Article
Biochemistry & Molecular Biology
Daniel W. Bak, Eranthie Weerapana
Summary: This study describes a chemoproteomic strategy that monitors changes in the reactivity of Fe-S cysteine ligands to inform on Fe-S cluster occupancy and demonstrates its utility in Escherichia coli. The results show global disruptions in Fe-S incorporation in cells cultured under iron-depleted conditions, identify Fe-S client proteins reliant on scaffold, carrier, and chaperone proteins within the Isc Fe-S biogenesis pathway, and identify two previously unannotated Fe-S proteins, TrhP and DppD.
NATURE CHEMICAL BIOLOGY
(2023)
Editorial Material
Cell Biology
Sarah E. Bondos, A. Keith Dunker, Vladimir N. Uversky
Summary: The sequence -> structure -> function paradigm is primarily applicable to enzymes, transmembrane proteins, and signaling domains, while the sequence -> IDP/IDR ensemble -> function paradigm is primarily applicable to signaling and regulatory proteins and regions. Disorder contributes to signaling in a broad spectrum of species, playing diverse roles in responding to signals and orchestrating organismal processes.
CELL COMMUNICATION AND SIGNALING
(2021)
Article
Biochemistry & Molecular Biology
Parool Gupta, Rani Mansuri, Priya Priydarshni, Sachidananda Behera, Amir Zaidi, Shamshun Nehar, Ganesh Chandra Sahoo, Krishna Pandey, Vahab Ali
Summary: This study revealed the interaction between two proteins, Cfd1 and Nbp35, in L. donovani, forming a stable complex involved in the cellular process of Fe-S cluster biogenesis and transfer. The upregulation of Cfd1 and Nbp35 proteins in drug-resistant parasites leads to increased Fe-S protein levels, promoting parasite survival under drug pressure.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Melissa Jansing, Steffen Mielenbrink, Hannah Rosenbach, Sabine Metzger, Ingrid Span
Summary: This study compares the effects of three different maturation strategies on three well-established [4Fe-4S] proteins. The results show that co-expression of the genes for iron-sulfur cluster biogenesis pathway can improve protein yield and cluster content. In vivo maturation can reduce the formation of iron-sulfur aggregates that commonly occur in chemical reconstitution. The study also demonstrates the potential of using in vivo maturation strategies for proteins previously only matured by chemical reconstitution.
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY
(2023)
Article
Microbiology
Ashutosh S. Tripathi, Kushi Anand, Mayashree Das, Ruchika Annie O'Niel, Chandrani Thakur, Raghunatha Reddy R. L., Raju Rajmani, Nagasuma Chandra, Sunil Laxman, Amit Singh
Summary: This study identifies a novel critical protein, SufT, in Mtb that plays an important role in the maturation of Fe-S clusters. SufT interacts with other proteins to regulate Fe-S cluster biogenesis in Mtb and affects the survival, metabolism, and infectivity of Mtb.
Article
Plant Sciences
Jonathan Przybyla-Toscano, Andrew E. Maclean, Marina Franceschetti, Daniela Liebsch, Florence Vignols, Olivier Keech, Nicolas Rouhier, Janneke Balk
Summary: NFU4 and NFU5 proteins in plants have a housekeeping function and are involved in the lipoylation process of mitochondrial dehydrogenases, providing Fe-S clusters to lipoyl synthase.
Article
Biochemistry & Molecular Biology
Chie Ueda, Michelle Langton, Jiahua Chen, Maria-Eirini Pandelia
Summary: HBx protein, a key regulatory factor of hepatitis B virus, is associated with liver diseases. This study reveals that HBx protein binds to Fe-S cluster and undergoes a reductive transformation similar to Fe-S scaffold proteins. This discovery uncovers previously unknown molecular properties of HBx protein and provides insights into the roles of HBx-related iron regulation and reactive oxygen species in liver tumorigenesis.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Review
Biochemistry & Molecular Biology
Leszek Rydz, Maria Wrobel, Halina Jurkowska
Summary: Mitochondria are crucial organelles for the synthesis of Fe-S clusters, with sulfurtransferases playing a key role. Fe-S clusters are essential for Fe-S proteins, susceptible to oxidative stress but capable of being resynthesized or repaired. Sulfurtransferases are involved in the formation, maturation, and reconstitution of Fe-S clusters.
Article
Chemistry, Inorganic & Nuclear
Juan He, Jia Wei, Gan Xu, Xu-Dong Chen
Summary: The rational construction of versatile Mo-Fe-S cubane clusters was achieved using a LEGO strategy, providing a controlled synthesis method for biomimetic chemistry.
