Article
Biochemical Research Methods
Alya Hussain, Natasia Paukovich, Morkos A. Henen, Beat Vogeli
Summary: This article introduces the application of the exact nuclear Overhauser enhancement (eNOE) methodology in NMR spectroscopy, which improves the resolution of structure calculation and allows the identification of different conformations of macromolecules. The article reviews the technical development and biological applications in this field.
Article
Chemistry, Multidisciplinary
Peter Kiraly, Nicolas Kern, Mateusz P. Plesniak, Mathias Nilsson, David J. Procter, Gareth A. Morris, Ralph W. Adams
Summary: The article introduces a new approach to selectively excite proton NMR signals using a fast, single-scan method, addressing the issue of signal overlap in traditional methods. Through selective 1D NOESY experiments, the relative configuration can be more effectively determined. This new method has the potential to be widely applied in other experiments.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Radiology, Nuclear Medicine & Medical Imaging
Jing Cui, Yu Zhao, Feng Wang, Daniel F. Gochberg, Zhongliang Zu
Summary: Through in vivo and ex vivo experiments, it is suggested that the NOE(-1.6) is not mainly derived from blood but may be vasculature dependent.
MAGNETIC RESONANCE IN MEDICINE
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
Dushyant Kumar, Blake Benyard, Narayan Datt Soni, Anshuman Swain, Neil Wilson, Ravinder Reddy
Summary: This study demonstrates the feasibility of brain lipid mapping using an easily implementable transient NOE (tNOE) approach at 7T.
MAGNETIC RESONANCE IN MEDICINE
(2023)
Review
Chemistry, Physical
Pedro Lameiras, Jean-Marc Nuzillard
Summary: The nuclear Overhauser effect (NOE) is a result of cross-relaxation between nuclear spins mediated by dipolar coupling, becoming increasingly important in determining through-space atom proximity relationships within molecules. The efficiency of NOE depends on the molecular rotational correlation time, and increasing solution viscosity can reveal otherwise unobservable NOEs.
PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY
(2021)
Article
Chemistry, Physical
P. P. Kobchikova, S. Efimov, I. A. Khodov, V. V. Klochkov
Summary: In this study, cyclosporins D, E, and G were characterized by NMR spectroscopy and molecular dynamics simulation to investigate their structure features and backbone flexibility. It was found that these peptides share common characteristics, with the exception of CsE, which lacks backbone dynamics at the nanosecond timescale, raising questions about its biological activity.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Radiology, Nuclear Medicine & Medical Imaging
Jing Cui, Casey Sun, Zhongliang Zu
Summary: This study proposes a new method, called 2 pi-CEST, using a low-duty-cycle pulsed-CEST sequence with an asymmetric analysis to quantify NOE and reduce the contribution from APT. Compared to the conventional asymmetric analysis, 2 pi-CEST detects NOE more accurately and requires less scan time.
MAGNETIC RESONANCE IN MEDICINE
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Jing Cui, Yu Zhao, Casey Sun, Junzhong Xu, Zhongliang Zu
Summary: The purpose of this study is to evaluate the contribution of confounding factors (T-1 weighting and magnetization transfer) to the CEST ratio (CESTR)-quantified amide proton transfer (APT) and nuclear Overhauser enhancement (NOE) (-3.5) in tumors. A signal model was provided to analyze the effects of these factors, and the relative contribution was calculated in a rat tumor model. The correlation between CESTR and solute concentration (f(s)) was assessed.
MAGNETIC RESONANCE IN MEDICINE
(2023)
Article
Energy & Fuels
Peng Liu, Yuanyuan Zhang, Tieying Pan, Dexiang Zhang, Lishi Chen, Changrong Sun
Summary: The conversion of coal to material or chemical substances through pyrolysis is an important method for achieving carbon neutrality. This study focuses on accurately quantifying the carbon structural types of complex coal in order to predict pyrolysis behavior. The study utilizes C-13 NMR Cp/MAS TOSS spectra to quantify the carbon structural types in coal, and verifies the accuracy of this method using the H/C atomic ratio and aromaticity. Pyrolysis behavior is predicted using pyrolysis Gas Chromatography-Mass Spectrometer (Py-GC-MS), thermogravimetric analysis (TG), and fix-bed slow pyrolysis based on the correction of carbon structure. The results demonstrate that the corrected H/C atomic ratio and aromaticity align with the experimental values, and the correction carbon structure evolution during pyrolysis is consistent with general conclusions and Py-GC-MS analysis. This study provides fundamental insights for the conversion of carbon material to chemicals and can guide accurate calculation and simulations in quantum chemistry.
