Article
Biochemistry & Molecular Biology
Ekaterina Georgieva, Yanka Karamalakova, Georgi Arabadzhiev, Vasil Atanasov, Rositsa Kostandieva, Mitko Mitev, Vanya Tsoneva, Yovcho Yovchev, Galina Nikolova
Summary: The main factors in COVID-19 pathology are the abnormal generation of free radicals and oxidative stress, which can cause extensive structural changes at the cellular and molecular levels. The concentration of human serum albumin is crucial for maintaining plasma oncotic pressure, nutrient and drug transport, drug therapy effectiveness, and prevention of drug toxicity. Low albumin levels and structural defects in the protein may lead to ineffective therapy, frequent complications, and high mortality rates.
Article
Biochemistry & Molecular Biology
Emilien Etienne, Annalisa Pierro, Ketty C. Tamburrini, Alessio Bonucci, Elisabetta Mileo, Marlene Martinho, Valerie Belle
Summary: Site-directed spin labeling (SDSL) combined with continuous wave electron paramagnetic resonance (cw EPR) spectroscopy is a powerful technique to study protein dynamics. Numerical simulation using SimLabel, a graphical user interface (GUI) of Matlab, is proposed to analyze SDSL-EPR spectra and provide quantitative information on protein dynamics. Guidelines for simulating X-band cw-EPR spectra of nitroxide labeled proteins at room temperature are presented.
Article
Chemistry, Applied
Jacqueline Lux, Mykhailo Azarkh, Laura Fitzner, Julia K. Keppler, Karin Schwarz, Malte Drescher, Anja Steffen-Heins
Summary: SDSL of natural beta-lactoglobulin revealed that different spin labels bind to specific sites to varying extents, affecting the formation of amyloid-like structures. The spatial distribution of labels within protein aggregates was confirmed to be similar to a string of pearls, indicating a potential mechanism for amyloid formation.
FOOD HYDROCOLLOIDS
(2021)
Article
Chemistry, Physical
Joshua L. Wort, Swati Arya, Katrin Ackermann, Alan J. Stewart, Bela E. Bode
Summary: Pulse-dipolar EPR is an attractive method for structural characterization in solution, especially when paired with genetically encoded self-assembling spin labels and Cu-II-chelates. The combination of room-temperature isothermal titration calorimetry and cryogenic relaxation-induced dipolar modulation enhancement showed that the double-histidine motif spin labeling with Cu-II-nitrilotriacetic acid is robust against competition from Zn-II-NTA and maintains high nM binding affinity even under acidic and basic conditions. The strategy is well-suited for diverse biological applications, with the requirement of other metal ion cofactors or slightly acidic pH not necessarily being prohibitive.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Food Science & Technology
Hui Li, Yanxiong Pan, Zhongyu Yang, Jiajia Rao, Bingcan Chen
Summary: This review article discusses the use of SDSL-EPR technology to reveal the structure and dynamics of food proteins on an atomic level, emphasizing the importance of protein structure and dynamics for functionality. Overall, SDSL-EPR can help improve the understanding of the relationship between structure and functionality of food proteins.
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Shutian Lu, Catherine R. R. Fowler, Brian Ream, Sheela M. M. Waugh, Theresa M. M. Russell, John C. C. Rohloff, Larry Gold, Jason P. P. Cleveland, Stefan Stoll
Summary: Recent developments in aptamer chemistry have provided new opportunities for protein biosensing tools. This study presents a method that uses immobilized slow off-rate modified aptamers (SOMAmers) labeled with a nitroxide radical to detect protein binding. The rotational mobility of the spin label is changed by protein binding, which is detected using solution-state electron paramagnetic resonance (EPR) spectroscopy.
Review
Biochemistry & Molecular Biology
Keyun Huang, Xianyang Fang
Summary: RNAs are essential biomolecules that are closely associated with various cellular processes and human diseases. Investigating the structure, dynamics, and functional connections of RNA using magnetic resonance techniques such as NMR and EPR spectroscopies is crucial for understanding their biological functions and developing RNA-based therapeutics.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Polymer Science
Uwe Lappan, Carolin Naas, Ulrich Scheler
Summary: This study utilizes cationic charged chitosan and weak polyacid poly(ethylene-alt-maleic acid) to create polyelectrolyte multilayers (PEMs). By attaching a nitroxide spin-label to the polyacid, the rotational dynamics of the polymer backbone in the swollen state of the PEMs are studied using electron paramagnetic resonance spectroscopy. The study reveals that PEMs with an even number of layers exhibit a superposition of two spectral components, a major slow-motion component from protonated amino groups compensating chain segments of the chitosan, and a minor fast-motion component believed to originate from loops and tails of the polyacid chain at the PEMs' surface.
