Article
Materials Science, Multidisciplinary
E. Vavilova, T. Vasilchikova, A. Vasiliev, D. Mikhailova, V. Nalbandyan, E. Zvereva, S. Streltsov
Summary: Recent theoretical studies suggest that Kitaev physics and spin-liquid states can be found not only in alpha-RuCl3 and iridates, but also in traditional 3d transition metal compounds. Through various measurements like magnetometry, thermodynamics, and NMR, the material Na3Co2SbO6 was investigated, revealing a comprehensive phase diagram. The results show the antiferromagnetic structure transforms under an external magnetic field, gradual development of saturation phase, and evidence of gapped behavior in certain regions of the phase diagram.
Article
Biochemistry & Molecular Biology
Zhaoyong Xi, Tatiana V. Ilina, Michel Guerrero, Lixin Fan, Nicolas Sluis-Cremer, Yun-Xing Wang, Rieko Ishima
Summary: This study revealed the impact of the L289K mutation in HIV-1 reverse transcriptase on its structure and function. The results showed that the L289K mutation in the p51 subunit reduces the formation of the heterodimer with p66, providing insights into the mechanism of p66 homodimer formation.
Article
Chemistry, Multidisciplinary
Anais M. E. Cassaignau, Tomasz Wlodarski, Sammy H. S. Chan, Lauren F. Woodburn, Ivana V. Bukvin, Julian O. Streit, Lisa D. Cabrita, Christopher A. Waudby, John Christodoulou
Summary: The study characterizes interactions between the ribosome surface and unfolded nascent chains, with the strongest interactions found in the C-terminal segment essential for folding. Quantitative agreement is demonstrated between these interactions and the energetics of co-translational folding. Competition between folding and binding provides a simple, dynamic mechanism for the modulation of co-translational folding by the ribosome.
Article
Biochemistry & Molecular Biology
Mette Ahrensback Roesgaard, Jeppe E. Lundsgaard, Estella A. Newcombe, Nina L. Jacobsen, Francesco Pesce, Emil E. Tranchant, Soren Lindemose, Andreas Prestel, Rasmus Hartmann-Petersen, Kresten Lindorff-Larsen, Birthe B. Kragelund
Summary: By comparing the effects of aspartate and glutamates in intrinsically disordered proteins, the study found that while the variants support similar function and global dimensions, they differ in binding affinities and population of local transient structural elements, indicating potential roles in functional diversity.
Article
Biochemistry & Molecular Biology
Hyun Sun Cho, Friedrich Schotte, Valentyn Stadnytskyi, Philip Anfinrud
Summary: Time-resolved small- and wide-angle X-ray scattering studies of proteins in solution using the pump-probe approach can provide structural information from intermediates across different length and time scales. While promising, only a fraction of the potential information encoded in scattering data has been extracted so far. The article discusses the methodology, summarizes recent results, and explores the potential for extracting additional information from these scattering curves.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2021)
Article
Materials Science, Multidisciplinary
A. Kurbakov, A. E. Susloparova, V. Y. Pomjakushin, Y. Skourski, E. L. Vavilova, T. M. Vasilchikova, G. Raganyan, A. N. Vasiliev
Summary: The magnetic properties of the trigonal layered quaternary tellurate Na2MnTeO6 have been studied, and it has been found to have a commensurate 120 degrees spin helix magnetic structure with a certain ordering temperature and 2D short-range correlations.
