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Recent Advances in Self-Assembled Peptides

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: closed (1 February 2019) | Viewed by 40531

Special Issue Editor

Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019-0065, USA
Interests: de novo peptide design and self-assembly; bioorganic chemistry; supramolecular chemistry; antimicrobial peptides; cell penetrating peptides; peptide–polymer conjugates; cancer nanotechnology; antimicrobial nanomaterials; drug delivery; gene delivery; self-assembling hydrogel

Special Issue Information

Dear Colleagues,

The last two decades have witnessed great achievements in the design and self-assembly of peptides to generate functional materials. Peptides, as the molecular building blocks, can be either de novo designed or engineered, based on naturally derived sequences that self-assemble into highly ordered nanostructures and nanostructured networks. From a fundamental viewpoint, the self-assembly strategy, in combination with new peptide design principles and chemistry has provided powerful tools to fabricate a wide range of thermodynamically stable and kinetically trapped nanostructures, as well as dynamic and smart nanostructures and materials in response to specific triggers. Comprehensive structural characterization of these hierarchical structures and fundamental analysis and understanding of their thermodynamics and kinetics are crucial to develop self-assembled, well-regulatedpeptides. From the viewpoint of practical applications, the main focus is to develop optimal functionality of self-assembled peptides. Pre-functionalization of the molecular building blocks and post-modification of the self-assembly are both effective methods to endow functions on self-assembled peptides and both are being extensively explored with regard to a variety of nanotechnological and biotechnological applications.

The main aim of this Special Issue is to create an open forum where researchers can share their new methods, results, perspectives and insights, and work together to address emerging issues of both fundamental and practical significance in peptide self-assembly. Contributions to this issue, both in the form of original research or review articles, may cover all aspects of peptide self-assembly and multidisplinnary studies offering new principles, methodologies/strategies and insights are particularly welcome.

Assoc. Prof. Dr. He Dong
Guest Editor

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. Molecules 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 2700 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

  • De novo peptide design and self-assembly
  • Computational approaches in the design of self-assembling peptides
  • Microscopic/spectroscopic tools for the study of self-assembling peptide structures
  • Functional peptide nanomaterials
  • Stimuli-responsive peptide self-assembly
  • Peptide-based hydrogels
  • Hybrid peptide-based materials
  • Biointerface and microdevices based on self-assembled peptides
  • Technological and biomedical applications of self-assembled peptides

Published Papers (9 papers)

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Editorial

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3 pages, 151 KiB  
Editorial
Editorial to the Special Issue—“Recent Advances in Self-Assembled Peptides”
by He Dong
Molecules 2019, 24(17), 3089; https://doi.org/10.3390/molecules24173089 - 26 Aug 2019
Cited by 1 | Viewed by 1697
Abstract
Peptide self-assembly is an interdisciplinary research area involving chemistry, life science, and materials science [...] Full article
(This article belongs to the Special Issue Recent Advances in Self-Assembled Peptides)

