
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7
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Kapp-Joswig JO, Keller BG. CommonNNClustering─A Python Package for Generic Common-Nearest-Neighbor Clustering. J Chem Inf Model 2023; 63:1093-1098. [PMID: 36744824 DOI: 10.1021/acs.jcim.2c01493] [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: 02/07/2023]
Abstract
Density-based clustering procedures are widely used in a variety of data science applications. Their advantage lies in the capability to find arbitrarily shaped and sized clusters and robustness against outliers. In particular, they proved effective in the analysis of molecular dynamics simulations, where they serve to identify relevant, low-energetic molecular conformations. As such, they can provide a convenient basis for the construction of kinetic (core-set) Markov-state models. Here we present the open-source Python project CommonNNClustering, which provides an easy-to-use and efficient reimplementation of the common-nearest-neighbor (CommonNN) method. The package provides functionalities for hierarchical clustering and an evaluation of the results. We put our emphasis on a generic API design to keep the implementation flexible and open for customization.
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Affiliation(s)
- Jan-Oliver Kapp-Joswig
- Department of Theoretical Chemistry, Freie Universität Berlin, Arnimallee 22, 14195Berlin, Germany
| | - Bettina G Keller
- Department of Theoretical Chemistry, Freie Universität Berlin, Arnimallee 22, 14195Berlin, Germany
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8
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Wenz MT, Bertazzon M, Sticht J, Aleksić S, Gjorgjevikj D, Freund C, Keller BG. Target Recognition in Tandem WW Domains: Complex Structures for Parallel and Antiparallel Ligand Orientation in h-FBP21 Tandem WW. J Chem Inf Model 2022; 62:6586-6601. [PMID: 35347992 DOI: 10.1021/acs.jcim.1c01426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Protein-protein interactions often rely on specialized recognition domains, such as WW domains, which bind to specific proline-rich sequences. The specificity of these protein-protein interactions can be increased by tandem repeats, i.e., two WW domains connected by a linker. With a flexible linker, the WW domains can move freely with respect to each other. Additionally, the tandem WW domains can bind in two different orientations to their target sequences. This makes the elucidation of complex structures of tandem WW domains extremely challenging. Here, we identify and characterize two complex structures of the tandem WW domain of human formin-binding protein 21 and a peptide sequence from its natural binding partner, the core-splicing protein SmB/B'. The two structures differ in the ligand orientation and, consequently, also in the relative orientation of the two WW domains. We analyze and probe the interactions in the complexes by molecular simulations and NMR experiments. The workflow to identify the complex structures uses molecular simulations, density-based clustering, and peptide docking. It is designed to systematically generate possible complex structures for repeats of recognition domains. These structures will help us to understand the synergistic and multivalency effects that generate the astonishing versatility and specificity of protein-protein interactions.
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Affiliation(s)
- Marius T Wenz
- Institute for Chemistry and Biochemistry, Molecular Dynamics Group, Freie Universität Berlin, Arnimallee 22, Berlin 14195, Germany
| | - Miriam Bertazzon
- Institute for Chemistry and Biochemistry, Protein Biochemistry Group, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Jana Sticht
- Institute for Chemistry and Biochemistry, Protein Biochemistry Group, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany.,Core Facility BioSupraMol, Freie Universität Berlin, Takustrasse 3, Berlin 14195, Germany
| | - Stevan Aleksić
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach, Germany
| | - Daniela Gjorgjevikj
- Institute for Chemistry and Biochemistry, Protein Biochemistry Group, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Christian Freund
- Institute for Chemistry and Biochemistry, Protein Biochemistry Group, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Bettina G Keller
- Institute for Chemistry and Biochemistry, Molecular Dynamics Group, Freie Universität Berlin, Arnimallee 22, Berlin 14195, Germany
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9
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Wehrhan L, Leppkes J, Dimos N, Loll B, Koksch B, Keller BG. Water Network in the Binding Pocket of Fluorinated BPTI-Trypsin Complexes─Insights from Simulation and Experiment. J Phys Chem B 2022; 126:9985-9999. [PMID: 36409613 DOI: 10.1021/acs.jpcb.2c05496] [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: 11/22/2022]
Abstract
Structural waters in the S1 binding pocket of β-trypsin are critical for the stabilization of the complex of β-trypsin with its inhibitor bovine pancreatic trypsin inhibitor (BPTI). The inhibitor strength of BPTI can be modulated by replacing the critical lysine residue at the P1 position by non-natural amino acids. We study BPTI variants in which the critical Lys15 in BPTI has been replaced by α-aminobutyric acid (Abu) and its fluorinated derivatives monofluoroethylglycine (MfeGly), difluoroethylglycine (DfeGly), and trifluoroethylglycine (TfeGly). We investigate the hypothesis that additional water molecules in the binding pocket can form specific noncovalent interactions with the fluorinated side chains and thereby act as an extension of the inhibitors. We report potentials of mean force (PMF) of the unbinding process for all four complexes and enzyme activity inhibition assays. Additionally, we report the protein crystal structure of the Lys15MfeGly-BPTI-β-trypsin complex (pdb: 7PH1). Both experimental and computational data show a stepwise increase in inhibitor strength with increasing fluorination of the Abu side chain. The PMF additionally shows a minimum for the encounter complex and an intermediate state just before the bound state. In the bound state, the computational analysis of the structure and dynamics of the water molecules in the S1 pocket shows a highly dynamic network of water molecules that does not indicate a rigidification or stabilizing trend in regard to energetic properties that could explain the increase in inhibitor strength. The analysis of the energy and the entropy of the water molecules in the S1 binding pocket using grid inhomogeneous solvation theory confirms this result. Overall, fluorination systematically changes the binding affinity, but the effect cannot be explained by a persistent water network in the binding pocket. Other effects, such as the hydrophobicity of fluorinated amino acids and the stability of the encounter complex as well as the additional minimum in the potential of mean force in the bound state, likely influence the affinity more directly.
