Article
Green & Sustainable Science & Technology
Matthias Thomitzek, Oke Schmidt, Gabriela Ventura Silva, Hassan Karaki, Mark Lippke, Ulrike Krewer, Daniel Schroeder, Arno Kwade, Christoph Herrmann
Summary: The application of batteries in electric vehicles and stationary energy-storage systems is promising, but the battery production process is complex and has untapped potential. This study presents a framework that predicts the impact of processes on battery performance and provides decision support to improve production efficiency.
Article
Genetics & Heredity
Gopinath Chattopadhyay, Jayantika Bhowmick, Kavyashree Manjunath, Shahbaz Ahmed, Parveen Goyal, Raghavan Varadarajan
Summary: Global suppressor mutations have been found to rescue defects caused by loss-of-function mutations in proteins by enhancing the foldability of buried site mutants and increasing in-vivo solubilities and regain-of-function phenotypes.
Article
Biochemistry & Molecular Biology
Christoph Kaiser, Marc Vogel, Bettina Appel, Julia Weigand, Sabine Mueller, Beatrix Suess, Josef Wachtveitl
Summary: Engineering in vitro selected RNA aptamers into in vivo functional riboswitches is a challenge in molecular biology. Magnesium ions play a crucial role in the folding process.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Analytical
Gabriela Sanchez-Reyes, Heiner Graalfs, Mathias Hafner, Christian Frech
Summary: Ion exchange chromatography is a commonly used unit operation for the purification of therapeutic proteins, but its performance is influenced by a complex interplay of various parameters. Batch variations in ion exchange resins play a significant role in the robustness of downstream processing steps, with ligand density being a key factor affecting protein adsorption and separation performance. Using a model-based approach can help in understanding the impact of parameter variations, like ligand density, on the overall process.
JOURNAL OF SEPARATION SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Paul T. Kim, Robin Winter, Djork-Arne Clevert
Summary: Research suggests that unsupervised learned representations can predict protein-ligand binding more effectively than handcrafted ones. Various protein and molecule embedding methods have been developed based on different language modeling methods.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biology
Mathias C. Eymery, Andrew A. McCarthy, Jens Hausmann
Summary: This study demonstrates the potent inhibitory effect of Delta 9-tetrahydrocannabinol (THC) on the catalysis of autotaxin (ATX), as well as the binding interface between ATX and THC by X-ray crystallography. Cellular experiments confirm the inhibitory effect of THC in the ATX-LPA signaling pathway. These findings highlight a functional interaction between THC and autotaxin-LPA signaling and provide insights for medicinal cannabis therapy.
LIFE SCIENCE ALLIANCE
(2023)
Article
Chemistry, Multidisciplinary
Hemashree Golla, Adithi Kannan, Soundhararajan Gopi, Sowmiya Murugan, Lakshmi R. Perumalsamy, Athi N. Naganathan
Summary: The fluctuations in protein's native ensemble play a significant role in its functioning and determining the functional output is confounded by multiple variables. Through the study of the FF1 domain in human p190A RhoGAP protein, it was discovered that phosphorylation of a buried tyrosine, which is crucial in transcriptional activity, is regulated through the modulation of structural coupling and native ensemble characteristics. The unfavorable charge-charge interactions were found to be important in governing this functional event.
ACS CENTRAL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Jonathan E. Barnes, Craig R. Miller, Frederick Marty Ytreberg
Summary: This study explores the mechanisms driving pairwise epistasis between two amino acid mutations in protein-protein binding affinity and protein folding stability. Statistical models were developed using experimental protein structures and free energy data, and it was discovered that increasing the distance between mutation sites reduces epistasis. The results provide insights into important factors contributing to epistasis in protein systems.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2022)
Review
Biochemistry & Molecular Biology
Pol Fernandez-Gonzalez, Aina Mas-Sanchez, Pere Garriga
Summary: Dietary polyphenols, such as flavonoids, show potential benefits in protecting against retinal degenerative diseases by stabilizing visual photoreceptor proteins and offsetting the harmful effects of mutations. Current therapies for such diseases are lacking, leading to renewed interest in developing novel ligands to target these proteins. Further research is needed to fully understand the effects of polyphenol compounds on retinal degenerative diseases.