Research

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15 pages, 2543 KiB  
Article
Aβ(M1–40) and Wild-Type Aβ40 Self-Assemble into Oligomers with Distinct Quaternary Structures
by Jacob L. Bouchard, Taylor C. Davey and Todd M. Doran
Molecules 2019, 24(12), 2242; https://doi.org/10.3390/molecules24122242 - 15 Jun 2019
Cited by 2 | Viewed by 2833
Abstract
Amyloid-β oligomers (AβOs) self-assemble into polymorphic species with diverse biological activities that are implicated causally to Alzheimer’s disease (AD). Synaptotoxicity of AβO species is dependent on their quaternary structure, however, low-abundance and environmental sensitivity of AβOs in vivo have impeded a thorough assessment [...] Read more.
Amyloid-β oligomers (AβOs) self-assemble into polymorphic species with diverse biological activities that are implicated causally to Alzheimer’s disease (AD). Synaptotoxicity of AβO species is dependent on their quaternary structure, however, low-abundance and environmental sensitivity of AβOs in vivo have impeded a thorough assessment of structure–function relationships. We developed a simple biochemical assay to quantify the relative abundance and morphology of cross-linked AβOs. We compared oligomers derived from synthetic Aβ40 (wild-type (WT) Aβ40) and a recombinant source, called Aβ(M1–40). Both peptides assemble into oligomers with common sizes and morphology, however, the predominant quaternary structures of Aβ(M1–40) oligomeric states were more diverse in terms of dispersity and morphology. We identified self-assembly conditions that stabilize high-molecular weight oligomers of Aβ(M1–40) with apparent molecular weights greater than 36 kDa. Given that mixtures of AβOs derived from both peptides have been shown to be potent neurotoxins that disrupt long-term potentiation, we anticipate that the diverse quaternary structures reported for Aβ(M1–40) oligomers using the assays reported here will facilitate research efforts aimed at isolating and identifying common toxic species that contribute to synaptic dysfunction. Full article
(This article belongs to the Special Issue Recent Advances in Self-Assembled Peptides)
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13 pages, 2340 KiB  
Article
Rippled β-Sheet Formation by an Amyloid-β Fragment Indicates Expanded Scope of Sequence Space for Enantiomeric β-Sheet Peptide Coassembly
by Jennifer M. Urban, Janson Ho, Gavin Piester, Riqiang Fu and Bradley L. Nilsson
Molecules 2019, 24(10), 1983; https://doi.org/10.3390/molecules24101983 - 23 May 2019
Cited by 25 | Viewed by 5348
Abstract
In 1953, Pauling and Corey predicted that enantiomeric β-sheet peptides would coassemble into so-called “rippled” β-sheets, in which the β-sheets would consist of alternating l- and d-peptides. To date, this phenomenon has been investigated primarily with amphipathic peptide sequences composed of [...] Read more.
In 1953, Pauling and Corey predicted that enantiomeric β-sheet peptides would coassemble into so-called “rippled” β-sheets, in which the β-sheets would consist of alternating l- and d-peptides. To date, this phenomenon has been investigated primarily with amphipathic peptide sequences composed of alternating hydrophilic and hydrophobic amino acid residues. Here, we show that enantiomers of a fragment of the amyloid-β (Aβ) peptide that does not follow this sequence pattern, amyloid-β (16–22), readily coassembles into rippled β-sheets. Equimolar mixtures of enantiomeric amyloid-β (16–22) peptides assemble into supramolecular structures that exhibit distinct morphologies from those observed by self-assembly of the single enantiomer pleated β-sheet fibrils. Formation of rippled β-sheets composed of alternating l- and d-amyloid-β (16–22) is confirmed by isotope-edited infrared spectroscopy and solid-state NMR spectroscopy. Sedimentation analysis reveals that rippled β-sheet formation by l- and d-amyloid-β (16–22) is energetically favorable relative to self-assembly into corresponding pleated β-sheets. This work illustrates that coassembly of enantiomeric β-sheet peptides into rippled β-sheets is not limited to peptides with alternating hydrophobic/hydrophilic sequence patterns, but that a broader range of sequence space is available for the design and preparation of rippled β-sheet materials. Full article
(This article belongs to the Special Issue Recent Advances in Self-Assembled Peptides)
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10 pages, 200 KiB  
Communication
Challenges in Translating from Bench to Bed-Side: Pro-Angiogenic Peptides for Ischemia Treatment
by Karel Petrak, Ravi Vissapragada, Siyu Shi, Zain Siddiqui, Ka Kyung Kim, Biplab Sarkar and Vivek A. Kumar
Molecules 2019, 24(7), 1219; https://doi.org/10.3390/molecules24071219 - 28 Mar 2019
Cited by 7 | Viewed by 2765
Abstract
We describe progress and obstacles in the development of novel peptide-hydrogel therapeutics for unmet medical needs in ischemia treatment, focusing on the development and translation of therapies specifically in peripheral artery disease (PAD). Ischemia is a potentially life-threatening complication in PAD, which affects [...] Read more.
We describe progress and obstacles in the development of novel peptide-hydrogel therapeutics for unmet medical needs in ischemia treatment, focusing on the development and translation of therapies specifically in peripheral artery disease (PAD). Ischemia is a potentially life-threatening complication in PAD, which affects a significant percentage of the elderly population. While studies on inducing angiogenesis to treat PAD were started two decades ago, early results from animal models as well as clinical trials have not yet been translated into clinical practice. We examine some of the challenges encountered during such translation. We further note the need for sustained angiogenic effect involving whole growth factor, gene therapy and synthetic growth factor strategies. Finally, we discuss the need for tissue depots for de novo formation of microvasculature. These scaffolds can act as templates for neovasculature development to improve circulation and healing at the preferred anatomical location. Full article
(This article belongs to the Special Issue Recent Advances in Self-Assembled Peptides)
17 pages, 6354 KiB  
Article
Engineering Peptide-Based Polyelectrolyte Complexes with Increased Hydrophobicity
by Sara Tabandeh and Lorraine Leon
Molecules 2019, 24(5), 868; https://doi.org/10.3390/molecules24050868 - 01 Mar 2019
Cited by 47 | Viewed by 4591
Abstract
Polyelectrolyte complexation is a versatile platform for the design of self-assembled materials. Here we use rational design to create ionic hydrophobically-patterned peptides that allow us to precisely explore the role of hydrophobicity on electrostatic self-assembly. Polycations and polyanions were designed and synthesized with [...] Read more.
