Article
Biochemistry & Molecular Biology
Giulia Giubertoni, Federico Caporaletti, Steven J. Roeters, Adam S. Chatterley, Tobias Weidner, Peter Laity, Chris Holland, Sander Woutersen
Summary: The mechanical properties of biomaterials are influenced by the interactions and conformations of their protein building blocks. Infrared spectroscopy is a commonly used method for studying molecular structures, and polarized two-dimensional infrared spectroscopy (2D-IR) is applied in this study to identify the protein secondary structures in native silk films. The results show changes in the secondary structure due to hydration, with an increase in random coil content and a decrease in helical content.
Article
Chemistry, Physical
Elisa Steinruecken, Till Wissel, Martin Brodrecht, Hergen Breitzke, Julia Regentin, Gerd Buntkowsky, Michael Vogel
Summary: A variety of amino-acid functionalized silica pores with diameters of about 6 nm were prepared, and the temperature-dependent reorientation dynamics of water in these confinements were studied. The reorientation dynamics of water strongly depends on the chemistry of the inner surfaces, with different surfaces showing rotational correlation times varying by about two orders of magnitude.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Collin G. Borcik, Isaac R. Eason, Boden Vanderloop, Benjamin J. Wylie
Summary: This study presents a cost-effective method for the enrichment of cholesterol using H-2 and C-13 labeling. The labeling pattern of cholesterol is characterized and its utility in reporting cholesterol dynamics and orientation in various environments is demonstrated. The flexibility and universality of this labeling technique allow it to be widely applied to different lipid molecules and natural products.
Article
Chemistry, Physical
Euihyun Lee, Xiao You, Carlos R. Baiz
Summary: Studies have shown that the inverted-headgroup has no effect on the carbonyl H-bond populations or the interfacial water H-bond dynamics in lipids, but disrupts the H-bond structure of carbonyl-associated waters in the DOCPe bilayer, especially within the second hydration shell.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Mounesha N. Garaga, Laura Murdock, Tawhid Pranto, Sophia Suarez, Brian C. Benicewicz, Steven G. Greenbaum
Summary: This study presents a molecular-level view of the structural changes in polybenzimidazole (PBI) membranes doped with phosphoric acid (PA) using a new membrane fabrication technique. The modified PA doped membranes showed unprecedented ionic conductivity at high temperatures, comparable to the starting PBI gel membranes prepared by the commonly used PPA process, while also exhibiting enhanced mechanical properties. Multiple nuclear magnetic resonance (NMR) techniques were used to characterize the structure and dynamics of the modified film and the original gel PBI membranes, revealing an increase in proton diffusivity and strong binding between the phosphate groups and the PBI polymer backbone in the modified membrane.
JOURNAL OF POWER SOURCES
(2023)
Article
Chemistry, Physical
Kris Strunge, Tucker Burgin, Thaddeus W. Golbek, Steven J. Roeters, Jim Pfaendtner, Tobias Weidner
Summary: α-synuclein folds into a defined secondary structure at the air-water interface, promoting its aggregation and fibrillation. Understanding the role of hydrophobic surfaces in this process is important for studying severe brain disorders such as Parkinson's disease.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Rafael L. Schoch, Gilad Haran, Frank L. H. Brown
Summary: Recent single-molecule measurements have observed dynamic lipid-lipid correlations in membranes with high spatial and temporal resolution. Theoretical expressions are derived to infer experimentally measurable correlations from the diffusion matrix. The theoretical predictions match well with Brownian dynamics simulations of experimental measurements. Membrane protein diffusion measurement, along with lipid diffusion measurements, could help resolve experimental ambiguities in certain black lipid membranes.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Biophysics
Ladislav Bartos, Ivo Kabelka, Robert Vacha
Summary: This study demonstrates that transmembrane proteins with hydrophilic patches can enhance the translocation of amphiphilic peptides by stabilizing them in the membrane. However, optimal amphiphilicity is critical as peptides can become overstabilized in the transmembrane state, hindering their dissociation from proteins and limiting translocation.
BIOPHYSICAL JOURNAL
(2021)
Article
Pharmacology & Pharmacy
Claudia Herrera-Leon, Francisco Ramos-Martin, Hassan El Btaouri, Viviane Antonietti, Pascal Sonnet, Laurent Martiny, Fabrizia Zevolini, Chiara Falciani, Catherine Sarazin, Nicola D'Amelio
Summary: This study demonstrates that specific arrangements of amino acids in anticancer peptides significantly impact their activity, with changes in amino acid order or substitutions in key motifs affecting the efficacy against cancer cell lines. The study also reveals that the insertion capability in cancer-mimicking membranes is crucial for the activity of the peptides, with specific amino acids playing a role in anchoring and insertion into these membranes.
