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Protein and Nucleotide Engineering for Diagnoses and Biosensing II
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Protein and Nucleotide Engineering for Diagnoses and Biosensing II

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: 30 April 2024 | Viewed by 3967

Special Issue Editors

Prof. Dr. Koji Sode

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Guest Editor
Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill (UNC) and North Carolina State University, Chapel Hill, NC, USA
Interests: protein engineering; enzyme engineering; biosensors; biosensing; biomedical engineering; biomolecular engineering
Special Issues, Collections and Topics in MDPI journals
Dr. Takenori Satomura

E-Mail Website
Guest Editor
Department of Applied Chemistry and Biotechnology, Faculty of Engineering /Graduate School of Engineering, University of Fukui, Fukui, Japan
Interests: protein
Special Issues, Collections and Topics in MDPI journals
Dr. Wataru Yoshida

E-Mail Website
Guest Editor
School of Bioscience and Biotechnology, Graduate School of Bionics, Tokyo University of Technology, Hachioji, Japan
Interests: aptamers; DNA methylation; DNA quadruplex; biosensing
Special Issues, Collections and Topics in MDPI journals
Dr. Moon Il Kim

E-Mail Website
Guest Editor
Department of BioNano Technology, Gachon University, Gyeonggi 13120, Republic of Korea
Interests: nano-biosensor; biosynthesis of drug candiates & drug delivery; cell-based biosensors & anti-bacterial assay; in vitro biosynthesis of nanoparticles
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The development and innovation of methods and devices for monitoring metabolites, biomarkers, and drugs used for medical treatments are strongly dependent on the availability of the molecular recognition elements—biosensing molecules. These include proteins such as enzymes, antibodies, binding proteins, and receptors, as well as their mimics such as enzyme-mimicking nanomaterials (nanozymes). Additionally included are nucleotides such as DNA aptamers and RNA aptamers, along with their mimics such as peptide nucleic acids, which specifically recognize and bind to the target molecules. Recent progress made in the technologies used for designing and engineering these molecules, together with advances made in the variety of simulations and prediction tools used for engineering proteins/nucleotides, are accelerating the development of engineering biosensing molecules for use in diagnosis and biosensing technologies, which will provide a new future for biosensing technologies.

Following our great success in the former Special Issue, “Protein and Nucleotide Engineering for Diagnoses and Biosensing”, we are very excited to invite you to contribute to the Special Issue “Protein and Nucleotide Engineering for Diagnoses and Biosensing II”. This Special issue aims to provide a summary of the field; to explore recent advances made in the discovery, design, and engineering of proteins and nucleotides for use in diagnosis and biosensing; and to discuss how we can utilize these for the development of future biosensing technologies. We invite authors to submit original research articles related to any of these aspects. We also welcome review articles which cover the specific topics in this research area.

Prof. Dr. Koji Sode
Dr. Takenori Satomura
Dr. Wataru Yoshida
Prof. Dr. Moon Il Kim
Guest 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 special issue 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.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • proteins
  • enzymes
  • antibodies
  • binding proteins
  • aptamers
  • nanozymes
  • biosensors
  • diagnosis

Published Papers (2 papers)

