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Multidisciplinary Sciences
Huaying Zhao, Di Wu, Sergio A. Hassan, Ai Nguyen, Jiji Chen, Grzegorz Piszczek, Peter Schuck
Summary: The N-protein of SARS-CoV-2 plays a crucial role in viral assembly and RNA scaffolding. It promotes LLPS, forming dense droplets that aid in the assembly of ribonucleoprotein particles. Through experiments, simulations, and mutational analysis, researchers have discovered an unknown oligomerization site that contributes to LLPS and is necessary for the assembly of protein-nucleic acid complexes. This finding presents a potential target for antiviral therapeutics.
Review
Biochemistry & Molecular Biology
Steven O. Smith
Summary: Class A G protein-coupled receptors, which have evolved to recognize a wide range of ligands, possess a highly conserved core within their seven-transmembrane helix framework. However, there is still no consensus on the mechanism of ligand binding coupling or the roles of specific residues within the core. Recent insights from crystallography and NMR spectroscopy provide a new perspective on decomposing the core into its essential structural and functional elements, shedding new light on this important region.
TRENDS IN BIOCHEMICAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Naohiro Kon, Hsin-tzu Wang, Yoshiaki S. Kato, Kyouhei Uemoto, Naohiro Kawamoto, Koji Kawasaki, Ryosuke Enoki, Gen Kurosawa, Tatsuto Nakane, Yasunori Sugiyama, Hideaki Tagashira, Motomu Endo, Hideo Iwasaki, Takahiro Iwamoto, Kazuhiko Kume, Yoshitaka Fukada
Summary: Temperature compensation of circadian rhythms is achieved through NCX-mediated Ca2+ signaling, which plays essential roles in maintaining temperature-compensated oscillations.
Article
Biochemistry & Molecular Biology
Ugochukwu K. Ihenacho, Rafael Toro, Rana H. Mansour, R. Blake Hill
Summary: A study found that mitochondrial fission protein 1 (FIS1) is conserved in all eukaryotes. The researchers conducted experiments using different variants and found that a noncanonical insert sequence of FIS1 plays an important role in mitochondrial morphology and recruitment of certain proteins.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Cell Biology
Sezen Meydan, Gessica C. Barros, Vanessa Simoes, Lana Harley, Blanche K. Cizubu, Nicholas R. Guydosh, Gustavo M. Silva
Summary: Under oxidative stress conditions, the E2 ubiquitin conjugase Rad6 mediates K63-linked ubiquitination of ribosomes, leading to ribosome pausing at specific amino acid motifs and ribosome collisions. These redoxpausing signatures are independent of the ribosome-associated quality control (RQC) pathway and Rad6 is also required to inhibit overall translation during oxidative stress, resulting in increased expression of antioxidant genes. The absence of Rad6 affects translation during oxidative stress and impacts the activation of the integrated stress response (ISR) pathway.
Article
Biochemistry & Molecular Biology
Rebecca K. Lau, Eray Enustun, Yajie Gu, Justin Nguyen, Kevin D. Corbett
Summary: Bacteria have evolved diverse immune systems to protect themselves from phage infection. Researchers have discovered a transcriptional regulator module associated with hundreds of CBASS immune systems and demonstrated its role in driving the expression of the CBASS system in response to DNA damage. This finding highlights a mechanism by which bacterial immune systems can sense and respond to cellular stress.
Article
Biochemistry & Molecular Biology
Argha Mitra, Arijit Sarkar, Marton Richard Szabo, Attila Borics
Summary: Recent advancements in experimental structural biology have provided high-resolution structures of G protein-coupled receptors, shedding light on the mechanisms of transition between active and inactive states. Molecular dynamics simulations demonstrate that external stimulus transmission to the intracellular surface of the receptor involves subtle movements of polar amino acid side chains.
Article
Biochemistry & Molecular Biology
Seong-Cheol Park, Jong-Kook Lee, Young-Min Kim, Jung Ro Lee
Summary: Due to the emergence of drug-resistant pathogens, scientists have discovered antimicrobial peptides (AMPs) with high antibacterial activity and cell selectivity. By modifying the amino acids in the peptide chain, they have enhanced the antimicrobial effects and salt tolerance, while reducing cytotoxicity.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Janne M. Bibbe, Gert Vriend
Summary: G protein-coupled receptors play key roles in physiological processes and are important drug targets. Conserved GPCR sequence motifs create weak spots in transmembrane helices, allowing for ligand binding and signaling. Activation of GPCRs involves helix motions and deformations facilitated by weak spots, which are more conserved than the motifs causing them and are crucial for understanding the activation process and designing drugs.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Biology
Rui P. Silva, Yimin Huang, Annalee W. Nguyen, Ching-Lin Hsieh, Oladimeji S. Olaluwoye, Tamer S. Kaoud, Rebecca E. Wilen, Ahlam N. Qerqez, Jun-Gyu Park, Ahmed M. Khalil, Laura R. Azouz, Kevin C. Le, Amanda L. Bohanon, Andrea M. DiVenere, Yutong Liu, Alison G. Lee, Dzifa A. Amengor, Sophie R. Shoemaker, Shawn M. Costello, Eduardo A. Padlan, Susan Marqusee, Luis Martinez-Sobrido, Kevin N. Dalby, Sheena D'Arcy, Jason S. McLellan, Jennifer A. Maynard, Leslie Goo
Summary: Understanding the protective potential of conserved epitopes in SARS-CoV-2 and other coronaviruses is crucial for addressing the current pandemic and future outbreaks. Researchers have identified a highly conserved epitope in the S2 domain of beta-coronaviruses, specifically in the hinge region. An antibody called RAY53 targets this epitope and has been found to mediate immune responses against SARS-CoV-2 spike protein. However, mutations in the hinge region and other spike protein changes may impact antibody binding and evade existing serum antibodies. This study provides valuable insights into the targeting of S2 core epitopes and the limitations of this approach.