Article
Chemistry, Medicinal
Ryuhei Harada, Rikuri Morita, Yasuteru Shigeta
Summary: The free-energy profile of a compound is crucial in evaluating membrane permeation and can be calculated using molecular dynamics simulations. However, existing methods often fail to sample rare events in membrane permeation accurately. In this study, a hybrid conformational search method combining rare-event sampling methods and Markov state models was proposed to calculate the free-energy profiles and membrane permeability of seven compounds with good correlation to experimental measurements.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Polymer Science
Amulya K. Pervaje, Melissa A. Pasquinelli, Saad A. Khan, Erik E. Santiso
Summary: In this paper, a multiscale approach is presented to predict the mechanical properties of polypropylene fibers based on chemical and physical characteristics. The method relies on validation with experimental data and utilizes molecular simulations and neural network models to predict parameters for a chosen constitutive model.
Article
Chemistry, Physical
Giovanni Bressan, Jasper J. van Thor
Summary: This study presents an analytical expression to describe the orientational part of molecular response, which is evaluated for different conditions. Results obtained in the strong-field conditions suggest that careful analysis of two-dimensional spectroscopic experimental data should include laser pulse intensity considerations.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Olga Yu. Selyutina, Anna V. Mastova, Nikolay E. Polyakov
Summary: Q1 can form chelate complexes with transition metal ions, enhancing its penetration ability in the cell membrane, and it can affect lipid mobility in the bilayer, which is important for understanding Q1's biological activity.
Article
Multidisciplinary Sciences
You-jin Jung, Hyoseok Kim, Hae-Kap Cheong, Yong-beom Lim
Summary: The authors demonstrate a strategy to enhance the magnetic responsiveness of self-assembled peptide nanostructures by combining the concepts of perfect alpha-helix and rod-coil supramolecular building blocks. They develop a monomeric, nonpolar, and perfect alpha-helix and use it as the rod block of rod-coil amphiphiles for fabricating responsive assemblies.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Adam S. Chatterley, Thaddeus W. Golbek, Tobias Weidner
Summary: This study demonstrates a new approach to measuring the structure of proteins at aqueous interfaces using two-dimensional infrared (2D-IR) spectroscopy of protein stabilized emulsions. By measuring the 2D-IR spectra of emulsions stabilized by model peptides, the folding of the peptides at the interface was clearly observed. This method provides detailed information about the interfacial protein structure, which is crucial for understanding their function.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Immunology
Christian Mink, Erik Strandberg, Parvesh Wadhwani, Manuel N. Melo, Johannes Reichert, Irene Wacker, Miguel A. R. B. Castanho, Anne S. Ulrich
Summary: BP100 is a short, designer-made membrane-active peptide with antimicrobial, cell-penetrating, and fusogenic properties. Its amphipathic helical structure resembles that of pore forming magainin-like peptides, showing high antimicrobial activity.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Oleg Babii, Sergii Afonin, Christian Diel, Marcel Huhn, Jennifer Dommermuth, Tim Schober, Serhii Koniev, Andrii Hrebonkin, Alexander Nesterov-Mueller, Igor V. Komarov, Anne S. Ulrich
Summary: Chemical modification of a bicyclic peptide scaffold led to the development of photoswitchable inhibitors based on diarylethene for serine protease Bos taurus trypsin 1 (T1). These inhibitors exhibited low nanomolar K-i values and a 20-fold activity modulation under irradiation. The study also demonstrated the feasibility of manipulating enzyme activity in time and space.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Nithin Suryadevara, Ansgar Pausch, Eufemio Moreno-Pineda, Asato Mizuno, Jochen Buerck, Ananya Baksi, Tim Hochdoerffer, Ivan Salitros, Anne S. Ulrich, Manfred M. Kappes, Volker Schuenemann, Wim Klopper, Mario Ruben
Summary: Enantiomerically pure Fe(II) grid complexes were successfully prepared by designing novel chiral ligands, allowing for the fabrication of magneto-chiral molecular devices. The chiral resolution of these complexes enables controlled programmable separation before synthesis. The experimental and calculated CD spectra showed good agreement, confirming the enantiomeric purity of the complexes.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Parvesh Wadhwani, Saiguru Sekaran, Erik Strandberg, Jochen Burck, Archana Chugh, Anne S. Ulrich
Summary: The seven peptides from the latarcin family fold into amphiphilic alpha-helices in the presence of lipids, with different levels of aggressiveness and selectivity in antimicrobial activity. Ltc2a stands out as the most aggressive peptide, whereas Ltc1, Ltc3a, Ltc4a, and Ltc5a show efficient and selective antibacterial effects. The other two peptides, Ltc6a and Ltc7, do not have strong antimicrobial activities but can disturb model bilayers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Polymer Science
Shouliang Nie, Karl-Friedrich Ratzsch, Stephan L. Grage, Jonas Keller, Anne S. Ulrich, Jorge Lacayo-Pineda, Manfred Wilhelm
Summary: The cross-linking process of natural rubber was studied for the first time using a combination of rheology and time-domain NMR methods. It was found that the conformational flexibility of network chains in natural rubber is affected by the efficiency of vulcanization.
Article
Chemistry, Multidisciplinary
Sergii Afonin, Serhii Koniev, Laetitia Preau, Masanari Takamiya, Alexander Strizhak, Oleg Babii, Andrii Hrebonkin, Vasyl G. Pivovarenko, Margitta Dathe, Ferdinand le Noble, Sepand Rastegar, Uwe Straehle, Anne S. Ulrich, Igor Komarov
Summary: This study successfully utilized fluorescent labeling of peptides with an amino acid bearing a fluorophore, demonstrating the importance of fluorescent labeling in studying peptide activity. The behavior of labeled peptides was observed in human cells and zebrafish embryos using various techniques.