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Research

15 pages, 1995 KiB  
Article
Development of a Versatile Method to Construct Direct Electron Transfer-Type Enzyme Complexes Employing SpyCatcher/SpyTag System
by Takumi Yanase, Junko Okuda-Shimazaki, Ryutaro Asano, Kazunori Ikebukuro, Koji Sode and Wakako Tsugawa
Int. J. Mol. Sci. 2023, 24(3), 1837; https://doi.org/10.3390/ijms24031837 - 17 Jan 2023
Cited by 3 | Viewed by 2206
Abstract
The electrochemical enzyme sensors based on direct electron transfer (DET)-type oxidoreductase-based enzymes are ideal for continuous and in vivo monitoring. However, the number and types of DET-type oxidoreductases are limited. The aim of this research is the development of a versatile method to [...] Read more.
The electrochemical enzyme sensors based on direct electron transfer (DET)-type oxidoreductase-based enzymes are ideal for continuous and in vivo monitoring. However, the number and types of DET-type oxidoreductases are limited. The aim of this research is the development of a versatile method to create a DET-type oxidoreductase complex based on the SpyCatcher/SpyTag technique by preparing SpyCatcher-fused heme c and SpyTag-fused non-DET-type oxidoreductases, and by the in vitro formation of DET-type oxidoreductase complexes. A heme c containing an electron transfer protein derived from Rhizobium radiobacter (CYTc) was selected to prepare SpyCatcher-fused heme c. Three non-DET-type oxidoreductases were selected as candidates for the SpyTag-fused enzyme: fungi-derived flavin adenine dinucleotide (FAD)-dependent glucose dehydrogenase (GDH), an engineered FAD-dependent d-amino acid oxidase (DAAOx), and an engineered FMN-dependent l-lactate oxidase (LOx). CYTc-SpyCatcher (CYTc-SC) and SpyTag-Enzymes (ST-GDH, ST-DAAOx, ST-LOx) were prepared as soluble molecules while maintaining their redox properties and catalytic activities, respectively. CYTc-SC/ST-Enzyme complexes were formed by mixing CYTc-SpyCatcher and SpyTag-Enzymes, and the complexes retained their original enzymatic activity. Remarkably, the heme domain served as an electron acceptor from complexed enzymes by intramolecular electron transfer; consequently, all constructed CYTc-SC/ST-Enzyme complexes showed DET ability to the electrode, demonstrating the versatility of this method. Full article
(This article belongs to the Special Issue Protein and Nucleotide Engineering for Diagnoses and Biosensing II)
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11 pages, 1977 KiB  
Article
Development of Alkaline Phosphatase-Fused Mouse Prion Protein and Its Application in Toxic Aβ Oligomer Detection
by Kaori Tsukakoshi, Rikako Kubo and Kazunori Ikebukuro
Int. J. Mol. Sci. 2022, 23(23), 14588; https://doi.org/10.3390/ijms232314588 - 23 Nov 2022
Cited by 1 | Viewed by 1091
Abstract
Amyloid β (Aβ) oligomers play a key role in the progression of Alzheimer’s disease (AD). Multiple forms of Aβ assemblies have been identified by in vitro and in vivo analyses; however, it is uncertain which oligomer is highly neurotoxic. Thus, understanding the pathogenesis [...] Read more.
Amyloid β (Aβ) oligomers play a key role in the progression of Alzheimer’s disease (AD). Multiple forms of Aβ assemblies have been identified by in vitro and in vivo analyses; however, it is uncertain which oligomer is highly neurotoxic. Thus, understanding the pathogenesis of AD by detecting toxic Aβ oligomers is crucial. In this study, we report a fusion protein of cellular prion protein (PrPc) and alkaline phosphatase (ALP) from Escherichia coli as a sensing element for toxic Aβ oligomers. Since the N-terminus domain of PrPc (residue 23–111) derived from mice is known to bind to toxic Aβ oligomers in vitro, we genetically fused PrPc23–111 to ALP. The developed fusion protein, PrP–ALP, retained both the binding ability of PrPc and enzymatic activity of ALP. We showed that PrP–ALP strongly bound to high molecular weight (HMW) oligomers but showed little or no affinity toward monomers. The observation that PrP–ALP neutralized the toxic effect of Aβ oligomers indicated an interaction between PrP–ALP and toxic HMW oligomers. Based on ALP activity, we succeeded in detecting Aβ oligomers. PrP–ALP may serve as a powerful tool for detecting toxic Aβ oligomers that may be related to AD progression. Full article
(This article belongs to the Special Issue Protein and Nucleotide Engineering for Diagnoses and Biosensing II)
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