Article
Biochemistry & Molecular Biology
Nadezda A. Penkova, Mars G. Sharapov, Nikita Penkov
Summary: The hydration shells of DNA were studied in solution by terahertz time-domain spectroscopy, revealing differences from undisturbed water in terms of the presence of strongly bound water molecules, a higher number of free molecules, and an increased number of hydrogen bonds. Salts in the solution had varying effects on hydration, with MgCl2 having minimal alteration and KCl significantly attenuating hydration effects.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Nikita Penkov
Summary: This research focuses on the dynamic hydration characteristics of carbohydrates in aqueous solutions using terahertz time-domain spectroscopy analysis. It reveals that all analyzed carbohydrates increase the binding degree of water, with monosaccharides showing higher numbers of hydrogen bonds and free water molecules but polysaccharides exhibiting less apparent hydration depending on the type of glycosidic bonds.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Monika Bokor, Eszter Hazy, Agnes Tantos
Summary: Parkinson's disease is caused by aggregation of the protein alpha-synuclein, and the variants A30P and E46K have different hydration properties and compactness compared to the wild-type and A53T variants. The E46K variant has a more compact structure and altered water-protein interactions.
Article
Chemistry, Physical
Valeria Conti Nibali, Francesco Sacchetti, Alessandro Paciaroni, Caterina Petrillo, Mounir Tarek, Giovanna D'Angelo
Summary: Understanding the internal dynamics of proteins is essential for understanding their functions. Recent research has revealed that proteins exhibit complex and coordinated motions on the sub-picosecond timescale, which have significant impacts on their functional mechanisms. By analyzing molecular dynamics simulations using an interacting-mode model, it has been discovered that proteins possess multiple acoustic-like and low-frequency optic-like modes that interfere with each other. This new understanding provides insights into the molecular mechanisms underlying energy redistribution processes in proteins.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Physics, Fluids & Plasmas
Zhang-Hu Hu, Wen-Ping Lv, De-Xuan Hui, Xiao-Juan Wang, You-Nian Wang
Summary: Potassium ion channels play a crucial role in cellular electrical excitability and maintaining resting potential. This study demonstrates that an external terahertz wave can enhance the permeation efficiency of the KcsA channel through the effective response of K+ ions.
Article
Chemistry, Multidisciplinary
Qi Li, Johanna Kolbel, Margaret P. Davis, Timothy M. Korter, Andrew D. Bond, Terrence Threlfall, J. Axel Zeitler
Summary: Terahertz time-domain spectroscopy in a transmission geometry combined with visual analysis was used to investigate the crystallization process of MgSO4 solution. The method allowed the extraction of information about the liquid phase before and during crystallization, aiding the investigation of solvation dynamics and the behavior of molecular species at phase boundaries.
CRYSTAL GROWTH & DESIGN
(2022)
Editorial Material
Cell Biology
Qi Zhang, Yihong Ye
Summary: In yeast, the vacuole-associated Rsp5 ubiquitin ligase utilizes a substrate adaptor Ssh4 to recognize membrane helices in Ypq1, targeting the lysine transporter for lysosomal degradation during lysine starvation.
JOURNAL OF CELL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Seyeon Kim, Jin Kyung Park, So-Jung Park, Byeongmoon Jeong
Summary: Oligonucleotides of different bases were investigated for their ice recrystallization inhibition (IRI) activity. The degree of polymerization of oligothymines was also tested. Among them, T20 showed the best IRI performance, indicating its effectiveness in preventing ice recrystallization. The IRI mechanism was further explored, and it was found that the hydrophobic interactions of T20 in the interface layer might contribute to its IRI activity.
Article
Polymer Science
Zhengyu Piao, Jin Kyung Park, Madhumita Patel, Hyun Jung Lee, Byeongmoon Jeong
Summary: This study found that poly(L-alanine-co-L-lysine) (PAK) exhibits IRI activity similar to poly(vinyl alcohol) and generates cubic-to-spherical shaped ice crystals, showing superior performance. In contrast, poly(L-alanine-co-L-aspartic acid) (PAD) and poly(ethylene glycol) (PEG) with similar molecular weights did not provide significant IRI activity. FTIR and circular dichroism spectroscopies indicated that PAK forms alpha-helices, while PAD forms random coils in water. Additionally, dynamic ice shaping study suggested strong interaction between PAK and ice crystals, while PAD and PEG only weakly interact.
