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Designer Biopolymers: Self-Assembling Proteins and Nucleic Acids

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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: closed (31 October 2019) | Viewed by 53349

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Prof. Dr. Ayae Sugawara-Narutaki

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Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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Dr. Yukiko Kamiya

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Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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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

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Keywords

de novo protein design
Artificial nucleic acid/peptide
Self-assembling peptide/protein
DNA nanotechnology
Nanofiber and gel of nucleic acid/protein/peptide
Stimuli-responsive designer biopolymers
Tissue engineering scaffold

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Designer Biopolymers: Self-Assembling Proteins and Nucleic Acids 2020 in International Journal of Molecular Sciences (10 articles)

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Editorial

Jump to: Research, Review

3 pages, 171 KiB

Open AccessEditorial

Designer Biopolymers: Self-Assembling Proteins and Nucleic Acids

by Ayae Sugawara-Narutaki and Yukiko Kamiya

Int. J. Mol. Sci. 2020, 21(9), 3276; https://doi.org/10.3390/ijms21093276 - 6 May 2020

Cited by 1 | Viewed by 2055

Abstract

Nature has evolved sequence-controlled polymers such as DNA and proteins over its long history [...] Full article

(This article belongs to the Special Issue Designer Biopolymers: Self-Assembling Proteins and Nucleic Acids)

Research

Jump to: Editorial, Review

14 pages, 2524 KiB

Open AccessArticle

Self-Association of Antimicrobial Peptides: A Molecular Dynamics Simulation Study on Bombinin

by Peicho Petkov, Elena Lilkova, Nevena Ilieva and Leandar Litov

Int. J. Mol. Sci. 2019, 20(21), 5450; https://doi.org/10.3390/ijms20215450 - 1 Nov 2019

Cited by 20 | Viewed by 4074

Abstract

Antimicrobial peptides (AMPs) are a diverse group of membrane-active peptides which play a crucial role as mediators of the primary host defense against microbial invasion. Many AMPs are found to be fully or partially disordered in solution and to acquire secondary structure upon interaction with a lipid membrane. Here, we report molecular dynamics simulations studies on the solution behaviour of a specific AMP, bombinin H2. We show that in monomeric form in water solution the peptide is somewhat disordered and preferably adopts a helix-loop-helix conformation. However, when more than a single monomer is placed in the solution, the peptides self-associate in aggregates. Within the aggregate, the peptides provide each other with an amphipathic environment that mimics the water–membrane interface, which allows them to adopt a single-helix structure. We hypothesise that this is the mechanism by which bombinin H2 and, possibly, other small linear AMPs reach the target membrane in a functional folded state and are able to effectively exert their antimicrobial action on it. Full article

(This article belongs to the Special Issue Designer Biopolymers: Self-Assembling Proteins and Nucleic Acids)

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27 pages, 19967 KiB

Open AccessArticle

Examination of Adsorption Orientation of Amyloidogenic Peptides Over Nano-Gold Colloidal Particle Surfaces

by Kazushige Yokoyama, Kieran Brown, Peter Shevlin, Jack Jenkins, Elizabeth D’Ambrosio, Nicole Ralbovsky, Jessica Battaglia, Ishan Deshmukh and Akane Ichiki

Int. J. Mol. Sci. 2019, 20(21), 5354; https://doi.org/10.3390/ijms20215354 - 28 Oct 2019

