Article
Biochemistry & Molecular Biology
Mark A. Nakasone, Karolina A. Majorek, Mads Gabrielsen, Gary J. Sibbet, Brian O. Smith, Danny T. Huang
Summary: This study elucidates the mechanism of processive K48-linked polyUb chain formation by UBE2K, including acceptor Ub recognition and multivalent Ub-binding feature.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Joanne L. Usher, Alvaro Sanchez-Martinez, Ana Terriente-Felix, Po-Lin Chen, Juliette J. Lee, Chun-Hong Chen, Alexander J. Whitworth
Summary: The PINK1-Parkin pathway can promote mitochondrial turnover independently of canonical autophagy. The detection of Ser65-phosphorylated ubiquitin (pS65-Ub) can be used to analyze the function of the Pink1-Parkin pathway in Drosophila.
Article
Cell Biology
Stefanie Chan, Emma Smith, Yuan Gao, Julian Kwan, Benjamin C. Blum, Andrew M. Tilston-Lunel, Isabella Turcinovic, Xaralabos Varelas, Maria Dafne Cardamone, Stefano Monti, Andrew Emili, Valentina Perissi
Summary: GPS2 functions as a tumor suppressor in breast cancer, and its loss enhances cancer cell proliferation and tumor growth through uncontrolled activation of AKT signaling. The study suggests that GPS2 could serve as a potential biomarker for a subset of breast cancers responsive to PI3K inhibitors.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Avinash K. Singh, Sumit Murmu, Artur Krezel
Summary: Post-translational modifications (PTMs) of proteins, such as ubiquitination, play important regulatory roles in cellular processes. Defects in the ubiquitination process are associated with diseases, making it crucial to develop efficient methods for studying and targeting this process. This report describes the development of a simple and efficient chemoenzymatic strategy for synthesizing homogeneous ubiquitin conjugates, providing a valuable tool for understanding the complexity of ubiquitination and designing therapeutics.
Article
Biochemistry & Molecular Biology
Siqi Shen, Gregory A. Davidson, Kun Yang, Zhihao Zhuang
Summary: The study used photoactivatable PCNA and Ub-PCNA probes to identify direct interactions of the Pol η catalytic core with both sides of the PCNA ring in the polymerase complex. This provides important insights for investigating PCNA-containing complexes involved in DNA replication, repair, and damage tolerance.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Pharmacology & Pharmacy
Yanyu Jiang, Shuaishuai Ni, Biying Xiao, Lijun Jia
Summary: This review summarizes the functions, clinical significance, and regulatory mechanisms of Ub and Ubl pathways in tumorigenesis, as well as the current progress of small-molecular drug discovery.
ACTA PHARMACEUTICA SINICA B
(2023)
Review
Biochemistry & Molecular Biology
Julia Koehler Leman, Georg Kuenze
Summary: Nuclear magnetic resonance (NMR) spectroscopy allows for the study of protein structures and dynamics. Although it can be challenging to collect sufficient NMR data for complex proteins, computational modeling techniques, such as those provided by the Rosetta software, can supplement sparse data and improve structure determination. This review provides an overview of the computational protocols in Rosetta for modeling protein structures from NMR data, including new developments for paramagnetic NMR, hydrogen-deuterium exchange, and chemical shifts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Mohd Shariq, Neha Quadir, Anwar Alam, Sheeba Zarin, Javaid A. Sheikh, Neha Sharma, Jasmine Samal, Uzair Ahmad, Indu Kumari, Seyed E. Hasnain, Nasreen Z. Ehtesham
Summary: Intracellular pathogens exploit the cellular ubiquitination process to evade host immunity. Ubiquitin modification, as a way to regulate cellular functions, is used by pathogens to subvert host defenses. The hijacking of host ubiquitination system allows pathogens to escape immune responses and enhance their virulence by manipulating host autophagy.
Article
Astronomy & Astrophysics
Yu-Kuo Hsiao, Yao Yu
Summary: In the B+ -> D(+)D(-)K(+) decay, LHCb has reported the observation of open-charm exotic states with four different quark flavors, proposing a process to confirm this discovery. The estimates suggest that these states are accessible to the LHCb experiment, paving the way for further research in b-baryon decays.
