Article
Biochemical Research Methods
Veronica Saez-Jimenez, Simone Scrima, Matteo Lambrughi, Elena Papaleo, Valeria Mapelli, Martin K. M. Engqvist, Lisbeth Olsson
Summary: Pathway engineering is commonly used to improve the production of metabolites, but low catalytic activity can create bottlenecks in specific reaction steps. This study successfully obtained mutant variants of (R)-2-hydroxyglutarate dehydrogenase with a 100-fold higher catalytic efficiency, paving the way for the bio-based production of adipic acid. Rational analysis revealed that mutation A206V played a key role in the improved activity.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Shohei Mine, Makoto Nakabayashi, Kazuhiko Ishikawa
Summary: Aldehyde dehydrogenase (ALDH) is widely distributed in nature and plays a crucial role in aldehyde detoxification. Thermostable ALDH from Sulfolobus tokodaii has high activity towards acetaldehyde and can be potentially used as a biosensor. However, the crystal structure of this thermostable ALDH with high activity towards acetaldehyde has not been reported. This study successfully determined the crystal structure of recombinant thermostable ALDH from S. tokodaii in complex with NADP, which provides insights for further studies on catalytic mechanisms and applications.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Maria Dumina, Dmitry Zhdanov, Alexander Zhgun, Marina Pokrovskaya, Svetlana Aleksandrova, Alexander Veselovsky, Michael El'darov
Summary: Researchers have successfully increased the activity and cytotoxicity of a thermophilic L-ASNase through the construction of a double mutant. This was achieved by modifying two adjacent amino acid residues in the substrate-binding site of the enzyme.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Seiya Watanabe, Yohsuke Murase, Yasunori Watanabe, Yasuhiro Sakurai, Kunihiko Tajima
Summary: Seiya Watanabe et al. report the crystal structures of two distinct members of the Aconitase X subfamily, which contain [Fe-S] clusters different from other aconitases. This study provides insight into the molecular evolution of the aconitase superfamily.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Michelangelo Simongini, Andrea Puglisi, Filippo Genovese, Alejandro Hochkoeppler
Summary: The tetrameric enzyme rbLDH from rabbit skeletal muscle undergoes dissociation and loses enzyme activity under acidic conditions. Trehalose, a disaccharide, has been shown to stabilize proteins and enzymes, but its effect on the dissociation of protein oligomers is unknown. Our study found that trehalose can prevent the dissociation of rbLDH induced by acidic conditions, while maltose and cellobiose enhance the dissociation.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2023)
Article
Biotechnology & Applied Microbiology
Yong Guo, Jingjing Huo, Runchao Bai, Jingyuan Zhang, Jipeng Yao, Kaijie Ma, Zengtao Zhang, Haigang Li, Chun Zhang
Summary: This study confirms the essential role of free cysteine residues in tetrameric formation and stability of mammalian uricase. Mutations or blockage of Cys188 and Cys195 significantly disrupt the formation and stability of the tetrameric structure, highlighting the importance of free thiols in Cys residues.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Jiaqi Li, Guangbo Kang, Jiewen Wang, Haibin Yuan, Yili Wu, Shuxian Meng, Ping Wang, Miao Zhang, Yuli Wang, Yuanhang Feng, He Huang, Ario de Marco
Summary: Routinely screened antibody fragments often require further in vitro maturation for optimal biophysical properties. In vitro strategies can introduce random mutations into the sequences and select for improved ligands under more stringent conditions. Rational approaches aim to identify specific residues involved in biophysical mechanisms and evaluate mutations to improve characteristics. Understanding antigen-antibody interactions is crucial for reliable development, with deep learning methods promising for accelerating model building.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Alberto Pietro Pasti, Valentina Rossi, Giuseppina Di Stefano, Maurizio Brigotti, Alejandro Hochkoeppler
Summary: The study reveals that human LDH-A undergoes homotropic allosteric transitions when exposed to acidic pH, while displaying Michaelis-Menten kinetics at pH values equal to or higher than 7.0. Additionally, citrate, isocitrate, and malate activate human LDH-A, with citrate and isocitrate leading to major effects, and the allosteric kinetics in human LDH-A is accompanied by the dissociation of the enzyme tetramer under acidic conditions. Furthermore, a negative feedback between lactic acidosis and human LDH-A activity is observed, indicating a complex regulation of this feedback by pyruvate and intermediates of the Krebs cycle.
