Review
Biochemistry & Molecular Biology
Fabian Hia, Osamu Takeuchi
Summary: The central dogma of molecular biology states that genetic information is transferred from nucleic acid to proteins. Recent research has highlighted the importance of mRNA regulation in controlling protein abundances, with a specific focus on codon bias and optimality. This system allows different organisms or cell types to coordinate physiological pathways in response to various stress or growth conditions.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Chemistry, Medicinal
Madita Wolter, Dario Valenti, Peter J. Cossar, Stanimira Hristeva, Laura M. Levy, Thorsten Genski, Torsten Hoffmann, Luc Brunsveld, Dimitrios Tzalis, Christian Ottmann
Summary: This study describes the systematic bottom-up development of a reversible covalent PPI stabilizer and investigates how its chemical properties affect the structural changes in the ternary 14-3-3/p65/molecular glue complex, ultimately leading to increased stability and high cooperativity.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Construction & Building Technology
Chunyang Yu, Chunyi Cui, Jiuye Zhao, Junjie Zheng
Summary: By combining the foam drying process with carbonation stabilization and introducing ground steel slag into dredged slurries, a more efficient and economical way of recycling dredged materials can be achieved with increased drying rate. After carbonation stabilization, the strength of the modified soil significantly increases, with the product mainly consisting of highly polymerized calcium carbonate.
CONSTRUCTION AND BUILDING MATERIALS
(2021)
Article
Cell Biology
Anja J. Engel, Marina Kithil, Markus Langhans, Oliver Rauh, Matea Cartolano, James L. Van Etten, Anna Moroni, Gerhard Thiel
Summary: The study found that biased frequency of synonymous codons can affect protein localization within cells, thus modulating protein function through different steps such as transcription, translation, and folding.
Article
Computer Science, Information Systems
Xueyan Liu, Bo Yang, Hechang Chen, Katarzyna Musial, Hongxu Chen, Yang Li, Wanli Zuo
Summary: Stochastic blockmodel (SBM) is a widely used statistical network representation model with good interpretability and flexibility. Learning an optimal SBM is an NP-hard problem, resulting in limitations for its applications in large-scale networks. A novel redefined SBM with Poisson distribution and its block-wise learning algorithm have been proposed in this work to efficiently analyze large-scale networks, outperforming state-of-the-art methods in terms of accuracy and scalability.
ACM TRANSACTIONS ON KNOWLEDGE DISCOVERY FROM DATA
(2021)
Article
Biotechnology & Applied Microbiology
Alexander L. Cope, Michael A. Gilchrist
Summary: Our study quantifies codon-specific shifts in natural selection related to protein structure in S. cerevisiae and E. coli using an explicit population genetics approach. We find that selection on codon usage varies only slightly between different secondary structures and between structured and intrinsically-disordered regions. Our results also contradict previous findings by showing that selection on codon usage only varies slightly at the termini of helices in E. coli. Additionally, we demonstrate that the previous observation of non-optimal codons being enriched at the beginning of helices in S. cerevisiae was due to failure to control for confounding factors, rather than selection for cotranslational folding.
Article
Biophysics
Haojie Jin, Jiaqi Zhang, Yan Wang, Wanzhao Ge, Yike Jing, Xiaoyu Cao, Yixin Huo, Yujie Fu
Summary: In this study, a live-cell bio-monitoring system was proposed to assess phenylalanine bioavailability in real time in cyanobacteria based on codon de-generacy and species-specific usage bias. Increasing intracellular phenylalanine bioavailability could promote cell growth and provide a screening method for phenylalanine content.
BIOSENSORS & BIOELECTRONICS
(2024)
Article
Engineering, Multidisciplinary
G. Machin, M. Sadli, J. Pearce, J. Engert, R. M. Gavioso
Summary: This article outlines the implications of redefining the kelvin in terms of the Boltzmann constant in 2019. It describes the progress made towards realizing the redefined kelvin and outlines the prospects for temperature traceability into the 2030s.
Article
Multidisciplinary Sciences
Kazuki Saito, Hanna Kratzat, Annabelle Campbell, Robert Buschauer, A. Maxwell Burroughs, Otto Berninghausen, L. Aravind, Rachel Green, Roland Beckmann, Allen R. Buskirk
Summary: A new rescue factor, SmrB, with endonuclease activity has been discovered. It cleaves mRNAs upstream of stalled ribosomes, allowing the ribosome rescue factor tmRNA to rescue upstream ribosomes.
