Article
Engineering, Biomedical
Peng Hou, Yu Sun, Weichao Yang, Hongliu Wu, Luyuan Sun, Xinjie Xiu, Chaoyang Xiu, Xiaonong Zhang, Wen Zhang
Summary: Magnesium ion (Mg2+) stimulates osteogenesis and activates the transcription of OPN through the CaM/CaMKIV/CREB1 signaling pathway, leading to increased cell proliferation and OPN expression.
JOURNAL OF BIOMEDICAL MATERIALS RESEARCH PART B-APPLIED BIOMATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Jio Song, Eung Take Lee, Ji Hyun Lee, Gyu Hyun Kim, Yong Hyun Lee, Jae Kweon Park
Summary: The purpose of this study is to improve the method for characterizing enzyme kinetics on chitin and address the inconvenience of colloidal chitin production and use. By partially hydrolyzing and acetylating high molecular weight chitosan, a low molecular weight substrate was prepared. The study confirmed the activity of chitinase under optimal reaction conditions using acetylated low molecular weight chitin.
PROCESS BIOCHEMISTRY
(2023)
Article
Chemistry, Organic
Asif Fazal, Jake Wheeler, Michael E. Webb, Ryan F. Seipke
Summary: SurE is a peptide cyclase essential for the production of surugamide antibiotics. However, the substrate specificity of this enzyme is not well understood. In order to address this issue, researchers developed a new assay to investigate the chemical space of the N-terminal substrate residue.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Sumita Roy, Mirella Vivoli Vega, Jessica R. Ames, Nicole Britten, Amy Kent, Kim Evans, Michail N. Isupov, Nicholas J. Harmer
Summary: N-acetyl-D-glucosamine (GlcNAc) is an important component in bacterial cell walls and its metabolism starts with phosphorylation to GlcNAc-6-phosphate. The ROK kinase NagK is responsible for this step in bacteria. In this study, the structure of NagK in complex with GlcNAc and ATP analog AMP-PNP was solved, revealing conformational changes and a sequential random enzyme mechanism. Molecular dynamics modeling and site-directed mutagenesis further confirmed the essential catalytic metal and base residues. Overall, this study provides comprehensive insights into the activity of ROK kinases.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Letter
Chemistry, Physical
Dan Su, Tatsiana Kosciuk, Hening Lin
Summary: This article concludes that binding affinity is crucial for in vivo substrate specificity and proposes a method to identify substrate proteins for enzymes by utilizing existing interactome data. The Reply aims to clarify important points in the original article.
Article
Microbiology
Bradley Benjamin, Yehuda Goldgur, Nikolaus Jork, Henning J. J. Jessen, Beate Schwer, Stewart Shuman
Summary: The fission yeast Schizosaccharomyces pombe phosphate regulon is sensitive to the level of the inositol pyrophosphate signaling molecule 1,5-IP8. The enzyme Asp1, consisting of a kinase domain and a pyrophosphatase domain, plays a crucial role in determining the dynamics of IP8. Crystal structures of the Asp1 kinase domain reveal its conformational changes upon ligand binding and its substrate specificity. Wild-type Asp1 kinase can utilize N-6-benzyl-ATP as a phosphate donor.
Article
Chemistry, Physical
Dan Su, Tatsiana Kosciuk, Min Yang, Ian R. Price, Hening Lin
Summary: Kinetic parameters are commonly used to characterize enzymes, but the substrate specificity of enzymes like NMT1 is actually determined by their binding affinity for different substrates rather than traditional kinetic values. Understanding this allows for the discovery of new substrate proteins through interactions with enzymes that catalyze post-translational modifications.
Article
Biochemistry & Molecular Biology
Ilona Faustova, Kaidi Moll, Ervin Valk, Mart Loog, Mihkel Ord
Summary: Cyclins not only activate CDK complexes, but also serve as docking scaffolds for CDK substrates and inhibitors. G1-cyclins in yeast play a specific role in promoting bud growth and polarization, essential for cell survival. The discovery of a specific docking motif in G1-cyclins expands our understanding of cyclin specificity mechanisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Physical
Sai Pooja Mahajan, Yashes Srinivasan, Jason W. Labonte, Matthew P. DeLisa, Jeffrey J. Gray
Summary: This study decoded the sequence and structural motifs determining peptide substrate preferences for the GalNAc-T2 isoform, revealing enzyme features that lead to finely tuned specificity for a broad range of peptide substrates. Computational scanning and experimental validation successfully discriminated glycosylatable peptides with high efficiency, providing insights for designing enzyme variants with tailored specificity in the future.