News Item
Biochemistry & Molecular Biology
Sven M. Lange, Yogesh Kulathu
Summary: Different types of ubiquitin chains serve as distinct cellular signals, with the new synthetic antigen-binding fragment sAB-K29 specifically recognizing K29-linked diubiquitin and linking K29 chains to proteotoxic stress and their accumulation in midbodies during mitosis.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Tomoki Sorada, Daichi Morimoto, Erik Walinda, Kenji Sugase
Summary: Cyclic ubiquitin chains, although expected to restrict flexibility, can still be recognized by various proteins. Cleavage of the cyclic chain results in a partially accessible conformation, induced by interaction with specific recognition patches on ubiquitin subunits.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Sarah F. Ruidiaz, Jesper E. Dreier, Rasmus Hartmann-Petersen, Birthe B. Kragelund
Summary: Two IDPs, DSS1 and CSNAP, have differences in structure and function, with even subtle sequence variance potentially leading to different functional traits. These traits may impact their ability to engage in multiple interactions, thus affecting their interactome sizes.
Review
Biochemistry & Molecular Biology
Shashank Bangalore Srikanta, Nicolas Cermakian
Summary: Circadian clocks are internal timing systems that enable organisms to adjust their behavioral and physiological rhythms to daily changes in the environment. Post-translational modifications, including ubiquitination and deubiquitination, play key roles in regulating the stability, activity, localization, and interactions of clock proteins, ultimately influencing the pace of circadian clocks and their responses to external cues.
JOURNAL OF NEUROCHEMISTRY
(2021)
Article
Agriculture, Dairy & Animal Science
Yuxuan Sun, Ying Zhu, Peng Cheng, Mengqian Zhang, Na Wang, Zhongkai Cui, Min Wei, Wenteng Xu
Summary: Ubiquitin ligase (E3) plays a versatile role in gonadal development and spermatogenesis in mammals, while its function in fish is little reported. In this study, a Z-chromosome linked ubiquitin ligase rchy1 in C. semilaevis (Cs-rchy1) was cloned and characterized, demonstrating its potential involvement in gonadal differentiation and gametogenesis.
Article
Astronomy & Astrophysics
Tian-Ge Li, Zhuo Gao, Guan-Ying Wang, De-Min Li, En Wang, Jingya Zhu
Summary: In this study, we evaluated the strong decays of K-0*(1950) and K-0*(2130) using the relativized quark model. Our results suggest that K-0*(2130) can be assigned as K-0*(3(3)P(0)), while K-0*(1950) is difficult to explain as a q (q) over bar meson. Additionally, we predicted the mass and width of the K-0*(2(3)P(0)) and K-0*(4(3)P(0)) states.
Article
Biochemistry & Molecular Biology
Fa-An Chao, Domarin Khago, R. Andrew Byrd
JOURNAL OF BIOMOLECULAR NMR
(2020)
Editorial Material
Multidisciplinary Sciences
R. Andrew Byrd
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Clemens Anklin, R. Andrew Byrd
Summary: Multi-resonance NMR experiments can manipulate spin interactions by independently combining RF fields, but the practical implementation may face interference from combination bands. A facile approach of time sharing the application of individual frequencies can resolve this issue and increase sensitivity.
JOURNAL OF BIOMOLECULAR NMR
(2021)
Article
Biochemical Research Methods
Fa-An Chao, Yue Zhang, R. Andrew Byrd
Summary: NMR relaxation dispersion experiments are widely used to study conformational exchange in biological systems, with recent improvements in computational techniques and theoretical breakthroughs enabling quantitative data analysis of complex exchange models. However, the topology of a given exchange model plays a crucial role in solving the Bloch-McConnell equation, and the lack of theoretical analysis on exchange topologies at n-site exchange limits further progress. Using graph theory, the topological complexity of n-site exchange is revealed, and machine learning is introduced as an alternative method to select exchange models based on relaxation dispersion data.
JOURNAL OF MAGNETIC RESONANCE
(2021)
Article
Biochemistry & Molecular Biology
Ian J. Fucci, R. Andrew Byrd
Summary: Nuclear magnetic resonance (NMR) provides site-specific information on local environments through chemical shifts and is widely used in protein studies. Nightshift is a Python utility and library that allows users to plot simulated NMR spectra from assigned chemical shifts in the BMRB, enabling the preview or examination of a wide range of protein spectra.