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Affiliation(s)
- Leon Wehrhan
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 22, Berlin14195, Germany
| | - Jakob Leppkes
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 20, Berlin14195, Germany
| | - Nicole Dimos
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, Berlin14195, Germany
| | - Bernhard Loll
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, Berlin14195, Germany
| | - Beate Koksch
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 20, Berlin14195, Germany
| | - Bettina G Keller
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 22, Berlin14195, Germany
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10
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Yao G, Kosol S, Wenz MT, Irran E, Keller BG, Trapp O, Süssmuth RD. The occurrence of ansamers in the synthesis of cyclic peptides. Nat Commun 2022; 13:6488. [PMID: 36310176 PMCID: PMC9618573 DOI: 10.1038/s41467-022-34125-8] [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: 05/20/2022] [Accepted: 10/14/2022] [Indexed: 12/25/2022] Open
Abstract
α-Amanitin is a bicyclic octapeptide composed of a macrolactam with a tryptathionine cross-link forming a handle. Previously, the occurrence of isomers of amanitin, termed atropisomers has been postulated. Although the total synthesis of α-amanitin has been accomplished this aspect still remains unsolved. We perform the synthesis of amanitin analogs, accompanied by in-depth spectroscopic, crystallographic and molecular dynamics studies. The data unambiguously confirms the synthesis of two amatoxin-type isomers, for which we propose the term ansamers. The natural structure of the P-ansamer can be ansa-selectively synthesized using an optimized synthetic strategy. We believe that the here described terminology does also have implications for many other peptide structures, e.g. norbornapeptides, lasso peptides, tryptorubins and others, and helps to unambiguously describe conformational isomerism of cyclic peptides.
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Affiliation(s)
- Guiyang Yao
- grid.6734.60000 0001 2292 8254Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany ,grid.8547.e0000 0001 0125 2443Center for Innovative Drug Discovery, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences, Fudan University, Shanghai, PR China
| | - Simone Kosol
- grid.6734.60000 0001 2292 8254Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Marius T. Wenz
- grid.14095.390000 0000 9116 4836Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Elisabeth Irran
- grid.6734.60000 0001 2292 8254Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Bettina G. Keller
- grid.14095.390000 0000 9116 4836Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Oliver Trapp
- grid.5252.00000 0004 1936 973XDepartment of Chemistry and Pharmacy, Ludwig-Maximilians-University, Butenandtstr. 5-13, 81377 Munich, Germany ,grid.429508.20000 0004 0491 677XMax-Planck-Institute for Astronomy, Königstuhl 17, 69117 Heidelberg, Germany
| | - Roderich D. Süssmuth
- grid.6734.60000 0001 2292 8254Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
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11
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Tiemann M, Nawrotzky E, Schmieder P, Wehrhan L, Bergemann S, Martos V, Song W, Arkona C, Keller BG, Rademann J. A Formylglycine-Peptide for the Site-Directed Identification of Phosphotyrosine-Mimetic Fragments. Chemistry 2022; 28:e202201282. [PMID: 35781901 PMCID: PMC9804470 DOI: 10.1002/chem.202201282] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 04/25/2022] [Indexed: 01/05/2023]
Abstract
Discovery of protein-binding fragments for precisely defined binding sites is an unmet challenge to date. Herein, formylglycine is investigated as a molecular probe for the sensitive detection of fragments binding to a spatially defined protein site . Formylglycine peptide 3 was derived from a phosphotyrosine-containing peptide substrate of protein tyrosine phosphatase PTP1B by replacing the phosphorylated amino acid with the reactive electrophile. Fragment ligation with formylglycine occurred in situ in aqueous physiological buffer. Structures and kinetics were validated by NMR spectroscopy. Screening and hit validation revealed fluorinated and non-fluorinated hit fragments being able to replace the native phosphotyrosine residue. The formylglycine probe identified low-affinity fragments with high spatial resolution as substantiated by molecular modelling. The best fragment hit, 4-amino-phenyl-acetic acid, was converted into a cellularly active, nanomolar inhibitor of the protein tyrosine phosphatase SHP2.
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Affiliation(s)
- Markus Tiemann
- Department of Biology, Chemistry, PharmacyInstitute of PharmacyFreie Universität BerlinKönigin-Luise-Strasse 2+414195BerlinGermany
| | - Eric Nawrotzky
- Department of Biology, Chemistry, PharmacyInstitute of PharmacyFreie Universität BerlinKönigin-Luise-Strasse 2+414195BerlinGermany
| | - Peter Schmieder
- Leibniz Institute of Molecular Pharmacology (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
| | - Leon Wehrhan
- Department of Biology, Chemistry, PharmacyInstitute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Silke Bergemann
- Department of Biology, Chemistry, PharmacyInstitute of PharmacyFreie Universität BerlinKönigin-Luise-Strasse 2+414195BerlinGermany
| | - Vera Martos
- Leibniz Institute of Molecular Pharmacology (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
| | - Wei Song
- Department of Biology, Chemistry, PharmacyInstitute of PharmacyFreie Universität BerlinKönigin-Luise-Strasse 2+414195BerlinGermany
| | - Christoph Arkona
- Department of Biology, Chemistry, PharmacyInstitute of PharmacyFreie Universität BerlinKönigin-Luise-Strasse 2+414195BerlinGermany
| | - Bettina G. Keller
- Department of Biology, Chemistry, PharmacyInstitute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Jörg Rademann
- Department of Biology, Chemistry, PharmacyInstitute of PharmacyFreie Universität BerlinKönigin-Luise-Strasse 2+414195BerlinGermany
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12
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Kieninger S, Keller BG. GROMACS Stochastic Dynamics and BAOAB Are Equivalent Configurational Sampling Algorithms. J Chem Theory Comput 2022; 18:5792-5798. [DOI: 10.1021/acs.jctc.2c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stefanie Kieninger
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Arnimallee 22, D-14195 Berlin, Germany
| | - Bettina G. Keller
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Arnimallee 22, D-14195 Berlin, Germany
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13
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Accorsi M, Tiemann M, Wehrhan L, Finn LM, Cruz R, Rautenberg M, Emmerling F, Heberle J, Keller BG, Rademann J. Pentafluorophosphato‐Phenylalanines: Amphiphilic Phosphotyrosine Mimetics Displaying Fluorine‐Specific Protein Interactions. Angew Chem Int Ed Engl 2022; 61:e202203579. [PMID: 35303375 PMCID: PMC9323422 DOI: 10.1002/anie.202203579] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Indexed: 11/10/2022]
Abstract
Phosphotyrosine residues are essential functional switches in health and disease. Thus, phosphotyrosine biomimetics are crucial for the development of chemical tools and drug molecules. We report here the discovery and investigation of pentafluorophosphato amino acids as novel phosphotyrosine biomimetics. A mild acidic pentafluorination protocol was developed and two PF5‐amino acids were prepared and employed in peptide synthesis. Their structures, reactivities, and fluorine‐specific interactions were studied by NMR and IR spectroscopy, X‐ray diffraction, and in bioactivity assays. The mono‐anionic PF5 motif displayed an amphiphilic character binding to hydrophobic surfaces, to water molecules, and to protein‐binding sites, exploiting charge and H−F‐bonding interactions. The novel motifs bind 25‐ to 30‐fold stronger to the phosphotyrosine binding site of the protein tyrosine phosphatase PTP1B than the best current biomimetics, as rationalized by computational methods, including molecular dynamics simulations.