Article
Biochemistry & Molecular Biology
Dylan Valleau, Saima M. Sidik, Luiz C. Godoy, Yamilex Acevedo-Sanchez, Charisse Flerida A. Pasaje, My-Hang Huynh, Vern B. Carruthers, Jacquin C. Niles, Sebastian Lourido
Summary: The microneme protein CLAMP, along with the invasion-associated SPATR and a previously uncharacterized protein CLAMP-linked invasion protein (CLIP), forms a complex that is essential for rhoptry discharge following host-cell contact. Phylogenetic analysis suggests that the essential complex components are present across apicomplexans.
Article
Chemistry, Organic
Matteo Pollastrini, Luca Pasquinelli, Marcin Gorecki, Federica Balzano, Lorenzo Cupellini, Filippo Lipparini, Gloria Uccello Barretta, Fabio Marchetti, Gennaro Pescitelli, Gaetano Angelici
Summary: We demonstrated that the cooperative effect of four amino acid units is sufficient to form a preferential structure in solution. By analyzing spectroscopic and chiroptical properties, supported by X-ray crystallography and computational studies, we shed light on this rare secondary structure.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Biochemical Research Methods
Yakun Fang, Fan Liu, Yi Shi, Ting Yang, Chaojuan Liang, Yu Xin, Guiyang Shi, Liang Zhang
Summary: This study investigated the thermostable skeleton and mechanism of action of the lipase TrLipB from Thermomicrobium roseum. The results showed that substitutions at specific sites affected the thermostability and catalytic efficiency of the enzyme.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Martyna Gajos, Olga Jasnovidova, Alena van Boemmel, Susanne Freier, Martin Vingron, Andreas Mayer
Summary: Research reveals widespread RNA polymerase pausing in human cells, mostly occurring along the gene-body of transcribed genes rather than in promoter-proximal regions. Machine learning modeling identifies DNA sequence properties underlying transcriptional pausing, suggesting potential functional roles of exact pause locations in gene expression.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Immunology
Ya-Ling Huang, Tsun-Mei Lin, Shu-Ying Wang, Jen-Ren Wang
Summary: By conducting large-scale sequence analysis, researchers identified the distribution and location of conserved residues in VP1 protein of enteroviruses, which is important for the development of antiviral drug candidates against enteroviruses.
JOURNAL OF MICROBIOLOGY IMMUNOLOGY AND INFECTION
(2022)
Article
Pharmacology & Pharmacy
Carla Sosa-Alvarado, Aurelio Hernandez-Mendez, M. Teresa Romero-Avila, Omar B. Sanchez-Reyes, Yoshinori Takei, Gozoh Tsujimoto, Akira Hirasawa, J. Adolfo Garcia-Sainz
EUROPEAN JOURNAL OF PHARMACOLOGY
(2015)
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Biochemistry & Molecular Biology
Naoki Kimata, Andreyah Pope, Omar B. Sanchez-Reyes, Markus Eilers, Chikwado A. Opefi, Martine Ziliox, Philip J. Reeves, Steven O. Smith
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2016)
Article
Biochemistry & Molecular Biology
Naoki Kimata, Andreyah Pope, Omar B. Sanchez-Reyes, Markus Eilers, Chikwado A. Opefi, Martine Ziliox, Philip J. Reeves, Steven O. Smith
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2016)
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Pharmacology & Pharmacy
Omar B. Sanchez-Reyes, M. Teresa Romero-Avila, Jean A. Castillo-Badillo, Yoshinori Takei, Akira Hirasawa, Gozoh Tsujimoto, Rafael Villalobos-Molina, J. Adolfo Garcia-Sainz
EUROPEAN JOURNAL OF PHARMACOLOGY
(2014)
Article
Multidisciplinary Sciences
Jean A. Castillo-Badillo, Omar B. Sanchez-Reyes, Marco A. Alfonzo-Mendez, Teresa Romero-Avila, Guadalupe Reyes-Cruz, J. Adolfo Garcia-Sainz
Article
Biophysics
Omar B. Sanchez-Reyes, Aidan L. G. Cooke, Dale B. Tranter, Dawood Rashid, Markus Eilers, Philip J. Reeves, Steven O. Smith
BIOPHYSICAL JOURNAL
(2017)