Cited by 9 | Viewed by 6003

Abstract

The adsorption of amyloidogenic peptides, amyloid beta 1–40 (Aβ_1–40), alpha-synuclein (α-syn), and beta 2 microglobulin (β2m), was attempted over the surface of nano-gold colloidal particles, ranging from d = 10 to 100 nm in diameter (d). The spectroscopic inspection between pH 2 and pH 12 successfully extracted the critical pH point (pH_o) at which the color change of the amyloidogenic peptide-coated nano-gold colloids occurred due to aggregation of the nano-gold colloids. The change in surface property caused by the degree of peptide coverage was hypothesized to reflect the ΔpH_o, which is the difference in pH_o between bare gold colloids and peptide coated gold colloids. The coverage ratio (Θ) for all amyloidogenic peptides over gold colloid of different sizes was extracted by assuming Θ = 0 at ΔpH_o = 0. Remarkably, Θ was found to have a nano-gold colloidal size dependence, however, this nano-size dependence was not simply correlated with d. The geometric analysis and simulation of reproducing Θ was conducted by assuming a prolate shape of all amyloidogenic peptides. The simulation concluded that a spiking-out orientation of a prolate was required in order to reproduce the extracted Θ. The involvement of a secondary layer was suggested; this secondary layer was considered to be due to the networking of the peptides. An extracted average distance of networking between adjacent gold colloids supports the binding of peptides as if they are “entangled” and enclosed in an interfacial distance that was found to be approximately 2 nm. The complex nano-size dependence of Θ was explained by available spacing between adjacent prolates. When the secondary layer was formed, Aβ_1–40 and α-syn possessed a higher affinity to a partially negative nano-gold colloidal surface. However, β2m peptides tend to interact with each other. This difference was explained by the difference in partial charge distribution over a monomer. Both Aβ_1–40 and α-syn are considered to have a partial charge (especially δ+) distribution centering around the prolate axis. The β2m, however, possesses a distorted charge distribution. For a lower Θ (i.e., Θ <0.5), a prolate was assumed to conduct a gyration motion, maintaining the spiking-out orientation to fill in the unoccupied space with a tilting angle ranging between 5° and 58° depending on the nano-scale and peptide coated to the gold colloid. Full article

(This article belongs to the Special Issue Designer Biopolymers: Self-Assembling Proteins and Nucleic Acids)

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11 pages, 6019 KiB

Open AccessCommunication

miR-7 Knockdown by Peptide Nucleic Acids in the Ascidian Ciona intestinalis

by Silvia Mercurio, Silvia Cauteruccio, Raoul Manenti, Simona Candiani, Giorgio Scarì, Emanuela Licandro and Roberta Pennati

Int. J. Mol. Sci. 2019, 20(20), 5127; https://doi.org/10.3390/ijms20205127 - 16 Oct 2019

Cited by 10 | Viewed by 2851

Abstract

Peptide Nucleic Acids (PNAs) are synthetic mimics of natural oligonucleotides, which bind complementary DNA/RNA strands with high sequence specificity. They display numerous advantages, but in vivo applications are still rare. One of the main drawbacks of PNAs application is the poor cellular uptake that could be overcome by using experimental models, in which microinjection techniques allow direct delivery of molecules into eggs. Thus, in this communication, we investigated PNAs efficiency in miR-7 downregulation and compared its effects with those obtained with the commercially available antisense molecule, Antagomir (Dharmacon) in the ascidian Ciona intestinalis. Ascidians are marine invertebrates closely related to vertebrates, in which PNA techniques have not been applied yet. Our results suggested that anti-miR-7 PNAs were able to reach their specific targets in the developing ascidian embryos with high efficiency, as the same effects were obtained with both PNA and Antagomir. To the best of our knowledge, this is the first evidence that unmodified PNAs can be applied in in vivo knockdown strategies when directly injected into eggs. Full article

(This article belongs to the Special Issue Designer Biopolymers: Self-Assembling Proteins and Nucleic Acids)

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13 pages, 4681 KiB

Open AccessArticle

Hydroxyapatite Formation on Self-Assembling Peptides with Differing Secondary Structures and Their Selective Adsorption for Proteins

by Suzuka Kojima, Hitomi Nakamura, Sungho Lee, Fukue Nagata and Katsuya Kato

Int. J. Mol. Sci. 2019, 20(18), 4650; https://doi.org/10.3390/ijms20184650 - 19 Sep 2019