INORGANIC CHEMISTRY
(2022)
Article
Chemistry, Inorganic & Nuclear
Lian Xue, Gan Xu, Zheng Wang, Xu-Dong Chen
Summary: Mimicking the nitrogenase FeMo cofactor has been a longstanding challenge in synthetic inorganic chemistry and bioinorganic chemistry. The discovery of an interstitial light atom, later identified as carbide, made this task even more difficult. A controlled synthetic strategy named redox metathesis was utilized to successfully synthesize nitride-incorporated edge-bridged double cubane (N-EBDC) W-Fe-S clusters, with various terminal ligand substitutions affecting the cluster cores' structures and redox behaviors. This study provides valuable insights for the structural and functional mimicking of nitrogenase Fe-S clusters.
DALTON TRANSACTIONS
(2021)
Review
Microscopy
Tiara V. Hinton, Sharon Batelu, Noah Gleason, Timothy L. Stemmler
Summary: Fe-S clusters play crucial roles in biochemical pathways in living organisms, synthesizing through mitochondrial and cytosolic pathways in eukaryotes. Deficiency in Fe-S clusters can be detrimental to cell and organism viability.
Article
Biochemistry & Molecular Biology
Przemyslaw Wieczorek, Artur Jarmolowski, Zofia Szweykowska-Kulinska, Maciej Kozak, Michal Taube
Summary: MicroRNA biogenesis in plants involves the assembly of molecular processes governed by three proteins: DCL1, SERRATE, and HYL1. HYL1 protein acts as a crucial player by binding to double-stranded RNA and facilitating the excision of miRNA from primary miRNA transcripts. HYL1 protein is also involved in loading miRNA molecules onto AGO1 endonuclease, and its phosphorylation status regulates miRNA levels. The C-terminal domain of HYL1 protein plays a role in dimer formation and stabilization.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2023)
Article
Biochemistry & Molecular Biology
Mirjana M. Maljkovic, Nenad S. Mitic, Alexandre G. de Brevern
Summary: This study focuses on predicting Protein Blocks (PBs) from amino acid sequences using different data mining approaches and machine learning algorithms. The constructed models show varying importance of input attributes among algorithms. Utilizing information about amino acids in intrinsically disordered regions and repeats can improve the prediction accuracy for some PBs.
Article
Chemistry, Physical
Xiaoqiang Du, Jiaxin Li, Kaicheng Tong, Xiaoshuang Zhang
Summary: In this study, an efficient quinary sulfur selenide metal material was synthesized and applied in supercapacitors. The material exhibited high specific capacitance and excellent cycling stability, showing potential for energy conversion and transportation applications.
JOURNAL OF ALLOYS AND COMPOUNDS
(2022)
Article
Multidisciplinary Sciences
Beth Kelly, Gustavo E. Carrizo, Joy Edwards-Hicks, David E. Sanin, Michal A. Stanczak, Chantal Priesnitz, Lea J. Flachsmann, Jonathan D. Curtis, Gerhard Mittler, Yaarub Musa, Thomas Becker, Joerg M. Buescher, Erika L. Pearce
Summary: The behavior of Dictyostelium discoideum is dependent on nutrients, existing as unicellular organisms in the presence of sufficient food and aggregating into multicellular organisms upon starvation. The generation of reactive oxygen species due to nutrient limitation leads to the sequestration of cysteine in the antioxidant glutathione, limiting its sulfur atom usage and maintaining the organism in a nonproliferating state conducive to multicellular development. This mechanism of signaling through reactive oxygen species highlights the roles of oxygen and sulfur as simple signaling molecules in dictating cell fate in early eukaryotes, with implications for responses to nutrient fluctuations in multicellular eukaryotes.
