Article
Chemistry, Multidisciplinary
Jan H. Overbeck, Jennifer Vogele, Felix Nussbaumer, Elke Duchardt-Ferner, Christoph Kreutz, Jens Wohnert, Remco Sprangers
Summary: The synthetic neomycin-sensing riboswitch interacts with neomycin, ribostamycin, and paromomycin. However, only neomycin can efficiently repress translation initiation due to differences in ligand:riboswitch dynamics. Five complementary fluorine-based NMR methods were used to accurately quantify dynamics in the riboswitch complexes and identified four structurally different states. These findings highlight the potential of F-19 NMR methods in characterizing complex exchange processes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Biochemistry & Molecular Biology
Vitaly Volkov, Alexander Chernyak, Nikita A. Slesarenko, Irina A. Avilova
Summary: This review focuses on the progress of solvation and mobility studies in solid electrolyte, particularly ion-exchange membranes and composite materials, using NMR techniques. The applications of various NMR techniques are discussed, and comparisons are made between diffusion coefficients and ionic conductivity data. The microscopic mechanism of ionic transfer is also explored.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Chemistry, Multidisciplinary
Hans Agren, Olle Bjorneholm, Gunnar Ohrwall, Vincenzo Carravetta, Arnaldo Naves de Brito
Summary: We unraveled the microscopic properties of ethanol-water solutions at different concentrations through experimental and theoretical simulations. At low concentrations, ethanol molecules form a film at the surface, while complex intermolecular interactions occur in the bulk.
ACCOUNTS OF CHEMICAL RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Stacey Wardenfelt, Xinyao Xiang, Mouzhe Xie, Lei Yu, Lei Bruschweiler-Li, Rafael Bruschweiler
Summary: This study utilizes a new method to investigate the dynamics of protein interactions with nanoparticles. The results indicate that the interaction between proteins and silica nanoparticles of different sizes is not significant, and the backbone dynamics are confined to sub-nanosecond timescales.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Markus Zweckstetter
Summary: The AlphaFold2 method has shown the ability to accurately predict protein structures in solution, matching well with experimental data, and holds promise as a powerful tool for studying structural changes in proteins.
Review
Biochemistry & Molecular Biology
Vitaly I. Volkov, Olga V. Yarmolenko, Alexander V. Chernyak, Nikita A. Slesarenko, Irina A. Avilova, Guzaliya R. Baymuratova, Alena V. Yudina
Summary: This review summarizes the development of different types of novel polymer electrolytes for lithium power sources in the past decade, focusing on their compositions, conductivity, and ion transport mechanism. The use of NMR techniques, quantum chemical calculations, and ionic conductivity methods has provided insights into the nanochannel structure, ion complexes, and mobilities of cations and anions in polymer electrolytes.
Review
Biochemistry & Molecular Biology
Francisco Javier Canada, Angeles Canales, Pablo Valverde, Beatriz Fernandez de Toro, Monica Martinez-Orts, Paola Oquist Phillips, Amaia Pereda
Summary: Carbohydrates, either as free molecules or conjugated with other biomolecules, play important roles in various biological processes. Nuclear Magnetic Resonance spectroscopy (NMR) is a versatile tool for studying the structures and interactions of carbohydrates, providing information about their sequences, structures, and local geometries. Labeling carbohydrates with 13C enhances the resolution and detail of the analyzed structures. Moreover, combining NMR with molecular modeling and theoretical calculations offers insights into the conformational flexibility of carbohydrates. Additionally, the use of partially oriented media or paramagnetic perturbations allows for the study of longer and branched glycan chains. This review presents examples and an overview of recent and relevant NMR applications in the field of glycobiology.