Cited by 16 | Viewed by 3959

Abstract

Self-assembling peptides have been employed as biotemplates for biomineralization, as the morphologies and sizes of the inorganic materials can be easily controlled. We synthesized two types of highly ordered self-assembling peptides with different secondary structures and investigated the effects of secondary structures on hydroxyapatite (HAp) biomineralization of peptide templates. All as-synthesized HAp-peptides have a selective protein adsorption capacity for basic protein (e.g., cytochrome c and lysozyme). Moreover, the selectivity was improved as peptide amounts increased. In particular, peptide–HAp templated on β-sheet peptides adsorbed more cytochrome c than peptide–HAp with α-helix structures, due to the greater than 2-times carboxyl group density at their surfaces. It can be expected that self-assembled peptide-templated HAp may be used as carriers for protein immobilization in biosensing and bioseparation applications and as enzyme-stabilizing agents. Full article

(This article belongs to the Special Issue Designer Biopolymers: Self-Assembling Proteins and Nucleic Acids)

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19 pages, 4075 KiB

Open AccessArticle

Effect of the Hydrophilic-Hydrophobic Balance of Antigen-Loaded Peptide Nanofibers on Their Cellular Uptake, Cellular Toxicity, and Immune Stimulatory Properties

by Tomonori Waku, Saki Nishigaki, Yuichi Kitagawa, Sayaka Koeda, Kazufumi Kawabata, Shigeru Kunugi, Akio Kobori and Naoki Tanaka

Int. J. Mol. Sci. 2019, 20(15), 3781; https://doi.org/10.3390/ijms20153781 - 2 Aug 2019

Cited by 13 | Viewed by 4314

Abstract

Recently, nanofibers (NFs) formed from antigenic peptides conjugated to β-sheet-forming peptides have attracted much attention as a new generation of vaccines. However, studies describing how the hydrophilic-hydrophobic balance of NF components affects cellular interactions of NFs are limited. In this report, three different NFs were prepared by self-assembly of β-sheet-forming peptides conjugated with model antigenic peptides (SIINFEKL) from ovalbumin and hydrophilic oligo-ethylene glycol (EG) of differing chain lengths (6-, 12- and 24-mer) to investigate the effect of EG length of antigen-loaded NFs on their cellular uptake, cytotoxicity, and dendritic cell (DC)-stimulation ability. We used an immortal DC line, termed JAWS II, derived from bone marrow-derived DCs of a C57BL/6 p53-knockout mouse. The uptake of NFs, consisting of the EG 12-mer by DCs, was the most effective and activated DC without exhibiting significant cytotoxicity. Increasing the EG chain length significantly reduced cellular entry and DC activation by NFs. Conversely, shortening the EG chain enhanced DC activation but increased toxicity and impaired water-dispersibility, resulting in low cellular uptake. These results show that the interaction of antigen-loaded NFs with cells can be tuned by the EG length, which provides useful design guidelines for the development of effective NF-based vaccines. Full article

(This article belongs to the Special Issue Designer Biopolymers: Self-Assembling Proteins and Nucleic Acids)

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14 pages, 1877 KiB

Open AccessArticle

Mutational and Combinatorial Control of Self-Assembling and Disassembling of Human Proteasome α Subunits

by Taichiro Sekiguchi, Tadashi Satoh, Eiji Kurimoto, Chihong Song, Toshiya Kozai, Hiroki Watanabe, Kentaro Ishii, Hirokazu Yagi, Saeko Yanaka, Susumu Uchiyama, Takayuki Uchihashi, Kazuyoshi Murata and Koichi Kato

Int. J. Mol. Sci. 2019, 20(9), 2308; https://doi.org/10.3390/ijms20092308 - 9 May 2019

