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, Physical
Xue-Ni Hou, Naotaka Sekiyama, Yasuko Ohtani, Feng Yang, Yohei Miyanoiri, Ken-ichi Akagi, Xun-Cheng Su, Hidehito Tochio
Summary: This study utilized paramagnetic NMR spectroscopy to investigate the conformational space of linear diubiquitin, revealing that the molecule prefers to sample particular regions of conformational space. By combining these findings with data on charge-reversal derivatives, structural insights into the binding events of linear diubiquitin were obtained.
Review
Biochemistry & Molecular Biology
Julia Koehler Leman, Georg Kuenze
Summary: Nuclear magnetic resonance (NMR) spectroscopy allows for the study of protein structures and dynamics. Although it can be challenging to collect sufficient NMR data for complex proteins, computational modeling techniques, such as those provided by the Rosetta software, can supplement sparse data and improve structure determination. This review provides an overview of the computational protocols in Rosetta for modeling protein structures from NMR data, including new developments for paramagnetic NMR, hydrogen-deuterium exchange, and chemical shifts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Chandrashekhar Honrao, Nathalie Teissier, Bo Zhang, Robert Powers, Elizabeth M. O'Day
Summary: The addition of a gadolinium-based PRE agent can enhance the sensitivity of NMR spectral data, improve the detection of a wide range of metabolites, and increase the repeatability of intensity measurements in metabolomics samples.
Article
Biochemical Research Methods
Jose P. Carvalho, Wassilios Papawassiliou, Andrew J. Pell
Summary: This article presents a combination of solid-state NMR methods for extracting the 23Na shift and quadrupolar parameters in the structurally complex NaMnO2 Na-ion cathode material. By combining multiple experiments, the shift and quadrupolar parameters for observed Na environments were determined and showed agreement with theoretical models.
JOURNAL OF MAGNETIC RESONANCE
(2022)
Article
Biochemistry & Molecular Biology
Marta Bonaccorsi, Tanguy Le Marchand, Guido Pintacuda
Summary: Magic-Angle Spinning Nuclear Magnetic Resonance (MAS NMR) is a rapidly developing technique that complements solution NMR, X-ray crystallography, and electron microscopy for the biophysical characterization of microcrystalline, poorly crystalline or disordered protein samples. MAS NMR is ideal for investigating both structures and dynamics, and has been increasingly applied in structural biology research in recent years to describe conformational dynamics in various systems.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Rui Cordeiro, Maria J. Beira, Carlos Cruz, Joao L. Figueirinhas, Marta C. Corvo, Pedro L. Almeida, Andreia A. Rosatella, Carlos A. M. Afonso, Carla I. Daniel, Pedro J. Sebastiao
Summary: This study aims to characterize a set of systems based on ionic liquids and DMSO mixtures, revealing that DMSO can tune the local order of these systems and relaxation enhancement. The study presents a method of characterizing paramagnetic ionic systems and obtaining a consistent analysis for samples with different co-solvent concentrations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Andrew J. Pell
Summary: This paper discusses the paramagnetic shift in nuclear magnetic resonance (NMR) and shows that traditional Redfield theory fails to predict it, while the recently-introduced Lindbladian theory can accurately do so, applicable to dynamic nuclear polarization and beyond. The formalism is tested through simulations of various case studies, proving its effectiveness in predicting paramagnetic shifts and relaxation-induced linewidths in pNMR.
JOURNAL OF MAGNETIC RESONANCE
(2021)
Article
Chemistry, Analytical
Alan Wong
Summary: High-Resolution Magic-Angle Spinning (HRMAS) NMR spectroscopy is considered an essential technique in metabolomics for assessing the biochemical composition of tissue samples. HRMAS localized profiling shows promise for spatial resolution of metabolic profiles within the sampling tissues.
ANALYTICAL METHODS
(2023)
Review
Chemistry, Physical
Kai Xue, Riddhiman Sarkar, Zdenek Tosner, Bernd Reif
Summary: Proton detection in solid state NMR is continuously advancing, and current achievements include the necessity of deuteration for optimal spectral quality, the superiority of 13CH3 isotopomers for methyl groups at high MAS frequencies, and the sensitivity enhancement with increased static magnetic field.
PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY
(2022)
Article
Biochemical Research Methods
Evgeny Nimerovsky, Stefan Becker, Loren B. Andreas
Summary: In this study, we investigate the windowed sequence for cross polarization (wCP) and find that it has additional matching conditions compared to traditional cross polarization. By considering the flip angle of the pulse, we observe a striking similarity between wCP and CP transfer conditions. Using spin-1/2 formalism and average Hamiltonian theory, we derive an analytical approximation that matches these observed transfer conditions. Data recorded at spectrometers with different external magnetic fields show that these transfers and the selectivity of CP are related to flip angle (average nutation).