Review
Biochemistry & Molecular Biology
Jin Hae Kim, Jameson R. Bothe, T. Reid Alderson, John L. Markley
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
(2015)
Article
Chemistry, Multidisciplinary
Jin Hae Kim, Javier Oroz, Markus Zweckstetter
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2016)
Review
Biochemistry & Molecular Biology
Thomas Reid Alderson, Jin Hae Kim, John Lute Markley
Article
Biochemistry & Molecular Biology
Javier Oroz, Jin Hae Kim, Bliss J. Chang, Markus Zweckstetter
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Javier Oroz, Jin Hae Kim, Bliss J. Chang, Markus Zweckstetter
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2017)
Article
Multidisciplinary Sciences
K. Ogata, S. Jeon, D. -S. Ko, I. S. Jung, J. H. Kim, K. Ito, Y. Kubo, K. Takei, S. Saito, Y. -H. Cho, H. Park, J. Jang, H. -G. Kim, J. -H. Kim, Y. S. Kim, W. Choi, M. Koh, K. Uosaki, S. G. Doo, Y. Hwang, S. Han
NATURE COMMUNICATIONS
(2018)
Article
Chemistry, Multidisciplinary
Jin Hae Kim, T. Reid Alderson, Ronnie O. Frederick, John L. Markley
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2014)
Review
Biochemistry & Molecular Biology
Federica Saponaro, Jin Hae Kim, Grazia Chiellini
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Review
Biochemistry & Molecular Biology
Jin-Beom Si, Bokyung Kim, Jin Hae Kim
Summary: TTR is a crucial transporter of thyroid hormone and retinol binding protein in human plasma and cerebrospinal fluid, yet it is also known for its amyloidogenic nature leading to various amyloidoses. Research has shown that decreased stability of TTR's native tetrameric conformation is the main cause of these diseases, and recent multidisciplinary investigations have shed light on the mechanistic details of TTR amyloidogenic transformation. Special emphasis has been placed on identifying novel structural features in amyloidogenic species of TTR and discussing the proteolysis-induced fragmentation mechanism that promotes TTR amyloidosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Bokyung Kim, Young Ho Ko, Massimiliano Runfola, Simona Rapposelli, Gabriella Ortore, Grazia Chiellini, Jin Hae Kim
Summary: Thyromimetics, with physicochemical characteristics similar to thyroid hormones, have shown promise as novel therapeutics for neurodegenerative and metabolic pathologies. Particularly, compounds like sobetirome, IS25, and TG68 have been identified as TTR stabilizers and efficient suppressors of TTR aggregation, suggesting their potential as multi-functional therapeutic molecules for TTR-related pathologies, including neurodegenerative diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biology
Srinivasan Muniyappan, Yuxi Lin, Young-Ho Lee, Jin Hae Kim
Summary: Oxygen is essential for maintaining biomolecular structures, regulating physiological processes, and facilitating biomolecular interactions. Oxygen-17 (O-17) has been proposed as a valuable probe to provide detailed information about the physicochemical properties of proteins. Recent advancements in O-17 NMR spectroscopy have revolutionized this methodology, making it a unique and widely applicable tool for determining protein structure and dynamics.
Article
Multidisciplinary Sciences
Jin Hae Kim, Hyokeun Park, Tae-Gon Kim, Hyunmi Lee, Shinae Jun, Eunha Lee, Woo Sung Jeon, Jaegwan Chung, In-Sun Jung
Summary: Colloidal quantum-dots are attractive for optoelectronic applications due to their easy maneuverability, high functionality, wide applicability, and low cost. A new method has been developed to disrupt the interaction between the inorganic particle and organic ligands on the surface of QDs, facilitating accurate analysis of the ligands.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Wonjin Yang, Beom Soo Kim, Srinivasan Muniyappan, Young-Ho Lee, Jin Hae Kim, Wookyung Yu
Summary: Monomer dissociation and misfolding of transthyretin (TTR) are crucial factors in TTR amyloidosis, which causes severe human diseases. Studies have shown that stability of the DAGH beta-sheet and conformational perturbations in TTR may lead to aggregation. MD simulation techniques can provide new insights into transient yet important structural states of amyloidogenic proteins.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Hong-Guen Lee, Jin Hae Kim, Tumpa Gorai, Young Ho Ko, Haw-Young Kwon, Wooseong Chung, Ilha Hwang, Sungsu Lim, Yun Kyung Kim, Kwanwoo Shin, Young-Tae Chang, Kimoon Kim, Kyeng Min Park
Summary: This study presents a new supramolecular approach using a synthetic cell system to control the initiation of protein aggregation and mimic various conditions of lipid membranes. The approach enables systematic investigations of membrane-dependent effects on protein aggregation by visualization. The concurrent use of synthetic cells and natural cells demonstrates the potential of this approach for studying inter- and intracellularly transmittable protein aggregation.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemical Research Methods
Bokyung Kim, Jin Hae Kim
Summary: In this study, various structural features of TTR were investigated using solution-state nuclear magnetic resonance (NMR) spectroscopy, with successful backbone NMR signal assignments reported. The chemical shift information obtained will serve as a valuable basis for further structural and functional studies of TTR.
JOURNAL OF THE KOREAN MAGNETIC RESONANCE SOCIETY
(2021)