Cited by 5 | Viewed by 5438

Abstract

Eukaryotic proteasomes harbor heteroheptameric α-rings, each composed of seven different but homologous subunits α1–α7, which are correctly assembled via interactions with assembly chaperones. The human proteasome α7 subunit is reportedly spontaneously assembled into a homotetradecameric double ring, which can be disassembled into single rings via interaction with monomeric α6. We comprehensively characterized the oligomeric state of human proteasome α subunits and demonstrated that only the α7 subunit exhibits this unique, self-assembling property and that not only α6 but also α4 can disrupt the α7 double ring. We also demonstrated that mutationally monomerized α7 subunits can interact with the intrinsically monomeric α4 and α6 subunits, thereby forming heterotetradecameric complexes with a double-ring structure. The results of this study provide additional insights into the mechanisms underlying the assembly and disassembly of proteasomal subunits, thereby offering clues for the design and creation of circularly assembled hetero-oligomers based on homo-oligomeric structural frameworks. Full article

(This article belongs to the Special Issue Designer Biopolymers: Self-Assembling Proteins and Nucleic Acids)

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10 pages, 1884 KiB

Open AccessArticle

Molecular and Structural Basis of the Proteasome α Subunit Assembly Mechanism Mediated by the Proteasome-Assembling Chaperone PAC3-PAC4 Heterodimer

by Tadashi Satoh, Maho Yagi-Utsumi, Kenta Okamoto, Eiji Kurimoto, Keiji Tanaka and Koichi Kato

Int. J. Mol. Sci. 2019, 20(9), 2231; https://doi.org/10.3390/ijms20092231 - 7 May 2019

Cited by 18 | Viewed by 4535

Abstract

The 26S proteasome is critical for the selective degradation of proteins in eukaryotic cells. This enzyme complex is composed of approximately 70 subunits, including the structurally homologous proteins α1–α7, which combine to form heptameric rings. The correct arrangement of these α subunits is essential for the function of the proteasome, but their assembly does not occur autonomously. Assembly of the α subunit is assisted by several chaperones, including the PAC3-PAC4 heterodimer. In this study we showed that the PAC3-PAC4 heterodimer functions as a molecular matchmaker, stabilizing the α4-α5-α6 subcomplex during the assembly of the α-ring. We solved a 0.96-Å atomic resolution crystal structure for a PAC3 homodimer which, in conjunction with nuclear magnetic resonance (NMR) data, highlighted the mobility of the loop comprised of residues 51 to 61. Based on these structural and dynamic data, we created a three-dimensional model of the PAC3-4/α4/α5/α6 quintet complex, and used this model to investigate the molecular and structural basis of the mechanism of proteasome α subunit assembly, as mediated by the PAC3-PAC4 heterodimeric chaperone. Our results provide a potential basis for the development of selective inhibitors against proteasome biogenesis. Full article

(This article belongs to the Special Issue Designer Biopolymers: Self-Assembling Proteins and Nucleic Acids)

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Review

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22 pages, 4153 KiB

Open AccessReview

Self-Assembling Peptides and Their Application in the Treatment of Diseases

by Sungeun Lee, Trang H.T. Trinh, Miryeong Yoo, Junwu Shin, Hakmin Lee, Jaehyeon Kim, Euimin Hwang, Yong-beom Lim and Chongsuk Ryou

Int. J. Mol. Sci. 2019, 20(23), 5850; https://doi.org/10.3390/ijms20235850 - 21 Nov 2019

Cited by 149 | Viewed by 9528

Abstract

Self-assembling peptides are biomedical materials with unique structures that are formed in response to various environmental conditions. Governed by their physicochemical characteristics, the peptides can form a variety of structures with greater reactivity than conventional non-biological materials. The structural divergence of self-assembling peptides allows for various functional possibilities; when assembled, they can be used as scaffolds for cell and tissue regeneration, and vehicles for drug delivery, conferring controlled release, stability, and targeting, and avoiding side effects of drugs. These peptides can also be used as drugs themselves. In this review, we describe the basic structure and characteristics of self-assembling peptides and the various factors that affect the formation of peptide-based structures. We also summarize the applications of self-assembling peptides in the treatment of various diseases, including cancer. Furthermore, the in-cell self-assembly of peptides, termed reverse self-assembly, is discussed as a novel paradigm for self-assembling peptide-based nanovehicles and nanomedicines. Full article

