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Applied Sciences
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Innovation in Biomolecular Sciences and Engineering
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Innovation in Biomolecular Sciences and Engineering

A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Applied Biosciences and Bioengineering".

Deadline for manuscript submissions: closed (31 January 2022) | Viewed by 26643

Special Issue Editors

Prof. Dr. Hidehiko Hirakawa

E-Mail Website
Guest Editor
Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8577, Japan
Interests: protein engineering; protein assembly; enzyme immobilization; oxidoreductases
Dr. Yusaku Miyama

E-Mail Website
Guest Editor
Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
Interests: chemical biology; cell biology; protein degradation; nuclear receptor; natural product chemistry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We are inviting manuscript submissions to our Special Issue on Innovation in Biomolecular Sciences and Engineering.

Biomolecules have sophisticated functions and strictly regulate biological events, interacting with other molecules. The combination of novel scientific insights of biomolecules with synthetic molecules and biomolecules that did not originally co-exist is a key of innovation in life sciences, generating functional molecular architectures and leading to the discovery of surprising biological findings.

This Special Issue aims to cover multidisciplinary studies, which include unclassified research, in accordance with conventional research fields, on biomolecules, including nucleic acids, proteins, and lipids. The topics of interest include chemical and nonchemical approaches to adding new functionalities or regulating functions of biomolecules, engineering of biomacromolecules, discovery of new functions, and novel applications of biomolecules. The issue also focuses on chemical and genetic approaches to manipulating intracellular biomolecules and cellular functions, including post-translational control of cellular protein function or stability and protein labeling. Review articles as well as original research articles which will bring new insights into the applied sciences of biomolecules are also welcome.

Prof. Dr. Hidehiko Hirakawa
Prof. Dr. Yusaku Miyamae
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. Applied Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). 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

  • biocatalyst;
  • bioconjugation;
  • biochemistry;
  • biohybrid materials;
  • biomacromolecules;
  • cellular engineering;
  • chemical biology;
  • self-assembly;
  • synthetic biology;
  • protein degradation

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Published Papers (5 papers)

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Review

14 pages, 2338 KiB  
Review
Recent Advances in Protein Caging Tools for Protein Photoactivation
by Satoshi Yamaguchi
Appl. Sci. 2022, 12(8), 3750; https://doi.org/10.3390/app12083750 - 8 Apr 2022
Cited by 3 | Viewed by 1914
Abstract
In biosciences and biotechnologies, it is recently critical to promote research regarding the regulation of the dynamic functions of proteins of interest. Light-induced control of protein activity is a strong tool for a wide variety of applications because light can be spatiotemporally irradiated [...] Read more.
In biosciences and biotechnologies, it is recently critical to promote research regarding the regulation of the dynamic functions of proteins of interest. Light-induced control of protein activity is a strong tool for a wide variety of applications because light can be spatiotemporally irradiated in high resolutions. Therefore, synthetic, semi-synthetic, and genetic engineering techniques for photoactivation of proteins have been actively developed. In this review, the conventional approaches will be outlined. As a solution for overcoming barriers in conventional ones, our recent approaches in which proteins were chemically modified with biotinylated caging reagents are introduced to photo-activate a variety of proteins without genetic engineering and elaborate optimization. This review mainly focuses on protein caging and describes the concepts underlying the development of reported approaches that can contribute to the emergence of both novel protein photo-regulating methods and their killer applications. Full article
(This article belongs to the Special Issue Innovation in Biomolecular Sciences and Engineering)
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18 pages, 4085 KiB  
Review
Sequence-Specific Recognition of Double-Stranded DNA by Peptide Nucleic Acid Forming Double-Duplex Invasion Complex
by Yuichiro Aiba, Masanari Shibata and Osami Shoji
Appl. Sci. 2022, 12(7), 3677; https://doi.org/10.3390/app12073677 - 6 Apr 2022
Cited by 5 | Viewed by 4016
Abstract
Peptide nucleic acid (PNA) is an analog of natural nucleic acids, where the sugar-phosphate backbone of DNA is replaced by an electrostatically neutral N-(2-aminoethyl)glycine backbone. This unique peptide-based backbone enables PNAs to form a very stable duplex with the complementary nucleic acids [...] Read more.
Peptide nucleic acid (PNA) is an analog of natural nucleic acids, where the sugar-phosphate backbone of DNA is replaced by an electrostatically neutral N-(2-aminoethyl)glycine backbone. This unique peptide-based backbone enables PNAs to form a very stable duplex with the complementary nucleic acids via Watson–Crick base pairing since there is no electrostatic repulsion between PNA and DNA·RNA. With this high nucleic acid affinity, PNAs have been used in a wide range of fields, from biological applications such as gene targeting, to engineering applications such as probe and sensor developments. In addition to single-stranded DNA, PNA can also recognize double-stranded DNA (dsDNA) through the formation of a double-duplex invasion complex. This double-duplex invasion is hard to achieve with other artificial nucleic acids and is expected to be a promising method to recognize dsDNA in cellula or in vivo since the invasion does not require the prior denaturation of dsDNA. In this paper, we provide basic knowledge of PNA and mainly focus on the research of PNA invasion. Full article
(This article belongs to the Special Issue Innovation in Biomolecular Sciences and Engineering)
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Graphical abstract

