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Topical Collection "State-of-the-Art Macromolecules in Japan"

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A topical collection in International Journal of Molecular Sciences (ISSN 1422-0067). This collection belongs to the section "Macromolecules".

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Editors

Prof. Dr. Ryoichi Arai

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Collection Editor

Faculty of Textile Science and Technology, Department of Applied Biology, Shinshu University, Nagano, Japan
Interests: protein engineering; structural biology; biotechnology; synthetic biology

Dr. Shunsuke Tomita

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Collection Editor

Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8560, Japan
Interests: biomacromolecules; biosensors; liquid–liquid phase separation
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Prof. Dr. Tamotsu Zako

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Collection Editor

Department of Chemistry, Ehime University, Ehime, Japan
Interests: nanoparticle; sensitive detection; amyloid

Prof. Dr. Masafumi Yohda

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Collection Editor

Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
Interests: chaperone; olfaction; structural biology

Prof. Dr. Masafumi Odaka
E-Mail Website
Collection Editor

Department of Life Science, Akita University, Akita, Japan
Interests: enzyme; structural biology; computational biology

Topical Collection Information

Dear Colleagues,

Molecules are the smallest units of materials. Among them, macromolecules are huge molecules, usually diameter ranging from about 10 to 1,000 nm. Our lives depend on various macromolecules, plastics, resins, and fibers. Our bodies are also made of macromolecules, such as proteins, nucleic acids, sugar chains. Most macromolecules are polymers. Proteins are polymers of amino acids. Nylon is a polyamide polymer. The development of novel materials and the advancement of life science depend on the studies of macromolecules.

Macromolecular science pursues a deeper understanding of the structure, property, and reactivity of macromolecules.

Macromolecular science and technology is multi-disciplinary research that combines physics, chemistry, biology, and engineering. A large number of research teams in Japan from different institutions and universities are working together and devoting considerable efforts to develop and study various macromolecules. This Topic Collection is committed to providing an overview of the macromolecular sciences and technologies in Japan.

Prof. Dr. Ryoichi Arai
Dr. Shunsuke Tomita
Prof. Dr. Tamotsu Zako
Prof. Dr. Masafumi Yohda
Prof. Dr. Masafumi Odaka
Collection Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the collection website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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Keywords

protein
supramolecule
biomaterials
enzyme
polymers
nanoparticle

Published Papers (5 papers)

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2023

Jump to: 2022

19 pages, 4154 KiB

Open AccessArticle

Development of Mn²⁺-Specific Biosensor Using G-Quadruplex-Based DNA

and

Int. J. Mol. Sci. 2023, 24(14), 11556; https://doi.org/10.3390/ijms241411556 - 17 Jul 2023

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Abstract

Metal ions are used in various situations in living organisms and as a part of functional materials. Since the excessive intake of metal ions can cause health hazards and environmental pollution, the development of new molecules that can monitor metal ion concentrations with high sensitivity and selectivity is strongly desired. DNA can form various structures, and these structures and their properties have been used in a wide range of fields, including materials, sensors, and drugs. Guanine-rich sequences respond to metal ions and form G-quadruplex structures and G-wires, which are the self-assembling macromolecules of G-quadruplex structures. Therefore, guanine-rich DNA can be applied to a metal ion-detection sensor and functional materials. In this study, the IRDAptamer library originally designed based on G-quadruplex structures was used to screen for Mn²⁺, which is known to induce neurodegenerative diseases. Circular dichroism and fluorescence analysis using Thioflavin T showed that the identified IRDAptamer sequence designated MnG4C1 forms a non-canonical G-quadruplex structure in response to low concentrations of Mn²⁺. A serum resistance and thermostability analysis revealed that MnG4C1 acquired stability in a Mn²⁺-dependent manner. A Förster resonance energy transfer (FRET) system using fluorescent molecules attached to the termini of MnG4C1 showed that FRET was effectively induced based on Mn²⁺-dependent conformational changes, and the limit of detection (LOD) was 0.76 µM for Mn²⁺. These results suggested that MnG4C1 can be used as a novel DNA-based Mn²⁺-detecting molecule. Full article

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2022

Jump to: 2023

9 pages, 2043 KiB

Open AccessCommunication

Relative Nuclease Resistance of a DNA Aptamer Covalently Conjugated to a Target Protein

Yudai Tabuchi

Jay Yang

and

Masumi Taki

Int. J. Mol. Sci. 2022, 23(14), 7778; https://doi.org/10.3390/ijms23147778 - 14 Jul 2022

Cited by 4 | Viewed by 1545

Abstract

A major obstacle to the therapeutic application of an aptamer is its susceptibility to nuclease digestion. Here, we confirmed the acquisition of relative nuclease resistance of a DNA-type thrombin binding aptamer with a warhead (TBA₃) by covalent binding to a target protein in the presence of serum/various nucleases. When the thrombin-inhibitory activity of TBA₃ on thrombin was reversed by the addition of the complementary strand, the aptamer was instantly degraded by the nucleases, showing that the properly folded/bound aptamer conferred the resistance. Covalently binding aptamers possessing both a prolonged drug effect and relative nuclease resistance would be beneficial for in vivo translational applications. Full article