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Affiliation(s)
- Matteo Accorsi
- Department of Biology, Chemistry, Pharmacy Institute of Pharmacy Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Germany
| | - Markus Tiemann
- Department of Biology, Chemistry, Pharmacy Institute of Pharmacy Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Germany
| | - Leon Wehrhan
- Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Lauren M. Finn
- Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Ruben Cruz
- Department of Physics Freie Universität Berlin Arnimallee 14 14195 Berlin Germany
| | - Max Rautenberg
- Bundesanstalt für Materialforschung und -prüfung (BAM) Richard-Willstätter-Str.11 12489 Berlin Germany
| | - Franziska Emmerling
- Bundesanstalt für Materialforschung und -prüfung (BAM) Richard-Willstätter-Str.11 12489 Berlin Germany
| | - Joachim Heberle
- Department of Physics Freie Universität Berlin Arnimallee 14 14195 Berlin Germany
| | - Bettina G. Keller
- Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Jörg Rademann
- Department of Biology, Chemistry, Pharmacy Institute of Pharmacy Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Germany
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14
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Accorsi M, Tiemann M, Wehrhan L, Finn LM, Cruz R, Rautenberg M, Emmerling F, Heberle J, Keller BG, Rademann J. Pentafluorophosphato‐Phenylalanines: Amphiphilic Phosphotyrosine Mimetics Displaying Fluorine‐Specific Protein Interactions. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Matteo Accorsi
- Freie Universität Berlin: Freie Universitat Berlin Department of Biology, Chemistry, Pharmacy; Institute of Pharmacy GERMANY
| | - Markus Tiemann
- Freie Universität Berlin: Freie Universitat Berlin Department of Biology, Chemistry, Pharmacy, Institute of Pharmacy GERMANY
| | - Leon Wehrhan
- Freie Universität Berlin: Freie Universitat Berlin Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry GERMANY
| | - Lauren M. Finn
- Freie Universität Berlin: Freie Universitat Berlin Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry GERMANY
| | - Ruben Cruz
- Freie Universität Berlin: Freie Universitat Berlin Department of Physics GERMANY
| | - Max Rautenberg
- Bundesanstalt für Materialforschung und -prüfung: Bundesanstalt fur Materialforschung und -prufung Structure Analysis GERMANY
| | - Franziska Emmerling
- Bundesanstalt für Materialforschung und -prüfung: Bundesanstalt fur Materialforschung und -prufung Structural Analytics GERMANY
| | - Joachim Heberle
- Freie Universität Berlin: Freie Universitat Berlin Department of Physics GERMANY
| | - Bettina G. Keller
- Freie Universität Berlin: Freie Universitat Berlin Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry GERMANY
| | - Jörg Rademann
- Freie Universitat Berlin, Institute of Pharmacy Medicinal Chemistry Königin-Luise-Str. 2+4 14195 Berlin GERMANY
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15
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Leppkes J, Dimos N, Loll B, Hohmann T, Dyrks M, Wieseke A, Keller BG, Koksch B. Fluorine-induced polarity increases inhibitory activity of BPTI towards chymotrypsin. RSC Chem Biol 2022; 3:773-782. [PMID: 35755190 PMCID: PMC9175108 DOI: 10.1039/d2cb00018k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/06/2022] [Indexed: 11/21/2022] Open
Abstract
Substituting the P1 position in bovine pancreatic trypsin inhibitor (BPTI) is known to heavily influence its inhibitory activity towards serine proteases. Side-chain fluorinated aliphatic amino acids have been shown to alter numerous properties of peptides and proteins and thus are of interest in the context of BPTI. In our study, we systematically investigated the site-specific incorporation of non-canonical amino acids into BPTI by microwave-assisted solid-phase peptide synthesis (SPPS). Inhibitor activity of the variants was tested towards the serine protease α-chymotrypsin. We observed enhanced inhibition of two fluorinated BPTIs compared to wild type and hydrocarbon variants. To further investigate the complexes, we performed X-ray structure analysis. Our findings underline the power fluorine offers as a tool in protein engineering to beneficially alter the effects on phenomena as protein–protein interactions. Site-specific incorporation of fluorine into bovine pancreatic trypsin inhibitor (BPTI) through chemical protein synthesis, followed by investigations of influence of fluorine on inhibition properties towards serine protease chymotrypsin.![]()
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Affiliation(s)
- Jakob Leppkes
- Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 20 14195 Berlin Germany
| | - Nicole Dimos
- Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Structural Biochemistry, Freie Universität Berlin Takustr. 6 14195 Berlin Germany
| | - Bernhard Loll
- Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Structural Biochemistry, Freie Universität Berlin Takustr. 6 14195 Berlin Germany
| | - Thomas Hohmann
- Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 20 14195 Berlin Germany
| | - Michael Dyrks
- Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 20 14195 Berlin Germany
| | - Ariane Wieseke
- Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 20 14195 Berlin Germany
| | - Bettina G Keller
- Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Beate Koksch
- Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 20 14195 Berlin Germany
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16
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Yao G, Knittel CH, Kosol S, Wenz MT, Keller BG, Gruß H, Braun AC, Lutz C, Hechler T, Pahl A, Süssmuth RD. Iodine-Mediated Tryptathionine Formation Facilitates the Synthesis of Amanitins. J Am Chem Soc 2021; 143:14322-14331. [PMID: 34459587 DOI: 10.1021/jacs.1c06565] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Synthetic methods on the macrocyclization of peptides are of high interest since they facilitate the synthesis of various types of potentially bioactive compounds, e.g. addressing targets like protein-protein-interactions. Herein, we report on an efficient method to construct tryptathionine-cross-links in peptides between the amino acids Trp and Cys. This reaction not only is the basis for the total synthesis of the death cap toxin α-amanitin but also provides rapid access to various new amanitin analogues. This study for the first time presents a systematic compilation of structure-activity relations (SAR) of amatoxins with regard to RNA polymerase II inhibition and cytotoxicity with one amanitin derivative of superior RNAP II inhibition. The present approach paves the way for the synthesis of structurally diverse amatoxins as future payloads for antibody-toxin conjugates in cancer therapy.