Article
Multidisciplinary Sciences
Aya Okuda, Masahiro Shimizu, Ken Morishima, Rintaro Inoue, Nobuhiro Sato, Reiko Urade, Masaaki Sugiyama
Summary: Multi-domain proteins exhibit various domain conformations under physiological conditions to regulate their functions through conformational changes. ER-60, a typical MDP protein folding enzyme, is found to have different domain conformations in solution depending on the redox state, with oxidized and reduced ER-60 structures differing from each other. Structural modeling with coarse-grained molecular dynamics simulation indicates that the distance between the two edge domains of oxidized ER-60 is longer and one edge domain has a more flexible conformation compared to reduced ER-60.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Multidisciplinary
Emma E. Cawood, G. Marius Clore, Theodoros K. Karamanos
Summary: The T193A mutation in DNAJB6 reduces self-oligomerization and anti-aggregation activity while increasing the rate of formation of a partially folded state. This highlights the importance of chaperone dynamics in regulating protein aggregation and suggests potential therapeutic avenues targeting specific substrates.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Engineering, Chemical
Danuta Kruk, Malgorzata Florek-Wojciechowska, Elzbieta Masiewicz, Mecit Oztop, Anna Ploch-Jankowska, Piotr Duda, Slawomir Wilczynski
Summary: H-1 NMR relaxometry studies on different types of cheese have revealed two fractions of water with significantly different dynamical properties, referred to as confined-water and free-water. The dynamics of water molecules in the cheese matrix are much slower than bulk water, and the differences in water behavior and macroscopic properties of cheese are related to the relative populations of these fractions and the portion of water molecules bound to proteins.
JOURNAL OF FOOD ENGINEERING
(2021)
Article
Chemistry, Multidisciplinary
Anton Abyzov, Eckhard Mandelkow, Markus Zweckstetter, Nasrollah Rezaei-Ghaleh
Summary: The dynamics of a 441-residue long intrinsically disordered protein (IDP), tau protein, were investigated in the temperature range of 0-25 degrees C. The results suggest that at higher temperatures, the fast backbone conformational fluctuations and slower chain segmental motions of the protein might become inseparable. This study demonstrates the remarkable dynamic plasticity of this prototypical IDP and highlights the need for dynamic studies of IDPs at multiple temperatures.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Review
Biochemistry & Molecular Biology
Kai Zumpfe, Albert A. Smith
Summary: Relaxation in nuclear magnetic resonance is a powerful method for obtaining dynamics information about molecular systems, but biomolecular systems are generally too complex for full characterization using NMR data alone. The Lipari-Szabo model-free analysis captures the full information content of NMR relaxation data when all internal motion of a molecule in solution is sufficiently fast. Various methods, such as model-free, spectral density mapping, and LeMaster's approach, form a class of analysis methods where the behavior of fitted parameters has a well-defined relationship to the distribution of correlation times of motion. Of these methods, only detectors are generally applicable to solid-state NMR relaxation data.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Food Science & Technology
Takumi Mitsudome
Summary: Proton T2 relaxation is correlated with water content and aggregation of bovine lactoferrin powders during storage at different temperatures. The change in T2 relaxation time is influenced by factors such as monomer loss rate, water content, and storage temperature.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Vaibhav Kumar Shukla, Lucas Siemons, D. Flemming Hansen
Summary: Enzymes sample various conformations, and the dynamic sampling of conformations determines both enzymatic activity and inhibitor potency. Precise structures alone often cannot explain the effect of mutations on enzymatic activity and drug potency.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biophysics
Yuhao Ma, Marcello Tonelli, Larry D. Unsworth
Summary: This research investigates the impact of protein carbamylation on the physicochemical properties and adsorption to surfaces, showing that carbamylation significantly alters protein tertiary structure and surface charge, affecting adsorption.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2021)
Article
Biochemical Research Methods
Liliya Vugmeyster, Dmitry Ostrovsky, Alexander Greenwood, Riqiang Fu
Summary: Experimental and computational approaches for measuring 2H rotating frame NMR relaxation for solid samples under magic angle spinning conditions are demonstrated in this study. The technique is validated for different MAS rates and sample applications through comprehensive consideration of motional parameters and experimental computational factors.
JOURNAL OF MAGNETIC RESONANCE
(2022)
Article
Biochemistry & Molecular Biology
Petr Konarev, Melissa A. Graewert, Cy M. Jeffries, Masakazu Fukuda, Taisiia A. Cheremnykh, Vladimir V. Volkov, Dmitri Svergun
Summary: SAXS is commonly used for structural analysis of biological macromolecules in solution, and combining SAXS with chromatography setups has become popular in research. The computer program EFAMIX, based on evolving factor analysis (EFA), efficiently restores scattering and concentration profiles of components from mixed SAXS data, proving useful for interpretation and analysis of fractions in the sample.