CURRENT MEDICINAL CHEMISTRY
(2022)
Correction
Chemistry, Physical
K. J. Mallikarjunaiah, Jacob J. Kinnun, Horia I. Petrache, Michael F. Brown
Summary: The study corrected the NMR spectroscopy of flexible lipid nanomaterials, providing data support for more accurate research on this type of material.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Plant Sciences
Emily B. Crull, Ajay N. Jain, Paul C. D. Hawkins, Ann E. Cleves, Edmund I. Graziani, R. Thomas Williamson
Summary: Rapamycin, a well-known natural product with various biological activities, has been extensively studied since its discovery over fifty years ago. Although it adopts a single conformation in the solid state, it exists as a mixture of two conformations in solution. Previous studies have suggested that the minor conformer is the cis amide based on the analogy to FK-506, but its characterization remained incomplete. By using NMR techniques and computational methods, the solution structure of the minor conformer of rapamycin was revealed to be a trans amide species with rotation around the ester linkage.
JOURNAL OF NATURAL PRODUCTS
(2023)
Article
Biochemistry & Molecular Biology
Yulian Gavrilov, Andreas Prestel, Kresten Lindorff-Larsen, Kaare Teilum
Summary: Slow conformational changes are important for protein function, but their impact on the overall folding stability is not well understood. This study investigates the effects of L49I and I57V substitutions on the slow conformational dynamics of CI2. The results show that these substitutions have minimal impact on the structure of the excited state, but the stability of the excited state is influenced by the stability of the main state. The interactions between substituted residues and water molecules play a role in linking subtle structural changes to slow conformational changes in the protein.
Article
Biochemistry & Molecular Biology
Lukasz T. Olenginski, Wojciech K. Kasprzak, Christina Bergonzo, Bruce A. Shapiro, Theodore K. Dayie
Summary: In this study, the dynamics of hepatitis B virus RNA were investigated using nuclear magnetic resonance and molecular dynamics simulations. The results highlight the functional importance of RNA dynamics in various processes such as viral polymerase binding, packaging, and reverse transcription during viral replication.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Cell Biology
Fabian Bumbak, Miquel Pons, Asuka Inoue, Juan Carlos Paniagua, Fei Yan, Hongwei Wu, Scott A. Robson, Ross A. D. Bathgate, Daniel J. Scott, Paul R. Gooley, Joshua J. Ziarek
Summary: Nuclear magnetic resonance (NMR) studies have shown that fast methyl sidechain dynamics can provide information about entropically-driven allostery. This study focuses on the fast dynamics of a thermostabilized G protein-coupled receptor (GPCR), neurotensin receptor 1 (NTS1), using 13C epsilon-methionine chemical shift-based global order parameters. The results indicate the presence of substates with different lifetimes in the NTS1 solution ensemble, and the rapid fluctuations of individual methionine residues are correlated with ligand pharmacology, suggesting a role for sub-microsecond dynamics and conformational entropy in GPCR ligand discrimination.
Article
Pharmacology & Pharmacy
Morgane Adelaide, Evgeniy Salnikov, Francisco Ramos-Martin, Christopher Aisenbrey, Catherine Sarazin, Burkhard Bechinger, Nicola D'Amelio
Summary: SAAP-148 is an antimicrobial peptide derived from LL-37 with excellent activity against drug-resistant bacteria and biofilms. Its mechanism of action at the molecular level has not been explored despite its optimal pharmacological properties.
Article
Multidisciplinary Sciences
Enrico Rennella, Danny D. Sahtoe, David Baker, Lewis E. Kay
Summary: With recent advancements in calculating protein structures from amino acid sequences using AI algorithms, the next important step is to understand how dynamics is encoded in the primary protein sequence to improve function prediction. This study emphasizes the significance of dynamics in modulating the function of a designed protein called C34, which binds β-strands. By investigating the structural dynamics of C34 using NMR spectroscopy, the researchers show that manipulating conformations can enhance functionality in protein design.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Energy & Fuels
Qingtao Zhang, Gang Zhou, Yingying Hu, Mengyao Xing, Rui Zhang, Pengfei Wang, Shengyong Hu
Summary: With the advancement of coal mine mechanization and automation, the dust concentration at production sites has increased, posing threats to workers' safety and mine production. Through experiments and simulations, the wetting mechanisms of coal dust were explored, along with the effects of different surfactants on the wetting of lignite. The research provides insights into the wetting dynamic characteristics and mechanisms of lignite at a micro level, offering scientific guidance for clean mine production.
