Article
Biochemistry & Molecular Biology
Kritika Kumari, Marina Warepam, Aniket Kumar Bansal, Tanveer Ali Dar, Vladimir N. Uversky, Laishram Rajendrakumar Singh
Summary: TMAO is a significant metabolite derived from various organic compounds, with diverse biological functions in humans. Studies have shown its crucial impact on protein folding and cell cycle, potentially leading to protein misfolding and the development of related diseases.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Plant Sciences
Zsolt Gulyas, Blanka Moncsek, Kamiran Aron Hamow, Pal Straner, Zoltan Tolnai, Eszter Badics, Norbert Incze, Eva Darko, Valeria Nagy, Andras Perczel, Laszlo Kovacs, Vilmos Soos
Summary: This study characterizes D27-LIKE1 in Arabidopsis and highlights its important physiological and enzymatic functions related to carotenoids. The results show that D27-LIKE1 has multi-substrate specificity and may regulate carotenoid cis pools and the biosynthesis pathways of strigolactones and ABA.
Article
Biochemistry & Molecular Biology
Fanni Sebak, Janos Szolomajer, Nandor Papp, Gabor K. Toth, Andrea Bodor
Summary: The type of neighboring amino acids, especially aromatic and positively charged sidechains, has been found to affect the cis-Pro content. These findings can assist in the design of protein regions with specific cis-Pro content and contribute to a better understanding of the roles and functions of IDPs.
FRONTIERS IN BIOSCIENCE-LANDMARK
(2023)
Article
Chemistry, Physical
Junggil Kim, Sang Kyu Kim
Summary: The photofragmentation dynamics of the cis and trans isomers of 1,2-dibromoethylene were studied using multiphoton excitation, revealing isomer-specific reactivity. The Br-2(+) product ion from the cis isomer preferentially originates from a specific photon energy for unimolecular reactions, while anisotropic kinetic energy components of Br+ and Br-2(+) from the trans isomer appear at higher photon energies. The transition dipole moment of the strongest oscillator strength indicates the orientation of the transition for the trans and cis isomers, leading to fast anisotropic components in the product distributions.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Fanni Sebak, Peter Ecsedi, Wolfgang Bermel, Burkhard Luy, Laszlo Nyitray, Andrea Bodor
Summary: This study introduces two new NMR experiments to identify proline cis/trans isomers in proteins, detecting minor conformers present in 4-15%, and analyzes the impact of CK2 phosphorylation on the cis/trans-proline equilibrium. Statistical analysis indicates that the amino acid type also affects the distribution of cis/trans-proline.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Applied
Jolanta Konieczkowska, Mariola Siwy
Summary: This work investigates the thermal cis-trans isomerization in solid-state for poly(ether imide)s and poly(ester imide)s with azobenzene or azo pyridine moieties. The study explores the relationship between various material aspects such as polyimide structure, molar mass, azo dye content, d-spacing value, polymer film thickness, and thermal cis-trans isomerization. The reversibility of the trans-cis-trans reaction was studied using different irradiation wavelengths. This is the first comprehensive article on solid-state cis-trans isomerization for azo polyimides.
Article
Physics, Fluids & Plasmas
Izabela Sliwa, Pavel Maslennikov, Alex Zakharov
Summary: A molecular model is proposed to describe the effective anchoring energy of a liquid crystal system. The model explains the mechanism behind the anchoring transition caused by structural changes in the photosensitive azobenzene layer.
Article
Chemistry, Physical
Abhigyan Sengupta, Lorenz E. Rognoni, Ulrich Merkel, Gabriel Zoldak, Matthias Rief
Summary: Prolyl isomerization catalyzed by the PPIase enzyme plays a crucial role in cellular signaling and molecular timing. This study demonstrates a 25-fold acceleration of trans-cis isomerization rate and a stabilization effect on the cis-isomer by SlyD in a single-molecule experiment with FlnA20 protein.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biochemical Research Methods
Xiang Chen, Justin M. Mirazee, Katarzyna A. Skorupka, Hiroshi Matsuo, Philippe Youkharibache, Naomi Taylor, Kylie J. Walters
Summary: T cells engineered to express CARs have transformative therapeutic possibilities. CD8 alpha hinge exhibits structural plasticity and local structural motifs that are important for relaying and amplifying antigen-binding effects.
