Article
Multidisciplinary Sciences
Xiangnan Sun, Linqian Jing, Fengwei Li, Meina Zhang, Xiaotong Diao, Jingjing Zhuang, Fraydoon Rastinejad, Dalei Wu
Summary: This study describes the structural characteristics of NPAS4-ARNT and NPAS4-ARNT2 heterodimers, revealing the unique domain conformation of NPAS4 itself and its differential configuration with ARNT and ARNT2. The study also demonstrates the variable conformations of the PAS-A domains of ARNT and ARNT2 within these heterodimers. These findings provide molecular insights into the architecture of NPAS4 protein and expand the repertoire of heterodimerization patterns within the bHLH-PAS family.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Developmental Biology
Rebecca Oramas, Elizabeth M. Knapp, Baosheng Zeng, Jianjun Sun
Summary: In this study, it was found that both Sim and Tgo transcription factors play important roles in promoting follicle maturation and ovulation in Drosophila.
Article
Biochemistry & Molecular Biology
Yating Wang, Zhiai Xi, Xiuhong Wang, Yuyu Zhang, Yongguo Liu, Shuai Yuan, Shirui Zhao, Jiping Sheng, Demei Meng
Summary: In this study, 10 putative bHLH transcription factors were identified in the edible mushroom A. bisporus, and their role in postharvest development was investigated. The results suggest that these bHLH proteins play a crucial role in the regulation of arginine catabolism and control of postharvest mushroom development.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Chao Ding, Junzhao Gao, Shiya Zhang, Ning Jiang, Dongtao Su, Xinzheng Huang, Zhao Zhang
Summary: This study conducted a comprehensive analysis of the bHLH gene family in roses, revealing their characteristics in terms of gene structure, expression, and function, and identified potential genes associated with resistance to B. cinerea infection.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Jiayi Chen, Fangfang Xie, Kamran Shah, Canbin Chen, Jianmei Zeng, Jiaxuan Chen, Zhike Zhang, Jietang Zhao, Guibing Hu, Yonghua Qin
Summary: In this study, 165 HubHLH genes were identified, and their functions related to betalain biosynthesis in pitaya were revealed. HubHLH159 gene showed high expression level in red-pulp pitaya, and promoted betalain biosynthesis by activating the expression of HuADH1, HuCYP76AD1-1, and HuDODA1.
Article
Multidisciplinary Sciences
Lin Zhang, Wei Chen, Rongrong Liu, Ben Shi, Youju Shu, Haoyu Zhang
Summary: This study identified 122 bHLH family members in the physic nut genome database, demonstrating their essential roles in plant development and abiotic stress. These genes were distributed on specific chromosomes and could be divided into 28 subfamilies. Syntenic analysis and gene expression profiles revealed their association with salinity and drought stresses, as well as their high expression in various tissues. Furthermore, the protein interaction network indicated their involvement in growth, development, and stress signal transduction pathways.
Article
Chemistry, Physical
Stefano Motta, Alessandro Pandini, Arianna Fornili, Laura Bonati
Summary: This study used steered molecular dynamics simulations and self-organizing maps (SOMs) to uncover two unfolding pathways for ARNT PAS-B, in line with AFM experimental findings. Analysis revealed a stable conformation along one pathway, potentially representing a structural model for the intermediate state detected by AFM.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Plant Sciences
Moyan Jia, Jacob Munz, Jenny Lee, Nolan Shelley, Yuan Xiong, Sunjoo Joo, EonSeon Jin, Jae-Hyeok Lee
Summary: Our study identified and characterized the bHLH factor NRI1 in Chlamydomonas, which is required to repress the use of alternative nitrogen sources. NRI1 functions as a critical repressor and coordinates diverse nitrogen starvation-induced responses, providing a crucial first step in understanding how plants and algae cope with fluctuating nitrogen availability.
Article
Plant Sciences
Yang Liu, Ling Lin, Yang Liu, Qiong Mo, Damao Zhang, Weidong Li, Xingyao Xiong, Xiaoying Yu, Yanlin Li
Summary: This study identified the bHLH transcription factor family in Loropetalum chinense var. rubrum and investigated its role in anthocyanin synthesis. Six candidate genes were identified and the function of LcbHLH156 in regulating anthocyanin synthesis was validated. These results provide a foundation for further research on the regulation mechanism of leaf colors in L. chinense var. rubrum.