Article
Crystallography
Jing Dai, Boris B. Kharkov, Sergey V. Dvinskikh
Article
Engineering, Chemical
Nanta Sophonrat, Linda Sandstrom, Rikard Svanberg, Tong Han, Sergey Dvinskikh, Claudio M. Lousada, Weihong Yang
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
(2019)
Article
Chemistry, Multidisciplinary
Sergey Dvinskikh
Article
Crystallography
Jing Dai, Debashis Majhi, Boris B. Kharkov, Sergey Dvinskikh
Article
Biochemistry & Molecular Biology
Debashis Majhi, Andrei Komolkin, Sergey Dvinskikh
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Multidisciplinary Sciences
Debashis Majhi, Sergey V. Dvinskikh
Summary: Ionic liquid crystals exhibit liquid-crystalline behavior and are stabilized by electrostatic, hydrogen bonding, and van der Waals interactions. Dicationic ionic liquid crystals, with two single-charged ions linked by a spacer, display similar local order and alignment as monocationic salts. Bond order parameters in dicationic smectic phase are lower compared to double-chain monocationic analogs, indicating reduced van der Waals forces.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Physical
Debashis Majhi, Boris B. Kharkov, Sergey Dvinskikh
Summary: Dipolar NMR spectroscopy is a powerful analytical tool for studying structural and dynamic properties of solids at the molecular level. An approach to determine the signs of dipolar couplings in liquid crystals is presented, where sign information can be directly obtained from one-dimensional NMR spectra in samples spinning slightly off the magic angle. This method can be used to develop an experimental strategy for sign-sensitive measurements of heteronuclear dipolar couplings in anisotropic soft materials.
CHEMICAL PHYSICS LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Lukas Marcos Celada, Judith Martin, Sergey V. Dvinskikh, Peter Olsen
Summary: Biopolymers, especially cellulose, play a vital role in transitioning to a circular economy and reducing reliance on fossil fuels. However, modifying cellulose hydroxyls is a challenge due to the similarity of their chemical features with water. To address this, we developed bio-based ionic liquids that can activate cellulose without disturbing its crystalline ordering. One specific ionic liquid showed high activation in heterogeneous conditions, resulting in over 30% conversion of cellulose hydroxyls. This work opens new perspectives for cellulose derivatization while maintaining sustainability.
Article
Chemistry, Physical
Fredrik Grote, Alexander Lyubartsev, Sergey V. Dvinskikh, Vibhu Rinwa, Jan Holmbaeck
Summary: Binary mixtures of ethanol and phospholipids DOPC and DOPE were investigated for topical drug delivery applications using computer simulation and experimental approach. Molecular dynamics simulations and experimental measurements were used to compute and validate properties such as diffusion coefficients, relaxation times, and viscosity. The simulations revealed that the structure of ethanol-DOPC mixtures remains unchanged while ethanol-DOPE mixtures undergo structural rearrangements, indicating the stronger aggregation tendency of DOPE. These findings provide valuable insights into the development of advanced drug delivery formulations.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Debashis Majhi, Jing Dai, Sergey Dvinskikh
Summary: This study investigates the hydrogen-bonding interaction in imidazolium-based mesogenic ionic liquids in different phases using solid-state nuclear magnetic resonance (NMR). The results show that the more basic anions form stronger hydrogen bonds in the smectic phase. The strength of the hydrogen bonds slightly decreases in the mesophase compared to the isotropic phase. Additionally, the cation structural modification does not significantly affect the hydrogen bond strength as long as the aprotic nature of the material is preserved.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Debashis Majhi, Jing Dai, Andrei Komolkin, Sergey Dvinskikh
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2020)
Meeting Abstract
Biochemistry & Molecular Biology
B. Kharkov, I. Podkorytov, S. Bondarev, M. Belousov, G. Zhuravleva, N. Skrynnikov
Article
Chemistry, Physical
Boris Kharkov, Xueyou Duan, Emily S. Tovar, James W. Canary, Alexej Jerschow
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2019)