JOURNAL OF MAGNETIC RESONANCE
(2022)
Article
Polymer Science
Yurachat Janpatompong, Kamil Suwada, Michael L. Turner, Guillaume De Bo
Summary: Understanding the stability of conjugated polymers towards mechanical stimuli is crucial for optimizing their use in electronic and optoelectronic devices. Mechanochemistry is a field that aims to control mechanical forces for chemical changes, and it can also be used to study the stability of conjugated polymers. Ultrasonication is a technique that can be used to test the mechanical integrity of phenylenevinylene block copolymers and demonstrate their stability to mechanical forces, making them suitable for flexible organic electronics.
Article
Chemistry, Multidisciplinary
Patrick M. Killoran, George S. M. Hanson, Sanne J. M. Verhoork, Madeleine Smith, Davide Del Gobbo, Lu-Yun Lian, Christopher R. Coxon
Summary: A method using 4-fluorophenylalanine as a reporter group for F-19 NMR was developed to measure the conformational status of peptidylprolyl bonds in peptide models. This method was applied to study the prolyl bond status in pentapeptide models of the intrinsically disordered region of alpha-synuclein. It was demonstrated that F-19 NMR is a valuable tool for studying proline isomerism under different conditions.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Zhao Gao, Fei Yan, Lulu Shi, Yifei Han, Shuai Qiu, Juan Zhang, Feng Wang, Si Wu, Wei Tian
Summary: Photoisomeric supramolecular assemblies have been a hot topic in recent years. In general, the photoisomerization process from irregular aggregates to regular assemblies leads to the destruction of assemblies. However, through the conversion from planar to nonplanar photoisomer, a converse sol-to-gel transition has been achieved. A well-designed acylhydrazone-linked monomer, with imine for trans-cis interconversion and amide for intermolecular hydrogen bonding, is used to drive the photoisomerization-induced self-assembly. The counterintuitive sol-to-gel transition is attributed to the partial trans->cis photoisomerization of acylhydrazone, which changes the stacking mode of monomers. This reversible phase transition also holds potential for miniature materials, as demonstrated in the formation of in situ valves in microfluidic devices.
Article
Biochemistry & Molecular Biology
Huan-Hua Xu, Liang Yang, Ming-Xia Tang, An-Ping Ye, Bo-Dan Tu, Zhen-Hong Jiang, Jian-Feng Yi
Summary: This study found that the degree of isomerization of lobeline has a significant impact on its respiratory excitatory effects. The respiratory excitatory effect was significantly reduced with the administration of trans-lobeline injections compared to cis-lobeline injections. The study also discovered that isomerization is a one-way reaction catalyzed by temperature, with pH as the key factor. Lobeline, as a nonselective antagonist with high affinity for nicotinic acetylcholine receptors, has shown potential in the treatment of addiction and nervous system disorders.
Article
Chemistry, Physical
Taposi Chatterjee, Ersad Hossain, Samim Khan, Sourav Roy, Saikh Mohammad Wabaidur, Md Ataul Islam, Seikh Mafiz Alam, Mohammad Hedayetullah Mir
Summary: A Zn(II) based two-dimensional metal-organic framework (MOF) 1 has been synthesized by a slow diffusion method. Compound 1 exhibits photoluminescence property and undergoes in situ cis,cis- to cis,trans-isomerization under visible light. Non-covalent interactions within compound 1 have been investigated using Hirshfeld surface analysis.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Article
Chemistry, Multidisciplinary
Xia Yu, Yuzhang Meng, Hao Zhang, Junbo Guo, Shixian Wang, Hui Li, Jun Hu, Min-Hui Li
Summary: This study synthesized and characterized two pure stereoisomers, trans- and cis-TPE-2GA, which exhibited different aggregation-induced emission, self-assembly properties, and crystallinity. The cis-TPE-2GA showed mechano-chromic properties and a lower energy gap, higher quantum yield, and longer lifetime compared to trans-TPE-2GA, explaining their differences in fluorescence and mechano-chromic properties.
