Article
Plant Sciences
Carol Bvindi, Sanghun Lee, Liang Tang, Michael V. Mickelbart, Ying Li, Tesfaye Mengiste
Summary: This study investigated the role of histone lysine methylations in biotic and abiotic stress responses in tomatoes. Mutations in the SDG33 and SDG34 genes resulted in altered methylations and gene expressions, as well as improved tolerance to drought and resistance to a fungal pathogen.
Article
Biochemistry & Molecular Biology
Sarfraz Sehrish, Wahid Sumbal, Meili Xie, Chuanji Zhao, Rong Zuo, Feng Gao, Shengyi Liu
Summary: This study identified 122 SDGs in the B. napus genome through genome-wide analysis. BnSDGs were classified into seven classes and segmental duplication played a role in their evolution. BnSDGs were closely associated with histone and non-histone methylation and stress response, and they were important for plant development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Diane Erdmann, Jean Contreras, Remy A. Le Meur, Bruno Vitorge, Vincent Saverat, Ambre Tafit, Corinne Jallet, Veronique Cadet-Daniel, Corentin Bon, Phannarath Phansavath, Virginie Ratovelomanana-Vidal, Albert Jeltsch, Sophie Vichier-Guerre, J. Inaki Guijarro, Paola B. Arimondo
Summary: Epigenetics plays a crucial role in disease research, and researchers have designed analogues to probe MBD2, gaining valuable insights for further studies.
ACS CHEMICAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Rinko Nakamura, Jun-ichi Nakayama
Summary: Histones, the building blocks of nucleosomes, undergo various post-translational modifications, including methylation. The SUV39H family of histone methyltransferases is evolutionarily conserved and plays a crucial role in forming higher-order chromatin structures. By catalyzing the methylation of histone H3 lysine 9, they create a binding site for heterochromatin protein 1, which contributes to the formation of heterochromatin. Studies on the fission yeast Clr4 have provided important insights into the regulatory mechanisms of this enzyme family, which can be compared to other histone methyltransferases.
Article
Biochemistry & Molecular Biology
Hiroshi Otsuka, Kei Endo, Miki Wada, Koichi Ito
Summary: Translation elongation is hindered by obstacles like rare codons or RNA structures, causing ribosomal stalling. Ribosome rescue pathways resolve persistent stalling states. The study identified the critical regions in ribosomal proteins S20 and Asc1 required for ribosome rescue, and revealed their interaction with the E3 ubiquitin ligase Hel2 and their crucial role at the collided ribosome interface.
Article
Biochemistry & Molecular Biology
Chengcheng Zhang, Yuan Tian, Shuang Song, Lu Zhang, Yunkun Dang, Qun He
Summary: The deposition of H2A.Z and deacetylation of histone H3 lysine 56 play crucial roles in restricting heterochromatin spreading.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Immunology
Francesco Coppolino, Letizia Romeo, Giampiero Pietrocola, Germana Lentini, Giuseppe Valerio De Gaetano, Giuseppe Teti, Roberta Galbo, Concetta Beninati
Summary: The study identified the importance of Plg's K4 Kringle domain in binding to the bacterial protein PbsP, with lysine binding sites in the Plg molecule playing a key role in the interaction. Interestingly, mutating lysine residues in PbsP did not decrease its ability to bind Plg, indicating a novel bacterial sequence that can interact with lysine binding sites in the Plg molecule.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yunfeng Yang, Junfeng Liu, Xiaofei Fu, Fan Zhou, Shuo Zhang, Xuemei Zhang, Qihong Huang, Mart Krupovic, Qunxin She, Jinfeng Ni, Yulong Shen
Summary: Cell cycle regulation is crucial for all forms of life. A transcription factor called aCcr1 and its viral homologs control cell division in Sulfolobales. Over-expression of aCcr1 and its viral homologs leads to growth retardation and cell division failure, while its over-expression downregulates 17 genes, including cdvA. This study provides insights into the conserved mechanism of cell division regulation in archaeal cells and the manipulation of host cell cycle by viruses.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Xuan Xie, Shaogang Wang, Mingyi Li, Lei Diao, Xingyu Pan, Jijun Chen, Weiguo Zou, Xu Zhang, Wenfeng Feng, Lan Bao
Summary: The post-translational modification α-TubK40me3 plays a crucial role in neuronal polarization and migration by promoting microtubule formation. This modification is enriched in the mouse cerebral cortex during embryonic development, and its deficiency leads to defects in neuronal migration that can be rescued by overexpression of specific proteins. Additionally, α-TubK40me3 potently promotes tubulin nucleation and is involved in tubulin acetylation regulation, highlighting its importance in microtubule dynamics and neuronal development.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Heloise Grunchec, Jerome Deraze, Delphine Dardalhon-Cumenal, Valerie Ribeiro, Anne Coleno-Costes, Karine Dias, Sebastien Bloyer, Emmanuele Mouchel-Vielh, Frederique Peronnet, Helene Thomassin
Summary: The ribosomal protein uL11 plays a crucial role in translational efficiency, and its transcriptional regulation is potentially modulated through the modification of lysine 3 in its N-terminal end. Mutation studies highlight the importance of lysine 3 modification in both the function and transcriptional regulation of uL11.