BIOSCIENCE REPORTS
(2022)
Article
Chemistry, Physical
Qinyuan Ma, Xiaoxiao Wang, Fang Luan, Ping Han, Xue Zheng, Yanmiao Yin, Xianghe Zhang, Yaning Zhang, Xiuzhen Gao
Summary: This study reveals the existence of divergent evolution in the meso-diaminopimelate dehydrogenase (meso-DAPDH) family and investigates the function of an indel loop in CgDAPDH. The results demonstrate that the indel loop plays a crucial role in the catalytic cycle of CgDAPDH, maintaining the correct conformation of the protein and stabilizing the hydrogen-bond network. However, it is not the driving force for the divergent evolution of the meso-DAPDH family.
Article
Biochemistry & Molecular Biology
Mohammed Hamed Alqarni, Ahmed Ibrahim Foudah, Magdy Mohamed Muharram, Haritium Budurian, Nikolaos E. Labrou
Summary: AMPS-HDB reacts covalently with CbFDH, leading to complete inactivation of the enzyme activity, while NAD(+) and NADH protect CbFDH from inactivation by AMPS-HDB. Molecular modelling studies identified Arg174 as the target for AMPS-HDB, confirmed by site-directed mutagenesis.
Review
Biotechnology & Applied Microbiology
Zarina Iqbal, Saima Sadaf
Summary: Generating functional protein variants with novel or improved characteristics can be achieved through rational design and directed evolution. In laboratory evolution, new tools and methods are needed to create genetic diversity and identify variants with desired traits. Building large libraries of target molecules and protocols to alter their properties has been a challenge in directed evolution experiments.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Genetics & Heredity
Xin Tang, Lulu Chang, Shujie Gu, Hao Zhang, Yong Q. Chen, Haiqin Chen, Jianxin Zhao, Wei Chen
Summary: The research shows that IPMDH affects fatty acid metabolism in two fungi by regulating the metabolism of branched-chain amino acids, providing a potential strategy to increase lipid production.
FUNGAL GENETICS AND BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Luca Giacinto Iacovino, Martina Rossi, Giuseppina Di Stefano, Valentina Rossi, Claudia Binda, Maurizio Brigotti, Fabio Tomaselli, Alberto Pietro Pasti, Fabrizio Dal Piaz, Stefano Cerini, Alejandro Hochkoeppler
Summary: Lactate dehydrogenase plays an important role in generating lactate under conditions of muscle fatigue or limited oxygen availability. This study reveals that rabbit skeletal muscle LDH undergoes allosteric transitions in response to pH changes, and the dissociation of LDH counteracts lactic acidosis, with citrate and pyruvate regulating the enzyme's conformational changes.
Article
Chemistry, Physical
Bo Hyun Choi, Sung Hui Kim, Pyung Cheon Lee
Summary: The study investigated the relationship between the structure and CDB-introducing capability of Phytoene desaturase CrtI, identifying three key amino acids that significantly determined carotenoid profiles. The mutated amino acids were found to be located in the membrane-binding domain of CrtI, influencing the FAD binding region and subsequently affecting the desaturation level in phytoene. These findings contribute to a better understanding of the function and regulation of CrtI in carotenoid biosynthesis.