JOURNAL OF MAGNETIC RESONANCE
(2023)
Article
Chemistry, Multidisciplinary
Jan Blahut, Arthur L. Lejeune, Sebastian Ehrling, Irena Senkovska, Stefan Kaskel, Florian M. Wisser, Guido Pintacuda
Summary: A toolbox for rapid characterization of powdered samples of paramagnetic metal-organic frameworks by H-1-detected solid-state NMR was presented, with tailored radiofrequency irradiation schemes and fast MAS rates helping to overcome sensitivity and resolution limits. The approach was demonstrated on DUT-8(Ni) to detect and assign H-1 and C-13 resonances of organic linkers in a few hours with only 1-2 mg of sample, providing information on structure, dynamics, and metal electronic properties. The experiments revealed new possibilities for describing local and global structural changes and correlating them to electronic and magnetic properties of the assemblies.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemical Research Methods
Daniel Jardon-Alvarez, Tahel Malka, Johan van Tol, Yishay Feldman, Raanan Carmieli, Michal Leskes
Summary: This study maps the fluctuations of the magnetic moment of unpaired electron spins by analyzing the ratio between longitudinal and transverse nuclear relaxation times. This analysis helps explain the evolution of NMR lineshapes and DNP enhancements as a function of the concentration of paramagnetic species and temperature.
JOURNAL OF MAGNETIC RESONANCE
(2022)
Article
Chemistry, Physical
Thomas Biedenbaender, Edvards R. Bensons, Bjoern Corzilius
Summary: With the increasing size of molecules in structural biology, site-specificity and sensitivity enhancement methods in solid-state magic-angle spinning NMR spectroscopy are becoming more crucial. SCREAM-DNP, a method exploiting selective dynamic groups within molecules, has been developed to enhance NMR signals. In this study, rotational resonance (R-2) is reintroduced during SCREAM-DNP to further enhance experiment selectivity. The analysis of polarization buildup dynamics in a model system demonstrates that dipolar-recoupled transfer rates exceed DNP buildup dynamics, enabling selective and efficient hyperpolarization of larger distances.
Article
Chemistry, Physical
Frederic A. Perras, Tian Wei Goh, Wenyu Huang
Summary: Due to their high gyromagnetic ratio, measuring distances and correlations involving protons is of considerable interest. However, such measurements are complicated by the recoupling of chemical shift anisotropy (CSA). Recent research has shown that adding CSA refocusing periods during 1H-X dipolar recoupling improves the stability and performance of sequences.
SOLID STATE NUCLEAR MAGNETIC RESONANCE
(2022)
Article
Biochemistry & Molecular Biology
Darryl Aucoin, Yongjie Xia, Theint Theint, Philippe S. Nadaud, Krystyna Surewicz, Witold K. Surewicz, Christopher P. Jaroniec
JOURNAL OF STRUCTURAL BIOLOGY
(2019)
Article
Multidisciplinary Sciences
Hai Wang, Zan Gao, Xuanyou Liu, Pranay Agarwal, Shuting Zhao, Daniel W. Conroy, Guang Ji, Jianhua Yu, Christopher P. Jaroniec, Zhenguo Liu, Xiongbin Lu, Xiaodong Li, Xiaoming He
NATURE COMMUNICATIONS
(2018)
Article
Chemistry, Physical
Matthew D. Shannon, Theint Theint, Dwaipayan Mukhopadhyay, Krystyna Surewicz, Witold K. Surewicz, Dominique Marion, Paul Schanda, Christopher P. Jaroniec
Article
Chemistry, Multidisciplinary
Theint Theint, Yongjie Xia, Philippe S. Nadaud, Dwaipayan Mukhopadhyay, Charles D. Schwieters, Krystyna Surewicz, Witold K. Surewicz, Christopher P. Jaroniec
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2018)
Article
Chemistry, Multidisciplinary
Alberto Perez, Kari Gaalswyk, Christopher P. Jaroniec, Justin L. MacCallum
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2019)
Article
Biochemical Research Methods
Christopher P. Jaroniec
JOURNAL OF MAGNETIC RESONANCE
(2019)
Article
Biochemical Research Methods
Alia Hassan, Caitlin M. Quinn, Jochem Struppe, Ivan V. Sergeyev, Chunting Zhang, Changmiao Guo, Brent Runge, Theint Theint, Hanh H. Dao, Christopher P. Jaroniec, Melanie Berbon, Alons Lends, Birgit Habenstein, Antoine Loquet, Rainer Kuemmerle, Barbara Perrone, Angela M. Gronenborn, Tatyana Polenova
JOURNAL OF MAGNETIC RESONANCE
(2020)
Article
Chemistry, Multidisciplinary
Sevastyan O. Rabdano, Matthew D. Shannon, Sergei A. Izmailov, Nicole Gonzalez Salguero, Mohamad Zandian, Rudra N. Purusottam, Michael G. Poirier, Nikolai R. Skrynnikov, Christopher P. Jaroniec