Article
Physics, Applied
Vasileios Balos, Patrick Muller, Gerhard Jakob, Mathias Klaui, Mohsen Sajadi
Summary: The approach utilizes spintronic THz emitters to measure the dielectric response of liquids, imprinting the liquid's complex refractive index and dielectric response into the radiated electromagnetic field by bringing the liquid in contact with the emitter. Water is used as a test liquid, and its dielectric loss and permittivity in the range of 0.3-15 THz are determined.
APPLIED PHYSICS LETTERS
(2021)
Article
Chemistry, Physical
Lucas W. Henderson, Edie M. Sharon, Amit K. S. Gautam, Adam J. Anthony, Martin F. Jarrold, David H. Russell, Andreas Matouschek, David E. Clemmer
Summary: Mass spectrometry studies show that the stability of S. cerevisiae 20S proteasome undergoes related configurations and transitions during temperature changes, possibly linked to the opening of the proteolytic core. The study indicates that the proteasome remains intact and all transitions are reversible. Three types of structures are identified based on thermodynamic analysis: energetically stabilized closed configurations, high-entropy precursor states, and open pore structures. Opening of the 20S pore in the absence of the regulatory unit involves a charge-priming process. However, only a small fraction of precursor configurations actually open to expose the catalytic cavity.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Hangxin Liu, Shuqing Xiang, Haomiao Zhu, Li Li
Summary: The study found that the dynamics of protein-water change at different temperatures and mutation levels affect protein's amplitude fluctuations and hydrogen bond loss. The results also suggest that protein activation is related to the hydrogen bonding between local hydration water and the protein as well as other waters.
Article
Chemistry, Physical
Yusuke Shuto, Erik Walinda, Daichi Morimoto, Kenji Sugase
Summary: Weak electric fields disrupt the local structure of proteins and induce rotational mobility of hydration water. The alignment tendency of bulk water with electric fields is stronger than that of hydration water. The findings emphasize the importance of local dipoles and their electric polarizability in net-uncharged biomolecules.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Multidisciplinary
Bhawna Rana, David J. Fairhurst, Kailash C. Jena
Summary: The Hofmeister effect, which refers to the ability of ions to induce conformational changes in macromolecules, was investigated using surface-specific sum frequency generation (SFG) vibrational spectroscopy at the air/ polyvinylpyrrolidone (PVP)/water interface. The study revealed that ions can order water molecules in a manner consistent with the Hofmeister series, but do not significantly affect the structure of PVP macromolecules. However, the orientation angle of vinyl chain CH2 groups in PVP was found to be influenced by ions in a manner consistent with the Hofmeister series.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Mantu Santra, Aniruddha Seal, Kankana Bhattacharjee, Suman Chakrabarty
Summary: This study systematically investigates the localization, structure, dynamics, and energetics of water molecules in the channel of KR2 rhodopsin in its resting/dark state. The research shows significant structural and dynamical heterogeneity of the water molecules in these cavities, with very rare exchange between them. The translational and rotational dynamics of buried water are strongly influenced by protein cavity size and local interactions, exhibiting classic trapped diffusion and rotational anisotropy.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Meeting Abstract
Biophysics
David Gnutt, Jonas Ahlers, Benedikt Koenig, Matthias Heyden, Simon Ebbinghaus
BIOPHYSICAL JOURNAL
(2018)
Article
Chemistry, Multidisciplinary
David Gnutt, Stepan Timr, Jonas Ahlers, Benedikt Koenig, Emily Manderfeld, Matthias Heyden, Fabio Sterpone, Simon Ebbinghaus
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2019)
Article
Chemistry, Multidisciplinary
Benjamin Haemisch, Roland Pollak, Simon Ebbinghaus, Klaus Huber
CHEMISTRY-A EUROPEAN JOURNAL
(2020)
Article
Chemistry, Physical
Stepan Timr, David Gnutt, Simon Ebbinghaus, Fabio Sterpone
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2020)
Article
Chemistry, Multidisciplinary
Lukas J. Patalag, Somayeh Ahadi, Olesia Lashchuk, Peter G. Jones, Simon Ebbinghaus, Daniel B. Werz
Summary: The study demonstrates a straightforward synthetic route to water-soluble, uncharged BODIPY derivatives using unprocessed reducing sugar substrates, showing high fluorescence efficiency and compatibility with various postfunctionalizations. The Knoevenagel condensations result in red and far-red fluorescent glycoconjugates with high hydrophilicity, and the synthetic outcome is confirmed through X-ray crystallography and photophysical investigations. Cell experiments further illustrate efficient cell uptake and differential cell targeting based on chiral information integration.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Nirnay Samanta, Sara S. Ribeiro, Mailin Becker, Emeline Laborie, Roland Pollak, Stepan Timr, Fabio Sterpone, Simon Ebbinghaus