Review
Chemistry, Multidisciplinary
Marko Grabarics, Maike Lettow, Carla Kirschbaum, Kim Greis, Christian Manz, Kevin Pagel
Summary: Cells encode information in biopolymers, but little is known about the sugar code and biological roles of these molecules. The complexity of carbohydrate structures has made their analysis challenging, but recent advances in mass spectrometry have revolutionized glycan analysis.
Article
Chemistry, Analytical
Priyanka Bansal, Ahmed Ben Faleh, Stephan Warnke, Thomas R. Rizzo
Summary: Glycans, present on the surface of cells in all living organisms, play crucial roles in biological processes. However, the complexity of their isomeric structures poses challenges for structural characterization. Researchers have developed a method combining ion-mobility spectrometry, collision-induced dissociation, and cryogenic infrared spectroscopy to determine the structure of positional isomers of N-glycans. This approach enables the identification of previously difficult-to-obtain analytical standards and facilitates glycan analysis.
Article
Biochemical Research Methods
Gergo Peter Szekeres, Kevin Pagel, Zsuzsanna Heiner
Summary: Analyzing the interactions between GAGs and cell membranes is challenging, but recent advancements in analytical methods and synthesis technology have made progress in this field. The development of laser technology, particularly nonlinear spectroscopic methods, such as vibrational sum-frequency generation spectroscopy, has the potential to unravel the complex structures of biological interfaces in real-time.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Carla Kirschbaum, Kim Greis, Sandy Gewinner, Wieland Schoellkopf, Gerard Meijer, Gert von Helden, Kevin Pagel
Summary: Tandem mass spectrometry plays a crucial role in elucidating lipid structures, with the coordination of silver ions enabling differentiation of glycerophospholipid isomers. Gas-phase infrared spectroscopy confirms the generation of dioxolane-type fragments from silver-adducted glycerophospholipids, providing qualitative explanations for the fragmentation behaviors of different isomers. This study demonstrates the significant contribution of gas-phase IR spectroscopy to understanding lipid dissociation mechanisms and the effects of coordinating cations.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Christian Manz, Michael Goetze, Clemens Frank, Andreas Zappe, Kevin Pagel
Summary: LC-MS is an important tool for the comprehensive characterization of N-glycans. However, the measurement times of HILIC chromatography remain a bottleneck in glycan analysis. This study demonstrates the use of an internal calibration strategy to speed up glycan analysis by reducing the number of utilized calibrant. The minimized calibrant shows accurate calibration and can be applied in HPLC runs without modification.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Kim Greis, Carla Kirschbaum, Martin I. Taccone, Michael Goetze, Sandy Gewinner, Wieland Schoellkopf, Gerard Meijer, Gert von Helden, Kevin Pagel
Summary: mRNA-based vaccines have become crucial during the COVID-19 pandemic. This study investigates the mechanism of backbone cleavage of RNA strands and the tautomerization of cytosine in the gas phase using experimental and theoretical approaches. The findings have important implications for the development and analysis of mRNA vaccines.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Organic
Kim Greis, Carla Kirschbaum, Giulio Fittolani, Eike Mucha, Rayoon Chang, Gert von Helden, Gerard Meijer, Martina Delbianco, Peter H. Seeberger, Kevin Pagel
Summary: This study investigates the influence of fluorination on the structure of the glycosyl cation, an intermediate in glycosylation reactions. The results reveal that C3 and C6 fluorination of glucosyl building blocks can alter the structure of the glycosyl cation, with neighboring group participation being the dominant motif.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Chemistry, Analytical
Ahmed Ben Faleh, Stephan Warnke, Teun Van Wieringen, Ali H. Abikhodr, Thomas R. Rizzo
Summary: The combination of high-resolution ion mobility spectrometry and cryogenic vibrational spectroscopy offers a rapid and efficient method for separating and identifying isomeric and isobaric metabolites. Ion mobility enables the separation of isomers in milliseconds, while cryogenic IR spectroscopy provides clear IR fingerprints for molecular identification. Additionally, our approach allows for automatic identification of metabolite isomers by comparing their IR fingerprints with those in a database, eliminating the need for analytical standards. We demonstrate the principle of this approach by constructing a database of IR fingerprints for eight isomeric/isobaric metabolites and using it for identification in mixtures. Furthermore, our fast IR fingerprinting technology allows for rapid probing of IR fingerprints as molecules elute from an LC column. This approach has great potential to enhance metabolomics workflows in terms of accuracy, speed, and cost.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Organic