Article
Biophysics
Tingting Wang, Yanqing Ran, Yifei He, Lei Shi, Baizhao Zeng, Faqiong Zhao
Summary: Programmed death ligand-1 (PD-L1) is a key factor in tumor immune escape by suppressing T-cell activity, making the detection of PD-L1 levels crucial for tumor prognosis. A dual-mode analytical device using a hybrid material and self-powered photoelectrochemical system has been developed for ultrasensitive detection of PD-L1. Both the sensitivity and specificity of the device are high, with a detection limit of 0.29 pg mL-1. This portable sensing chip shows promising potential as a clinical diagnosis tool.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Chemistry, Multidisciplinary
Nancy Wiebelhaus, Niven Singh, Peng Zhang, Stephen L. Craig, David N. Beratan, Michael C. Fitzgerald
Summary: This study utilizes protein folding stability measurements and the SPROX and LiP techniques to discover protein-xenon interactions on the proteomic scale. The results enrich our understanding of biologically relevant xenon interactions.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemical Research Methods
Laura Marie Helleckes, Michael Osthege, Wolfgang Wiechert, Eric von Lieres, Marco Oldiges
Summary: High-throughput experimentation has revolutionized data-driven experimental sciences and opened the door to the application of machine learning techniques. Data quality and the quantification of random effects are crucial for data analysis. Calibration is an important element in experimental sciences and univariate calibration, especially involving non-linear saturation effects, is often performed in life sciences to extract quantitative information. Adequate calibration models that describe both the input/output relationship and measurement noise are required. However, statistically robust calibration modeling remains a challenge.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Victor Antontsev, Aditya Jagarapu, Yogesh Bundey, Hypatia Hou, Maksim Khotimchenko, Jason Walsh, Jyotika Varshney
Summary: The study demonstrates how a computational platform integrating machine learning optimization with mechanistic modeling can accurately predict compound plasma concentration profiles and tissue-plasma partition coefficients by varying the lipophilicity descriptor logP. The optimized simulations generated outputs in under 5 hours, indicating high efficiency and scalability of the framework for assessing mechanistic relationships in pharmacokinetic-pharmacodynamic phenomena.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Shiwei Wang, Juan Xie, Jianfeng Pei, Luhua Lai
Summary: CavityPlus is a comprehensive web server for detecting potential binding sites in protein structures. The upgraded version, CavityPlus 2022, includes improved speed and accuracy in cavity detection, as well as new modules for drug repurposing and protein function studies.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Analytical
Kenneth R. Wehmeyer, Ryan J. White, Peter T. Kissinger, Andwilliam R. Heineman
Summary: The development of electrochemical affinity assays and sensors allows for selective and sensitive detection of target analytes, with recent advancements focusing on improving sensitivity and user-friendly features.
ANNUAL REVIEW OF ANALYTICAL CHEMISTRY, VOL 14, 2021
(2021)
Article
Biophysics
Wei Huang, Krishnakumar M. Ravikumar, Mark R. Chance, Sichun Yang
BIOPHYSICAL JOURNAL
(2015)
Article
Biochemistry & Molecular Biology
Wei Huang, Krishnakumar M. Ravikumar, Marc Parisien, Sichun Yang
JOURNAL OF STRUCTURAL BIOLOGY
(2016)
Review
Biochemistry & Molecular Biology
Harry Scott, Wei Huang, James G. Bann, Derek J. Taylor
Article
Multidisciplinary Sciences
Wei Huang, Yi Peng, Janna Kiselar, Xuan Zhao, Aljawharah Albaqami, Daniel Mendez, Yinghua Chen, Srinivas Chakravarthy, Sayan Gupta, Corie Ralston, Hung-Ying Kao, Mark R. Chance, Sichun Yang
NATURE COMMUNICATIONS
(2018)
Article
Biochemistry & Molecular Biology
Wilnelly Hernandez-Sanchez, Wei Huang, Brian Plucinsky, Nelson Garcia-Vazquez, Nathaniel J. Robinson, William P. Schiemann, Anthony J. Berdis, Emmanuel Skordalakes, Derek J. Taylor
Article
Microbiology
Chih-Chia Su, Christopher E. Morgan, Sekhar Kambakam, Malligarjunan Rajavel, Harry Scott, Wei Huang, Corey C. Emerson, Derek J. Taylor, Phoebe L. Stewart, Robert A. Bonomo, Edward W. Yu
Article
Microbiology
Christopher E. Morgan, Wei Huang, Susan D. Rudin, Derek J. Taylor, James E. Kirby, Robert A. Bonomo, Edward W. Yu
Article
Biochemistry & Molecular Biology
Daniel Leonard, Wei Huang, Sudeh Izadmehr, Caitlin M. O'Connor, Danica D. Wiredja, Zhizhi Wang, Nilesh Zaware, Yinghua Chen, Daniela M. Schlatzer, Janna Kiselar, Nikhil Vasireddi, Stefan Schuechner, Abbey L. Perl, Matthew D. Galsky, Wenqing Xu, David L. Brautigan, Egon Ogris, Derek J. Taylor, Goutham Narla
Article
Cell Biology
Yuxin Wang, Qiaoling Song, Wei Huang, Yuxi Lin, Xin Wang, Chenyao Wang, Belinda Willard, Chenyang Zhao, Jing Nan, Elise Holvey-Bates, Zhuoya Wang, Derek Taylor, Jinbo Yang, George R. Stark
Summary: Type I interferons (IFN-I) play a crucial role in protecting against viral infections, with STAT2 being a key component in driving gene expression in response to IFN-I. The phosphorylation of STAT2 at T404 acts as a critical conformational switch, disrupting an inactive STAT1-STAT2 dimer and enhancing the antiviral defense response to IFN-I. Additionally, virus infection-induced activation of IKK-epsilon can directly phosphorylate T404, further facilitating the antiviral defense mechanism.