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Affiliation(s)
- Guiyang Yao
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Caroline H Knittel
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Simone Kosol
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Marius T Wenz
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Bettina G Keller
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Hendrik Gruß
- Heidelberg Pharma Research GmbH, Gregor-Mendel-Straße 22, 68526 Ladenburg, Germany
| | - Alexandra C Braun
- Heidelberg Pharma Research GmbH, Gregor-Mendel-Straße 22, 68526 Ladenburg, Germany
| | - Christian Lutz
- Heidelberg Pharma Research GmbH, Gregor-Mendel-Straße 22, 68526 Ladenburg, Germany
| | - Torsten Hechler
- Heidelberg Pharma Research GmbH, Gregor-Mendel-Straße 22, 68526 Ladenburg, Germany
| | - Andreas Pahl
- Heidelberg Pharma Research GmbH, Gregor-Mendel-Straße 22, 68526 Ladenburg, Germany
| | - Roderich D Süssmuth
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
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17
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Donati L, Weber M, Keller BG. Markov models from the square root approximation of the Fokker-Planck equation: calculating the grid-dependent flux. J Phys Condens Matter 2021; 33:115902. [PMID: 33352543 DOI: 10.1088/1361-648x/abd5f7] [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] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Molecular dynamics (MD) are extremely complex, yet understanding the slow components of their dynamics is essential to understanding their macroscopic properties. To achieve this, one models the MD as a stochastic process and analyses the dominant eigenfunctions of the associated Fokker-Planck operator, or of closely related transfer operators. So far, the calculation of the discretized operators requires extensive MD simulations. The square-root approximation of the Fokker-Planck equation is a method to calculate transition rates as a ratio of the Boltzmann densities of neighboring grid cells times a flux, and can in principle be calculated without a simulation. In a previous work we still used MD simulations to determine the flux. Here, we propose several methods to calculate the exact or approximate flux for various grid types, and thus estimate the rate matrix without a simulation. Using model potentials we test computational efficiency of the methods, and the accuracy with which they reproduce the dominant eigenfunctions and eigenvalues. For these model potentials, rate matrices with up to [Formula: see text] states can be obtained within seconds on a single high-performance compute server if regular grids are used.
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Affiliation(s)
- Luca Donati
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustraße 3, D-14195 Berlin, Germany
| | - Marcus Weber
- Zuse Institute Berlin, Takustr. 7, 14195 Berlin, Germany
| | - Bettina G Keller
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustraße 3, D-14195 Berlin, Germany
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18
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Abstract
Path reweighting is a principally exact method to estimate dynamic properties from biased simulations-provided that the path probability ratio matches the stochastic integrator used in the simulation. Previously reported path probability ratios match the Euler-Maruyama scheme for overdamped Langevin dynamics. Since molecular dynamics simulations use Langevin dynamics rather than overdamped Langevin dynamics, this severely impedes the application of path reweighting methods. Here, we derive the path probability ratio ML for Langevin dynamics propagated by a variant of the Langevin Leapfrog integrator. This new path probability ratio allows for exact reweighting of Langevin dynamics propagated by this integrator. We also show that a previously derived approximate path probability ratio Mapprox differs from the exact ML only by O(ξ4Δt4) and thus yields highly accurate dynamic reweighting results. (Δt is the integration time step, and ξ is the collision rate.) The results are tested, and the efficiency of path reweighting is explored using butane as an example.
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Affiliation(s)
- S Kieninger
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Arnimallee 22, D-14195 Berlin, Germany
| | - B G Keller
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Arnimallee 22, D-14195 Berlin, Germany
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19
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Kieninger S, Donati L, Keller BG. Dynamical reweighting methods for Markov models. Curr Opin Struct Biol 2020; 61:124-131. [PMID: 31958761 DOI: 10.1016/j.sbi.2019.12.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/13/2019] [Accepted: 12/26/2019] [Indexed: 12/21/2022]
Abstract
Conformational dynamics is essential to biomolecular processes. Markov State Models (MSMs) are widely used to elucidate dynamic properties of molecular systems from unbiased Molecular Dynamics (MD). However, the implementation of reweighting schemes for MSMs to analyze biased simulations is still at an early stage of development. Several dynamical reweighing approaches have been proposed, which can be classified as approaches based on (i) Kramers rate theory, (ii) rescaling of the probability density flux, (iii) reweighting by formulating a likelihood function, (iv) path reweighting. We present the state-of-the-art and discuss the methodological differences of these methods, their limitations and recent applications.
