Article
Biochemistry & Molecular Biology
Aakriti Upadhyay, Chinwe Ekenna
Summary: Understanding the binding behavior and conformational dynamics of intrinsically disordered proteins (IDPs) is crucial. We proposed an algorithm that explores IDP binding behavior with protein complexes by extracting topological and geometric features from the protein surface model. Our method outperformed the compared methods in computation performance and binding affinity in experimental conformations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Engineering, Chemical
Ana Freitas, Lucilia Domingues, Tatiana Q. Aguiar
Summary: This study evaluated the feasibility of using bare silica as a matrix for protein purification/immobilization, and the results showed that unmodified silica matrices can effectively purify His-tagged proteins, with the combination of tags being advantageous for immobilization purposes.
SEPARATION AND PURIFICATION TECHNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Rakesh Trivedi, Hampapathalu Adimurthy Nagarajaram
Summary: This review discusses different aspects of disordered proteins and protein regions, as well as the experimental and computational methods used to characterize them. Additionally, the role of disordered proteins in diseases and their potential as drug targets are explored.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
H. Jane Dyson
Summary: Viruses infect all kingdoms of life and employ disordered proteins to accomplish various functions. Disordered proteins have been discovered in almost all viruses studied, regardless of the viral genome composition or the viral capsid configuration. This review presents a collection of stories illustrating the diverse functions of disordered proteins in viruses, providing a survey of the field's expansion.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Soumyanetra Chandra, Kavyashree Manjunath, Aparna Asok, Raghavan Varadarajan
Summary: Unlike globular proteins, the mutational effects on IDPs' function are not well-studied. By conducting Deep Mutational Scanning on a mutant library of the CcdA IDP displayed on yeast surface, the study sheds light on the sequence-function relationships. The research also reveals that a single ligand concentration can be used to quantitatively estimate the relative binding constants for a large number of protein variants, thanks to IDPs' extended interface.
Article
Biochemistry & Molecular Biology
Uros Zavrtanik, San Hadzi, Jurij Lah
Summary: The study characterizes the high affinity interaction between the intrinsically disordered HigA2 antitoxin and its globular target HigB2 toxin. Through experimental decomposition of the association parameters, it is found that the energy optimization of the HigA2-HigB2 interface is similar to that of globular ultra-high affinity complexes. Other ultra-high affinity IDP-target systems suggest that a strategy based on entropy optimization can also achieve picomolar affinities.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Shangbo Ning, Hong-Jun Chao, Shuangli Li, Rui Zhou, Lei Zou, Xu Zhang, Jun Liu, Dazhong Yan, Mojie Duan
Summary: This study investigates the molecular mechanism of phosphorylation regulation on the auto-inhibition of Ets-1 using molecular simulations and biochemical experiments. The results suggest that both steric hindrance and allosteric regulation are involved in the DNA-binding inhibitory effect caused by phosphorylation, with steric effects playing a greater role.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biotechnology & Applied Microbiology
Stefan Rauwolf, Tobias Steegmuller, Sebastian Patrick Schwaminger, Sonja Berensmeier
Summary: Silica is widely used for chromatography resins due to its high mechanical strength, column efficiency, easy manufacturing, and low cost. This study demonstrated that the octapeptide (RH)4 can be used as a peptide tag for high-purity protein purification on bare silica, achieving high affinity through an ion pairing mechanism. The purification process showed high purity, recovery rate, and ability to enhance purity through overloading the column, making it independent from buffer choice and cost-effective compared to surface functionalization.
ENGINEERING IN LIFE SCIENCES
(2021)
Review
Chemistry, Multidisciplinary
Matti Mar, Kateryna Nitsenko, Petur O. Heidarsson
Summary: Eukaryotic transcription factors play a crucial role in integrating molecular feedback and regulating gene expression. They consist of structured DNA-binding domains and long intrinsically disordered regions (IDRs). The dynamic multifunctionality of IDRs is essential for their functions in genome regulation. This review analyzes the chemical features of TF IDRs and their involvement in protein interactions, DNA binding, chromatin opening, and phase separation. Suggestions are given for future research to integrate experiments and simulations in understanding TF functions.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Vladimir D. Manyilov, Nikolay S. Ilyinsky, Semen V. Nesterov, Baraa M. G. A. Saqr, Guy W. Dayhoff, Egor V. Zinovev, Simon S. Matrenok, Alexander V. Fonin, Irina M. Kuznetsova, Konstantin K. Turoverov, Valentin Ivanovich, Vladimir N. Uversky
Summary: This article examines the impact of intrinsically disordered proteins and regions on aging-related processes. The findings indicate that these disordered components play significant roles in aging, particularly in genome regulation.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Attila Meszaros, Kevin Muwonge, Steven Janvier, Junaid Ahmed, Peter Tompa
Summary: Intrinsically disordered proteins (IDPs) lack well-defined 3D structures and can interact promiscuously due to their high flexibility. This unique property allows them to play diverse regulatory roles in cellular processes. However, their exposed structural state makes them more susceptible to proteolytic degradation compared to globular proteins.