Article
Biochemistry & Molecular Biology
Sven Wernersson, Romel Bobby, Liz Flavell, Alexander G. Milbradt, Geoffrey A. Holdgate, Kevin J. Embrey, Mikael Akke
Summary: This study investigates the dynamics and interactions of bromodomains in the BRD4 protein and their binding to a peptide corresponding to the tail of histone 4. The results show that the peptide has lower affinity for the domains in the tandem construct compared to the isolated domains. Additionally, the peptide binding induces dimerization in certain regions of the domains and alters their dynamics.
Article
Chemistry, Physical
Matthias Dreydoppel, Mikael Akke, Ulrich Weininger
Summary: Aromatic ring flips are an important characteristic of protein dynamics and can be studied using NMR spectroscopy. Recent advances have improved the characterization of these flips across different time scales, but there are diverging views on the fluidity or solidity of the protein interior. This study resolves these issues by measuring residual dipolar coupling-mediated exchange contributions using NMR relaxation dispersion experiments.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Cell Biology
Mateusz Molon, Karolina Stepien, Patrycja Kielar, Bela Vasileva, Bonka Lozanska, Dessislava Staneva, Penyo Ivanov, Monika Kula-Maximenko, Eliza Molestak, Marek Tchorzewski, George Miloshev, Milena Georgieva
Summary: The interaction between chromatin proteins Hho1p and Arp4p plays a significant role in the ageing of mitotically active yeast cells, and disrupting this interaction can lead to premature ageing phenotypes.
Article
Biochemistry & Molecular Biology
Sven Wernersson, Simon Birgersson, Mikael Akke
Summary: Protein-ligand-exchange kinetics is crucial for the duration of biochemical signals and its role in drug design. This study investigates the effect of the solvent dimethyl sulfoxide (DMSO) on protein-ligand binding. Results show that increasing DMSO concentration leads to decreased affinity and slower association rate, while dissociation rate is less affected. Only a small fraction of binding attempts result in successful complex formation.
Article
Biochemistry & Molecular Biology
Iain M. Hay, Maria Shamin, Eve R. Caroe, Ahmed S. A. Mohanned, Dmitri I. Svergun, Cy M. Jeffries, Stephen C. Graham, Hayley J. Sharpe, Janet E. Deane
Summary: Type IIB receptor protein tyrosine phosphatases mediate cell adhesion and signaling through their extracellular and cytoplasmic domains, respectively. The crystal structure of PTPRK has revealed an intermembrane adhesion mode consistent with other family members. Comparison with PTPRM structure suggests that conformational differences between the domains may contribute to homophilic specificity. Analysis of the full-length PTPRM and PTPRK proteins using small-angle X-ray scattering reveals rigid extended conformations and one residue difference at the interaction interface that affects dimer formation.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Goksin Liu, Erhan Ekmen, Farzaneh Jalalypour, Haydyn D. T. Mertens, Cy M. Jeffries, Dmitri Svergun, Ali Rana Atilgan, Canan Atilgan, Zehra Sayers
Summary: This study combines molecular dynamics (MD) simulations with small angle x-ray scattering (SAXS) measurements to investigate the range of conformations and populations of a pH/ionic strength (IS) sensitive protein. The protein studied is the periplasmic ferric binding protein A (FbpA) involved in iron capture from higher organisms by bacteria. The study reveals the detectable changes in conformational distribution of FbpA under different conditions, but detection of conformational changes due to point mutation D52A and changes in ionic strength has been challenging.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Mikael Akke, Ulrich Weininger
Summary: Aromatic residues play an important role in the protein core, interacting tightly with surrounding side chains. The rotations, or flips, of phenylalanine and tyrosine residues are mediated by breathing motions, creating void volume around the aromatic ring. Recent advancements in NMR methods have allowed for studying the mechanisms and energetics of aromatic ring flips, which can provide valuable insights into protein dynamics.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Biochemistry & Molecular Biology
Gabriela Guedez, Gabriele Loers, Cy M. Jeffries, Sandra Kozak, Rob Meijers, Dmitri I. Svergun, Melitta Schachner, Christian Loew
Summary: The cell adhesion molecule L1 plays crucial roles in neural development, regeneration, synaptic plasticity, and tumor cell migration. L1 is a member of the immunoglobulin superfamily and consists of Ig-like domains and fibronectin type III homologous repeats. The second Ig-like domain is involved in cell binding, and the fibronectin type III homologous repeats contribute to signal transduction.