Article
Microbiology
Yakun Fang, Fan Liu, Yi Shi, Ting Yang, Yu Xin, Zhenghua Gu, Guiyang Shi, Liang Zhang
Summary: TrLipE is a thermophilic lipase with potential commercial applications due to its catalytic ability under extreme conditions. By constructing chimeras between TrLipE and structurally similar enzymes, it was found that these chimeras had similar pH range and optimum pH as TrLipE but a narrower temperature range of 40-80 degrees C. Most chimeras showed lower Km and higher kcat values compared to TrLipE when using p-nitrophenol esters as substrates.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Pavlina Nekvasilova, Natalia Kulik, Michael Kotik, Lucie Petraskova, Kristyna Slamova, Vladimir Kren, Pavla Bojarova
Summary: By targeting a mutation hotspot on the active site, researchers successfully changed the substrate specificity of β-N-acetylhexosaminidase. The best single mutant variant showed an 8-fold increase in selectivity towards GlcNAc, and some variants exhibited stronger transglycosylation capabilities compared to the wild-type.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Takfarinas Kentache, Leopold Thabault, Gladys Deumer, Vincent Haufroid, Raphael Frederick, Carole L. Linster, Alessio Peracchi, Maria Veiga-da-Cunha, Guido T. Bommer, Emile Van Schaftingen
Summary: N-acetylneuraminate (Neu5Ac) is a sugar commonly found in vertebrates and some bacteria, serving as an energy source for certain prokaryotes like Escherichia coli. The aldolase NanA in E. coli and its human homolog NPL were found to preferentially metabolize the open form of Neu5Ac. Additionally, the Neu5Ac anomerase NanM was able to stimulate the utilization of both beta and alpha-anomers by NanA in vitro.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Hieu Nguyen, Arminja N. Kettenbach
Summary: Dynamic protein phosphorylation and dephosphorylation play critical roles in cellular signaling and biological functions. Dysregulation of these processes has been linked to various human diseases. This review focuses on the mechanisms controlling the specific dephosphorylation of proteins. The majority of serine/threonine dephosphorylation is catalyzed by highly conserved phosphoprotein phosphatase (PPP) catalytic subunits, which form holoenzymes with regulatory and scaffolding subunits. PPP holoenzymes recognize phosphorylation site consensus motifs and interact with short linear motifs (SLiMs) or structural elements distal to the phosphorylation site. Recent advances in understanding the mechanisms of PPP site-specific dephosphorylation preference and substrate recruitment are discussed, with emphasis on their roles in regulating cell division.
TRENDS IN BIOCHEMICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Jose Carlos Bozelli, Jenny Yune, Daisuke Takahashi, Fumio Sakane, Richard M. Epand
Summary: The physical properties of membranes determine the substrate acyl chain specificity of human DGK alpha, affecting its enzymatic activity and ability to differentiate between DAG molecular species. Changes in membrane morphology, particularly the presence of physically curved membrane structures, impact the specificity of DGK alpha for certain DAG pools, adding a layer of regulation to the interconversion between DAG and PA. This suggests a fine-tuned signaling system dependent on the levels and molecular species of DAG and PA regulated by the interplay between membrane physical and chemical properties.
Article
Chemistry, Multidisciplinary
Elias Englund, Matthias Schmidt, Alberto A. Nava, Anna Lechner, Kai Deng, Renee Jocic, Yingxin Lin, Jacob Roberts, Veronica T. Benites, Ramu Kakumanu, Jennifer W. Gin, Yan Chen, Yuzhong Liu, Christopher J. Petzold, Edward E. K. Baidoo, Trent R. Northen, Paul D. Adams, Leonard Katz, Satoshi Yuzawa, Jay D. Keasling
Summary: This study successfully altered the extension substrates of modular polyketide synthases (PKSs) by exchanging acyltransferase (AT) domains, resulting in the synthesis of 13 structurally different polyketides in vitro. The results greatly enhance our understanding of rare AT domains and demonstrate the benefit of using PKS engineering strategy to produce novel chemicals in vitro.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)