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Affiliation(s)
- Stefanie Kieninger
- Freie Universität Berlin, Department of Biology, Chemistry, Pharmacy, Arnimallee 22, D-14194 Berlin, Germany
| | - Luca Donati
- Freie Universität Berlin, Department of Biology, Chemistry, Pharmacy, Arnimallee 22, D-14194 Berlin, Germany
| | - Bettina G Keller
- Freie Universität Berlin, Department of Biology, Chemistry, Pharmacy, Arnimallee 22, D-14194 Berlin, Germany.
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20
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Abstract
C-type lectins are the largest and most diverse family of mammalian carbohydrate-binding proteins. They share a common protein fold, which provides the unifying basis for calcium-mediated carbohydrate recognition. Their involvement in a multitude of biological functions is remarkable. Here, we review the variety of tasks these lectins are involved in alongside with the structural demands on the overall protein architecture. Subtle changes of the protein structure are implemented to cope with such diverse functional requirements. The presence of a high level of structural dynamics over a broad palette of time scales is paired with the presence of secondary binding sites and allosteric coordination of remote sites and renders this lectin fold a highly adaptable scaffold.
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Affiliation(s)
- Bettina G Keller
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Christoph Rademacher
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany; Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, 14424 Potsdam, Germany.
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21
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Yao G, Joswig J, Keller BG, Süssmuth RD. Total Synthesis of the Death Cap Toxin Phalloidin: Atropoisomer Selectivity Explained by Molecular‐Dynamics Simulations. Chemistry 2019; 25:8030-8034. [DOI: 10.1002/chem.201901888] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Guiyang Yao
- Institut für ChemieTechnische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
| | - Jan‐Oliver Joswig
- Department of Biology, Chemistry, PharmacyFreie Universität Berlin Takustrasse 3 14195 Berlin Germany
| | - Bettina G. Keller
- Department of Biology, Chemistry, PharmacyFreie Universität Berlin Takustrasse 3 14195 Berlin Germany
| | - Roderich D. Süssmuth
- Institut für ChemieTechnische Universität Berlin Strasse des 17. Juni 124 10623 Berlin Germany
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22
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Kiran P, Bhatia S, Lauster D, Aleksić S, Fleck C, Peric N, Maison W, Liese S, Keller BG, Herrmann A, Haag R. Exploring Rigid and Flexible Core Trivalent Sialosides for Influenza Virus Inhibition. Chemistry 2018; 24:19373-19385. [PMID: 30295350 PMCID: PMC6587447 DOI: 10.1002/chem.201804826] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 09/22/2018] [Indexed: 12/25/2022]
Abstract
Herein, the chemical synthesis and binding analysis of functionalizable rigid and flexible core trivalent sialosides bearing oligoethylene glycol (OEG) spacers interacting with spike proteins of influenza A virus (IAV) X31 is described. Although the flexible Tris-based trivalent sialosides achieved micromolar binding constants, a trivalent binder based on a rigid adamantane core dominated flexible tripodal compounds with micromolar binding and hemagglutination inhibition constants. Simulation studies indicated increased conformational penalties for long OEG spacers. Using a systematic approach with molecular modeling and simulations as well as biophysical analysis, these findings emphasize on the importance of the scaffold rigidity and the challenges associated with the spacer length optimization.
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Affiliation(s)
- Pallavi Kiran
- Institut für Chemie und Biochemie Organische ChemieFreie Universität BerlinTakustr. 314195BerlinGermany
| | - Sumati Bhatia
- Institut für Chemie und Biochemie Organische ChemieFreie Universität BerlinTakustr. 314195BerlinGermany
| | - Daniel Lauster
- Institut für Biologie, Molekulare Biophysik, IRI Life SciencesHumboldt-Universität zu BerlinInvalidenstr. 4210115BerlinGermany
| | - Stevan Aleksić
- Institut für Chemie und Biochemie, Physikalische und Theoretische ChemieFreie Universität BerlinTakustr. 314195BerlinGermany
| | - Carsten Fleck
- Fachbereich ChemieInstitut für PharmazieUniversität HamburgBundesstr. 4520146HamburgGermany
| | - Natalija Peric
- Fachbereich ChemieInstitut für PharmazieUniversität HamburgBundesstr. 4520146HamburgGermany
| | - Wolfgang Maison
- Fachbereich ChemieInstitut für PharmazieUniversität HamburgBundesstr. 4520146HamburgGermany
| | - Susanne Liese
- Department of MathematicsUniversity of Oslo, P.O Box1053 Blinder0316OsloNorway
- Department of PhysicsFreie Universität BerlinArnimallee 1414195BerlinGermany
| | - Bettina G. Keller
- Institut für Chemie und Biochemie, Physikalische und Theoretische ChemieFreie Universität BerlinTakustr. 314195BerlinGermany
| | - Andreas Herrmann
- Institut für Biologie, Molekulare Biophysik, IRI Life SciencesHumboldt-Universität zu BerlinInvalidenstr. 4210115BerlinGermany
| | - Rainer Haag
- Institut für Chemie und Biochemie Organische ChemieFreie Universität BerlinTakustr. 314195BerlinGermany
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23
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Abstract
In recent years, for the analysis of molecular processes, the estimation of time-scales and transition rates has become fundamental. Estimating the transition rates between molecular conformations is-from a mathematical point of view-an invariant subspace projection problem. We present a method to project the infinitesimal generator acting on function space to a low-dimensional rate matrix. This projection can be performed in two steps. First, we discretize the conformational space in a Voronoi tessellation, then the transition rates between adjacent cells is approximated by the geometric average of the Boltzmann weights of the Voronoi cells. This method demonstrates that there is a direct relation between the potential energy surface of molecular structures and the transition rates of conformational changes. We will show also that this approximation is correct and converges to the generator of the Smoluchowski equation in the limit of infinitely small Voronoi cells. We present results for a two dimensional diffusion process and alanine dipeptide as a high-dimensional system.