Article
Biochemistry & Molecular Biology
Krishnamurthy Subramanian, Bryan Payne, Felix Feyertag, David Alvarez-Ponce
Summary: This is an online database that provides codon usage statistics for all species in RefSeq, allowing users to search for specific species or taxonomic groups and access relevant statistical tables.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biotechnology & Applied Microbiology
Kunshan Liu, Yaqi Ouyang, Ru Lin, Chenyu Ge, Mian Zhou
Summary: Codon usage bias plays an important role in regulating gene expression levels, mRNA and protein stabilities in P. pastoris. Extreme codon optimization in genes with strong negative correlation between codon usage bias and protein structural disorder tendency may not be favored, and may affect protein structural conformation more severely in structural disordered proteins.
JOURNAL OF BIOTECHNOLOGY
(2022)
Article
Chemistry, Applied
Kei Nomura, Madoka Sakai, Hitomi Ohboshi, Akihiro Nakamura
Summary: The optimal extraction conditions for water-soluble lentil polysaccharide were found to be at 120°C for 90 minutes, with yields as high as 23.3% at pH 4 and 19.6% at pH 8. Two extractions at different pH values showed variations in composition and molecular mass, but both displayed a multi-branched structure.
FOOD HYDROCOLLOIDS
(2021)
Review
Biochemistry & Molecular Biology
Veymar G. Tacias-Pascacio, Roberto Morellon-Sterling, Daniel Castaneda-Valbuena, Angel Berenguer-Murcia, Majid Rasool Kamli, Olga Tavano, Roberto Fernandez-Lafuente
Summary: This paper reviews the immobilization of papain on different supports for the first time, with a special focus on the preparation of magnetic biocatalysts and specific problems related to the immobilization of proteases. The benefits of proper immobilization and potential artifacts are discussed.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Immunology
Pankaj Gurjar, Noushad Karuvantevida, Igor Vladimirovich Rzhepakovsky, Azmat Ali Khan, Rekha Khandia
Summary: The study identified specific molecular patterns in the structural genes of the SARS-CoV-2 delta variant, including an abundance of T nucleotides, underrepresentation of certain dinucleotides, and specific codon usage preferences. The virus uses these patterns to reduce translation rate and facilitate correct protein folding. This information can be utilized to design an attenuated vaccine candidate against the SARS-CoV-2 delta variant.
Article
Chemistry, Analytical
Lars Kolbowski, Lutz Fischer, Juri Rappsilber
Summary: Cross-linking mass spectrometry is transitioning to enable structural systems biology, with MS3-based approaches for identifying cross-linked peptides showing potential despite MS2-based methods currently outperforming.
ANALYTICAL CHEMISTRY
(2023)
Article
Biology
Tetsuya Sakurai, Mutsuko Kukimoto-Niino, Kazufumi Kunimura, Nana Yamane, Daiji Sakata, Ryosuke Aihara, Tomoharu Yasuda, Shigeyuki Yokoyama, Mikako Shirouzu, Yoshinori Fukui, Takehito Uruno
Summary: DOCK8 is a critical guanine-nucleotide exchange factor for the development and function of white blood cells, playing a vital role in spatial control of Cdc42 activity during interstitial leukocyte migration by binding to phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). The DHR-1 domain of DOCK8 contains basic residues that are responsible for stereospecific recognition of phosphoinositides, essential for its function.
LIFE SCIENCE ALLIANCE
(2021)
Article
Cell Biology
Kazue Terasawa, Yuji Kato, Yuta Ikami, Kensaku Sakamoto, Kazumasa Ohtake, Seisuke Kusano, Yuri Tomabechi, Mutsuko Kukimoto-Niino, Mikako Shirouzu, Jun-Lin Guan, Toshihide Kobayashi, Takanori Iwata, Tetsuro Watabe, Shigeyuki Yokoyama, Miki Hara-Yokoyama
Summary: This study demonstrated the direct homophilic interaction of mouse LAMP2A molecules and highlighted the importance of side A-specific homophilic interaction for the functional aspects of LAMP2A.
