Article
Biochemistry & Molecular Biology
Daniel Pushparaju Yeggoni, Shreya Dubey, Yusuf Zamal Mohammad, Aparna Rachamallu, Rajagopal Subramanyam
Summary: The study investigated the interaction between the phytochemical stigmasterol and human serum albumin under physiological conditions, revealing anti-inflammatory and anti-cancer properties of stigmasterol. Stigmasterol bound to a specific subdomain of HSA, altering the protein's secondary structure. Molecular docking and dynamic simulation further supported the binding mechanism between HSA and stigmasterol.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Masaki Miyaguchi, Yoichi Nakanishi, Andres D. Maturana, Kimihiko Mizutani, Tomoaki Niimi
Summary: This study reveals the changes in the interaction between the Robo2 ectodomain and NELL1/2 under acidic conditions, as well as the impact of alternative splicing isoforms of Robo2 on the conformation of the hairpin-like structure and the binding affinity with NELL1/2.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Chemistry, Physical
Roy Aerts, Jonathan Bogaerts, Wouter Herrebout, Christian Johannessen
Summary: This study compares the VCD and ROA spectra of the antibiotic glycopeptide vancomycin in order to determine its conformational ensemble. The results indicate that ROA is highly suitable for this task, while VCD is too sensitive to minor conformational changes, leading to unreliable analysis.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Applied
Qimeng Yao, Jiaqi Ma, Xuemin Chen, Guanghua Zhao, Jiachen Zang
Summary: The pigment astaxanthin, a carotenoid, is widely used in various industries. However, its low stability and poor water solubility can be overcome by binding it to proteins, which improves stability and bioavailability. This review summarizes multiple examples of protein-astaxanthin interactions, providing insights for carotenoid stabilization and color regulation.
Article
Biochemistry & Molecular Biology
Laura Morbiato, Celeste Quaggia, Luca Menilli, Chiara Dalla Torre, Antonio Barbon, Marta De Zotti
Summary: Peptaibols are proteolysis-resistant, membrane-active peptides with stable helical 3D structures. Medium-length peptaibols are of interest for studying peptide-membrane interaction. Electron paramagnetic resonance (EPR) is used for this purpose, but it requires synthesis of spin-labeled medium-length peptaibols.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Polymer Science
Fengyi Cao, Genxing Zhu, Meng Song, Xiaoli Zhao, Gangqing Ma, Mengqing Zhang
Summary: This study investigated the self-assembly mechanism of antimicrobial peptides and designed five PAF26 peptide derivatives with different numbers of aromatic amino acids. Characterizations using various techniques revealed that the number of aromatic amino acids affected the peptide's hydrogen bonding and aromatic stacking interactions, leading to significant differences in the secondary conformation and microscopic structure.
Article
Chemistry, Physical
Daocheng Lin, Na Li, Chengzhi Wei, Zhanzhong Wang
Summary: This study investigated the use of Ionic liquids (ILs) as additives to regulate lysozyme crystallization. It was found that the addition of ILs induced changes in the solution structure and increased the content of beta-sheet structures in lysozyme. Molecular simulation and docking analysis further revealed the binding between ILs and lysozyme molecules, suggesting that ILs can stably interact with lysozyme in solution.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Multidisciplinary
Laia Miret-Casals, Sander van de Putte, Dorien Aerssens, Julien Diharce, Pascal Bonnet, Annemieke Madder
Summary: In this study, a coiled-coil peptide dimer was used as a model system to investigate the reactivity of furan. Novel cross-link partners of furan warheads for site-specific cross-linking were discovered, and it was demonstrated that the activation of furan could lead to covalently connected coiled-coil motifs. The study also revealed the reaction of the activated furan warhead with cysteine and tyrosine, expanding the versatility of furan cross-link methodology.
