Henrike M. Müller‐Werkmeister

University of Potsdam

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R. J. Dwayne Miller

University of Toronto

Eike C. Schulz

Max Planck Institute for the Structure and Dynamics of Matter

Robin L. Owen

Diamond Light Source

D.A. Sherrell

Argonne National Laboratory

P. Mehrabi

Max Planck Institute for the Structure and Dynamics of Matter

Jens Bredenbeck

Goethe University Frankfurt

Friedjof Tellkamp

Max Planck Institute for the Structure and Dynamics of Matter

Antoine Sarracini

University of Toronto

Oliver P. Ernst

University of Toronto

Yannik Pfeifer

University of Potsdam

Cooperative Institutions

Max Planck Institute for the Structure and Dynamics of Matter

Universität Hamburg

University of Toronto

Center for Free-Electron Laser Science

SPring-8

Hamburg Centre for Ultrafast Imaging

Diamond Light Source

University of Potsdam

Japan Synchrotron Radiation Research Institute

Tohoku University

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Impact of Azidohomoalanine Incorporation on Protein Structure and Ligand Binding

ChemBioChem (2017)

Florian K. Lehner D. Kudlinzki Christian Richter Henrike M. Müller‐Werkmeister Katharina B. Eberl

The impact of the incorporation of a non-natural amino acid (NNAA) on protein structure, dynamics, and ligand binding has not been studied rigorously so far. NNAAs are regularly used to modify proteins post-translationally in vivo and in vitro through click chemistry. Herein, structural characterisation of the impact of the incorporation of azidohomoalanine (AZH) into the model protein domain PDZ3 is examined by means of NMR spectroscopy and X-ray crystallography. The structure and dynamics of the apo state of AZH-modified PDZ3 remain mostly unperturbed. Furthermore, the binding of two PDZ3 binding peptides are unchanged upon incorporation of AZH. The interface of the AZH-modified PDZ3 and an azulene-linked peptide for vibrational energy transfer studies has been mapped by means of chemical shift perturbations and NOEs between the unlabelled azulene-linked peptide and the isotopically labelled protein. Co-crystallisation and soaking failed for the peptide-bound holo complex. NMR spectroscopy, however, allowed determination of the protein-ligand interface. Although the incorporation of AZH was minimally invasive for PDZ3, structural analysis of NNAA-modified proteins through the methodology presented herein should be performed to ensure structural integrity of the studied target.

10.1002/cbic.201700437

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Citations (16)

Observation of counterion effects and dimensionality reduction in single-crystal (EDO-TTF)2SbF6 with ultrafast electron diffraction

EPJ Web of Conferences (2019)

Lai Chung Liu Yifeng Jiang Henrike M. Müller‐Werkmeister Cheng Lü Gustavo Moriena

Femtosecond electron diffraction is used to resolve structural dynamics in single-crystal (EDO-TTF)2XF6 (X = P, Sb). The retarded and lower-dimensional dynamics of the latter illustrate the dominant role of counterion motion in stabilizing electron transfer.

Crystal (programming language)

10.1051/epjconf/201920504007

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Antimicrobial Polymers of Linear and Bottlebrush Architecture: Probing the Membrane Interaction and Physicochemical Properties

Alain M. Bapolisi Patrycja Kielb Marek Bekir Anne‐Catherine Lehnen Christin Radon

Polymeric antimicrobial peptide mimics are a promising alternative for the future management of the daunting problems associated with antimicrobial resistance. However, the development of successful antimicrobial polymers (APs) requires careful control of factors such as amphiphilic balance, molecular weight, dispersity, sequence, and architecture. While most of the earlier developed APs focused on random linear copolymers, the development of APs with advanced architectures proved to be more potent in the mimicry of antimicrobial peptides. We recently developed multivalent bottlebrush APs with improved antibacterial and hemocompatibility profiles, outperforming their linear counterparts. Understanding the rationale behind the outstanding biological activity of these newly developed antimicrobials is vital to further improving their performance. This work investigates the physicochemical properties governing the differences in activity between linear and bottlebrush architectures using diverse spectroscopic and microscopic techniques. Linear copolymers are more solvated, thermo-responsive and possess facial amphiphilicity resulting in random aggregations when interacting with liposomes mimicking E. coli-membranes. The bottlebrush copolymers adopt a more stable secondary conformation in aqueous solution in comparison to linear copolymers, conferring rapid and more specific binding mechanism to membranes. The advantageous physicochemical properties of the bottlebrush topology seem to be a determinant factor in the activity of these promising APs.

Dispersity

Linear polymer

10.26434/chemrxiv-2022-tt8v7

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TakeTwo: an indexing algorithm suited to still images with known crystal parameters

Acta Crystallographica Section D Structural Biology (2016)

Helen M. Ginn Philip Roedig Anling Kuo Gwyndaf Evans Nicholas K. Sauter

The indexing methods currently used for serial femtosecond crystallography were originally developed for experiments in which crystals are rotated in the X-ray beam, providing significant three-dimensional information. On the other hand, shots from both X-ray free-electron lasers and serial synchrotron crystallography experiments are still images, in which the few three-dimensional data available arise only from the curvature of the Ewald sphere. Traditional synchrotron crystallography methods are thus less well suited to still image data processing. Here, a new indexing method is presented with the aim of maximizing information use from a still image given the known unit-cell dimensions and space group. Efficacy for cubic, hexagonal and orthorhombic space groups is shown, and for those showing some evidence of diffraction the indexing rate ranged from 90% (hexagonal space group) to 151% (cubic space group). Here, the indexing rate refers to the number of lattices indexed per image.