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Affiliation(s)
- Luca Donati
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
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24
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Affiliation(s)
- Luca Donati
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustraße 3, D-14195 Berlin, Germany
| | - Bettina G. Keller
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustraße 3, D-14195 Berlin, Germany
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25
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Hormann J, Malina J, Lemke O, Hülsey MJ, Wedepohl S, Potthoff J, Schmidt C, Ott I, Keller BG, Brabec V, Kulak N. Multiply Intercalator-Substituted Cu(II) Cyclen Complexes as DNA Condensers and DNA/RNA Synthesis Inhibitors. Inorg Chem 2018; 57:5004-5012. [DOI: 10.1021/acs.inorgchem.8b00027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jan Hormann
- Institut für Chemie und Biochemie, Anorganische Chemie, Freie Universität Berlin, Fabeckstr. 34/36, 14195 Berlin, Germany
| | - Jaroslav Malina
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 61265 Brno, Czech Republic
| | - Oliver Lemke
- Institut für Chemie und Biochemie, Physikalische und Theoretische Chemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Max J. Hülsey
- Institut für Chemie und Biochemie, Anorganische Chemie, Freie Universität Berlin, Fabeckstr. 34/36, 14195 Berlin, Germany
- Biochemistry Center, Heidelberg University, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Stefanie Wedepohl
- Institut für Chemie und Biochemie, Organische Chemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Jan Potthoff
- Institut für Chemie und Biochemie, Anorganische Chemie, Freie Universität Berlin, Fabeckstr. 34/36, 14195 Berlin, Germany
| | - Claudia Schmidt
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstr. 55, 38106 Braunschweig, Germany
| | - Ingo Ott
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstr. 55, 38106 Braunschweig, Germany
| | - Bettina G. Keller
- Institut für Chemie und Biochemie, Physikalische und Theoretische Chemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Viktor Brabec
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 61265 Brno, Czech Republic
| | - Nora Kulak
- Institut für Chemie und Biochemie, Anorganische Chemie, Freie Universität Berlin, Fabeckstr. 34/36, 14195 Berlin, Germany
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26
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Hassan I, Donati L, Stensitzki T, Keller BG, Heyne K, Imhof P. The vibrational spectrum of the hydrated alanine-leucine peptide in the amide region from IR experiments and first principles calculations. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.03.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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27
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Manz C, Yu Kobitski A, Samanta A, Keller BG, Jäschke A, Nienhaus GU. Energy Landscape Analysis of the Full-Length SAM-I Riboswitch using Single-Molecule FRET Spectroscopy. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.3692] [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: 11/26/2022] Open
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28
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Witek J, Mühlbauer M, Keller BG, Blatter M, Meissner A, Wagner T, Riniker S. Interconversion Rates between Conformational States as Rationale for the Membrane Permeability of Cyclosporines. Chemphyschem 2017; 18:3309-3314. [DOI: 10.1002/cphc.201700995] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Jagna Witek
- Laboratory of Physical Chemistry; ETH Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - Max Mühlbauer
- Laboratory of Physical Chemistry; ETH Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - Bettina G. Keller
- Department of Biology, Chemistry, Pharmacy; Freie Universität Berlin; Takustrasse 3 14195 Berlin Germany
| | - Markus Blatter
- Novartis Institutes for BioMedical Research; Novartis Pharma AG; Novartis Campus 4056 Basel Switzerland
| | - Axel Meissner
- Novartis Institutes for BioMedical Research; Novartis Pharma AG; Novartis Campus 4056 Basel Switzerland
| | - Trixie Wagner
- Novartis Institutes for BioMedical Research; Novartis Pharma AG; Novartis Campus 4056 Basel Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry; ETH Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
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29
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Manz C, Kobitski AY, Samanta A, Keller BG, Jäschke A, Nienhaus GU. Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch. Nat Chem Biol 2017; 13:1172-1178. [DOI: 10.1038/nchembio.2476] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 08/03/2017] [Indexed: 11/09/2022]
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30
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Witek J, Keller BG, Blatter M, Meissner A, Wagner T, Riniker S. Correction to Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States. J Chem Inf Model 2017; 57:2393. [DOI: 10.1021/acs.jcim.7b00502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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)
- Jagna Witek
- Laboratory of Physical
Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Bettina G. Keller
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Markus Blatter
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4002 Basel, Switzerland
| | - Axel Meissner
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4002 Basel, Switzerland
| | - Trixie Wagner
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4002 Basel, Switzerland
| | - Sereina Riniker
- Laboratory of Physical
Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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Schumacher D, Lemke O, Helma J, Gerszonowicz L, Waller V, Stoschek T, Durkin PM, Budisa N, Leonhardt H, Keller BG, Hackenberger CPR. Broad substrate tolerance of tubulin tyrosine ligase enables one-step site-specific enzymatic protein labeling. Chem Sci 2017; 8:3471-3478. [PMID: 28507719 PMCID: PMC5418632 DOI: 10.1039/c7sc00574a] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [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: 02/07/2017] [Accepted: 03/18/2017] [Indexed: 12/31/2022] Open
Abstract
The broad substrate tolerance of tubulin tyrosine ligase enables its wide applicability for protein functionalization.
The broad substrate tolerance of tubulin tyrosine ligase is the basic rationale behind its wide applicability for chemoenzymatic protein functionalization. In this context, we report that the wild-type enzyme enables ligation of various unnatural amino acids that are substantially bigger than and structurally unrelated to the natural substrate, tyrosine, without the need for extensive protein engineering. This unusual substrate flexibility is due to the fact that the enzyme's catalytic pocket forms an extended cavity during ligation, as confirmed by docking experiments and all-atom molecular dynamics simulations. This feature enabled one-step C-terminal biotinylation and fluorescent coumarin labeling of various functional proteins as demonstrated with ubiquitin, an antigen binding nanobody, and the apoptosis marker Annexin V. Its broad substrate tolerance establishes tubulin tyrosine ligase as a powerful tool for in vitro enzyme-mediated protein modification with single functional amino acids in a specific structural context.