FRONTIERS IN CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Liwei Chang, Alberto Perez
Summary: AlphaFold has revolutionized structural biology by accurately predicting structures of proteins. Researchers have developed a competitive binding assay using AlphaFold to predict structures of receptors in the presence of multiple peptides. The assay can identify peptides with higher affinity and distinguish them from other peptides with statistical significance. Experimental validation on six protein receptors shows that the assay is best suited for medium to strong peptide binders with stable secondary structures.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Takatsugu Kosugi, Masahito Ohue
Summary: Over 930,000 protein-protein interactions (PPIs) have been identified, but targeting PPIs with conventional small molecules is challenging. A newly developed cyclic peptide complex offset, combined with AlphaFold2, can accurately predict the structure of target protein-cyclic peptide complexes and enable the design of putative cyclic peptide sequences targeting PPI.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Suzanne Morsch, Charlie R. Wand, Seyedgholamreza Emad, Stuart Lyon, Flor Siperstein, Mikhail Malanin, Julia Muche, Anja Caspari, Astrid Drechsler, Klaus-Jochen Eichhorn, Simon Gibbon
Summary: The hypothesis of this study is that interphase properties in composites, adhesives, and protective coatings can be predicted based on the interfacial interactions between polymeric precursor molecules and the inorganic surface during network formation. The researchers applied conventional analysis techniques, atomic force microscopy coupled with infrared (AFM-IR), and molecular dynamics simulations to investigate the molecular interactions and properties of nanocomposite specimens. The findings revealed the presence of under-cured interphase regions and the excess of epoxy functionality near the particle surfaces, and demonstrated the driving force for molecular orientation and raised Tg values in the goethite composite samples.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Yingying Qi, Daoning Zhou, Julian L. Kessler, Rongmao Qiu, S. Michael Yu, Gang Li, Zhao Qin, Yang Li
Summary: Collagen, as the most abundant human repeat protein, features a hallmark triple-helix structure influenced by the terminal repeats. Studies have shown that collagen-mimetic peptides with different terminal repeats may exhibit distinct end structures and stabilities.
Article
Biochemistry & Molecular Biology
Woong-Hee Shin, Keiko Kumazawa, Kenichiro Imai, Takatsugu Hirokawa, Daisuke Kihara
Summary: The driving mechanisms of many biological functions in a cell involve physical interactions between proteins. Protein-protein interactions (PPIs) also play a significant role in disease development, making them promising therapeutic targets in the pharmaceutical industry. This study introduces a novel method called protein-protein interaction-Surfer, which uses a three-dimensional Zernike descriptor (3DZD) to compare and quantify the similarity of local surface regions of PPIs. The performance of protein-protein interaction-Surfer was evaluated using datasets of PPIs, demonstrating its ability to identify similar potential drug binding regions without sequence and structure similarity.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Yuntao Li, Jinrong Yang, Xiao He
Summary: Protein binding onto a metal surface, such as gold nanoparticles, is important for biomedical applications. In this study, molecular dynamics simulations were used to investigate the adsorption process and conformational behavior of a collagen repetitive unit on a gold surface. The results provide insights into improving the design of protein-gold materials for medicinal purposes.
NANOSCALE ADVANCES
(2023)
Article
Chemistry, Physical
Kevin Scholten, Christian Merten
Summary: Thioureas are commonly used in supramolecular anion recognition. This research investigates a chiral tris(thiourea) compound and reveals the ambiguity in its conformational preferences in complexes. The study shows that the computational results depend on the computational level and relative energies chosen for the calculations.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Tino P. Golub, Ayham H. Abazid, Boris J. Nachtsheim, Christian Merten
Summary: In this study, vibrational circular dichroism (VCD) spectroscopy was used as an experimental technique to verify DFT-calculated chiral iodane structures. The research revealed that an undescribed cationic chiral iodane was the most common intermediate under oxidative conditions, with significant intramolecular interactions and no significant interactions with potential anionic ligands. Aggregation of the substrates resulted in the formation of a non-coordinating anionic hydrogen bonded complex.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Tino P. Golub, Malte Fessner, Elric Engelage, Christian Merten
Summary: In this study, the dynamic stereochemistry of a biphenyl-2,2'-bis(proline amide) catalyst in weakly and strongly hydrogen bonding solvents was characterized. The preferred axial stereochemistry of the catalyst was found to be determined by solute-solvent interactions, with explicit consideration of solvation with DMSO molecules being essential for accurate prediction. The study also investigated the stereochemistry of the enamines and imidazolidinones formed in the reaction, demonstrating that the VCD spectra analysis can directly deduce the stereochemistry without the need for further detailed analysis of NMR spectra. This study highlights the use of VCD spectroscopy for in situ characterization of intermediates in asymmetric catalysts.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Michael Kemper, Deborah A. Drost, Elric Engelage, Christian Merten