Orthorhombic crystal system

10.1107/s2059798316010706

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Citations (40)

Allostery in PDZ3: Using Unnatural Amino Acids as Site-Specific Reporters in IR Spectroscopy to Probe Allosteric Pathways

Biophysical Journal (2015)

Katharina B. Eberl Henrike M. Müller‐Werkmeister Martin Essig Jens Bredenbeck

PDZ domain

10.1016/j.bpj.2014.11.1021

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CCDC 2152408: Experimental Crystal Structure Determination

The Cambridge Structural Database (2022)

Cristian Cavedon Sebastian Gisbertz Susanne Reischauer Sarah Vogl Eric Sperlich

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

10.5517/ccdc.csd.cc2b7rjw

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Synthesis and characterisation of α-carboxynitrobenzyl photocaged l-aspartates for applications in time-resolved structural biology

RSC Advances (2019)

Joanna J. Zaitseva-Doyle Anke Puchert Yannik Pfeifer Hao Yan Briony A. Yorke

We report a new synthetic route to a series of α-carboxynitrobenzyl photocaged l -aspartates for application in time-resolved structural biology.

Structural Biology

10.1039/c9ra00968j

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Citations (4)

Anisotropy in Antimicrobial Bottle Brush Copolymers and Its Influence on Biological Activity

Advanced Functional Materials (2023)

Anne‐Catherine Lehnen Sergio Kogikoski Till Stensitzki Ahmad AlSawaf Alain M. Bapolisi

Abstract Antimicrobial polymers are a promising alternative to conventional antibiotics in the fight against antimicrobial resistance. Cationic bottle brush copolymers have shown to be superior to linear topologies in previous studies. Herein, the aspect ratio of such polymers is varied creating differently shaped confined unimolecular structures with varying degrees of side chain mobility. Using reversible addition‐fragmentation chain‐transfer (RAFT) polymerization, bottle brushes are produced in a one‐pot procedure. The morphology is confirmed by atomic force microscopy. The hydrophobicity, as determined via high performance‐liquid chromatography (HPLC) analysis, is drastically influenced by the topology. Using Fourier‐transform infrared (FTIR) spectroscopy, it is found that polymers with a high side chain mobility and increased global hydrophilicity, are less hydrated, and have stronger intramolecular hydrogen bonds. A phase segregated morphology leading to unimolecular micellization is assumed. Biological tests reveal increased antimicrobial activity for such segregated polymers. Their excellent hemocompatibility results in highly selective antimicrobial polymers whose adaptability seems to be a key feature in their excellent performance. This study highlights the tremendous importance of structural control in antimicrobial polymers.

Side chain

Cationic polymerization

Chain transfer

Raft

10.1002/adfm.202312651

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Citations (5)

Structural Dynamics upon Photoexcitation in a Spin Crossover Crystal Probed with Femtosecond Electron Diffraction

Angewandte Chemie International Edition (2017)

Yifeng Jiang Lai Chung Liu Henrike M. Müller‐Werkmeister Cheng Lü Dongfang Zhang

Abstract Photoexcitation of spin crossover (SCO) complexes can trigger extensive electronic spin transitions and transformation of molecular structure. However, the precise nature of the associated ultrafast structural dynamics remains elusive, especially in the solid state. Here, we studied a single‐crystal SCO material with femtosecond electron diffraction (FED). The unique capability of FED allows us to directly probe atomic motions and to track ultrafast structural changes within a crystal lattice. By monitoring the time‐dependent changes of the Bragg reflections, we observed the formation of a photoinduced structure similar to the thermally induced high‐spin state. The data and refinement calculations indicate the global structural reorganization within 2.3 ps, as the metal–ligand bond distribution narrows during intramolecular vibrational energy redistribution (IVR) driving the intermolecular rearrangement. Three independent dynamical group are identified to model the structural dynamics upon photoinduced SCO.

Photoexcitation

Spin Crossover

Dynamics

Crystal (programming language)

10.1002/anie.201702497

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Citations (49)

2D-IR spectroscopy of azide-labeled carbohydrates in H2O

The Journal of Chemical Physics (2024)

P. Gasse Till Stensitzki Henrike M. Müller‐Werkmeister

Carbohydrates constitute one of the key classes of biomacromolecules, yet vibrational spectroscopic studies involving carbohydrates remain scarce as spectra are highly congested and lack significant marker vibrations. Recently, we introduced and characterized a thiocyanate-labeled glucose [Gasse et al., J. Chem. Phys. 158, 145101 (2023)] demonstrating 2D-IR spectroscopy of carbohydrates using vibrational probes. Here, we build on that work and test azide groups as alternative for studies of carbohydrates to expand the available set of local probes. Many common carbohydrates with different azide labeling positions, such as galactose, glucose, or lactose, are readily available due to their application in click chemistry and hence do not require additional complex synthesis strategies. In this work, we have characterized azide-labeled glucose,, galactose, acetylglucosamine and lactose in water using IR and 2D-IR spectroscopy to test their potential for future applications in studies of carbohydrate-protein interactions. Our findings indicate that their absorption profiles and vibrational dynamics are primarily determined by the labeling position on the ring. However, we also observe additional variations between samples with the same labeling position. Furthermore, we demonstrate that their usage remains feasible at biologically relevant concentrations, highlighting their potential to probe more complex biological processes, i.e., enzymatic catalysis.

10.1063/5.0225308

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