Article
Biochemistry & Molecular Biology
Christopher E. Smith, Yien Che Tsai, Yu-He Liang, Domarin Khago, Jennifer Mariano, Jess Li, Sergey G. Tarasov, Emma Gergel, Borong Tsai, Matthew Villaneuva, Michelle E. Clapp, Valentin Magidson, Raj Chari, R. Andrew Byrd, Xinhua Ji, Allan M. Weissman
Summary: The study reveals a key role of the G2BR region of the ERAD accessory protein AUP1 in maintaining stability of the ERAD ubiquitin-conjugating enzyme UBE2G2. Additionally, G2BR(AUP1) is essential for both recruiting and activating UBE2G2 at the ER membrane during ERAD.
Article
Biochemistry & Molecular Biology
Caitlin M. Quinn, Shiping Xu, Guangjin Hou, Qingqing Chen, Deepak Sail, R. Andrew Byrd, Sharon Rozovsky
Summary: Sulfur-containing sites in proteins play crucial roles in protein structure and function. Selenium-77 can replace sulfur and be introduced into proteins without significant structural changes. However, there is currently no established method to accurately map the local environment around selenium sites. This study explores a method using correlations between selenium and carbon-13 to characterize the local environment of selenium sites in a model protein variant.
JOURNAL OF BIOMOLECULAR NMR
(2022)
Article
Chemistry, Multidisciplinary
Fa-An Chao, Srisathiyanarayanan Dharmaiah, Troy Taylor, Simon Messing, William Gillette, Dominic Esposito, Dwight Nissley, Frank McCormick, R. Andrew Byrd, Dhirendra K. Simanshu, Gabriel Cornilescu
Summary: This article investigates the influence of conformational dynamics of RAS proteins on their interactions with downstream effectors and explains and predicts the altered binding affinities of different mutants.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Jess Li, R. Andrew Byrd
Summary: This article presents a simple and effective method for producing highly deuterated proteins in Escherichia coli cells. The protocol combines common shaker flask growth method and the well-known pET system for large-scale recombinant protein expression. The optimized procedure allows for the production of a comparable quantity of deuterated protein compared to non-deuterated protein.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Eric M. Rosenberg Jr, Xiaoying Jian, Olivier Soubias, Hye-Young Yoon, Mukesh P. Yadav, Sarah Hammoudeh, Sandeep Pallikkuth, Itoro Akpan, Pei-Wen Chen, Tapan K. Maity, Lisa M. Jenkins, Marielle E. Yohe, R. Andrew Byrd, Paul A. Randazzo
Summary: The ADP-ribosylation factor (Arf) GTPases and their regulatory proteins are associated with cancer progression. NAV-2729 is a specific inhibitor of Arf6 and has been shown to reduce the progression of uveal melanoma. In this study, we assessed the inhibitory effects of NAV-2729 on the proliferation of different cell types and found that it inhibited proliferation in multiple cell lines. However, it did not correlate with Arf6 expression and knockdown of Arf6 did not affect cell viability or sensitivity to NAV-2729. We also identified other potential targets of NAV-2729, highlighting the complexity of defining small molecule targets.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Janusz Koscielniak, Jess Li, Deepak Sail, Rolf Swenson, Clemens Anklin, Sharon Rozovsky, R. Andrew Byrd
Summary: NMR spectroscopy has been widely used in proteins and biomolecules, but observing sulfur sites has been challenging. Recent studies have explored the use of Se-77 as a replacement for sulfur and applied Se-77 NMR in both solution and solid states. A double-labeling method using C-13 and Se-77 in proteins has been developed, enabling more sensitive triple-resonance schemes.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Meeting Abstract
Biophysics
Brianna M. Papoutsis, Olivier Soubias, Jess Li, Yue Zhang, Robert A. Byrd
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Olivier Soubias, Shashank Pant, Yue Zhang, Emad Tajkhorshid, Robert A. Byrd
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Yue Zhang, Olivier Soubias, Shashank Pant, Frank Heinrich, Alexander Vogel, Jess Li, Daniel Huster, Paul Randazzo, Mathias Losche, Emad Tajkhorshid, R. Andrew Byrd
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Olivier Soubias, Shashank Pant, Frank Heinrich, Yue Zhang, Paul Randazzo, Mathias Loesche, Emad Tajkhorshid, Robert A. Byrd
BIOPHYSICAL JOURNAL
(2021)