Review
Biochemistry & Molecular Biology
Hailey E. Edwards, Daniel A. Gorelick
Summary: Proteins containing basic helix-loop-helix (bHLH) and Per-Arnt-Sim (PAS) motifs act as transcription factors. These bHLH-PAS proteins play crucial and diverse roles in the body, including cell specification and differentiation during embryonic development, as well as the proper functioning of organs like the brain and liver in adulthood. They are divided into two classes, forming heterodimers to regulate transcription, with class I proteins being stimulus-specific and class II proteins being more ubiquitously expressed.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2022)
Article
Plant Sciences
Shanshan Jia, Xiaojie Liu, Xuejing Wen, Abdul Waheed, Yu Ding, Gulnaz Kahar, Xiaoshuang Li, Daoyuan Zhang
Summary: This study identified 184 putative MsbHLH genes in M. sieversii and studied their physicochemical properties. These genes play important roles in plant defense responses and are involved in protein-protein interactions. This study provides detailed insights into disease resistance in M. sieversii plants and offers candidate genes for resistance breeding.
Article
Biochemistry & Molecular Biology
Yue Wang, Youwen Zhuang, Jeffrey F. DiBerto, X. Edward Zhou, Gavin P. Schmitz, Qingning Yuan, Manish K. Jain, Weiyi Liu, Karsten Melcher, Yi Jiang, Bryan L. Roth, H. Eric Xu
Summary: Opioids are powerful painkillers with serious side effects. The study examines the binding and selectivity mechanisms of endogenous opioid peptides with opioid receptors, revealing a structural framework for the design of safer pain relief drugs.
Article
Biochemistry & Molecular Biology
David Jakubec, Petr Skoda, Radoslav Krivak, Marian Novotny, David Hoksza
Summary: This article presents significant enhancements to PrankWeb, including more accurate evolutionary conservation estimation and the ability to carry out LBS predictions using the AlphaFold model database.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Genetics & Heredity
Andrew T. Timberlake, Stephen McGee, Garrett Allington, Emre Kiziltug, Erin M. Wolfe, Amy L. Stiegler, Titus J. Boggon, May Sanyoura, Michelle Morrow, Tara L. Wenger, Erica M. Fernandes, Oana Caluseriu, John A. Persing, Sheng Chih Jin, Richard P. Lifton, Kristopher T. Kahle, Paul Kruszka
Summary: Craniosynostosis (CS) is the most common congenital cranial anomaly. Exome sequencing of 526 proband-parent trios with syndromic CS revealed a significant excess of damaging de novo variants (DNVs) in genes intolerant to loss-of-function variation. Several novel genes involved in chromatin modification and remodeling were identified, leading to major implications for genetic testing and counseling.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Horticulture
Tianjiao Shen, Xiaopeng Wen, Zhuang Wen, Zhilang Qiu, Qiandong Hou, Zhengchun Li, Lina Mei, Huanhuan Yu, Guang Qiao
Summary: The study identified 66 bHLH genes in the sweet cherry genome, classified into 17 subfamilies. Most members of the PavbHLH family were found to be involved in various processes in response to cold stress. Approximately 20 PavbHLH genes showed rapid induction of expression during low-temperature treatments, followed by a decrease in expression levels.
SCIENTIA HORTICULTURAE
(2021)
Article
Biochemistry & Molecular Biology
Youngchang Kim, Robert Jedrzejczak, Natalia I. Maltseva, Mateusz Wilamowski, Michael Endres, Adam Godzik, Karolina Michalska, Andrzej Joachimiak
Article
Biochemistry & Molecular Biology
Timothy A. Klein, Dirk W. Grebenc, Shil Y. Gandhi, Vraj S. Shah, Youngchang Kim, John C. Whitney
Summary: This study reveals the crystal structure of the extracellular T7SSb subunit EsaA from Streptococcus gallolyticus, suggesting its potential role as a receptor for lytic bacteriophages and in bacterial competition.