Article
Biochemistry & Molecular Biology
Ryushi Kawakami, Naoki Takami, Junji Hayashi, Kazunari Yoneda, Taketo Ohmori, Toshihisa Ohshima, Haruhiko Sakuraba
Summary: The crystal structures of Pseudomonas veronii L-arginine dehydrogenase in complex with different substrates were studied. The enzyme showed similarities with Archaeoglobus fulgidus L-AlaDH in terms of structure and specificity, but had different residues recognizing the substrates' amino groups.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Review
Astronomy & Astrophysics
Yuko Kawaguchi, Shin-ichi Yokobori, Hirofumi Hashimoto, Hajime Yano, Makoto Tabata, Hideyuki Kawai, Akihiko Yamagishi
Article
Biochemistry & Molecular Biology
Ryutaro Furukawa, Mizuho Nakagawa, Takuya Kuroyanagi, Shin-ichi Yokobori, Akihiko Yamagishi
JOURNAL OF MOLECULAR EVOLUTION
(2017)
Article
Biotechnology & Applied Microbiology
Yuhi Hamuro, Katsuya Tajima, Akiko Matsumoto-Akanuma, Sayaka Sakamoto, Ryutaro Furukawa, Akihiko Yamagishi, Naohito Ohno, Satoshi Akanuma
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2017)
Article
Biochemistry & Molecular Biology
Asuteka Nagao, Mitsuhiro Ohara, Kenjyo Miyauchi, Shin-ichi Yokobori, Akihiko Yamagishi, Kimitsuna Watanabe, Tsutomu Suzuki
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2017)
Article
Multidisciplinary Sciences
Emanuel Ott, Yuko Kawaguchi, Denise Koelbl, Palak Chaturvedi, Kazumichi Nakagawa, Akihiko Yamagishi, Wolfram Weckwerth, Tetyana Milojevic
Article
Multidisciplinary Sciences
Amanda K. Garcia, J. William Schopf, Shin-ichi Yokobori, Satoshi Akanuma, Akihiko Yamagishi
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2017)
Article
Biochemistry & Molecular Biology
Asuteka Nagao, Mitsuhiro Ohara, Kenjyo Miyauchi, Shin-ichi Yokobori, Akihiko Yamagishi, Kimitsuna Watanabe, Tsutomu Suzuki
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2017)
Article
Biotechnology & Applied Microbiology
Sota Yagi, Satoshi Akanuma, Asumi Kaji, Hiroya Niiro, Hayato Akiyama, Tatsuya Uchida, Akihiko Yamagishi
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2018)
Article
Multidisciplinary Sciences
Rei Shibue, Takahiro Sasamoto, Masami Shimada, Bowen Zhang, Akihiko Yamagishi, Satoshi Akanuma
SCIENTIFIC REPORTS
(2018)
Article
Multidisciplinary Sciences
Shota Nitahara, Shingo Kato, Akira Usui, Tetsuro Urabe, Katsuhiko Suzuki, Akihiko Yamagishi
Article
Astronomy & Astrophysics
Akihiko Yamagishi, Yuko Kawaguchi, Hirofumi Hashimoto, Hajime Yano, Eiichi Imai, Satoshi Kodaira, Yukio Uchihori, Kazumichi Nakagawa
Article
Microbiology
Emanuel Ott, Yuko Kawaguchi, Natalie Ozgen, Akihiko Yamagishi, Elke Rabbow, Petra Rettberg, Wolfram Weckwerth, Tetyana Milojevic
FRONTIERS IN MICROBIOLOGY
(2019)
Article
Multidisciplinary Sciences
Satoshi Akanuma, Mizumo Bessho, Hikono Kimura, Ryutaro Furukawa, Shin-ichi Yokobori, Akihiko Yamagishi
SCIENTIFIC REPORTS
(2019)
Article
Biochemistry & Molecular Biology
Ryutaro Furukawa, Shin-ichi Yokobori, Riku Sato, Taimu Kumagawa, Mizuho Nakagawa, Kazutaka Katoh, Akihiko Yamagishi
Summary: This study generated a composite phylogenetic tree for seven aminoacyl-tRNA synthetases (ARSs) and predicted the ancestral ARS sequences and amino acid specificity before the evolution of the last universal common ancestor. The results showed that the ancestral ARSs had substantial amino acid specificity and that the number of amino acid types aminoacylated by proteinaceous ARSs was limited before the appearance of a fuller range of proteinaceous ARS species.
JOURNAL OF MOLECULAR EVOLUTION
(2022)
Article
Katsuya Satoh, Hiroki Arai, Toshihiko Sanzen, Yuko Kawaguchi, Hidenori Hayashi, Shin-ichi Yokobori, Akihiko Yamagishi, Yutaka Oono, Issay Narumi
GENOME ANNOUNCEMENTS
(2018)