Article
Multidisciplinary Sciences
Andrew Keniry, Natasha Jansz, Linden J. Gearing, Iromi Wanigasuriya, Joseph Chen, Christian M. Nefzger, Peter F. Hickey, Quentin Gouil, Joy Liu, Kelsey A. Breslin, Megan Iminitoff, Tamara Beck, Andres Tapia del Fierro, Lachlan Whitehead, Andrew Jarratt, Sarah A. Kinkel, Phillippa C. Taberlay, Tracy Willson, Miha Pakusch, Matthew E. Ritchie, Douglas J. Hilton, Jose M. Polo, Marnie E. Blewitt
Summary: In this study, a replenishable female mouse embryonic stem cell system was developed to study X chromosome inactivation (XCI). Through a targeted genetic screen, the researchers identified the BAF complex as essential for creating nucleosome-depleted regions at promoters on the inactive X chromosome during the early stages of XCI establishment. This model system provides a valuable tool for discovering unknown factors involved in XCI and epigenetic silencing.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Takaki Okamoto, Kazuya Yamanaka, Yoshimitsu Hamano, Shingo Nagano, Tomoya Hino
Summary: In this study, the crystal structure of the adenylation domain of epsilon-PL synthetase was determined, providing insights into the precise interactions between the enzyme and L-Lys and its analogs. The findings contribute to a better understanding of the epsilon-PL synthesis mechanism and have implications for the successful application of NRPS adenylation domains in bioengineering.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Agriculture, Multidisciplinary
Mao-Song Pei, Hai-Nan Liu, Tong-Lu Wei, Da-Long Guo
Summary: A 4D label-free quantitative proteomics approach was used to study non-histone lysine methylation during grape berry ripening. A total of 822 methylation sites in 416 methylated proteins were identified, with a conserved motif of xxExxx_K_xxxxxx. Functional annotation showed that these non-histone proteins with methylated lysine residues were mainly associated with ripening and senescence, energy metabolism, oxidation-reduction process, and stimulus response. The study also investigated the correlation of methylated proteins with QTLs, SNPs, and selective regions associated with fruit quality and development.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Biology
Jorge Hernandez-Garcia, Borja Diego-Martin, Peggy Hsuanyu Kuo, Yasaman Jami-Alahmadi, Ajay A. Vashisht, James Wohlschlegel, Steven E. Jacobsen, Miguel A. Blazquez, Javier Gallego-Bartolome
Summary: In this study, a systematic analysis was conducted using multiple species to assess the conservation of known SWI/SNF subunits in eukaryotes. The researchers proposed the composition of a hypothetical ancestral SWI/SNF complex in the last eukaryotic common ancestor and uncovered a plant SWI/SNF complex similar to the animal BAF subclass. Additionally, a set of plant-specific subunits of unknown function was identified.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemical Research Methods
Qi Wang, Zhouxian Li, Jiahua Zhou, Yan Wang, Keyun Wang, Hongqiang Qin, Mingliang Ye
Summary: Protein methylation, especially on arginine and lysine residues, plays a critical role in cellular processes such as RNA splicing and DNA repair. A new chemical strategy has been developed to deplete histidine-containing peptides and improve the identification of low-abundance arginine/lysine methylpeptides. This method led to a 50% increase in methylation identifications, with a total of 333 forms identified in this study.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Multidisciplinary Sciences
Arvind S. Pillai, Shane A. Chandler, Yang Liu, Anthony Signor, Carlos R. Cortez-Romero, Justin L. P. Benesch, Arthur Laganowsky, Jay F. Storz, Georg K. A. Hochberg, Joseph W. Thornton
Article
Chemistry, Analytical
Shiyu Dong, Mehdi Shirzadeh, Liqi Fan, Arthur Laganowsky, David H. Russell
ANALYTICAL CHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Samantha Schrecke, Yun Zhu, Jacob W. McCabe, Mariah Bartz, Charles Packianathan, Minglei Zhao, Ming Zhou, David Russell, Arthur Laganowsky
