Article
Multidisciplinary Sciences
Terry Z. H. Gani, Zachariah J. Berkson, Ran Zhu, Jong Hun Kang, John R. Di Iorio, Ka Wing Chan, Daniel F. Consoli, Sohel K. Shaikh, Christophe Coperet, Yuriy Roman-Leshkov
Summary: The authors identify a dynamic site renewal and decay cycle, mediated by proton transfers involving proximal BrOnsted acidic OH groups, which operates concurrently with the Chauvin cycle and could address roadblocks associated with industrial metathesis processes. This cycle can be manipulated using small quantities of promoter olefins to drastically increase steady-state propylene metathesis rates, with negligible promoter consumption, showing potential applicability to other reactions. The increase in activity and reduction of operating temperature requirements were also observed on MoOx/SiO2 catalysts, indicating the broad scope of this strategy in addressing major challenges in industrial metathesis processes.
Article
Engineering, Environmental
Jing He, Peiwen Wu, Linlin Chen, Hongping Li, Mingqing Hua, Linjie Lu, Yongqing Wei, Yanhong Chao, ShuaiShuai Zhou, Wenshuai Zhu, Huaming Li
Summary: Ti3C2 MXene with dynamically-generated TiO2 active site shows enhanced catalytic oxidative desulfurization performance, attributed to its abundant interface engineering and loosely layered structure. The expanded slit layer in Ti3C2 MXene provides more pores and cavities for accelerated mass transfer, leading to efficient removal of sulfides in diesel. Additionally, the dynamically-generated active sites from continuous activation of molecular oxygen and Ti3C2 MXene play a key role in enhancing the catalytic activity.
CHEMICAL ENGINEERING JOURNAL
(2021)
Article
Cell Biology
Can Ozden, Roman Sloutsky, Tomohiro Mitsugi, Nicholas Santos, Emily Agnello, Christl Gaubitz, Joshua Foster, Emily Lapinskas, Edward A. Esposito, Takeo Saneyoshi, Brian A. Kelch, Scott C. Garman, Yasunori Hayashi, Margaret M. Stratton
Summary: This study investigates the activation mechanism of CaMKII using X-ray crystallography, molecular dynamics simulations, and biochemistry. The results show that contrary to the previously believed two distinct sites, activators and substrates actually bind to a single continuous site on the kinase domain. Through kinetic competition with the regulatory segment, high-affinity binding partners sustain the activity of CaMKII, allowing substrate phosphorylation.
Article
Chemistry, Physical
Setare Mostajabi Sarhangi, Dmitry V. Matyushov
Summary: This study investigates the process of electron transfer in the conductivity relay of azurin through theoretical analysis and molecular dynamics simulations. It is found that oxidation of tryptophan leads to electrowetting of the residue, resulting in nonparabolic free energy surfaces for electron transfer. The medium dynamics, including Stokes-shift dynamics and the modulation of electron tunneling through the donor-acceptor distance, affect protein electron transfer. The equilibrium donor-acceptor distance is determined by protein-water dynamics and is not affected by the probability of electron tunneling, which puts most intraprotein electron-transfer reactions under dynamical control.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Cell Biology
Haibo Dong, Yue Feng, Yang Yang, Yun Hu, Yimin Jia, Shu Yang, Nannan Zhao, Ruqian Zhao
Summary: The study identified a novel function of PCK2 in mediating LPS-induced inflammation and provided mechanistic insights into the regulation of inflammatory responses in Kupffer cells. PCK2 overexpression significantly increased inflammation markers, while PCK2 knockdown or inhibition mitigated LPS-induced inflammatory response in Kupffer cells. Additionally, PCK2 promoted protein phosphorylation of NF-kappa B and AKT/MAPK, the major signaling pathways controlling inflammatory cascade activation.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Qingda Wang, Huanjie Li, Yongzhen Xia, Luying Xun, Huaiwei Liu
Summary: This study presents a structure of Saccharomyces cerevisiae rhodanese 2 (RDL2) co-crystallized with thiosulfate, revealing the critical roles of Arg and Thr in sulfane sulfur transfer. It suggests that Arg may provide an acidic microenvironment for thiosulfate decomposition in RDL2. This finding may explain the catalyzing mechanism of rhodaneses.
Article
Plant Sciences
Minchae Kim, Soongon Jeong, Chae Woo Lim, Sung Chul Lee
Summary: Protein phosphorylation by kinase is crucial for adapting to drought stress conditions, and CaDIMK1 has been identified as a positive modulator of drought tolerance and ABA signal transduction in pepper plants.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Microbiology
Ting Lu, Yanping Zhu, Xue Ni, Xia Zhang, Yang Liu, Xiqing Cui, Xiuhua Pang
Summary: In this study, the critical residue D53 of the global regulator MtrA in Streptomyces venezuelae was identified as a potential phosphorylation site. Substitutions at the D53 site affected the ability of MtrA to bind its recognition sequences and resulted in aberrant production of chloramphenicol and jadomycin. The study demonstrates the importance of the predicted phosphorylation site D53 for the regulation of MtrA and suggests that MtrA functions in a phosphorylated form in Streptomyces.
