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Special Issue "Designer Biopolymers: Self-Assembling Proteins and Nucleic Acids 2020"

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

Deadline for manuscript submissions: 30 June 2020.

Special Issue Editors

Prof. Dr. Ayae Sugawara-Narutaki
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Guest Editor
Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
Special Issues and Collections in MDPI journals
Dr. Yukiko Kamiya
E-Mail Website
Guest Editor
Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues,

Nature has evolved sequence-controlled polymers like DNA and proteins over its long history. The recent rapid progress of synthetic chemistry, DNA recombinant technology, and computational science, as well as the elucidation of molecular mechanisms in biological processes, drive us to design ingenious polymers that are inspired by naturally occurring polymers but surpass them in specialized functions. The term “designer biopolymers” refers to polymers consisting of biological building units such as nucleotides, amino acids, and monosaccharides in a sequence-controlled manner. They may contain non-canonical nucleotides/amino acids/monosaccharides, or they may be conjugated to synthetic polymers to acquire specific functions in vitro and in vivo.

This Special Issue particularly focuses on the self-assembling aspect of designer biopolymers. Self-assembly is one common feature in biopolymers to realize their dynamic biological activities, and is strictly controlled by the sequence of biopolymers. In a broad sense, the self-assembly of biopolymers includes double-helix formation of DNA, protein folding, and higher-order protein assembly (e.g., viral capsids). Designer biopolymers are now going beyond what nature evolved: researchers have generated DNA origami, protein cages, peptide nanofibers, and gels. The aim of this Special Issue is to assemble the latest interdisciplinary work on self-assembling designer biopolymers to exchange ideas and encourage new lines of research.

Prof. Dr. Ayae Sugawara-Narutaki
Prof. Dr. Yukiko Kamiya
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 papers will be 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

  • de novo protein design
  • Artificial nucleic acids/peptides
  • Self-assembling peptides/proteins
  • DNA nanotechnology
  • Nanofibers and gels of nucleic acids/proteins/peptides
  • Stimuli-responsive designer biopolymers
  • Tissue engineering scaffolding

Related Special Issue

Published Papers (2 papers)

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Research

Open AccessArticle
Rheology of Dispersions of High-Aspect-Ratio Nanofibers Assembled from Elastin-Like Double-Hydrophobic Polypeptides
Int. J. Mol. Sci. 2019, 20(24), 6262; https://doi.org/10.3390/ijms20246262 - 12 Dec 2019
Abstract
Elastin-like polypeptides (ELPs) are promising candidates for fabricating tissue-engineering scaffolds that mimic the extracellular environment of elastic tissues. We have developed a “double-hydrophobic” block ELP, GPG, inspired by non-uniform distribution of two different hydrophobic domains in natural elastin. GPG has a block [...] Read more.
Elastin-like polypeptides (ELPs) are promising candidates for fabricating tissue-engineering scaffolds that mimic the extracellular environment of elastic tissues. We have developed a “double-hydrophobic” block ELP, GPG, inspired by non-uniform distribution of two different hydrophobic domains in natural elastin. GPG has a block sequence of (VGGVG)5-(VPGXG)25-(VGGVG)5 that self-assembles to form nanofibers in water. Functional derivatives of GPG with appended amino acid motifs can also form nanofibers, a display of the block sequence’s robust self-assembling properties. However, how the block length affects fiber formation has never been clarified. This study focuses on the synthesis and characterization of a novel ELP, GPPG, in which the central sequence (VPGVG)25 is repeated twice by a short linker sequence. The self-assembly behavior and the resultant nanostructures of GPG and GPPG were when compared through circular dichroism spectroscopy, atomic force microscopy, and transmission electron microscopy. Dynamic rheology measurements revealed that the nanofiber dispersions of both GPG and GPPG at an extremely low concentration (0.034 wt%) exhibited solid-like behavior with storage modulus G′ > loss modulus G” over wide range of angular frequencies, which was most probably due to the high aspect ratio of the nanofibers that leads to the flocculation of nanofibers in the dispersion. Full article
(This article belongs to the Special Issue Designer Biopolymers: Self-Assembling Proteins and Nucleic Acids 2020)
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Open AccessArticle
Hot Spots and Their Contribution to the Self-Assembly of the Viral Capsid: In Silico Prediction and Analysis
Int. J. Mol. Sci. 2019, 20(23), 5966; https://doi.org/10.3390/ijms20235966 - 27 Nov 2019
Abstract
The viral capsid is a macromolecular complex formed by a defined number of self-assembled proteins, which, in many cases, are biopolymers with an identical amino acid sequence. Specific protein–protein interactions (PPI) drive the capsid self-assembly process, leading to several distinct protein interfaces. Following [...] Read more.
The viral capsid is a macromolecular complex formed by a defined number of self-assembled proteins, which, in many cases, are biopolymers with an identical amino acid sequence. Specific protein–protein interactions (PPI) drive the capsid self-assembly process, leading to several distinct protein interfaces. Following the PPI hot spot hypothesis, we present a conservation-based methodology to identify those interface residues hypothesized to be crucial elements on the self-assembly and thermodynamic stability of the capsid. We validate the predictions through a rigorous physical framework which integrates molecular dynamics simulations and free energy calculations by Umbrella sampling and the potential of mean force using an all-atom molecular representation of the capsid proteins of an icosahedral virus in an explicit solvent. Our results show that a single mutation in any of the structure-conserved hot spots significantly perturbs the quaternary protein–protein interaction, decreasing the absolute value of the binding free energy, without altering the protein’s secondary nor tertiary structure. Our conservation-based hot spot prediction methodology can lead to strategies to rationally modulate the capsid’s thermodynamic properties. Full article
(This article belongs to the Special Issue Designer Biopolymers: Self-Assembling Proteins and Nucleic Acids 2020)
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