Article
Multidisciplinary Sciences
Jerzy Osipiuk, Saara-Anne Azizi, Steve Dvorkin, Michael Endres, Robert Jedrzejczak, Krysten A. Jones, Soowon Kang, Rahul S. Kathayat, Youngchang Kim, Vladislav G. Lisnyak, Samantha L. Maki, Vlad Nicolaescu, Cooper A. Taylor, Christine Tesar, Yu-An Zhang, Zhiyao Zhou, Glenn Randall, Karolina Michalska, Scott A. Snyder, Bryan C. Dickinson, Andrzej Joachimiak
Summary: The study focused on papain-like protease (PLpro) as a potential target for antivirals against SARS-CoV-2, identifying inhibitors and their interactions with the enzyme. The findings demonstrate the potential for developing high-affinity inhibitors through structure-based drug design efforts targeting PLpro.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Youngchang Kim, Jacek Wower, Natalia Maltseva, Changsoo Chang, Robert Jedrzejczak, Mateusz Wilamowski, Soowon Kang, Vlad Nicolaescu, Glenn Randall, Karolina Michalska, Andrzej Joachimiak
Summary: SARS-CoV-2 Nsp15 is a uridine-specific endoribonuclease that interferes with the innate immune response and is a potential target for therapeutic intervention. Studies have shown that Tipiracil inhibits the activity of Nsp15 by interacting with the uridine binding pocket. This discovery provides new insights for the development of drugs based on uracil scaffold.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Mateusz Wilamowski, Darren A. Sherrell, George Minasov, Youngchang Kim, Ludmilla Shuvalova, Alex Lavens, Ryan Chard, Natalia Maltseva, Robert Jedrzejczak, Monica Rosas-Lemus, Nickolaus Saint, Ian T. Foster, Karolina Michalska, Karla J. F. Satchell, Andrzej Joachimiak
Summary: The study elucidated the cap modification process of SARS-CoV-2 genome by Nsp16, investigated the structural changes during its methyltransferase activity, and provided evidence for Nsp16 as a potential drug target for viral proliferation inhibition.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biophysics
Mateusz Wilamowski, Michal Hammel, Wellington Leite, Qiu Zhang, Youngchang Kim, Kevin L. Weiss, Robert Jedrzejczak, Daniel J. Rosenberg, Yichong Fan, Jacek Wower, Jan C. Bierma, Altaf H. Sarker, Susan E. Tsutakawa, Sai Venkatesh Pingali, Hugh M. O'Neill, Andrzej Joachimiak, Greg L. Hura
Summary: The replication transcription complex (RTC) of the virus SARS-CoV-2 plays a crucial role in copying viral RNA and transcribing viral proteins. Through systematic structural investigations and various biophysical techniques, researchers have gained deeper insights into the assembly, mechanism, and potential disruption of RTC and its functions.
BIOPHYSICAL JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Leila T. Alexander, Rosalba Lepore, Andriy Kryshtafovych, Athanassios Adamopoulos, Markus Alahuhta, Ann M. Arvin, Yannick J. Bomble, Bettina Bottcher, Cecile Breyton, Valerio Chiarini, Naga Babu Chinnam, Wah Chiu, Krzysztof Fidelis, Rhys Grinter, Gagan D. Gupta, Marcus D. Hartmann, Christopher S. Hayes, Tatjana Heidebrecht, Andrea Ilari, Andrzej Joachimiak, Youngchang Kim, Romain Linares, Andrew L. Lovering, Vladimir V. Lunin, Andrei N. Lupas, Cihan Makbul, Karolina Michalska, John Moult, Prasun K. Mukherjee, William Sam Nutt, Stefan L. Oliver, Anastassis Perrakis, Lucy Stols, John A. Tainer, Maya Topf, Susan E. Tsutakawa, Mauricio Valdivia-Delgado, Torsten Schwede
Summary: The ability to predict protein structures in CASP14 has significantly improved, with many challenging targets modeled accurately. Experimentalists highlighted that computational models can accurately reproduce critical structural features and can guide further studies on biologically-relevant properties of proteins.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Chemistry, Medicinal
Gyan Modi, Gary M. Marqus, Mohana Rao Vippila, Deviprasad R. Gollapalli, Youngchang Kim, Adhar C. Manna, Shibin Chacko, Natalia Maltseva, Xingyou Wang, Ryan T. Cullinane, Yubo Zhang, Judy L. M. Kotler, Petr Kuzmic, Minjia Zhang, Ann P. Lawson, Andrzej Joachimiak, Ambrose Cheung, Barry B. Snider, David M. Rothstein, Gregory D. Cuny, Lizbeth Hedstrom
Summary: This study identified potent inhibitors of Staphylococcus aureus IMPDH with antibacterial activity, but the emergence of resistant strains raises questions about the vulnerability of IMPDH as a target for treating S. aureus infections, suggesting alternative functions of this protein may be involved in infection.
