Article
Multidisciplinary Sciences
Kevin Xiao, Homa Ghalei, Sohail Khoshnevis
Summary: RNA structure probing is a valuable method to investigate the three-dimensional structure of RNA. In this study, we analyze the effectiveness of guanine modification and uracil modification in yeast models. We find that phenylglyoxal (PGO) is the best guanine probe for structural probing in Saccharomyces cerevisiae and Candida albicans, and that uracils can be modified by Cyclohexyl-3-(2-Morpholinoethyl) Carbodiimide metho-p-Toluenesulfonate (CMCT) in S. cerevisiae. These findings provide valuable conditions and tools for studying RNA structure and function in yeast models.
Article
Biochemistry & Molecular Biology
Dalen Chan, Chao Feng, Whitney E. England, Dana Wyman, Ryan A. Flynn, Xiuye Wang, Yongsheng Shi, Ali Mortazavi, Robert C. Spitale
Summary: By combining icLASER and RNA flexibility data, researchers efficiently predict transcriptome-wide RNA-protein interactions and catalog RNA polyadenylation sites using RNA structure alone, showcasing the utility of designing novel chemical approaches for studying RNA biology.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biochemical Research Methods
Md Solayman, Thomas Litfin, Jaswinder Singh, Kuldip Paliwal, Yaoqi Zhou, Jian Zhan
Summary: Characterizing RNA structures and functions has traditionally focused on 2D secondary and 3D tertiary structures. However, recent advancements in understanding RNA solvent accessibility as a 1D representation highlight its importance in exploring complex structure-function relationships of RNAs.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Zhi Cheng, Charles Mobley, Sandeep K. Misra, Rama S. Gadepalli, Rachel Hammond, Leonid S. Brown, John M. Rimoldi, Joshua S. Sharp
Summary: Research shows that the membrane environment does not affect bulk solvent radical scavenging activity, but when present with proteins, the radical scavengers in the membrane compete for the local concentration of hydroxyl radicals, resulting in reduced oxidation of membrane proteins.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Nanoscience & Nanotechnology
Chen Yang, Xiaowen Shi, Luhe Qi, Xinyi Zhu, Jun Tong, Hongbing Deng, Yumin Du
Summary: This study demonstrates the storage and retrieval of structural information in hydrogel through electrically induced covalent cross-linking. By leveraging the diffusible feature of hydrogel, different micromorphology, chemical properties, and pH sensitivity are achieved in the written area, enabling dynamic information storage in 2D and 3D formats. The use of stable electrical inputs showcases the versatility in storing dynamic structural information and allows for recognition of the embedded information through chemical and physical variations.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Chemistry, Multidisciplinary
Rhianna J. Rowland, Yurong Chen, Imogen Breen, Liang Wu, Wendy A. Offen, Thomas J. Beenakker, Qin Su, Adrianus M. C. H. van den Nieuwendijk, Johannes M. F. G. Aerts, Marta Artola, Herman S. Overkleeft, Gideon J. Davies
Summary: The study synthesized a series of cyclophellitol epoxide and aziridine inhibitors and activity-based probes, revealing their binding modes with GBA and potential applications in GD treatment. A bi-functional aziridine ABP may serve as a more powerful imaging agent, but did not achieve additional benefits over the first generation ABPs.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Medicinal
Danni Rao, Tao Yang, Huixu Feng, Qi An, Shaofeng Zhang, Jinghua Yu, Xuelian Ren, Xingxing Diao, He Huang, Wei Tang, Shilin Xu
Summary: This study identifies a potent and selective covalent ZAP-70 inhibitor with anti-inflammatory activity, which effectively inhibits T cell activation and inflammatory cytokine production. The topical application of this inhibitor also shows promising efficacy in a psoriasis mouse model.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Julius Fuersch, Carsten Voormann, Kai-Michael Kammer, Florian Stengel
Summary: Small heat-shock proteins (sHSPs) play important roles in the cellular stress response across all species, primarily by binding early unfolding states of proteins to prevent aggregation. Research on yeast Hsp26 using cross-linking mass spectrometry (XL-MS) has provided detailed structural information on sHSP activation and client binding, revealing the significance of the middle domain in client-independent interaction and potential client specificity through additional binding sites within its alpha-crystallin domain and C-terminal extension.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Gregor Urban, Christophe N. Magnan, Pierre Baldi
Summary: Accurate prediction of protein secondary structure and solvent accessibility is crucial for studying protein evolution, structure, and predicting 3D protein structure. This study presents an improved version of SSpro/ACCpro predictors that utilize deep learning and enhanced features to achieve higher accuracy compared to previous versions.
Article
Chemistry, Medicinal
Manasi Gaikwad, Florian Richter, Rabea Goetz, Aline Doerrbaum, Lena Schumacher, Jason Tonillo, Christian Frech, Roland Kellner, Carsten Hopf
Summary: DEPC CL-MS is a useful method for evaluating structural changes and stability of mAbs. An aggregation-prone area in the CDR region was identified under heat stress. After long-term storage, DEPC CL-MS analysis further pinpointed structural disturbances of disulfide bonds at specific cysteines.
Article
Biochemistry & Molecular Biology
Laura Fourmois, Florent Poyer, Aude Sourdon, Delphine Naud-Martin, Sounderya Nagarajan, Rahima Chennoufi, Eric Deprez, Marie-Paule Teulade-Fichou, Florence Mahuteau-Betzer
Summary: Mitochondria-targeted fluorophores have been designed to monitor the mitochondrial status, with cationic derivatives shown to accumulate in mitochondria and translocate to the nucleus under depolarisation of the mitochondrial membrane. This reversible phenomenon suggests that these probes can be used to monitor Delta psi(m) variations.