MICROBIOLOGY SPECTRUM
(2022)
Article
Plant Sciences
Shuangxi Zhang, Huachun Sheng, Yue Ma, Yanping Wei, Dan Liu, Yanhua Dou, Huiying Cui, Boyou Liang, Johannes Liesche, Jisheng Li, Shaolin Chen
Summary: This study reveals that the phosphorylation of Arabidopsis cellulose synthase 1 (AtCESA1) plays a role in regulating pectin synthesis and methylesterification in seed coat mucilage. Through the construction of mutant and transgenic lines, it was found that the phosphorylation state of AtCESA1 at the T166 site can affect the cell wall organization, as well as the levels and methylesterification of pectin and cellulose in seeds. Therefore, the phosphorylation of AtCESA1 is important for the regulation of seed development.
JOURNAL OF PLANT PHYSIOLOGY
(2022)
Article
Microbiology
Krishna Kumar Singh, P. J. Athira, Neerupma Bhardwaj, Devendra Pratap Singh, Uchenna Watson, Deepak Kumar Saini
Summary: The study demonstrates that the essential response regulator protein MtrA in Mycobacterium tuberculosis undergoes non-enzymatic acetylation through acetyl phosphate, independent of phosphorylation. Acetylation of MtrA enhances its phosphorylation and interaction with its sensor kinase MtrB, while also affecting its DNA-binding ability on gene targets. Acetylation is proposed as a dominant post-translational modification overriding phosphorylation to regulate the activities of MtrA in M. tuberculosis.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Zhizeng Sun, Timothy Palzkill
Summary: The study identified essential active-site residues of the MCR-1 enzyme using deep sequencing, which are critical for its polymyxin resistance function. Approximately 75% of the residues examined were found to be essential for the enzyme's function, suggesting inhibitors binding near these sites will broadly inhibit MCR-1 and similar enzymes.
Article
Biochemistry & Molecular Biology
Claus Schmitz, Mariusz Madej, Zuzanna Nowakowska, Anna Cuppari, Anna Jacula, Miroslaw Ksiazek, Katarzyna Mikruta, Jerzy Wisniewski, Natalia Pudelko-Malik, Anshu Saran, Natalie Zeytuni, Piotr Mlynarz, Richard J. Lamont, Isabel Uson, Virginijus Siksnys, Jan Potempa, Maria Sola
Summary: The PglZ family of proteins belongs to the alkaline phosphatase superfamily, and the structure and function of PglZ family proteins have not been well studied. This research investigated the structure and function of PorX, an orphan response regulator containing a putative PglZ effector domain. PorX was found to have an active site cleft suitable for large substrates and acts as a phosphodiesterase on cyclic and linear oligonucleotides.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Alessandro Falconieri, Sara De Vincentiis, Valentina Cappello, Domenica Convertino, Ravi Das, Samuele Ghignoli, Sofia Figoli, Stefano Luin, Frederic Catala-Castro, Laura Marchetti, Ugo Borello, Michael Krieg, Vittoria Raffa
Summary: Mechanical force plays a crucial role in guiding axon outgrowth and synapse formation, and this process is known as stretch growth. However, the mechanism of how neurons convert mechanical input into signaling pathways is still not well understood. Additionally, the coordination between stretch growth and the addition of new mass along the axon remains unanswered. In this study, it is demonstrated that magnetic nano-pulling induces remodeling of the axonal cytoskeleton, leading to an increase in microtubule density and subsequent accumulation of organelles and signaling vesicles. This promotes local translation and sustains enhanced axon outgrowth and synapse maturation.