Article
Chemistry, Physical
Zhiwei Yan, Yue-Qi Ye, Rongchun Zhang
Summary: This article presents a novel HETCOR experiment method that allows sequential acquisition of C-13 and HETCOR spectra for both rigid and mobile components in a single experiment, resulting in significant time savings. The proposed method was demonstrated on small-molecule mixtures and polymer systems, showing potential for fast chemical shift resonance assignment and spectral editing in multiphase materials.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Chemistry, Physical
Denise Medeiros Selegato, Cesare Bracco, Carlotta Giannelli, Giacomo Parigi, Claudio Luchinat, Luca Sgheri, Enrico Ravera
Summary: Conformational variability and heterogeneity play vital roles in determining the function of biological macromolecules. Experimental access to this information is limited by the lack of observable parameters compared to the potentially infinite number of available conformational states. Computational methods, such as reweighting the initial conformational ensemble, have been proposed to address this challenge.
Article
Biochemical Research Methods
Peter Guntert
Summary: In this study, we derive the exact analytical results for the influence of isotropic, harmonic fluctuations of atom positions on Nuclear Overhauser effects (NOEs). The model takes into account steric repulsion and provides closed-form expressions for the expected values of general invertible functions of the distance between two atoms, with a special case of r(-6) for NOEs.
JOURNAL OF MAGNETIC RESONANCE
(2022)
Article
Biochemistry & Molecular Biology
Cristina Di Carluccio, Maria Concetta Forgione, Silvia Martini, Francesco Berti, Antonio Molinaro, Roberta Marchetti, Alba Silipo
Summary: Molecular recognition is crucial in biology, and the combination of NMR techniques with computational methods allows for the accurate determination of protein-ligand complex 3D models, providing key structural insights into ligand-receptor interactions.
CARBOHYDRATE RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Matthias Koeck, Thomas Lindel, Jochen Junker
Summary: The article describes the enhanced capability of WebCocon software in NMR data analysis, including the application of (4)J-HMBC and NOE data. Systematic studies of correlations in oxocyclostylidol and asperginol A demonstrate the software's superior performance.
Article
Biochemical Research Methods
Kurt Wuthrich
Summary: The development of protein structure determination by NMR in solution from 1968 to 1992 was driven by identifying NMR-accessible parameters and developing new experimental methods. Breakthroughs during the years 1976-1984 include the development of NOE experiments, solving the phase problem, generating distance geometry algorithms, and introducing two-dimensional NMR for improved spectral resolution.
JOURNAL OF MAGNETIC RESONANCE
(2021)
Correction
Chemistry, Physical
Carolin Seuring, Joeri Verasdonck, Philippe Ringler, Riccardo Cadalbert, Henning Stahlberg, Anja Bockmann, Beat H. Meier, Roland Riek
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Multidisciplinary
Anna Olerinyova, Adar Sonn-Segev, Joseph Gault, Cedric Eichmann, Johannes Schimpf, Adrian H. Kopf, Lucas S. P. Rudden, Dzmitry Ashkinadze, Radoslaw Bomba, Lukas Frey, Jason Greenwald, Matteo T. Degiacomi, Ralf Steinhilper, J. Antoinette Killian, Thorsten Friedrich, Roland Riek, Weston B. Struwe, Philipp Kukura
Summary: This study explores the application of mass photometry (MP) to Integral membrane proteins (IMPs) and membrane-mimetic systems at the single-particle level. By applying MP to amphipathic vehicles and lipid nanodiscs, the research characterizes particle size, sample purity, and heterogeneity, enabling high-resolution studies of membrane-protein structure and interactions. Evidence suggests that using native styrenemaleic acid nanodiscs could reveal new insights into the structure of membrane proteins compared to conventional detergent purification methods.
Article
Biophysics
Natasia Paukovich, Morkos A. Henen, Alya Hussain, Aaron Issaian, James M. Sikela, Kirk C. Hansen, Beat Vogeli
Summary: Olduvai protein domains, encoded by the NBPF gene family, have the largest copy number increase among protein-coding regions in the human genome. They are linked to human brain development, divergence from primate ancestors, and cognitive diseases like schizophrenia and autism spectrum disorder. This study focuses on the CON1 domain, which is associated with the severity of autism spectrum disorder, and confirms that CON1 is an intrinsically disordered protein.
BIOMOLECULAR NMR ASSIGNMENTS
(2022)
Article
Chemistry, Multidisciplinary
Saroj K. Rout, David Rhyner, Roland Riek, Jason Greenwald
Summary: This study demonstrates that the products of an amino acid condensation reaction, based on the templating nature of amyloids, can undergo self-replication to enhance yield and stereoselectivity. This finding further supports the potential role of amyloids in prebiotic molecular evolution.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
Patrick Vagenknecht, Artur Luzgin, Maiko Ono, Bin Ji, Makoto Higuchi, Daniela Noain, Cinzia A. Maschio, Jens Sobek, Zhenyue Chen, Uwe Konietzko, Juan A. Gerez, Roland Riek, Daniel Razansky, Jan Klohs, Roger M. Nitsch, Xose Luis Dean-Ben, Ruiqing Ni
Summary: This study demonstrated high-resolution imaging of tau protein in the whole brain of mice using non-invasive imaging technique. The results showed that the tau-targeted probe PBB5 specifically bound to tau protein and exhibited similar binding ability in diseased brain tissue.