Article
Multidisciplinary Sciences
Rebecca B. Berlow, H. Jane Dyson, Peter E. Wright
Summary: Intrinsically disordered proteins compete for binding to common regulatory targets to carry out their biological functions. The activation domains of HIF-1 alpha and CITED2 function as a unidirectional, allosteric molecular switch to control transcription of adaptive genes. The mechanistic details of this molecular switch were characterized through NMR spectroscopy and biophysical methods, revealing the contributions of individual binding motifs in CITED2. These findings provide insight into the complexity of molecular interactions involving disordered proteins and how they compete for occupancy of common targets.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Valentin Bauer, Boris Schmidtgall, Gergo Gogl, Jozica Dolenc, Judit Osz, Yves Nomine, Camille Kostmann, Alexandra Cousido-Siah, Andre Mitschler, Natacha Rochel, Gilles Trave, Bruno Kieffer, Vladimir Torbeev
Summary: This study utilized a specific amino acid substitution pattern to modify the free activation domain of transcriptional coactivator ACTR, resulting in increased binding affinity to CREB-binding protein. The X-ray structure of the modified ACTR domain - NCBD complex revealed a unique conformation of ACTR, demonstrating a strategy for characterizing individual conformational states of IDPs.
Article
Biochemical Research Methods
Yoko Ino, Yutaro Yamaoka, Kiho Tanaka, Kei Miyakawa, Mayuko Nishi, Yasuyoshi Hatayama, Hirokazu Kimura, Yayoi Kimura, Akihide Ryo
Summary: Peptide tag systems are widely used for protein detection and purification. We developed a novel tag system called HiP4 with a specific epitope sequence that overlaps with the conventional 6x histidine tag. By using this system, we developed a TAP-MS system for comprehensive protein interactome analysis, which showed low background and high selectivity in identifying novel protein interactions.
Article
Multidisciplinary Sciences
Susan K. Vester, Rolle Rahikainen, Irsyad N. A. Khairil Anuar, Rory A. Hills, Tiong Kit Tan, Mark Howarth
Summary: The authors developed a switchable protein purification method called SpySwitch, which enables gentle purification of proteins tagged with SpyTag. SpySwitch contains histidines that allow pH-dependent release of captured proteins, resulting in higher purity compared to traditional His-tag methods. Additionally, SpySwitch is thermosensitive, allowing protein capture and release at specific temperatures, making it suitable for direct assembly onto multimeric scaffolds. The study also demonstrated the application of SpySwitch in the purification of receptor-binding domains from coronaviruses and the recognition of these domains by antibodies.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Takeshi Ikeda, Kohei Ichikawa, Hajime Shigeto, Takenori Ishida, Ryuichi Hirota, Hisakage Funabashi, Akio Kuroda
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2019)
Article
Biotechnology & Applied Microbiology
Gamal Nasser Abdel-Hady, Takeshi Ikeda, Takenori Ishida, Hisakage Funabashi, Akio Kuroda, Ryuichi Hirota
Summary: In this study, a thermotolerant phosphite dehydrogenase from Ralstonia sp. 4506 (RsPtxD) was engineered to create a highly efficient and robust NADPH regeneration system. By changing specific amino acid residues, a mutant RsPtxD(HARRA) with significantly increased preference for NADP was obtained, displaying the highest catalytic efficiency among previously reported phosphite dehydrogenases. This mutant exhibited high thermostability and organic solvent tolerance, making it a promising alternative NADPH regeneration system for practical applications.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Correction
Biochemical Research Methods
Kei Motomura, Kosuke Sano, Satoru Watanabe, Akihiro Kanbara, Gamal Nasser Abdel-Hady, Takeshi Ikeda, Takenori Ishida, Hisakage Funabashi, Akio Kuroda, Ryuichi Hirota
ACS SYNTHETIC BIOLOGY
(2021)
Article
Plant Sciences
Narumi Toda, Hiroki Murakami, Akihiro Kanbara, Akio Kuroda, Ryuichi Hirota
Summary: The study on using phosphite (Pt) to suppress predatory zooplankton Poterioochromonas malhamensis showed that high concentrations of Pt reduced the grazing impact of P. malhamensis. Furthermore, the suppression effect of Pt was found to be dependent on the type of environmental water used, and under high Pt conditions, Paraphysomonas emerged as a dominant microorganism replacing P. malhamensis.