Kim Greis, Caleb E. Griesbach, Carla Kirschbaum, Gerard Meijer, Gert von Helden, Kevin Pagel, Mark W. Peczuh
Summary: Ferrier reactions involve Lewis acid activation of a cyclic enol ether to generate a glycosyl Ferrier cation through the departure of an allylic leaving group. The resulting cation undergoes attack and transposition, forming a new acetal linkage. This study focuses on the septanosyl Ferrier cation derived from a seven-membered ring carbohydrate-based oxepine. Experimental characterization of the ion, including gas-phase cryogenic IR spectroscopy and solution-phase Ferrier reactions, reveals a preference for contraction to five-membered ring structures in the cation.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Jerome Riedel, Gerard Meijer, Gert von Helden, Maike Lettow, Michael Gotze, Rebecca L. Miller, Geert-Jan Boons, Gergo Peter Szekeres, Kevin Pagel, Marko Grabarics
Summary: Glycosaminoglycans (GAGs), known for their diverse structures and importance in physiological processes, have gained attention in biochemical and biomedical research. Cryogenic gas-phase infrared (IR) spectroscopy has shown promise in identifying structural motifs of shorter GAG chains. This study used mass-selected heparan sulfate (HS) ions to extract characteristic vibrational features and employed random forest (RF) classifiers to discriminate between GAG classes and sulfate positions. The combination of gas-phase cryogenic IR ion spectroscopy and machine learning achieved high prediction accuracy for HS tetra- and hexasaccharides, demonstrating its importance in improving GAG sequencing and analysis of biomolecules.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemical Research Methods
Priyanka Bansal, Ahmed Ben Faleh, Stephan Warnke, Thomas R. Rizzo
Summary: The complex structure of glycans poses challenges in their characterization due to the presence of isomeric forms and isomeric fragments. A new approach combining IMS-CID-IMS with cryogenic infrared spectroscopy for glycan analysis has been developed. However, the lack of standards for identifying spectroscopic fingerprints of fragments remains a challenge. In this study, a multi-stage SLIM-based IMS-CID technique was used to generate second-generation fragments for detailed structural analysis of the first generation fragments.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Michael Goetze, Lukasz Polewski, Leila Bechtella, Kevin Pagel
Summary: This article introduces a 3D-printable nano-electrospray ionization (nano-ESI) source for Bruker instruments, which can be assembled by anyone with access to a 3D printer. The source can be fitted to any Bruker mass spectrometer with an ionBooster ESI source and only requires minor, reversible changes to the original Bruker hardware. The general utility of the source was demonstrated by recording high-resolution MS spectra of small molecules, intact proteins, as well as complex biological samples in negative and positive ion mode on two different Bruker instruments.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Chemistry, Analytical
Ali H. Abikhodr, Ahmed Ben Faleh, Stephan Warnke, Vasyl Yatsyna, Thomas R. Rizzo
Summary: High-resolution ion mobility spectrometry (IMS) combined with cryogenic infrared spectroscopy is a powerful technique for identifying oligosaccharides. However, the lack of extensive database and pure standards hinders its broad application. To overcome this, we propose a method that uses IMS to separate ion fragments produced by collision-induced dissociation (CID) and identifies them using the vibrational fingerprints of a few standards. This approach allows us to determine the structure of precursor molecules and add their vibrational fingerprints to the database. We demonstrate its application in identifying mobility-separated isomers in pooled human milk.
Article
Biochemistry & Molecular Biology
Ahed Almalla, Laura Elomaa, Lei''la Bechtella, Assal Daneshgar, Prabhu Yavvari, Zeinab Mahfouz, Peter Tang, Beate Koksch, Igor Sauer, Kevin Pagel, Karl Herbert Hillebrandt, Marie Weinhart
Summary: In this study, the potential of proteolytic enzymes including pepsin, papain, alpha-amylase, and collagenase to solubilize porcine liver dECM was compared. Papain, a plant-derived enzyme, was found to be a cost-effective alternative to animal-derived pepsin for dECM solubilization. Papain-digested dECM preserved its thermally triggered gelation properties similar to pepsin-digested dECM, and the resulting hydrogels demonstrated enhanced bioadhesiveness.