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Affiliation(s)
- Dominik Schumacher
- Department of Chemical-Biology , Leibniz-Institut für Molekulare Pharmakologie (FMP) , Robert-Rössle-Str. 10 , 13125 Berlin , Germany . .,Department of Chemistry , Humboldt Universität zu Berlin , Brook-Taylor-Strasse 2 , 12489 Berlin , Germany
| | - Oliver Lemke
- Department of Biology, Chemistry, Pharmacy , Freie Universität Berlin , Takustr. 3 , 14195 Berlin , Germany .
| | - Jonas Helma
- Department of Biology II , Ludwig Maximilians Universität München and Center for Integrated Protein Science Munich , Großhadenerstr. 2 , 82152 Martinsried , Germany
| | - Lena Gerszonowicz
- Department of Chemistry , Humboldt Universität zu Berlin , Brook-Taylor-Strasse 2 , 12489 Berlin , Germany
| | - Verena Waller
- Department of Biology II , Ludwig Maximilians Universität München and Center for Integrated Protein Science Munich , Großhadenerstr. 2 , 82152 Martinsried , Germany
| | - Tina Stoschek
- Department of Biology II , Ludwig Maximilians Universität München and Center for Integrated Protein Science Munich , Großhadenerstr. 2 , 82152 Martinsried , Germany
| | - Patrick M Durkin
- Department of Chemistry , TU Berlin , Müller-Breslau-Str. 10 , 10623 Berlin , Germany
| | - Nediljko Budisa
- Department of Chemistry , TU Berlin , Müller-Breslau-Str. 10 , 10623 Berlin , Germany
| | - Heinrich Leonhardt
- Department of Biology II , Ludwig Maximilians Universität München and Center for Integrated Protein Science Munich , Großhadenerstr. 2 , 82152 Martinsried , Germany
| | - Bettina G Keller
- Department of Biology, Chemistry, Pharmacy , Freie Universität Berlin , Takustr. 3 , 14195 Berlin , Germany .
| | - Christian P R Hackenberger
- Department of Chemical-Biology , Leibniz-Institut für Molekulare Pharmakologie (FMP) , Robert-Rössle-Str. 10 , 13125 Berlin , Germany . .,Department of Chemistry , Humboldt Universität zu Berlin , Brook-Taylor-Strasse 2 , 12489 Berlin , Germany
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Lemke O, Keller BG. Publisher’s Note: “Density-based cluster algorithms for the identification of core sets” [J. Chem. Phys. 145, 164104 (2016)]. J Chem Phys 2016; 145:199902. [DOI: 10.1063/1.4968513] [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: 11/14/2022] Open
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Affiliation(s)
- Oliver Lemke
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustraße 3, D-14195 Berlin, Germany
| | - Bettina G. Keller
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustraße 3, D-14195 Berlin, Germany
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Hanske J, Aleksić S, Ballaschk M, Jurk M, Shanina E, Beerbaum M, Schmieder P, Keller BG, Rademacher C. Intradomain Allosteric Network Modulates Calcium Affinity of the C-Type Lectin Receptor Langerin. J Am Chem Soc 2016; 138:12176-86. [DOI: 10.1021/jacs.6b05458] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jonas Hanske
- Department
of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
- Institute
of Chemistry and Biochemistry, Department of Biology, Chemistry, and
Pharmacy, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Stevan Aleksić
- Institute
of Chemistry and Biochemistry, Department of Biology, Chemistry, and
Pharmacy, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Martin Ballaschk
- Institute
of Chemistry and Biochemistry, Department of Biology, Chemistry, and
Pharmacy, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Marcel Jurk
- Department
of Bioinformatics, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Elena Shanina
- Department
of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
- Institute
of Chemistry and Biochemistry, Department of Biology, Chemistry, and
Pharmacy, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Monika Beerbaum
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Peter Schmieder
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Bettina G. Keller
- Institute
of Chemistry and Biochemistry, Department of Biology, Chemistry, and
Pharmacy, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Christoph Rademacher
- Department
of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
- Institute
of Chemistry and Biochemistry, Department of Biology, Chemistry, and
Pharmacy, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany
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Witek J, Keller BG, Blatter M, Meissner A, Wagner T, Riniker S. Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States. J Chem Inf Model 2016; 56:1547-62. [DOI: 10.1021/acs.jcim.6b00251] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jagna Witek
- Laboratory
of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Bettina G. Keller
- Department
of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Markus Blatter
- Novartis
Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4002 Basel, Switzerland
| | - Axel Meissner
- Novartis
Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4002 Basel, Switzerland
| | - Trixie Wagner
- Novartis
Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4002 Basel, Switzerland
| | - Sereina Riniker
- Laboratory
of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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Vitalini F, Noé F, Keller BG. Molecular dynamics simulations data of the twenty encoded amino acids in different force fields. Data Brief 2016; 7:582-90. [PMID: 27054161 PMCID: PMC4802541 DOI: 10.1016/j.dib.2016.02.086] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 02/23/2016] [Accepted: 02/29/2016] [Indexed: 11/26/2022] Open
Abstract
We present extensive all-atom Molecular Dynamics (MD) simulation data of the twenty encoded amino acids in explicit water, simulated with different force fields. The termini of the amino acids have been capped to ensure that the dynamics of the Φ and ψ torsion angles are analogues to the dynamics within a peptide chain. We use representatives of each of the four major force field families: AMBER ff-99SBILDN [1], AMBER ff-03 [2], OPLS-AA/L [3], CHARMM27 [4] and GROMOS43a1 [5], [6]. Our data represents a library and test bed for method development for MD simulations and for force fields development. Part of the data set has been previously used for comparison of the dynamic properties of force fields (Vitalini et al., 2015) [7] and for the construction of peptide basis functions for the variational approach to molecular kinetics [8].