Article
Instruments & Instrumentation
Hisakage Funabashi, Keisuke Nakatsuka, Shuhei Yoshida, Hajime Shigeto, Ryuichi Hirota, Takeshi Ikeda, Akio Kuroda
Summary: The design and feasibility of split G-quadruplex-based DNA nanotweezers that can detect short nucleic acids with a single-base mismatch are discussed. These nanotweezers exhibit peroxidase activity and can be used for homogeneous assay format to detect specific nucleic acids. Additionally, a new type of DNA-BNA chimera nanotweezers has been developed, which can distinguish different miRNA sequences based on the difference in melting temperature.
SENSORS AND MATERIALS
(2022)
Article
Biochemical Research Methods
Ryuichi Hirota, Zen-ichiro Katsuura, Naoki Momokawa, Hiroki Murakami, Satoru Watanabe, Takenori Ishida, Takeshi Ikeda, Hisakage Funabashi, Akio Kuroda
Summary: In this study, it was found that under specific conditions, a phosphite-dependent strain of Escherichia coli can generate escape mutants. The mutation occurs at position 210 of the transmembrane domain protein HtxC of the phosphorus compound transporter HtxBCDE. The replacement of a specific amino acid residue at this position can reduce the rate of escape mutant generation.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Hiroki Murakami, Kosuke Sano, Kei Motomura, Akio Kuroda, Ryuichi Hirota
Summary: Biological containment is a biosafety strategy used to prevent the spread of genetically modified organisms in natural ecosystems. A study assessed the risk of horizontal gene transfer (HGT) mediated escape in a phosphite-dependent cyanobacterium. The results showed that HGT from closely related species posed a high risk for escape, and inhibiting exogenous DNA uptake could enhance the robustness of the containment system.
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2023)
Article
Microbiology
Luke Bown, Ryuichi Hirota, Michelle N. Goettge, Jerry Cui, David T. Krist, Lingyang Zhu, Constantin Giurgiu, Wilfred A. van der Donk, Kou-San Ju, William W. Metcalf
Summary: The study reveals the biosynthetic pathway of phosphonothrixin, which can help design strains that overproduce this potentially useful herbicide.
JOURNAL OF BACTERIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Takeshi Ikeda
Summary: This review summarizes recent findings on bacterial extracellular and intracellular biosilicification. Topics discussed include bacterial extracellular biosilicification in geothermal environments, encapsulation of Bacillus spores within a silica layer, silicon accumulation in marine cyanobacteria, and the possible contribution of bacterial biosilicification to the global silicon cycle.
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Takenori Ishida, Takuma Hashimoto, Kanako Masaki, Hisakage Funabashi, Ryuichi Hirota, Takeshi Ikeda, Hideji Tajima, Akio Kuroda
SCIENTIFIC REPORTS
(2020)
Article
Chemistry, Analytical
Hajime Shigeto, Takuto Ono, Takeshi Ikeda, Ryuichi Hirota, Takenori Ishida, Akio Kuroda, Hisakage Funabashi
Article
Genetics & Heredity
Takenori Ishida, Nobutoshi Fujihara, Tomoki Nishimura, Hisakage Funabashi, Ryuichi Hirota, Takeshi Ikeda, Akio Kuroda
GENES AND ENVIRONMENT
(2019)
Article
Biochemical Research Methods
Juri Sakata, Toshifumi Tatsumi, Akira Sugiyama, Akihiro Shimizu, Yuya Inagaki, Hiroto Katoh, Takefumi Yamashita, Kazuki Takahashi, Sho Aki, Yudai Kaneko, Takeshi Kawamura, Mai Miura, Masazumi Ishii, Tsuyoshi Osawa, Toshiya Tanaka, Shumpei Ishikawa, Masanobu Tsukagoshi, Michael Chansler, Tatsuhiko Kodama, Motomu Kanai, Hidetoshi Tokuyama, Kenzo Yamatsugu
Summary: This study reports an expression, refolding, and purification method for antibody-mimetic drug conjugate (AMDC). The AMDC uses a variable heavy chain of heavy chain-only antibodies (VHHs) as the targeting protein and non-covalently binds to a potent DNA-alkylating drug. The AMDC shows strong cytotoxic effects on cancer cells.