Summary: The study shows that the two isoforms of K(2P)4.1 have distinct preferences for binding to lipids, including acyl chain length, position, and fatty acid linkage. Phosphatidic acid has the best activation effect on the channel.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Truc Viet Pham, Drake M. Mellott, Zahra Moghadamchargari, Kevin Chen, Inna Krieger, Arthur Laganowsky, James C. Sacchettini, Thomas D. Meek
Summary: This study identified cis-2,3-epoxysuccinate as the most potent inactivator of Mycobacterium tuberculosis ICL1, providing a new lead for the development of antituberculosis agents.
ACS CHEMICAL BIOLOGY
(2021)
Article
Chemistry, Analytical
Jacob W. McCabe, Mehdi Shirzadeh, Thomas E. Walker, Cheng-Wei Lin, Benjamin J. Jones, Vicki H. Wysocki, David P. Barondeau, David E. Clemmer, Arthur Laganowsky, David H. Russell
Summary: The stability and structure of proteins are influenced by various factors in their local environment, and a new variable-temperature electrospray ionization (vT-ESI) source has been developed to study the effects of temperature on protein folding and ligand binding. This apparatus allows for rapid and precise control of solution temperature changes, enabling research on temperature-dependent protein reactions with high efficiency.
ANALYTICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Zahra Moghadamchargari, Mehdi Shirzadeh, Chang Liu, Samantha Schrecke, Charles Packianathan, David H. Russell, Minglei Zhao, Arthur Laganowsky
Summary: This study investigated the interaction of oncogenic Ras mutants with SOS using native ion mobility-mass spectrometry and structural analysis, revealing different molecular assemblies and the potent modulatory effects of certain mutants on SOS. The findings provide insights into potential therapeutic interventions for Ras-driven cancers.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Analytical
Tarick J. El-Baba, Shannon A. Raab, Rachel P. Buckley, Christopher J. Brown, Corinne A. Lutomski, Lucas W. Henderson, Daniel W. Woodall, Jiangchuan Shen, Jonathan C. Trinidad, Hengyao Niu, Martin F. Jarrold, David H. Russell, Arthur Laganowsky, David E. Clemmer
Summary: The method characterizes the thermal stabilities of endogenous proteins and protein assemblies in complex mixtures by directly measuring melting transitions. Structural transitions related to protein complexes can be monitored based on changes in charge states and masses.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Linfeng Li, Bala C. Chenna, Kai S. Yang, Taylor R. Cole, Zachary T. Goodall, Miriam Giardini, Zahra Moghadamchargari, Elizabeth A. Hernandez, Jana Gomez, Claudia M. Calvet, Jean A. Bernatchez, Drake M. Mellott, Jiyun Zhu, Andrew Rademacher, Diane Thomas, Lauren R. Blankenship, Aleksandra Drelich, Arthur Laganowsky, Chien-Te K. Tseng, Wenshe R. Liu, A. Joshua Wand, Jorge Cruz-Reyes, Jair L. Siqueira-Neto, Thomas D. Meek
Summary: A novel class of self-masked aldehyde inhibitors has been developed for the major cysteine protease of Chagas disease, showing potent and reversible inhibition while potentially improving pharmacokinetic properties. The study also elucidated the kinetic and chemical mechanism of these inhibitors and applied the strategy to design anti-SARS-CoV-2 drugs.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Shannon A. Raab, Tarick J. El-Baba, Arthur Laganowsky, David H. Russell, Stephen J. Valentine, David E. Clemmer
Summary: The article discusses the impact of differences in time scales between protons and proteins on the conformation trapping during the electrospray process. It highlights the mechanisms of conformational changes and proton exchange at different time scales, as well as the immobilization of protons specific to protein conformations in the vacuum of the mass spectrometer.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Review
Biophysics
Arthur Laganowsky, David E. Clemmer, David H. Russell
Summary: This review highlights the application of vT-ESI-MS in studying the structures and thermodynamic properties of proteins and their interactions with ligands. The technology provides direct measurements of stability and heat-induced processes in different conformers of proteins.