Article
Biochemical Research Methods
Casimir Bamberger, Sandra Pankow, Salvador Martinez-Bartolome, Michelle Ma, Jolene Diedrich, Robert A. Rissman, John R. Yates
Summary: Covalent protein painting (CPP) is a mass spectrometry-based protein footprinting approach that quantifies the accessibility of lysine epsilon-amines for covalent modification on the surface of natively folded proteins. The research found that in Alzheimer's disease (AD), structural alterations extend beyond amyloid-beta (Aβ) and hyperphosphorylated tau to proteins such as tubulin-beta (TUBB) and succinate dehydrogenase (SHDB).
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Chemistry, Physical
Tiantian Dong, Pengyun Yu, Juan Zhao, Jianping Wang
Summary: This study focuses on improving the time resolution of structural analysis on biomolecules by synthesizing several 5-silylethynyl and 5-substituted phenylethynyl modified nucleosides. The results show that these compounds can serve as structurally sensitive infrared probes for monitoring the dynamic behaviors of polynucleotides.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Kyle S. Jiang, Gustavo M. Hobold, Rui Guo, Kyeong-Ho Kim, Aaron M. Melemed, Dongniu Wang, Lucia Zuin, Betar M. Gallant
Summary: This study investigates the correlation between the structural features of sulfonyl/sulfamoyl fluoride additives and the cycle performance of lithium-ion batteries. The results show that, in addition to coordination, the reactivity of the solvent and the structural features of the additives strongly regulate the cycling efficiency.
ACS ENERGY LETTERS
(2022)
Review
Biochemistry & Molecular Biology
Vivian S. Lin
Summary: The continued expansion of the chemical biology toolbox provides new opportunities to investigate the fundamental molecular mechanisms driving complex plant-microbe interactions. Through the use of metabolic labeling and activity-based probes, researchers can study the impacts of plant-associated microbes on plant growth, metabolism, and immune responses. While current studies mainly focus on the effects of pathogens on plants, chemical biology will also be valuable in exploring mutualistic associations between beneficial microbes and their plant hosts in the future.
Article
Biochemistry & Molecular Biology
Eizadora Yu, Sara P. Gaucher, Masood Z. Hadi
Article
Biotechnology & Applied Microbiology
Eizadora T. Yu, Frank J. Zendejas, Pamela D. Lane, Sara Gaucher, Blake A. Simmons, Todd W. Lane
JOURNAL OF APPLIED PHYCOLOGY
(2009)
Article
Biochemical Research Methods
Eizadora T. Yu, Arie Hawkins, Irwin D. Kuntz, Larry A. Rahn, Andrew Rothfuss, Kenneth Sale, Malin M. Young, Christine L. Yang, Carmen M. Pancerella, Daniele Fabris
JOURNAL OF PROTEOME RESEARCH
(2008)
Article
Biotechnology & Applied Microbiology
Eizadora T. Yu, Masood Z. Hadi
MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS
(2011)
Article
Multidisciplinary Sciences
Eizadora T. Yu, Arie Hawkins, Julian Eaton, Daniele Fabris
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2008)
Article
Biochemistry & Molecular Biology
Charmaine B. Mendoza, Dan Jethro M. Masacupan, Dessa Camille R. Batoctoy, Eizadora T. Yu, Arturo O. Lluisma, Lilibeth A. Salvador-Reyes
JOURNAL OF PEPTIDE SCIENCE
(2019)
Article
Multidisciplinary Sciences
Mac Kevin E. Braza, Jerrica Dominique N. Gazmen, Eizadora T. Yu, Ricky B. Nellas
SCIENTIFIC REPORTS
(2019)
Article
Microbiology
Megan M. Morris, Jeffrey A. Kimbrel, Haifeng Geng, Mary Bao Tran-Gyamfi, Eizadora T. Yu, Kenneth L. Sale, Todd W. Lane, Xavier Mayali
Summary: Bacteria play important roles in nutrient-rich aquatic environments, such as engineered algal biofuel systems, but our knowledge about the microbial ecology of algal cultivation systems remains limited. In this study, we used metagenomics to characterize the metabolic capacities of bacteria associated with the biofuel-relevant microalga Microchloropsis salina and predicted metabolic interactions between algae and manipulated communities of bacteria. These findings provide insights into the scalability of lab-based algal-bacterial interactions and offer a framework for empirical testing of genome-based metabolic predictions.
Article
Biochemical Research Methods
Qingrong Zhang, Eizadora T. Yu, Katherine A. Kellersberger, Elizabeth Crosland, Daniele Fabris
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2006)
Article
Biochemical Research Methods
OT Akinsiku, ET Yu, D Fabris
JOURNAL OF MASS SPECTROMETRY
(2005)
Article
Biochemical Research Methods
KA Kellersberger, ET Yu, SI Merenbloom, D Fabris
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2005)
Article
Biochemistry & Molecular Biology
ET Yu, QG Zhang, D Fabris
JOURNAL OF MOLECULAR BIOLOGY
(2005)
Article
Biochemical Research Methods
E Yu, D Fabris
ANALYTICAL BIOCHEMISTRY
(2004)
Article
Chemistry, Analytical
KA Kellersberger, E Yu, GH Kruppa, MM Young, D Fabris
ANALYTICAL CHEMISTRY
(2004)