PROTEIN EXPRESSION AND PURIFICATION
(2024)
Article
Biochemical Research Methods
Yao Wang, Shaoting Weng, Yajie Tang, Sen Lin, Xiayue Liu, Wenhui Zhang, Gang Liu, Boomi Pandi, Yinrong Wu, Lei Ma, Lin Wang
Summary: In this study, a high yield of recombinant CD20 and claudin 18.2 proteins was achieved using an in vitro coupled transcription-translation system. The results showed that rituximab has a high affinity with CD20 protein. This study provides a novel concept for promoting the expression of multi-pass transmembrane proteins and lays the foundation for large-scale industrial production of membrane-associated drug targets.
PROTEIN EXPRESSION AND PURIFICATION
(2024)
Article
Biochemical Research Methods
Xiaobing Chen, Zijuan Zou, Wei Li, Xu Dong, Yi Chen, Yan Lu, Mingyue Zhu, Mengsen Li, Bo Lin
Summary: In this study, the fusion protein ImI-AFP3, composed of alpha-Conotoxin ImI and human alpha fetoprotein domain 3 (AFP3), was found to inhibit the growth and migration of lung cancer cells and showed synergistic effects with the drug gefitinib. These findings suggest that ImI-AFP3 is a promising candidate for the development of anticancer drugs.
PROTEIN EXPRESSION AND PURIFICATION
(2024)
Article
Biochemical Research Methods
Angel Castillo-Corujo, Mirva J. Saaranen, Lloyd W. Ruddock
Summary: This study successfully expressed two Fabs antibodies in the cytoplasm of E. coli using the CyDisCo system, achieving high yields and biological activity under industrially relevant fermentation conditions.
PROTEIN EXPRESSION AND PURIFICATION
(2024)
Article
Biochemical Research Methods
Junling Guo, Zhongyi Cheng, Zhemin Zhou
Summary: This study focused on a halophilic archaeal nitrile hydratase (NHase) and found that it exhibited higher tolerance to substrates and products compared to NHases from other sources. The unique genetic structure of this highly stable archaeal NHase could provide a theoretical foundation for modifying and enhancing the industrial application of NHase.
PROTEIN EXPRESSION AND PURIFICATION
(2024)
Article
Biochemical Research Methods
Yunlong Shen, Ruirui Zhang, Xiaohua Jiang, Jinliang Yang
Summary: The study developed a monoclonal antibody, B1M023, that can bind to LILRB1 with high affinity and block its binding to HLA-G. This antibody can promote the activation and IFN-gamma secretion of T cells, suggesting its potential applications in concomitant diagnosis and tumor immunotherapy.
PROTEIN EXPRESSION AND PURIFICATION
(2024)
Article
Biochemical Research Methods
Jun Jiang, Zhengqiang Jiang, Qiaojuan Yan, Susu Han, Shaoqing Yang
Summary: A novel alginate lyase gene from a marine bacterium showed efficient enzyme activity and stability, producing high conversion ratios of alginate oligosaccharides.
PROTEIN EXPRESSION AND PURIFICATION
(2024)
Article
Biochemical Research Methods
Xianghua Xiong, Yujin Qiu, Jiahao Zheng, Ling Zhou, Qingyang Wang, Jinglun Pang, Weicai Zhang, Huipeng Chen, Gang Liu, Xiaodong Han
Summary: A specific monoclonal antibody ML419 has been found to disrupt the recognition between Botulinum neurotoxin serotype A (BoNT/A) and FGFR3, effectively preventing BoNT/A from entering neurons. In vivo experiments show that ML419 has a strong protective effect, making it a promising candidate for the development of therapeutics against BoNT/A.
PROTEIN EXPRESSION AND PURIFICATION
(2024)
Article
Biochemical Research Methods
Maria Rain Jennings, Soohyon Min, Grace S. Xu, Kassandra Homayuni, Bhavana Suresh, Yusef Amir Haikal, John Blazeck
Summary: This study successfully produced Homo sapiens adenosine deaminase isoform 1 (HsADA1) and its variants through optimizing the recombinant expression process. The D8N variant of HsADA1 was found to be about 30% less active than the wildtype, but it better retained its activity in human serum. Additionally, the study revealed a previously undescribed phenomenon involving albumin that contributed to the increased activity of HsADA1 and the D8N variant in serum.
PROTEIN EXPRESSION AND PURIFICATION
(2024)
Article
Biochemical Research Methods
Oinam Sangita Devi, Senjam Sunil Singh, K. Rana, Sorokhaibam Jibankumar Singh, Wayenbam Sobhachandra Singh
Summary: A new lectin with hemagglutination activity was purified from the rhizome of Xanthosoma violaceum Schott. The lectin showed different reactions towards human red blood cells of different blood groups. It exhibited optimal hemagglutination activity at specific temperature and pH range, and showed good stability.
PROTEIN EXPRESSION AND PURIFICATION
(2024)