ANNUAL REVIEW OF BIOPHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Pei Qiao, Samantha Schrecke, Jixing Lyu, Yun Zhu, Tianqi Zhang, Amanda Benavides, Arthur Laganowsky
Summary: The study found that Kir3.4 displays binding preferences for PIPs, and the interactions between Kir3.4 and PIPs are weaker compared to Kir3.2. Additionally, the type of acyl chains can influence the binding preferences of Kir3.4 for PIPs.
Article
Chemistry, Physical
Pei Qiao, Samantha Schrecke, Thomas Walker, Jacob W. McCabe, Jixing Lyu, Yun Zhu, Tianqi Zhang, Smriti Kumar, David Clemmer, David H. Russell, Arthur Laganowsky
Summary: This study used variable-temperature native mass spectrometry to investigate the thermodynamics of lipid binding events to the human G-protein-gated inward rectifier potassium channel, Kir3.2, revealing distinct thermodynamic strategies for different types of phosphatidylinositol and phosphorylated forms. The acyl chain of the lipid and the number of phosphate groups have significant impacts on the binding thermodynamics, with entropy and enthalpy playing key roles in the interactions.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Drake M. Mellott, Dan Torres, Inna Krieger, Scott A. Cameron, Zahra Moghadamchargari, Arthur Laganowsky, James C. Sacchettini, Thomas D. Meek, Lawrence D. Harris
Summary: The research shows that 5-NIC can serve as an effective inactivator of ICL1. Its design aims to lower the overall charge for improved cell permeability, facilitating the synthesis of pro-drug forms for M. tuberculosis cell-infection models.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemical Research Methods
Jacob W. McCabe, Benjamin J. Jones, Thomas E. Walker, Robert L. Schrader, Adam P. Huntley, Jixing Lyu, Nathan M. Hoffman, Gordon A. Anderson, Peter T. A. Reilly, Arthur Laganowsky, Vicki H. Wysocki, David H. Russell
Summary: This study presents a digital-waveform dual-quadrupole mass spectrometer to improve the performance of a drift tube FT-IMS high-resolution Orbitrap mass spectrometer in studying large proteins and protein complexes. The dual-quadrupole analyzer allows for low-energy collisional activation of ions and precise mass selection using digital-waveform technology, enhancing the capabilities of the instrument at a lower cost compared to traditional RF drivers.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Chemistry, Multidisciplinary
Mia L. Abramsson, Cagla Sahin, Jonathan T. S. Hopper, Rui M. M. Branca, Jens Danielsson, Mingming Xu, Shane A. Chandler, Nicklas Osterlund, Leopold L. Ilag, Axel Leppert, Joana Costeira-Paulo, Lisa Lang, Kaare Teilum, Arthur Laganowsky, Justin L. P. Benesch, Mikael Oliveberg, Carol Robinson, Erik G. Marklund, Timothy M. Allison, Jakob R. Winther, Michael Landreh
Summary: The presence of ionizable side chains in proteins affect their charging under native conditions, with preferential protonation sites. Absence of ionizable side chains results in similar charge state distributions under native-like and denaturing conditions, while an excess of ionizable side chains effectively modulates protein ion stability.