(This article belongs to the Special Issue Designer Biopolymers: Self-Assembling Proteins and Nucleic Acids)

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18 pages, 1199 KiB

Open AccessReview

Strategies to Obtain Designer Polymers Based on Cyanobacterial Extracellular Polymeric Substances (EPS)

by Sara B. Pereira, Aureliana Sousa, Marina Santos, Marco Araújo, Filipa Serôdio, Pedro Granja and Paula Tamagnini

Int. J. Mol. Sci. 2019, 20(22), 5693; https://doi.org/10.3390/ijms20225693 - 14 Nov 2019

Cited by 37 | Viewed by 5394

Abstract

Biopolymers derived from polysaccharides are a sustainable and environmentally friendly alternative to the synthetic counterparts available in the market. Due to their distinctive properties, the cyanobacterial extracellular polymeric substances (EPS), mainly composed of heteropolysaccharides, emerge as a valid alternative to address several biotechnological and biomedical challenges. Nevertheless, biotechnological/biomedical applications based on cyanobacterial EPS have only recently started to emerge. For the successful exploitation of cyanobacterial EPS, it is important to strategically design the polymers, either by genetic engineering of the producing strains or by chemical modification of the polymers. This requires a better understanding of the EPS biosynthetic pathways and their relationship with central metabolism, as well as to exploit the available polymer functionalization chemistries. Considering all this, we provide an overview of the characteristics and biological activities of cyanobacterial EPS, discuss the challenges and opportunities to improve the amount and/or characteristics of the polymers, and report the most relevant advances on the use of cyanobacterial EPS as scaffolds, coatings, and vehicles for drug delivery. Full article

(This article belongs to the Special Issue Designer Biopolymers: Self-Assembling Proteins and Nucleic Acids)

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15 pages, 3821 KiB

Open AccessReview

The ZT Biopolymer: A Self-Assembling Protein Scaffold for Stem Cell Applications

by Yevheniia Nesterenko, Christopher J. Hill, Jennifer R. Fleming, Patricia Murray and Olga Mayans

Int. J. Mol. Sci. 2019, 20(17), 4299; https://doi.org/10.3390/ijms20174299 - 3 Sep 2019

Cited by 5 | Viewed by 4209

Abstract

The development of cell culture systems for the naturalistic propagation, self-renewal and differentiation of cells ex vivo is a high goal of molecular engineering. Despite significant success in recent years, the high cost of up-scaling cultures, the need for xeno-free culture conditions, and the degree of mimicry of the natural extracellular matrix attainable in vitro using designer substrates continue to pose obstacles to the translation of cell-based technologies. In this regard, the ZT biopolymer is a protein-based, stable, scalable, and economical cell substrate of high promise. ZT is based on the naturally occurring assembly of two human proteins: titin-Z1Z2 and telethonin. These protein building blocks are robust scaffolds that can be conveniently functionalized with full-length proteins and bioactive peptidic motifs by genetic manipulation, prior to self-assembly. The polymer is, thereby, fully encodable. Functionalized versions of the ZT polymer have been shown to successfully sustain the long-term culturing of human embryonic stem cells (hESCs), human induced pluripotent stem cells (hiPSCs), and murine mesenchymal stromal cells (mMSCs). Pluripotency of hESCs and hiPSCs was retained for the longest period assayed (4 months). Results point to the large potential of the ZT system for the creation of a modular, pluri-functional biomaterial for cell-based applications. Full article

(This article belongs to the Special Issue Designer Biopolymers: Self-Assembling Proteins and Nucleic Acids)

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