Article
Chemistry, Medicinal
Dhanaji M. Lade, Roxy Nicoletti, James Mersch, Yehenew M. Agazie
Summary: SHP2 is an important oncogene in cancers driven by overexpression of receptor tyrosine kinases. In this study, we developed an optimized derivative BPDA2 as an SHP2 inhibitor with increased potency and selectivity, and demonstrated its efficacy and selectivity in cellular assays.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Callista B. Harper, Eva-Maria Blumrich, Michael A. Cousin
Summary: The study highlights the crucial role of the cytoplasmic C terminus of synaptophysin (Syp) in facilitating the accurate retrieval of synaptobrevin-II (SybII) during synaptic vesicle endocytosis. Neurons lacking Syp show defects in SybII retrieval, emphasizing the importance of a conformational change within the Syp C terminus for proper binding and retrieval. Importantly, the study suggests that Syp's presynaptic role is specifically related to the control of SybII retrieval, without affecting the kinetics of synaptic vesicle endocytosis at physiological temperatures.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Stephani C. Page, Ruth E. Silversmith, Edward J. Collins, Robert B. Bourret
Article
Biochemistry & Molecular Biology
Robert M. Immormino, Chrystal A. Starbird, Ruth E. Silversmith, Robert B. Bourret
Article
Microbiology
Stephani C. Page, Robert M. Immormino, Thane H. Miller, Robert B. Bourret
JOURNAL OF BACTERIOLOGY
(2016)
Article
Biochemistry & Molecular Biology
Ruth E. Silversmith, Boya Wang, Nanette B. Fulcher, Matthew C. Wolfgang, Robert B. Bourret
JOURNAL OF BIOLOGICAL CHEMISTRY
(2016)
Editorial Material
Microbiology
Robert B. Bourret
JOURNAL OF BACTERIOLOGY
(2017)
Editorial Material
Biochemistry & Molecular Biology
Robert Bourret, Karen Ottemann, John D. Helmann
MOLECULAR MICROBIOLOGY
(2017)
Editorial Material
Microbiology
Christine Josenhans, Robert B. Bourret, Karen Ottemann, Rasika Harshey, Ariane Briegel, Alan Wolfe, Birgit E. Scharf
Article
Microbiology
Philip B. Straughn, Luke R. Vass, Chase Yuan, Emily N. Kennedy, Clay A. Foster, Robert B. Bourret
JOURNAL OF BACTERIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Clay A. Foster, Ruth E. Silversmith, Robert M. Immormino, Luke R. Vass, Emily N. Kennedy, Yael Pazy, Edward J. Collins, Robert B. Bourret
Summary: Two-component signaling is a major mechanism through which microorganisms interact with their environments. The study focused on the role of certain variable residues in response regulators, revealing their effect on phosphorylation kinetics and activity. Additionally, the research identified how specific positions influence the receiver domain conformation.
Article
Microbiology
Emily N. Kennedy, Sarah A. Barr, Xiaolin Liu, Luke R. Vass, Yanan Liu, Zhihong Xie, Robert B. Bourret
Summary: Azorhizobium caulinodans is a nitrogen-fixing bacterium with a symbiotic relationship with plants that is important in lowland rice cultivation. The bacterium utilizes a unique chemotaxis system, with CheY1 and CheY2 playing key roles in the signaling pathway. A concerted mechanism involving CheA, CheY2, and CheZ is proposed as a novel scheme for regulating chemotactic responses.
JOURNAL OF BACTERIOLOGY
(2022)
Article
Microbiology
Robert B. Bourret, Clay A. Foster, William E. Goldman
Summary: The study revealed the diversity of receiver domains in fungal two-component regulatory systems, with significant differences in structure and function, suggesting their important roles in signal transduction; Fungal receiver domains exhibit unique amino acid patterns, proposing multiple experimentally testable hypotheses about the signal transduction mechanisms.
Article
Biochemistry & Molecular Biology
Luke R. Vass, Katie M. Branscum, Robert B. Bourret, Clay A. Foster
Summary: Domains are the fundamental building blocks of proteins, and their variability across different architectural contexts can provide insights into protein function and guide experimental priorities. In this study, we developed an approach to evaluate the variability in amino acid sequences of a single domain across different architectures, and applied it to CheW-like domains. We identified different classes of CheW-like domains with presumed functional differences, and also created a visualization method called SimpLogo for comparing and analyzing related protein sequences.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Luke R. Vass, Robert B. Bourret, Clay A. Foster
Summary: The ability to control microorganism locomotion in a dynamic environment provides them with a competitive advantage and drives the evolution of regulatory systems. Chemotaxis systems control motility and other cellular functions through the separation of receptor and kinase functions, linked by CheW scaffold proteins. Recent analysis on CheW-like domains in various proteins reveals different classes and architectures that exhibit specialized functional interactions. Co-occurrence analyses suggest synergy or antagonism among chemotaxis systems, and certain protein architectures preferentially occur with specific categories of these systems.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Review
Biochemistry & Molecular Biology
Emily N. Kennedy, Clay A. Foster, Sarah A. Barr, Robert B. Bourret
Summary: This article reviews several methods for using abundant sequence data to guide experimental research, including analyzing coevolutionary relationships, functional important residue positions, and domain variation prediction. These methods provide insights into the structure and function of protein families. Although applicable to different protein types, some of these methods have been used infrequently, offering new opportunities for research.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2022)