ACS INFECTIOUS DISEASES
(2021)
Article
Microbiology
Alfa Herrera, Youngchang Kim, Jiexi Chen, Robert Jedrzejczak, Shantanu Shukla, Natalia Maltseva, Grazyna Joachimiak, Lukas Welk, Grant Wiersum, Lukasz Jaroszewski, Adam Godzik, Andrzej Joachimiak, Karla J. F. Satchell
Summary: Alpha-pore-forming toxins (alpha-PFTs) are secreted by various bacteria and can form bi- or tripartite toxins, specifically targeting phagocytic cells.
JOURNAL OF BACTERIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Franz J. St John, Casey Crooks, Youngchang Kim, Kemin Tan, Andrzej Joachimiak
Summary: This report describes the first X-ray crystallographic structure models of a xylobiohydrolase (XBH) from Acetivibrio clariflavus, shedding light on the high functional specificity of this new bacterial GH30 XBH subfamily.
Article
Biochemical Research Methods
Gyorgy Babnigg, Darren Sherrell, Youngchang Kim, Jessica L. Johnson, Boguslaw Nocek, Kemin Tan, Danny Axford, Hui Li, Lance Bigelow, Lukas Welk, Michael Endres, Robin L. Owen, Andrzej Joachimiak
Summary: Protein crystals grown in microfluidic droplets provide an effective and robust platform for storing, transporting, and collecting crystallography data. This study describes the crystallization of human gut microbial hydrolases in microfluidic droplets and presents a sample-transport and data-collection approach that is inexpensive, convenient, and requires small amounts of protein. The research demonstrates the successful shipment of crystals grown in microfluidic droplets and their collection for data using a cost-effective method.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Instruments & Instrumentation
Darren A. Sherrell, Alex Lavens, Mateusz Wilamowski, Youngchang Kim, Ryan Chard, Krzysztof Lazarski, Gerold Rosenbaum, Rafael Vescovi, Jessica L. Johnson, Chase Akins, Changsoo Chang, Karolina Michalska, Gyorgy Babnigg, Ian Foster, Andrzej Joachimiak
Summary: Serial synchrotron crystallography is a method for studying protein structures using data collected from thousands of crystals at physiological temperature and reduced radiation damage. The Structural Biology Center used a new 3D-printed mesh-holder approach to optimize sample handling. By applying this system, two types of β-lactamases were successfully studied.
JOURNAL OF SYNCHROTRON RADIATION
(2022)
Article
Biochemistry & Molecular Biology
Seonghee Paek, Fumihiro Kawai, Nilamani Venisetty, Youngchang Kim, Hye-Jeong Yeo
Summary: The crystal structure of LptE in Campylobacter jejuni reveals insights into its function and allows for the proposal of the LPS transport system in this bacterium.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Microbiology
Timothy A. Klein, Dirk W. Grebenc, Prakhar Y. Shah, Owen D. McArthur, Brandon H. Dickson, Michael G. Surette, Youngchang Kim, John C. Whitney
Summary: Type VIIb secretion systems (T7SSb) are utilized by various Gram-positive bacteria to facilitate interbacterial killing and pathogenesis through the secretion of toxins. This study discovered two new protein families, Lap1 and Lap2, that interact with these toxins and are essential for their secretion, providing new insights into T7SSb-dependent toxin release from Gram-positive bacteria.
Article
Multidisciplinary Sciences
Shehryar Ahmad, Isis J. Gordon, Kara K. Tsang, Andrea G. Alexei, David Sychantha, Jake Colautti, Sarah L. Trilesky, Youngchang Kim, Boyuan Wang, John C. Whitney
Summary: Bacteria produce different nucleotide second messengers to adapt to their environment. This study reveals the distinct functions of nucleotide second messengers (p)ppGpp and (p)ppApp in bacteria, and identifies a family of hydrolases that specifically act on (p)ppApp. The research also demonstrates that these (p)ppApp hydrolases are widely distributed in bacteria and may play important roles in bacterial physiology.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