Editorial Material
Biochemistry & Molecular Biology
Wei Huang, Daniel Leonard, Derek J. Taylor
Summary: The highly conserved complex STRIPAK regulates the Hippo signaling pathway through phosphatase activity. The recent discovery of the core STRIPAK hub structure reveals how the striatins tetramerize to form a scaffolding platform for an intricate architecture, different from other protein phosphatase 2A (PP2A) complexes.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Eden M. Gallegos, Tanner D. Reed, Forge A. Mathes, Nelson V. Guevara, David B. Neau, Wei Huang, Marcia E. Newcomer, Nathaniel C. Gilbert
Summary: This study reveals two distinct conformations of 5-lipoxygenase (5-LOX) in its catalytic reaction through structural and dynamic experiments. By strategic mutations, researchers successfully unlocked a more open conformation and improved the enzyme's activity. These findings are of great importance for understanding the synthesis mechanism of leukotrienes.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Jiaqiang Zhu, Wei Huang, Jing Zhao, Loc Huynh, Derek J. Taylor, Michael E. Harris
Summary: This study reveals the conformational changes during the recognition process of bacterial RNase P using high-throughput enzymology and cryoEM. The specific pairing of precursor tRNA inhibits the formation of the catalytic conformation. Comparisons of different precursor tRNA structures show that RNase P primarily uses stacking interactions and shape complementarity to accommodate alternative sequences. The study uncovers the active site interactions and conformational changes of RNase P, laying the foundation for understanding the link between binding interactions and catalysis.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Thilini Abeywansha, Wei Huang, Xuan Ye, Allison Nawrocki, Xin Lan, Eckhard Jankowsky, Derek J. J. Taylor, Yi Zhang
Summary: Arginyl-tRNA-protein transferase 1 (ATE1) is a key regulator involved in protein homeostasis, stress response, cytoskeleton maintenance, and cell migration. The mechanism of how ATE1 hijacks tRNA and catalyzes the arginylation reaction from the ribosomal protein synthesis pathways remains unknown.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Wei Huang, Hongyun Li, Janna Kiselar, Stephen P. P. Fink, Sagar Regmi, Alexander Day, Yiyuan Yuan, Mark Chance, Joseph M. M. Ready, Sanford D. D. Markowitz, Derek J. J. Taylor
Summary: Inhibition of 15-prostaglandin dehydrogenase (15-PGDH) is a promising therapeutic target for regenerative medicine. We report the structure of 15-PGDH in complex with two different inhibitors. Unexpectedly, access to the binding pocket is regulated by a dynamic lid of the enzyme.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Sophie M. Travis, Brian P. Mahon, Wei Huang, Meisheng Ma, Michael J. Rale, Jodi Kraus, Derek J. Taylor, Rui Zhang, Sabine Petry
Summary: This study reveals the role of the augmin complex in microtubule branching through a structural model. By using cryo-electron microscopy and negative stain electron microscopy, the location and microtubule binding site of the augmin complex were identified. Evolutionary analysis shows that the structure and function of augmin are highly conserved across eukaryotes. These findings provide new insights into the mechanism of microtubule branching.
NATURE COMMUNICATIONS
(2023)