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING
(2022)
Article
Biochemistry & Molecular Biology
Dzmitry Ashkinadze, Piotr Klukowski, Harindranath Kadavath, Roland Riek, Peter Gu
Summary: This article presents an automated and unbiased method called PDBCor for detecting and analyzing correlated motions in experimental protein structures. The correlations extracted with PDBcor can be useful for subsequent experiments and validation.
Article
Biochemistry & Molecular Biology
Dzmitry Ashkinadze, Harindranath Kadavath, Roland Riek, Peter Guntert
Summary: Recent advances in liquid-state NMR allow the determination of multi-state protein conformations, providing insights into protein dynamics. The structural correlation measure, PDBcor, is introduced as a tool for multi-state protein structure analysis, enabling a comprehensive assessment of protein conformation clustering.
JOURNAL OF BIOMOLECULAR NMR
(2022)
Article
Multidisciplinary Sciences
Alexandra Born, Janne Soetbeer, Morkos A. Henen, Frauke Breitgoff, Yevhen Polyhach, Gunnar Jeschke, Beat Voegeli
Summary: Pin1 is a cell regulator with two domains. Ligand binding can change the conformation of these domains, thus affecting its catalytic site.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Ju-Sim Kim, Alexandra Born, James Karl A. Till, Lin Liu, Sashi Kant, Morkos A. Henen, Beat Vogeli, Andres Vazquez-Torres
Summary: The specific interaction between a sensor kinase and its response regulator ensures accurate partner selectivity in bacteria. The study reveals that conserved residues on the surface of thioredoxin play a crucial role in the interactions with structurally diverse response regulators.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Piotr Klukowski, Roland Riek, Peter Guentert
Summary: Nuclear Magnetic Resonance (NMR) spectroscopy is a widely used technique in structural biology but is limited by the tedious data analysis process. A team of researchers has developed a machine learning-based method called ARTINA, which can automatically analyze protein NMR data, providing signal positions, resonance assignments, and structures using only NMR spectra and protein sequences as input. Tested on a benchmark dataset, ARTINA demonstrated high accuracy in solving protein structures and assigning resonances, making the NMR analysis process more accessible to non-experts.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Christopher M. Clements, Beat Vogeli, Yiqun G. Shellman, Morkos A. Henen
Summary: This study characterized the structural features and dynamics of the SAM1 domain in SASH1 using various biophysical techniques. It was found that SAM1 primarily exists as a less compact monomer with a minor oligomer. NMR experiments revealed the presence of both a disordered monomer and a more structured oligomer in solution, and specific mutations increased its oligomerization. This study provides important evidence and framework for further understanding the mechanism of SAM domain oligomerization.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Parker J. Nichols, Jeffrey B. Krall, Morkos A. Henen, Beat Vogeli, Quentin Vicens
Summary: Z-RNA is a higher-energy, left-handed conformation of RNA with unknown function. Recent studies suggest that Z-RNA may play regulatory roles in the immune response. This article discusses the recognition of Z-RNA features in cellular RNAs, particularly retroelements, by a family of winged helix proteins, and their impact on host defense. The article also highlights the functional losses caused by mutations to specific Z-contacting amino acids. Knowledge gaps in this field are identified, and addressing them would greatly advance research in this area.
Article
Chemistry, Inorganic & Nuclear
Liliya Vugmeyster, Parker J. Nichols, Dmitry Ostrovsky, C. James McKnight, Beat Vogeli
Summary: Protein methyl groups have complex motional modes on different time scales. Detecting sub-nanosecond to nano-second time scale motions of methyl axes in small proteins in solutions is challenging. In this study, NMR relaxation interference was used to characterize the motions of methyl axes as a function of temperature in a small model protein. The results suggest the existence of slow motional modes and a coupling between slow internal motion and overall molecular tumbling at high temperatures.
Article
Biochemistry & Molecular Biology
Saumya M. De Silva, Alisha Dhiman, Surbhi Sood, Kilsia F. Mercedes, William J. Simmons, Morkos A. Henen, Beat Vogeli, Emily C. Dykhuizen, Catherine A. Musselman
Summary: PBRM1 is a subunit of the PBAF chromatin remodeling complex and is frequently mutated in clear cell renal cell carcinoma patients. It functions as a chromatin binding subunit and contains six tandem bromodomains which can bind nucleosomes acetylated at histone H3 lysine 14 (H3K14ac). In addition, the second and fourth bromodomains of PBRM1 also have the ability to bind double stranded RNA elements.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Oncology
Christopher M. Clements, Morkos A. Henen, Beat Voegeli, Yiqun G. Shellman
Summary: SAM domains play critical roles in various interactions relevant to tumorigenesis or metastasis of cancers, making them attractive targets for cancer therapies. This review focuses on the recent findings of SAM domains in proteins containing multiple SAM domains. It discusses the complexity of interactions and oligomerization arrangements due to intrinsic disorder of SAM domains and additional SAM domains in these proteins. The review also highlights the similarities among these proteins in their effects on cancer cell behaviors and their involvement in receptor-mediated signaling and neurology-related functions or diseases.