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Affiliation(s)
- F Vitalini
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustraße 3, D-14195 Berlin, Germany
| | - F Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, D-14195 Berlin, Germany
| | - B G Keller
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustraße 3, D-14195 Berlin, Germany
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Rakers C, Bermudez M, Keller BG, Mortier J, Wolber G. Computational close up on protein-protein interactions: how to unravel the invisible using molecular dynamics simulations? WIREs Comput Mol Sci 2015. [DOI: 10.1002/wcms.1222] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Christin Rakers
- Institute of Pharmacy; Freie Universität Berlin; Berlin Germany
| | - Marcel Bermudez
- Institute of Pharmacy; Freie Universität Berlin; Berlin Germany
| | - Bettina G. Keller
- Institute for Chemistry and Biochemistry; Freie Universität Berlin; Berlin Germany
| | - Jérémie Mortier
- Institute of Pharmacy; Freie Universität Berlin; Berlin Germany
| | - Gerhard Wolber
- Institute of Pharmacy; Freie Universität Berlin; Berlin Germany
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Abstract
![]()
We
have developed a hidden Markov model and optimization procedure
for photon-based single-molecule FRET data, which takes into account
the trace-dependent background intensities. This analysis technique
reveals an unprecedented amount of detail in the folding kinetics
of the Diels–Alderase ribozyme. We find a multitude of extended
(low-FRET) and compact (high-FRET) states. Five states were consistently
and independently identified in two FRET constructs and at three Mg2+ concentrations. Structures generally tend to become more
compact upon addition of Mg2+. Some compact structures
are observed to significantly depend on Mg2+ concentration,
suggesting a tertiary fold stabilized by Mg2+ ions. One
compact structure was observed to be Mg2+-independent,
consistent with stabilization by tertiary Watson–Crick base
pairing found in the folded Diels–Alderase structure. A hierarchy
of time scales was discovered, including dynamics of 10 ms or faster,
likely due to tertiary structure fluctuations, and slow dynamics on
the seconds time scale, presumably associated with significant changes
in secondary structure. The folding pathways proceed through a series
of intermediate secondary structures. There exist both compact pathways
and more complex ones, which display tertiary unfolding, then secondary
refolding, and, subsequently, again tertiary refolding.
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Affiliation(s)
- Bettina G Keller
- Freie Universität Berlin , Institute of Chemistry and Biochemistry, Takustr. 3, 14195 Berlin, Germany
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Affiliation(s)
- Feliks Nüske
- Department for Mathematics
and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
| | - Bettina G. Keller
- Department for Mathematics
and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
| | | | - Antonia S. J. S. Mey
- Department for Mathematics
and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
| | - Frank Noé
- Department for Mathematics
and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
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Abstract
Understanding how the chemical environment modulates the predominant conformations and kinetics of flexible molecules is a core interest of biochemistry and a prerequisite for the rational design of synthetic catalysts. This study combines molecular dynamics simulation and Markov state models (MSMs) to a systematic computational strategy for investigating the effect of the chemical environment of a molecule on its conformations and kinetics. MSMs allow quantities to be computed that are otherwise difficult to access, such as the metastable sets, their free energies, and the relaxation time scales related to the rare transitions between metastable states. Additionally, MSMs are useful to identify observables that may act as sensors for the conformational or binding state of the molecule, thus guiding the design of experiments. In the present study, the conformation dynamics of UDP-GlcNAc are studied in vacuum, water, water + Mg(2+), and in the protein UDP-GlcNAc 2-epimerase. It is found that addition of Mg(2+) significantly affects the conformational stability, thermodynamics, and kinetics of UDP-GlcNAc. In particular, the slowest structural process, puckering of the GlcNAc sugar, depends on the overall conformation of UDP-GlcNAc and may thus act as a sensor of whether Mg(2+) is bound or not. Interestingly, transferring the molecule from vacuum to water makes the protein-binding conformations UDP-GlcNAc first accessible, while adding Mg(2+) further stabilizes them by specifically associating to binding-competent conformations. While Mg(2+) is not cocrystallized in the UDP-GlcNAc 2-epimerase complex, the selectively stabilized Mg(2+)/UDP-GlcNAc complex may be a template for the bound state, and Mg(2+) may accompany the binding-competent ligand conformation to the binding pocket. This serves as a possible explanation of the enhanced epimerization rate in the presence of Mg(2+). This role of Mg(2+) has previously not been described and opens the question whether "binding co-factors" may be a concept of general relevance for protein-ligand binding.
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Affiliation(s)
- Martin Held
- Institute of Mathematics, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
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Keller BG, Long RE, Gold ED, Roth MD. Maxillary dental arch dimensions following pharyngeal-flap surgery. Cleft Palate J 1988; 25:248-57. [PMID: 3168269] [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] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Pharyngeal-flap surgery (PFS) is a surgical procedure utilized in the treatment of hypernasal speech. The purpose of this study was to evaluate the effect of PFS on the maxillary dental arch. Sixteen patients who had undergone PFS between the ages of 5 and 7 years were selected from the longitudinal growth study of the Lancaster Cleft Palate Clinic. Eight points were marked on the occlusal surfaces of serial maxillary dental models to determine arch width and length. These data were compared to a matched sample of patients from the same growth study who did not undergo PFS. The flap group demonstrated significant reduction in both arch width (at cuspids and molars) and arch length development compared to the control sample, following PFS. These results are not inconsistent with an hypothesis of dental-arch form changes related to possible airway obstruction following PFS, although data on the latter were not available on this sample.
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Affiliation(s)
- B G Keller
- Division of Orthodontics and Research, Lancaster Cleft Palate Clinic, PA 17602
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