Summary: The folding stability of SOD1 determines its association with SGs, regardless of aggregation. Specific protein-protein interactions within the cytoplasm compared to SGs play a role in determining the partitioning of folding states during heat stress.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Candice B. Raeburn, Angelique R. Ormsby, Dezerae Cox, Chloe A. Gerak, Christian Makhoul, Nagaraj S. Moily, Simon Ebbinghaus, Alex Dickson, Gawain McColl, Danny M. Hatters
Summary: This study investigates the role of quality control machinery in protecting proteins from misfolding and aggregation in different cellular compartments. The results show that the protection offered by the machinery is weaker in the nucleus compared to the cytosol, and the aggregation of mutant huntingtin exon 1 protein hinders the engagement of quality control machinery.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Nirnay Samanta, Yasser B. Ruiz-Blanco, Zamira Fetahaj, David Gnutt, Carter Lantz, Joseph A. Loo, Elsa Sanchez-Garcia, Simon Ebbinghaus
Summary: Protein misfolding and aggregation are common features of many neurodegenerative diseases. This study investigates the modulation mechanism of the unfolding and aggregation pathways of SOD1 protein, which is involved in ALS, by the supramolecular ligand CLR01. The results provide insights into the molecular mechanisms of how CLR01 affects the stability of SOD1 and suggest it as a potential target for the development of drugs against neurodegenerative diseases.
Article
Chemistry, Physical
Satyendra Rajput, Roland Pollak, Klaus Huber, Simon Ebbinghaus, Divya Nayar
Summary: The role of intracellular crowded environment in regulating protein aggregation is a complex and elusive mechanism. By studying a synthetic model for self-assembling proteins, it was found that ethylene glycol impedes the self-assembly of dye molecules, suggesting that a crowded environment can hinder the self-assembly of proteins. These findings have implications in understanding the impact of crowded environment on the free energy landscapes of proteins.
Article
Chemistry, Multidisciplinary
Alexander Christoph Hautke, Simon Ebbinghaus
Summary: Research has focused on the relationship between RNA molecules with trinucleotide repeat expansions and neurodegenerative diseases, primarily aiming to understand how they fold and function in disease progression. Functional studies in cells can reveal additional aspects of RNA behavior, while invitro studies mainly focus on sequence structure, stability, and self-assembly. Specific interactions with the unfolded state have been found to contribute to destabilization and aggregation of RNA in cellular lysate.
Article
Chemistry, Multidisciplinary
Christoph Rumancev, Tobias Voepel, Susan Stuhr, Andreas R. Gundlach, Tobias Senkbeil, Markus Osterhoff, Michael Sprung, Vasil M. Garamus, Simon Ebbinghaus, Axel Rosenhahn
Summary: Huntington's disease is a neurodegenerative disorder associated with the extension of polyglutamine in proteins, leading to the formation of amyloidal structures. By using nanoprobe small angle X-ray scattering in cellulo, the structure of Htt amyloid fibrils was investigated under cryogenic conditions, providing insights into aggregate formation without chemical fixation. It was also revealed that nanoprobe cryo-SAXS can serve as a powerful tool to study the kinetics of amyloid aggregate formation inside cells and understand how fibril formation can be influenced by drugs and external stimuli.
Article
Chemistry, Physical
Saikat Pal, Partha Pyne, Nirnay Samanta, Simon Ebbinghaus, Rajib Kumar Mitra
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2020)
Review
Chemistry, Multidisciplinary
Michael C. Owen, David Gnutt, Mimi Gao, Sebastian K. T. S. Warmlander, Juri Jarvet, Astrid Graslund, Roland Winter, Simon Ebbinghaus, Birgit Strodel
CHEMICAL SOCIETY REVIEWS
(2019)
Article
Biochemistry & Molecular Biology
David Gnutt, Linda Sistemich, Simon Ebbinghaus
FRONTIERS IN MOLECULAR BIOSCIENCES
(2019)
Article
Biophysics
Christoph Rumancev, Tobias Voepel, Susan Stuhr, Andreas von Gundlach, Tobias Senkbeil, Simon Ebbinghaus, Jan Garrevoet, Gerald Falkenberg, Bjoern De Samber, Laszlo Vincze, Axel Rosenhahn, Walter Schroeder
Summary: X-ray fluorescence analysis enables the study of trace element distributions in biological specimens under cryogenic conditions. The system described in this work was applied to analyze the elemental distribution in single HeLa cells.