Summary: The positively charged N-terminal histone tails interact with nucleosomal DNA, influencing their susceptibility to modifications and recognition by chromatin-binding proteins. The NMR data reveals that H4 tails are dynamically disordered in nucleosomes, showing a reduced conformational flexibility compared to free peptides. The findings suggest a fuzzy interaction between histone H4 tails and nucleosomal DNA, characterized by variable salt bridges and hydrogen bonds.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Physical
Mohamad Zandian, Nicole Gonzalez Salguero, Matthew D. Shannon, Rudra N. Purusottam, Theint Theint, Michael G. Poirier, Christopher P. Jaroniec
Summary: In this study, high-resolution NMR measurements were used to investigate the dynamics and interactions of H3 tails in nucleosome arrays with different lengths of linker DNA. The H3 tail dynamics in nucleosome arrays were found to be significantly attenuated compared to nucleosomes with or without linker DNA, but were not modulated by the specific linker DNA length investigated.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Zhe Qi, Krystyna Surewicz, Witold K. Surewicz, Christopher P. Jaroniec
Summary: In this study, the influence of the dynamic domain on the structure of the amyloid core region of huPrP23-144 was systematically evaluated. It was found that deleting a large portion of the N-terminal tail can result in amyloid fibrils with native-like core structure, while deleting additional flexible residues outside the core structure causes perturbation to the fibril structure.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Multidisciplinary Sciences
Daniel W. Conroy, Yu Xu, Honglue Shi, Nicole Gonzalez Salguero, Rudra N. Purusottam, Matthew D. Shannon, Hashim M. Al-Hashimi, Christopher P. Jaroniec
Summary: The majority of base pairs in DNA follow the canonical Watson-Crick geometry, but they can also adopt alternative Hoogsteen conformations which are important for biological function and mechanism. This study demonstrates that multidimensional dynamic nuclear polarization-enhanced solid-state NMR can be used as a spectroscopic tool to observe and distinguish between Watson-Crick and Hoogsteen base pairs in various DNA systems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Qiuye Li, Christopher P. Jaroniec, Witold K. Surewicz
Summary: This study presents a high-resolution cryo-EM structure of amyloid fibrils formed by human prion protein with the Y145Stop mutation associated with familial prion disease. The findings not only explain previous biochemical observations but also provide direct support for the conformational adaptability model of prion propagation.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sean T. Smrt, Nicole Gonzalez Salguero, Justin K. Thomas, Mohamad Zandian, Michael G. Poirier, Christopher P. Jaroniec
Summary: Chromatin, a dynamic protein-DNA complex that regulates eukaryotic genome accessibility and essential functions. Solid-state NMR techniques were used to investigate the conformational dynamics of histone H3 tails in nucleosome arrays with different DNA linker lengths. The chemical shifts and line broadening of certain residues at the H3-nucleosomal DNA interface varied in arrays with short DNA linkers compared to arrays with longer linkers, indicating increased nucleosome packing heterogeneity and structural strain.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Wenjun Sun, Olga O. Lebedenko, Nicole Gonzalez Salguero, Matthew D. Shannon, Mohamad Zandian, Michael G. Poirier, Nikolai R. Skrynnikov, Christopher P. Jaroniec
Summary: The nucleosome, the fundamental repeat unit of chromatin, consists of DNA and a histone protein octamer. The histone tails play important roles in chromatin compaction and regulation. This study investigates the conformation and interactions of histone H4 tails in nucleosomes using experimental results and molecular dynamics simulations.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biophysics
Hanh H. Dao, May Z. Hlaing, Yixuan Ma, Krystyna Surewicz, Witold K. Surewicz, Christopher P. Jaroniec
Summary: Solid-state NMR was used to establish the chemical shift assignments for amyloid fibrils formed by the A117V and M129V mutants of human PrP23-144, providing insights into the amyloid core regions and secondary protein structures. These mutants are associated with the development of Gerstmann-Straussler-Scheinker disease in the context of full-length PrP in vivo.
BIOMOLECULAR NMR ASSIGNMENTS
(2021)