Article
Biochemistry & Molecular Biology
Upasana Sridharan, Preethi Ragunathan, Seiki Kuramitsu, Shigeyuki Yokoyama, Thirumananseri Kumarevel, Karthe Ponnuraj
Summary: Carbonic anhydrases (CA) are a group of zinc metalloenzymes, with a newly identified gamma-class CA (Cag) from Geobacillus kaustophilus containing magnesium at its active site instead of the traditional zinc ion. While lacking some essential catalytic residues present in other gamma-CA's, Cag still shares certain conserved active site residues with characterized enzymes. Inductive Coupled Plasma - Optical Emission Spectrometry (ICP-OES) and NMR studies revealed the cambialistic nature of Cag, with the ability to bind both magnesium and zinc at its active site.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Medicine, General & Internal
Takaki Hiwasa, Hao Wang, Ken-ichiro Goto, Seiichiro Mine, Toshio Machida, Eiichi Kobayashi, Yoichi Yoshida, Akihiko Adachi, Tomoo Matsutani, Mizuki Sata, Kazumasa Yamagishi, Hiroyasu Iso, Norie Sawada, Shoichiro Tsugane, Mitoshi Kunimatsu, Ikuo Kamitsukasa, Masahiro Mori, Kazuo Sugimoto, Akiyuki Uzawa, Mayumi Muto, Satoshi Kuwabara, Yoshio Kobayashi, Mikiko Ohno, Eiichiro Nishi, Akiko Hattori, Masashi Yamamoto, Yoshiro Maezawa, Kazuki Kobayashi, Ryoichi Ishibashi, Minoru Takemoto, Koutaro Yokote, Hirotaka Takizawa, Takashi Kishimoto, Kazuyuki Matsushita, Sohei Kobayashi, Fumio Nomura, Takahiro Arasawa, Akiko Kagaya, Tetsuro Maruyama, Hisahiro Matsubara, Minako Tomiita, Shinsaku Hamanaka, Yushi Imai, Tomoo Nakagawa, Naoya Kato, Jiro Terada, Takuma Matsumura, Yusuke Katsumata, Akira Naito, Nobuhiro Tanabe, Seiichiro Sakao, Koichiro Tatsumi, Masaaki Ito, Fumiaki Shiratori, Makoto Sumazaki, Satoshi Yajima, Hideaki Shimada, Mikako Shirouzu, Shigeyuki Yokoyama, Takashi Kudo, Hirofumi Doi, Katsuro Iwase, Hiromi Ashino, Shu-Yang Li, Masaaki Kubota, Go Tomiyoshi, Natsuko Shinmen, Rika Nakamura, Hideyuki Kuroda, Yasuo Iwadate
Summary: The study identified antigens related to atherosclerosis through serum antibody levels, which can help predict the onset of AIS and provide significantly increased risk signals.
Article
Biophysics
Fahu He, Kanako Kuwasako, Masayuki Takizawa, Mari Takahashi, Kengo Tsuda, Takashi Nagata, Satoru Watanabe, Akiko Tanaka, Naohiro Kobayashi, Takanori Kigawa, Peter Guntert, Mikako Shirouzu, Shigeyuki Yokoyama, Yutaka Muto
Summary: Matrin-3 is a multifunctional protein with DNA-binding and RNA-binding activities, which are associated with nuclear matrix formation, transcriptional regulation, and mRNA metabolism. Pathogenic mutations in its disordered region cause ALS and FTD, linked to its RNA-binding activity mediated by the RRM domains.
BIOMOLECULAR NMR ASSIGNMENTS
(2022)
Article
Oncology
Yuta Ikami, Kazue Terasawa, Kensaku Sakamoto, Kazumasa Ohtake, Hiroyuki Harada, Tetsuro Watabe, Shigeyuki Yokoyama, Miki Hara-Yokoyama
Summary: This study reveals the direct interaction between Hsc70 and LAMP2A in chaperone-mediated autophagy (CMA), as well as the significance of the two-domain architecture of the lumenal domains of LAMP2A in this interaction.
EXPERIMENTAL CELL RESEARCH
(2022)
Article
Engineering, Biomedical
Eiji Kobayashi, Aishun Jin, Hiroshi Hamana, Kiyomi Shitaoka, Kazuto Tajiri, Seisuke Kusano, Shigeyuki Yokoyama, Tatsuhiko Ozawa, Tsutomu Obata, Atsushi Muraguchi, Hiroyuki Kishi
Summary: By analyzing T cells at the single-cell level on a microwell array, researchers discovered that T-cell activation can occur via both trans and cis interactions, and successfully cloned tumor-antigen-specific TCRs.