23 pages, 1892 KiB  
Review
RNA Interference-Based Pesticides and Antiviral Agents: Microbial Overproduction Systems for Double-Stranded RNA for Applications in Agriculture and Aquaculture
by Shuhei Hashiro and Hisashi Yasueda
Appl. Sci. 2022, 12(6), 2954; https://doi.org/10.3390/app12062954 - 14 Mar 2022
Cited by 12 | Viewed by 6764
Abstract
RNA interference (RNAi)-based pesticides are pest control agents that use RNAi mechanisms as the basis of their action. They are regarded as environmentally friendly and are a promising alternative to conventional chemical pesticides. The effective substance in RNAi-based pesticides is double-stranded RNA (dsRNA) [...] Read more.
RNA interference (RNAi)-based pesticides are pest control agents that use RNAi mechanisms as the basis of their action. They are regarded as environmentally friendly and are a promising alternative to conventional chemical pesticides. The effective substance in RNAi-based pesticides is double-stranded RNA (dsRNA) designed to match the nucleotide sequence of a target essential gene of the pest of concern. When taken up by the pest, this exerts an RNAi effect and inhibits some vital biochemical/biological process in the pest. dsRNA products are also expected to be applied for the control of viral diseases in aquaculture by RNAi, especially in shrimp farming. A critical issue in the practical application of RNAi agents is that production of the dsRNA must be low-cost. Here, we review recent methods for microbial production of dsRNAs using representative microorganisms (Escherichia coli, Pseudomonas syringae, Corynebacterium glutamicum, Chlamydomonas reinhardtii, and others) as host strains. The characteristics of each dsRNA production system are discussed. Full article
(This article belongs to the Special Issue Innovation in Biomolecular Sciences and Engineering)
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Figure 1

81 pages, 19455 KiB  
Review
Lipid Vesicles and Other Polymolecular Aggregates—From Basic Studies of Polar Lipids to Innovative Applications
by Peter Walde and Sosaku Ichikawa
Appl. Sci. 2021, 11(21), 10345; https://doi.org/10.3390/app112110345 - 3 Nov 2021
Cited by 17 | Viewed by 6647
Abstract
Lipid vesicles (liposomes) are a unique and fascinating type of polymolecular aggregates, obtained from bilayer-forming amphiphiles—or mixtures of amphiphiles—in an aqueous medium. Unilamellar vesicles consist of one single self-closed bilayer membrane, constituted by the amphiphiles and an internal volume which is trapped by [...] Read more.
Lipid vesicles (liposomes) are a unique and fascinating type of polymolecular aggregates, obtained from bilayer-forming amphiphiles—or mixtures of amphiphiles—in an aqueous medium. Unilamellar vesicles consist of one single self-closed bilayer membrane, constituted by the amphiphiles and an internal volume which is trapped by this bilayer, whereby the vesicle often is spherical with a typical desired average diameter of either about 100 nm or tens of micrometers. Functionalization of the external vesicle surface, basically achievable at will, and the possibilities of entrapping hydrophilic molecules inside the vesicles or/and embedding hydrophobic compounds within the membrane, resulted in various applications in different fields. This review highlights a few of the basic studies on the phase behavior of polar lipids, on some of the concepts for the controlled formation of lipid vesicles as dispersed lamellar phase, on some of the properties of vesicles, and on the challenges of efficiently loading them with hydrophilic or hydrophobic compounds for use as delivery systems, as nutraceuticals, for bioassays, or as cell-like compartments. Many of the large number of basic studies have laid a solid ground for various applications of polymolecular aggregates of amphiphilic lipids, including, for example, cubosomes, bicelles or—recently most successfully—nucleic acids-containing lipid nanoparticles. All this highlights the continued importance of fundamental studies. The life-saving application of mRNA lipid nanoparticle COVID-19 vaccines is in part based on year-long fundamental studies on the formation and properties of lipid vesicles. It is a fascinating example, which illustrates the importance of considering (i) details of the chemical structure of the different molecules involved, as well as (ii) physical, (iii) engineering, (iv) biological, (v) pharmacological, and (vii) economic aspects. Moreover, the strong demand for interdisciplinary collaboration in the field of lipid vesicles and related aggregates is also an excellent and convincing example for teaching students in the field of complex molecular systems. Full article
(This article belongs to the Special Issue Innovation in Biomolecular Sciences and Engineering)
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23 pages, 3404 KiB  
Review
Strategies for Post-Translational Control of Protein Expression and Their Applications
by Yuki Utsugi and Yusaku Miyamae
Appl. Sci. 2021, 11(18), 8300; https://doi.org/10.3390/app11188300 - 7 Sep 2021
Cited by 5 | Viewed by 4264
Abstract
Proteins are fundamental biomolecules of living cells, and their expression levels depend on the balance between the synthesis and degradation. Researchers often aim to control protein expression levels for the investigation of protein function and its relationship with physiological phenomena. The genetic manipulation [...] Read more.
Proteins are fundamental biomolecules of living cells, and their expression levels depend on the balance between the synthesis and degradation. Researchers often aim to control protein expression levels for the investigation of protein function and its relationship with physiological phenomena. The genetic manipulation of the target protein using CRISPR/Cas9, Cre/loxP, tetracyclin system, and RNA interference, are widely used for the regulation of proteins at the DNA, transcriptional, or mRNA level. However, the significant time delay in controlling protein levels is a limitation of these techniques; the knockout or knockdown effects cannot be observed until the previously transcribed and synthesized protein is degraded. Recently, researchers have developed various types of molecular tools for the regulation of protein expression at the post-translational level, which rely on harnessing cellular proteolytic machinery including ubiquitin–proteasome pathway, autophagy-lysosome pathway, and endocytosis. The post-translational control of protein expression using small molecules, antibodies, and light can offer significant advantages regarding speed, tunability, and reversibility. These technologies are expected to be applied to pharmacotherapy and cell therapy, as well as research tools for fundamental biological studies. Here, we review the established and recently developed technologies, provide an update on their applications, and anticipate potential future directions. Full article
(This article belongs to the Special Issue Innovation in Biomolecular Sciences and Engineering)
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