Summary: This article investigates the strength and role of a special kind of hydrogen bond called dihydrogen bond (DHB) in the self-aggregation of amine-borane adducts. The study shows that the stereochemistry at the nitrogen significantly influences the interaction enthalpy, suggesting that N-chiral amine boranes can be used to fine-tune the formation dynamics of assemblies in supramolecular chemistry.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Michael Kemper, Sven Reese, Elric Engelage, Christian Merten
Summary: The stabilization of chiral propeller conformations in triaryl compounds is challenging due to low racemization barriers. However, the incorporation of point-chiral alkylether chains and subsequent locking of the structure with ammonia can induce chiral conformational preferences in triaryl boranes. A four-point interaction involving Lewis-adduct formation and three hydrogen bonds was proposed as the stabilizing mechanism. DFT calculations predicted no significant preference for propeller handedness, but vibrational circular dichroism spectroscopy revealed a measurable excess of one propeller handedness. The steric demand of the amine was found to play a key role in the induction process and preventing blade rotations.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
V. U. Bhaskara Rao, Caiming Wang, Daniel P. Demarque, Corentin Grassin, Felix Otte, Christian Merten, Carsten Strohmann, Charles C. J. Loh
Summary: Site-selective functionalization is a significant synthetic strategy in organic synthesis. Chiral catalysis has been used to control the site selectivity in complex carbohydrate functionalizations, providing new routes to biologically relevant glycosides. However, the availability of robust catalytic systems to overcome multiple stereoselectivity challenges remains limited. In this study, we present a synergistic chiral Rh(I)- and organoboron-catalysed protocol for the synthesis of challenging but biologically relevant arylnaphthalene glycosides. Our method employs chiral Rh(I) catalysis for site-selective carbohydrate functionalization and demonstrates the utility of boronic acid as a compatible co-catalyst. The success of our method depends on the judicious choice of a suitable organoboron catalyst, and we show that multiple aspects of stereocontrol are simultaneously operative.
Article
Chemistry, Physical
Nora M. Kreienborg, Qin Yang, Corina H. Pollok, Julien Bloino, Christian Merten
Summary: The inclusion of anharmonicity in vibrational spectral analysis is mainly limited to small molecular systems. This limitation is due to the computational costs associated with larger systems and the lack of clear criteria for the identification of resonances. However, recent advances in vibrational perturbation theory (VPT2) have made it possible to handle resonance problems more transparently. This study demonstrates the importance of experimental benchmarking and highlights the mutual stimulation between experimental techniques and computational models.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Jie Liu, Shubhadip Mallick, Yusheng Xie, Corentin Grassin, Belen Lucas, Beate Schoelermann, Axel Pahl, Rebecca Scheel, Carsten Strohmann, Christoph Protzel, Thorsten Berg, Christian Merten, Slava Ziegler, Herbert Waldmann
Summary: Oxindoles and iso-oxindoles are natural product-derived scaffolds that inspire the design and synthesis of novel biologically relevant compounds. The spirocyclic connection of oxindoles with iso-oxindoles has not been explored by nature, but holds potential to create structurally related compounds with unique bioactivity. Therefore, efficient synthesis methods and identification of their cellular targets are highly desired.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Mechanics
Erik Willmann, Benjamin Boll, Moritz Scheel, Robert Horst Meissner, Bodo Fiedler
Summary: Estimating the damage state of composites is crucial in understanding the complex damage behavior of CFRP materials. This study investigated the effects of matrix cracks and different damage types on the vibro-acoustic modulation behavior of CFRP specimens under fatigue loading. The results showed that stiffness-reducing inter-fiber fractures and large-scale delaminations can be detected regardless of the laminate layup.
COMPOSITE STRUCTURES
(2023)
Article
Polymer Science
Niklas Neumann, Sascha Thinius, Gideon Abels, Andreas Hartwig, Katharina Koschek, Laura Boskamp
Summary: A synthesis approach was investigated for crosslinkable hyperbranched prepolymers with adjustable degrees of methylation and methacrylation, achieving full conversion of hydroxyl groups. The substitution degrees of methacrylate could be adjusted by catalyzed esterification using predefined partially methylated polyglycerol-based precursors. The combination of methacrylic anhydride, triethylamine, and 4-dimethylaminopyridine was proven effective for complete conversion of primary and secondary hydroxyl groups. NMR, IR, and Raman spectroscopy confirmed the insertion of methacrylic crosslinking groups in the polymeric backbone. The photopolymerization of obtained prepolymers resulted in higher crosslink density, stiffness, and glass transition temperature with increasing methacrylate content.