FRONTIERS IN CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Monica Gutierrez-Salazar, Eduardo Santamaria-Aranda, Louise Schaar, Jesus Salgado, Diego Sampedro, Victor A. Lorenz-Fonfria
Summary: The study presents a 24-residue hydrophobic α-helical polypeptide coupled with an azobenzene photoswitch, exhibiting a light-controlled TM/MI equilibrium in hydrated lipid bilayers. FTIR spectroscopy confirms the folding of trans KCALP-azo as a TM alpha-helix. Photoisomerization of the azobenzene moiety induces a reversible TM-to-MI transition in KCALP-azo, with cis KCALP-azo existing in a mixture of TM and MI states.
Article
Biochemistry & Molecular Biology
Stephan L. Grage, Sergii Afonin, Marco Ieronimo, Marina Berditsch, Parvesh Wadhwani, Anne S. Ulrich
Summary: The lateral pressure profile, an important physical property of lipid bilayers, can be manipulated and probed using peptides residing in different regions of the membrane, according to this study.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Igor Komarov, Ganna Tolstanova, Halyna Kuznietsova, Natalia Dziubenko, Petro Yanchuk, Lydia Y. Shtanova, Stanislav P. Veselsky, Liudmyla Garmanchuk, Nataliia Khranovska, Oleksandr Gorbach, Taisa Dovbynchuk, Petro Borysko, Oleg Babii, Tim Schober, Anne S. Ulrich, Sergii Afonin
Summary: The study analyzed the efficacy of a photoswitchable cytotoxic peptide LMB040 on chemically induced hepatocellular carcinoma model in immunocompetent rats, finding that initial application of a less toxic form followed by in vivo photoconversion led to higher overall survival of the animals and enhanced immune response compared to untreated animals.
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Beibei Meng, Stephan L. Grage, Oleg Babii, Masanari Takamiya, Neil MacKinnon, Tim Schober, Illia Hutskalov, Omar Nassar, Sergii Afonin, Serhii Koniev, Igor Komarov, Jan G. Korvink, Uwe Straehle, Anne S. Ulrich
Summary: A labeling strategy for in vivo F-19-MRI based on highly fluorinated, short hydrophilic peptide probes, is developed. These probes are functionalized further by a fluorophore and an alkyne moiety for bioconjugation. The design of the peptide probes ensures low cytotoxicity and high serum stability. The performance of these probes in F-19-MRI is demonstrated and they are found to exhibit high stability and long circulation times in living zebrafish embryos. Overall, these peptide probes are suitable for in vivo F-19-MRI applications.
Article
Biochemistry & Molecular Biology
Fabian Schweigardt, Erik Strandberg, Parvesh Wadhwani, Johannes Reichert, Jochen Buerck, Haroldo L. P. Cravo, Luisa Burger, Anne S. Ulrich
Summary: Amphipathic peptides exhibit antibiotic properties by permeabilizing cell membranes. KL peptides form amphipathic beta-strands in the presence of lipid bilayers and kill bacteria in a unique length-dependent manner. Experimental results demonstrate that KL peptides with 10-12 amino acids exhibit the best antimicrobial activity and low hemolytic side effects. The study suggests that the membrane disruption by KL peptides is achieved through a carpet mechanism.
Article
Chemistry, Physical
Frauke Greil, Rajalakshmi Punampalam, Torsten H. Walther, Stefan Heissler, Anne S. Ulrich
Summary: A novel solid phase of water stable at room temperature was believed to be accessible from hydrophilic surfaces by repeated perturbation of interfacial layers. However, a detailed biological and biochemical analysis revealed that the observed phenomena were likely due to accumulation of microbiological and organic contaminants, rather than a new solid phase of water. The same analysis also found that the presumed stable water aggregates in the lyophilized solid material consisted mainly of a conglomerate of bacteria, algae, and synthetic materials.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Meeting Abstract
Biophysics
Erik Strandberg, Fabian Schweigardt, Parvesh Wadhwani, Jochen Buerck, Anne S. Ulrich
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Parvesh Wadhwani, Saiguru Sekaran, Erik Strandberg, Jochen Burck, Archana Chugh, Anne S. Ulrich
BIOPHYSICAL JOURNAL
(2022)
Article
Chemistry, Physical
Vladimir Kubyshkin, Jochen Burck, Oleg Babii, Nediljko Budisa, Anne S. Ulrich
Summary: Circular dichroism is a conventional method for studying the secondary structures of peptides and proteins. The polyproline-II helix, while not exhibiting strictly conserved spectroscopic appearance, is significantly influenced by the surrounding solvent environment. Changes in solvation can lead to shifts and variations in the circular dichroism spectra, with new features potentially emerging in nonpolar environments. Additionally, the transition to a transmembrane state in isotropic liposomes is correlated with specific spectral changes, indicating the importance of considering the solvent environment in assessing circular dichroism spectra.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)