MACROMOLECULAR CHEMISTRY AND PHYSICS
(2023)
Review
Chemistry, Multidisciplinary
Annalisa Pierro, Malte Drescher
Summary: This Feature Article provides an overview of the recent advances in Site-directed Spin Labeling coupled to Electron Paramagnetic Resonance spectroscopy (SDSL-EPR) for studying biomolecules in living cells. The sensitivity, lack of background interference, and versatility of spin-labeling strategies make this approach highly promising for studying biomolecules in physiological environments.
CHEMICAL COMMUNICATIONS
(2023)
Article
Biology
Kevin Singewald, James A. Wilkinson, Sunil Saxena
Summary: Site-directed spin labeling with EPR allows for measuring residue-specific dynamics and distance distributions in biomolecules. Labeling proteins with a Cu(II)-NTA complex utilizing strategically placed histidine residues (dHis motif) overcomes limitations of typical spin labels. This approach provides unique structural constraints for integrative structural biophysics, complementing traditional techniques like NMR and crystallography.
Article
Biochemistry & Molecular Biology
Viranga W. Wimalasiri, Kinga A. Jurczak, Monika K. Wieliniec, Thushani D. Nilaweera, Robert K. Nakamoto, David S. Cafiso
Summary: Pulse EPR measurements provide information on distances and distance distributions in proteins. In this study, in vivo labeling of the E. coli outer membrane proteins BtuB and FecA were achieved using strains defective in the disulfide bond formation system. The in vivo measurements showed that the cellular environment affects the behavior of the extracellular loops of FecA, and the use of a DsbA minus strain improved the EPR signals and data obtained in vitro from BtuB.
Article
Chemistry, Organic
Yuliya F. Polienko, Natalia M. Kuprikova, Dmitriy A. Parkhomenko, Yuriy Gatilov, Elena Chernyak, Igor A. Kirilyuk
Summary: Nitroxides with spirocyclic moieties adjacent to the N-O group exhibit longer spin echo dephasing times between 80 and 295 K compared to tetramethyl nitroxides. New spin labels for site-directed spin labeling have been developed from 2,5-bis(spirocyclohexane)-substituted nitroxides of the pyrroline series, showing advantages in reduction stability and relaxation rates when compared to tetramethyl nitroxides.
Article
Biochemistry & Molecular Biology
Isao Suetake, Shigeaki Nakazawa, Kazunobu Sato, Risa Mutoh, Yuichi Mishima, Toru Kawakami, Toshiki Takei, Mikio Watanabe, Norio Sakai, Toshimichi Fujiwara, Takeji Takui, Makoto Miyata, Akira Shinohara, Hironobu Hojo, Toshiaki Arata
Summary: The study investigated the structural dynamics of HP1 proteins in heterochromatin formation, showing differences in spatial separation and mobility between HP1 alpha and HP1 gamma. HP1 alpha may exhibit an auto-inactivated state, potentially influencing its physiological role in heterochromatin formation.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biophysics
Eva R. Stockwald, Lena M. E. Steger, Stefanie Vollmer, Christina Gottselig, Stephan L. Grage, Jochen Buerck, Sergii Afonin, Julia Froebel, Anne -Sophie Bluemmel, Julia Setzler, Wolfgang Wenzel, Torsten H. Walther, Anne S. Ulrich
Summary: The TatA protein exports folded proteins across bacterial membranes through the Tat-dependent translocation pathway. The transmembrane α-helix of TatA is anchored to the lipid bilayer in an unusually short manner. The tilt angle of TatA's helix varies in different membranes.