Article
Biochemistry & Molecular Biology
Simon Christensen, Olof Stenstrom, Mikael Akke, Leif Bulow
Summary: Plant hemoglobins, known as phytoglobins, have significant roles in abiotic stress tolerance and can bind essential small metabolites. Moreover, phytoglobins can catalyze various oxidative reactions in vivo. This study identified the residues involved in dimer formation of a sugar beet phytoglobin using NMR relaxation experiments, which will contribute to a better understanding of phytoglobins' functions in plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Andras Lang, Alejandro Fernandez, Mireia Diaz-Lobo, Mar Vilanova, Francisco Cardenas, Margarida Gairi, Miquel Pons
Summary: Compared to well-studied regulatory mechanisms, the exact role of Src N-terminal regulatory element (SNRE) in modulating Src activity is still unclear. Phosphorylation of serine and threonine residues in SNRE can affect the interactions with the SH3 domain, potentially serving as an information transduction element. Positively charged sites in SNRE can interact with phosphorylated residues, leading to changes in acidity, local conformation, and functional unit formation. This study utilizes pH-dependent NMR measurements and single point mutations to analyze the electrostatic network in SNRE and provides an alternative method to identify interacting phosphorylated residues without mutations.
Article
Biochemistry & Molecular Biology
Aleix Tarres-Sole, Federica Battistini, Joachim M. Gerhold, Olivier Pietrement, Belen Martinez-Garcia, Elena Ruiz-Lopez, Sebastien Lyonnais, Pau Bernado, Joaquim Roca, Modesto Orozco, Eric Le Cam, Juhan Sedman, Maria Sola
Summary: A new mechanism of mitochondrial DNA compaction was discovered, in which the Gcf1p protein in Candida albicans utilizes its multiple domains to connect co-aligned DNA segments without altering DNA topology.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Carlos A. Elena-Real, Annika Urbanek, Lionel Imbert, Anna Morato, Aurelie Fournet, Frederic Allemand, Nathalie Sibille, Jerome Boisbouvier, Pau Bernado
Summary: A strategy for efficiently assigning frequencies to individual nuclei in large biomolecular machines and repetitive proteins using in vitro protein expression is presented. The approach was demonstrated to be applicable for NMR assignment in four proteins by introducing isotopically labeled alanines. The labeling method enabled unambiguous assignments in large protein assemblies and revealed the correlation between helical stability and homorepeat length in Phox2B. Selectively introducing alanines with distinct labeling patterns proves to be a powerful tool for studying challenging biomolecular systems.
ACS CHEMICAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Masakazu Fukuda, Melissa A. Graewert, Cy M. Jeffries, Dmitri I. Svergun, Tadao Yamazaki, Akiko Koga, Yuji Yamanaka
Summary: This study investigates the acidic variants of therapeutic monoclonal antibodies (mAbs) using a refolding approach. The results showed that these acidic variants are conformational variants with minor and localized conformational changes.
ANALYTICAL BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Stefano Da Vela, Giovanni Saudino, Francesca Lucarelli, Lucia Banci, Dmitri I. Svergun, Simone Ciofi-Baffoni
Summary: In humans, the biosynthesis and trafficking of mitochondrial [4Fe-4S]2+ clusters is a highly coordinated process that requires a complex protein machinery. Two [2Fe-2S]2+ clusters are converted into a [4Fe-4S]2+ cluster on an ISCA1-ISCA2 complex. NFU1 is the accessory protein that first receives the [4Fe-4S]2+ cluster from the ISCA1-ISCA2 complex.
JOURNAL OF MOLECULAR BIOLOGY
(2023)