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13 pages, 2678 KiB

Open AccessArticle

Long-Term Fluorescent Tissue Marking Using Tissue-Adhesive Porphyrin with Polycations Consisting of Quaternary Ammonium Salt Groups

and

Int. J. Mol. Sci. 2022, 23(8), 4218; https://doi.org/10.3390/ijms23084218 - 11 Apr 2022

Cited by 4 | Viewed by 1640

Abstract

Localization of tumors during laparoscopic surgery is generally performed by locally injecting India ink into the submucosal layer of the gastrointestinal tract using endoscopy. However, the location of the tumor is obscured because of the black-stained surgical field and the blurring caused by India ink. To solve this problem, in this study, we developed a tissue-adhesive porphyrin with polycations consisting of quaternary ammonium salt groups. To evaluate the ability of tissue-adhesive porphyrin in vivo, low-molecular-weight hematoporphyrin and tissue-adhesive porphyrin were injected into the anterior wall of the exposed stomach in rats. Local injection of low-molecular-weight hematoporphyrin into the anterior wall of the stomach was not visible even after 1 day because of its rapid diffusion. In contrast, the red fluorescence of the tissue-adhesive porphyrin was visible even after 7 days due to the electrostatic interactions between the positively-charged moieties of the polycation in the tissue-adhesive porphyrin and the negatively-charged molecules in the tissue. In addition, intraperitoneal injection of tissue-adhesive porphyrin in rats did not cause adverse effects such as weight loss, hepatic or renal dysfunction, or organ adhesion in the abdominal cavity. These results indicate that tissue-adhesive porphyrin is a promising fluorescent tissue-marking agent. Full article

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12 pages, 1789 KiB

Open AccessArticle

A Multi-Disulfide Receptor-Binding Domain (RBD) of the SARS-CoV-2 Spike Protein Expressed in E. coli Using a SEP-Tag Produces Antisera Interacting with the Mammalian Cell Expressed Spike (S1) Protein

Subbaian Brindha

and

Yutaka Kuroda

Int. J. Mol. Sci. 2022, 23(3), 1703; https://doi.org/10.3390/ijms23031703 - 01 Feb 2022

Cited by 13 | Viewed by 2583

Abstract

An Escherichia coli (E. coli) production of the receptor-binding domain (RBD) of the SARS-CoV-2 (isolate Wuhan-Hu-1) spike protein would significantly accelerate the search for anti-COVID-19 therapeutics because of its versatility and low cost. However, RBD contains four disulfide bonds and its expression in E. coli is limited by the formation of aberrant disulfide bonds resulting in inclusion bodies. Here, we show that a solubility-enhancing peptide (SEP) tag containing nine arginine residues (RBD-C9R) attached at the C-terminus can overcome this problem. The SEP-tag increased the expression in the soluble fraction and the final yield by five times (2 mg/L). The folding properties of the E. coli expressed RBD-C9R were demonstrated with biophysical characterization using RP-HPLC, circular dichroism, thermal denaturation, fluorescence, and light scattering. A quartz crystal microbalance (QCM) analysis confirmed the binding activity of RBD-C9R with ACE2, the host cell’s receptor. In addition, RBD-C9R elicited a Th-2 immune response with a high IgG titer in Jcl: ICR mice. The RBD-C9R antisera interacted with both itself and the mammalian-cell expressed spike protein (S1), as demonstrated by ELISA, indicating that the E. coli expressed RBD-C9R harbors native-like epitopes. Overall, these results emphasize the potential of our SEP-tag for the E. coli production of active multi-disulfide-bonded RBD. Full article

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19 pages, 3483 KiB

Open AccessArticle

Self-Assembling Lectin Nano-Block Oligomers Enhance Binding Avidity to Glycans

and

Int. J. Mol. Sci. 2022, 23(2), 676; https://doi.org/10.3390/ijms23020676 - 08 Jan 2022

Cited by 5 | Viewed by 2184

Abstract

Lectins, carbohydrate-binding proteins, are attractive biomolecules for medical and biotechnological applications. Many lectins have multiple carbohydrate recognition domains (CRDs) and strongly bind to specific glycans through multivalent binding effect. In our previous study, protein nano-building blocks (PN-blocks) were developed to construct self-assembling supramolecular nanostructures by linking two oligomeric proteins. A PN-block, WA20-foldon, constructed by fusing a dimeric four-helix bundle de novo protein WA20 to a trimeric foldon domain of T4 phage fibritin, self-assembled into several types of polyhedral nanoarchitectures in multiples of 6-mer. Another PN-block, the extender PN-block (ePN-block), constructed by tandemly joining two copies of WA20, self-assembled into cyclized and extended chain-type nanostructures. This study developed novel functional protein nano-building blocks (lectin nano-blocks) by fusing WA20 to a dimeric lectin, Agrocybe cylindracea galectin (ACG). The lectin nano-blocks self-assembled into various oligomers in multiples of 2-mer (dimer, tetramer, hexamer, octamer, etc.). The mass fractions of each oligomer were changed by the length of the linkers between WA20 and ACG. The binding avidity of the lectin nano-block oligomers to glycans was significantly increased through multivalent effects compared with that of the original ACG dimer. Lectin nano-blocks with high avidity will be useful for various applications, such as specific cell labeling. Full article

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Topical Collection "State-of-the-Art Macromolecules in Japan"

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Published Papers (5 papers)

2023

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2022

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