BIOPHYSICAL JOURNAL
(2023)
Review
Biochemistry & Molecular Biology
Dehua Pei, Ross E. Dalbey
Summary: This article provides an overview of systems and processes involved in the membrane translocation of folded proteins. It discusses various mechanisms for protein translocation, including pore/channel formation, local membrane disruption, membrane thinning, and transport by membrane vesicles. The article also introduces a newly discovered vesicular transport mechanism, vesicle budding and collapse, as a potential unifying mechanism for folded protein translocation processes.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Review
Biochemistry & Molecular Biology
Ben C. Berks
ANNUAL REVIEW OF BIOCHEMISTRY, VOL 84
(2015)
Article
Biology
Felicity Alcock, Phillip J. Stansfeld, Hajra Basit, Johann Habersetzer, Matthew A. B. Baker, Tracy Palmer, Mark I. Wallace, Ben C. Berks
Article
Multidisciplinary Sciences
Allister Crow, Nicholas P. Greene, Elise Kaplan, Vassilis Koronakis
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2017)
Article
Biology
Felicity Alcock, Merel P. M. Damen, Jesper Levring, Ben C. Berks
Article
Biochemistry & Molecular Biology
Marta Wojnowska, Joseph Gault, Shee Chien Yong, Carol V. Robinson, Ben C. Berks
Article
Multidisciplinary Sciences
Elise Kaplan, Nicholas P. Greene, Allister Crow, Vassilis Koronakis
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Review
Microbiology
Nicholas P. Greene, Elise Kaplan, Allister Crow, Vassilis Koronakis
FRONTIERS IN MICROBIOLOGY
(2018)
Article
Biochemical Research Methods
Elise Kaplan, Rachael Stone, Peter J. Hume, Nicholas P. Greene, Vassilis Koronakis
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2020)
Article
Microbiology
Rory Hennell James, Justin C. Deme, Andreas Kjaer, Felicity Alcock, Augustinas Silale, Frederic Lauber, Steven Johnson, Ben C. Berks, Susan M. Lea
Summary: The study reveals the internal structure and working mechanism of the gliding motility/type 9 protein secretion system motor, demonstrating that proton flow results in rotation of the GldM/PorM dimer inside the intra-membrane ring to drive processes at the bacterial outer membrane.
NATURE MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Augustinas Silale, Susan M. Lea, Ben C. Berks
Summary: During natural transformation, bacteria import extracellular DNA molecules into their genome using the protein ComEC. The C-terminal domain (CTD) of ComEC binds Mn2+ ions and exhibits Mn2+-dependent phosphodiesterase and nuclease activities. Inactivation of the CTD's enzymatic activity severely inhibits natural transformation in Bacillus subtilis.
MOLECULAR MICROBIOLOGY
(2021)
Editorial Material
Microbiology
Nicholas P. Greene, Vassilis Koronakis
Summary: The study shows that the three monomers within the CusA trimer can function independently in the presence of copper, contrary to the cooperative mechanism proposed for the multidrug exporting transporter. This provides a basis for further research on TEPs important for bacterial survival.
Article
Microbiology
Rory Hennell James, Justin C. Deme, Alicia Hunter, Ben C. Berks, Susan M. Lea
Summary: Gliding motility and protein secretion through the type IX secretion system (T9SS) are two specific features of the Bacteroidetes. These processes are energized by the GldLM motor complex, which converts the proton motive force into mechanical work. The structures of the GldLM motor complex from different Bacteroidetes species reveal a conserved architecture, but with species-specific differences at the N terminus of GldL. This study enhances our understanding of bacterial ion-driven motors and their role in T9SS and gliding motility.
Article
Biochemistry & Molecular Biology
Felicity Alcock, Ben C. Berks
Summary: This study reports the recovery of receptor complexes associated with elevated levels of TatA through detergent solubilization of membranes during active transport. By combining biochemical analysis and live cell fluorescence imaging, sub-steps in the Tat translocation cycle were resolved, and it was inferred that TatA assembly precedes the functional interaction with TatC. It was also observed that dissipation of the protonmotive force releases TatA oligomers from the assembled translocation site, suggesting that the TatA oligomer is assembled at the periphery of the receptor complex.
MOLECULAR MICROBIOLOGY
(2022)
Editorial Material
Multidisciplinary Sciences
Ben C. Berks
Summary: Membrane-spanning proteins play crucial roles in cells, and new findings challenge our current understanding of how these proteins are inserted into the membranes of animal cells.
Article
Multidisciplinary Sciences
Elise Kaplan, Nicholas P. Greene, Abigail E. Jepson, Vassilis Koronakis
Summary: In gram-negative bacteria, the Lol system plays a vital role in transporting triacylated lipoproteins from the inner membrane to the outer membrane. LolA, the periplasmic chaperone protein, is crucial for this process. This study presents the crystal structure of liganded LolA, providing molecular details of lipoprotein association and demonstrating how LolA accommodates different lipoproteins by interacting with their acyl chains. Additionally, the comparison of LolA structures reveals that the insertion of lipoprotein acyl chains disrupts the interaction between LolA and LolC. These findings contribute to a better understanding of the trafficking pathway in gram-negative bacteria.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)