Article
Chemistry, Multidisciplinary
Amir Kotobi, Lucas Schwob, Gregor B. Vonbun-Feldbauer, Mariana Rossi, Piero Gasparotto, Christian Feiler, Giel Berden, Jos Oomens, Bart Oostenrijk, Debora Scuderi, Sadia Bari, Robert H. Meissner
Summary: The authors accurately interpret and reproduce the experimental infrared spectra of a model peptide in the gas phase using a combination of replica-exchange molecular dynamics simulations, machine learning, and ab initio calculations. They evaluate the possibility of averaging representative structural contributions to obtain an accurate computed spectrum by partitioning the conformational phase space into subensembles of similar conformers and calculating the IR contribution of each representative conformer. Improvements achieved by decomposing clusters containing similar conformations into smaller subensembles provide strong evidence for the importance of assessing the conformational landscape and hydrogen bonding in deciphering important fingerprints in experimental spectroscopic data.
COMMUNICATIONS CHEMISTRY
(2023)
Article
Materials Science, Multidisciplinary
Vitus Hupp, Bernhard Schartel, Kerstin Flothmeier, Andreas Hartwig
Summary: This paper investigates the interaction between adhesive tapes and bonded materials during burning and the impact of flame retardancy on the burning behavior of adhesive tapes. It shows that the choice of carrier and substrates in bonds has the greatest influence on fire properties, changing the peak of heat release rate and the maximum average rate of heat emission by up to 25%.
FIRE AND MATERIALS
(2023)
Article
Engineering, Mechanical
Benjamin Boll, Lennart Dorendorf, Peter Oppermann, Erik Willmann, Bodo Fiedler, Bernd-Christian Renner, Marcus Rutner, Robert Horst Meissner
Summary: The vibroacoustic modulation (VAM) is a nonlinear ultrasonic testing method that utilizes the modulation of a high-frequency/low-amplitude probe wave with a low-frequency/high-amplitude pumping vibration, resulting in high sensitivities to damages in the structure. A synthetic generation of the VAM signal using probe measurements acquired at different stress levels is proposed, reducing the sensing requirements and decoupling VAM from the need for a constant recurrent frequency and amplitude of the natural vibration. This method opens the possibility of applying VAM to assess the structural health of complex structures.
MECHANICAL SYSTEMS AND SIGNAL PROCESSING
(2023)
Article
Chemistry, Multidisciplinary
Dan Wang, Milena Lippmann, Johannes Gaeding, Anita Ehnes, Dmitri Novikov, Robert Meissner, Oliver H. Seeck
Summary: In this work, the ordering structures of non-polar carbon tetrachloride liquid compressed to nano-scales between parallel substrates are studied. The theoretical considerations suggest that the confined parallel substrates induce orientational ordering of non-polar molecules. Molecular dynamic simulations demonstrate the relations between various ordered structures and the confined gap size. The experimental studies provide direct support to the suggested molecular orientation.
Article
Materials Science, Multidisciplinary
Kyriakos Karakyriazis, Vanessa Luehrs, Sebastian Stoesslein, Ingo Grunwald, Andreas Hartwig
Summary: Schiff base hydrogels have gained attention in the field of biomedical applications due to their reversible imine bonds and degradation properties. Commonly used multifunctional amines with low water solubility include bovine serum albumin and chitosan. Glutaric aldehyde, a toxic substance, is often used for Schiff base formation. In this study, a two-component Schiff-base-crosslinked hydrogel based on aminoterminated hyperbranched polyglycerol (hPG-NH2) and polyethyleneglycol dialdehyde (PEG-DA) was developed, showing promising mechanical properties. The hydrogels' mechanical properties were characterized using a texture analyzer, investigating the impact of solid content, component ratio, and pH on gel properties.
MATERIALS ADVANCES
(2023)
Article
Chemistry, Physical
Tim Wuerger, Linqian Wang, Darya Snihirova, Min Deng, Sviatlana Lamaka, David A. Winkler, Daniel Hoche, Mikhail L. Zheludkevich, Robert H. Meissner, Christian Feiler
Summary: This study evaluates the robustness and predictive performance of two QSPR models and proposes a multi-objective optimization method to accelerate the discovery of advanced battery systems.
JOURNAL OF MATERIALS CHEMISTRY A
(2022)