NATURE BIOMEDICAL ENGINEERING
(2022)
Article
Biophysics
Kanako Kuwasako, Sakura Suzuki, Nobukazu Nameki, Masayuki Takizawa, Mari Takahashi, Kengo Tsuda, Takashi Nagata, Satoru Watanabe, Akiko Tanaka, Naohiro Kobayashi, Takanori Kigawa, Peter Guentert, Mikako Shirouzu, Shigeyuki Yokoyama, Yutaka Muto
Summary: The structure and sequence characteristics of the KH domain of mtRbfA were studied, and differences were found compared to RbfA, which may be related to its function in ribosome biogenesis.
BIOMOLECULAR NMR ASSIGNMENTS
(2022)
Article
Biochemistry & Molecular Biology
K. Dhanalakshmi, Seiki Kuramitsu, Shigeyuki Yokoyama, Kumarevel Thirumananseri, Karthe Ponnuraj
Summary: This study reports the crystal structure of arginase from Thermus thermophilus (TtArginase), and compares it with other homologous structures. The results show that TtArginase is more stable compared to its mesophilic counterpart, Bacillus subtilis arginase (BsArginase). Additionally, the study reveals the critical role of metal ions in both the catalytic function and maintenance of proper active site geometry. These findings are important for optimizing the enzymatic action of arginase in various conditions.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
K. Dhanalakshmi, Seiki Kuramitsu, Shigeyuki Yokoyama, Thirumananseri Kumarevel, Karthe Ponnuraj
Summary: The crystal structure of pyrrolidone carboxyl peptidase from Thermus thermophilus (TtPCP) was solved and refined at 1.9 angstrom resolution using the molecular replacement method. Comparing TtPCP with its structural homologs, it was found that the putative thermal stability of TtPCP may be attributed to more intra and inter-molecular hydrogen bonds, hydrophobic and ion pair interactions. This structural information of TtPCP can contribute to understanding the intrinsic stability of thermophilic proteins and can be useful for protein engineering.
BIOPHYSICAL CHEMISTRY
(2023)
Editorial Material
Biochemistry & Molecular Biology
Kensaku Sakamoto
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Mutsuko Kukimoto-Niino, Kentaro Ihara, Chiemi Mishima-Tsumagari, Mio Inoue, Yoshinori Fukui, Shigeyuki Yokoyama, Mikako Shirouzu
Summary: This study reveals the crystal structures of the catalytic DHR2 domain of mouse DOCK10, complexed with either Cdc42 or Rac1, and uncovers the unique dual activation mechanism of DOCK10.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Tatsuo Yanagisawa, Eiko Seki, Hiroaki Tanabe, Yoshifumi Fujii, Kensaku Sakamoto, Shigeyuki Yokoyama
Summary: Pairs of pyrrolysyl-tRNA synthetase (PylRS) and tRNA(Pyl) from Methanosarcina mazei and Methanosarcina barkeri are used for site-specific incorporations of non-canonical amino acids into proteins. Mutations in Methanomethylophilus alvus PylRS allow efficient binding with N-e-((((E)-cyclooct-2-en-1-yl)oxy)carbonyl)-L-lysine (TCO*Lys) but not with N-e-(p-ethynylbenzyloxycarbonyl)-L-lysine (pEtZLys).
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Immunology
Seisuke Kusano, Sho Ueda, Daisuke Oryoji, Aya Toyoumi, Akiko Hashimoto-Tane, Hiroyuki Kishi, Hiroshi Hamana, Atsushi Muraguchi, Hui Jin, Hisashi Arase, Hiroko Miyadera, Reiko Kishikawa, Yasunobu Yoshikai, Hisakata Yamada, Ken Yamamoto, Yasuharu Nishimura, Takashi Saito, Takehiko Sasazuki, Shigeyuki Yokoyama
Summary: Cry j 1 is a major allergen in Japanese cedar pollens. The NF region of Cry j 1 peptide plays a role in enhancing T-cell activation. Mutation of Ser and Lys in the NF region to Glu reduces the affinity for HLA-DP5, antigen presentation, and T-cell activation.
INTERNATIONAL IMMUNOLOGY
(2023)