Polyelectrolyte complexation is a versatile platform for the design of self-assembled materials. Here we use rational design to create ionic hydrophobically-patterned peptides that allow us to precisely explore the role of hydrophobicity on electrostatic self-assembly. Polycations and polyanions were designed and synthesized with an alternating sequence of d- and l-chiral patterns of lysine or glutamic acid with either glycine, alanine or leucine due to their increasing hydrophobicity index, respectively. Two motifs were considered for the oppositely charged patterned peptides; one with equal residues of charged and uncharged amino acids and the other with increased charge density. Mass spectroscopy, circular dichroism, H- and F-NMR spectroscopy were used to characterize the polypeptides. Polyelectrolyte complexes (PECs) formed using the sequences were characterized using turbidity measurements, optical microscopy and infrared spectroscopy. Our results show that the critical salt concentration, a key measure of PEC stability, increased with both increasing charge density as well as hydrophobicity. Furthermore, by increasing the hydrophobicity, the amount of PEC formed increased with temperature, contrary to purely ionic PECs. Lastly, we assessed the encapsulation behavior of these materials using a hydrophobic dye. Concluding that encapsulation efficiency increased with hydrophobic content of the complexes providing insight for future work on the application of these materials for drug delivery. Full article
(This article belongs to the Special Issue Recent Advances in Self-Assembled Peptides)
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11 pages, 2366 KiB  
Article
Self-Assembly of Short Elastin-like Amphiphilic Peptides: Effects of Temperature, Molecular Hydrophobicity and Charge Distribution
by Meiwen Cao, Yang Shen, Yu Wang, Xiaoling Wang and Dongxiang Li
Molecules 2019, 24(1), 202; https://doi.org/10.3390/molecules24010202 - 08 Jan 2019
Cited by 32 | Viewed by 4940
Abstract
A novel type of self-assembling peptides has been developed by introducing the basic elastomeric β-turn units of elastin protein into the amphiphilic peptide molecules. The self-assembly behaviors of such peptides are affected by the overall molecular hydrophobicity, charge distribution and temperature. The molecules [...] Read more.
A novel type of self-assembling peptides has been developed by introducing the basic elastomeric β-turn units of elastin protein into the amphiphilic peptide molecules. The self-assembly behaviors of such peptides are affected by the overall molecular hydrophobicity, charge distribution and temperature. The molecules with higher hydrophobicity exhibit better self-assembling capability to form long fibrillar nanostructures. For some peptides, the temperature increase can not only promote the self-assembly process but also change the self-assembly routes. The self-assembly of the peptides with two charges centralized on one terminal show higher dependence on temperature than the peptides with two charges distributed separately on the two terminals. The study probes into the self-assembly behaviors of short elastin-like peptides and is of great help for developing novel self-assembling peptides with thermo sensitivity. Full article
(This article belongs to the Special Issue Recent Advances in Self-Assembled Peptides)
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13 pages, 4377 KiB  
Article
Shape Effects of Peptide Amphiphile Micelles for Targeting Monocytes
by Johan Joo, Christopher Poon, Sang Pil Yoo and Eun Ji Chung
Molecules 2018, 23(11), 2786; https://doi.org/10.3390/molecules23112786 - 27 Oct 2018
Cited by 13 | Viewed by 5258
Abstract
Peptide amphiphile micelles (PAMs) are a nanoparticle platform that have gained popularity for their targeting versatility in a wide range of disease models. An important aspect of micelle design is considering the type of hydrophobic moiety used to synthesize the PAM, which can [...] Read more.
Peptide amphiphile micelles (PAMs) are a nanoparticle platform that have gained popularity for their targeting versatility in a wide range of disease models. An important aspect of micelle design is considering the type of hydrophobic moiety used to synthesize the PAM, which can act as a contributing factor regarding their morphology and targeting capabilities. To delineate and compare the characteristics of spherical and cylindrical micelles, we incorporated the monocyte-targeting chemokine, monocyte chemoattractant protein-1 (MCP-1), into our micelles (MCP-1 PAMs). We report that both shapes of nanoparticles were biocompatible with monocytes and enhanced the secondary structure of the MCP-1 peptide, thereby improving the ability of the micelles to mimic the native MCP-1 protein structure. As a result, both shapes of MCP-1 PAMs effectively targeted monocytes in an in vitro binding assay with murine monocytes. Interestingly, cylindrical PAMs showed a greater ability to attract monocytes compared to spherical PAMs in a chemotaxis assay. However, the surface area, the multivalent display of peptides, and the zeta potential of PAMs may also influence their biomimetic properties. Herein, we introduce variations in the methods of PAM synthesis and discuss the differences in PAM characteristics that can impact the recruitment of monocytes, a process associated with disease and cancer progression. Full article
(This article belongs to the Special Issue Recent Advances in Self-Assembled Peptides)
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Review

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17 pages, 755 KiB  
Review
Fused in Sarcoma: Properties, Self-Assembly and Correlation with Neurodegenerative Diseases
by Chen Chen, Xiufang Ding, Nimrah Akram, Song Xue and Shi-Zhong Luo
Molecules 2019, 24(8), 1622; https://doi.org/10.3390/molecules24081622 - 24 Apr 2019
Cited by 49 | Viewed by 6374
Abstract
Fused in sarcoma (FUS) is a DNA/RNA binding protein that is involved in RNA metabolism and DNA repair. Numerous reports have demonstrated by pathological and genetic analysis that FUS is associated with a variety of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal [...] Read more.
Fused in sarcoma (FUS) is a DNA/RNA binding protein that is involved in RNA metabolism and DNA repair. Numerous reports have demonstrated by pathological and genetic analysis that FUS is associated with a variety of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration (FTLD), and polyglutamine diseases. Traditionally, the fibrillar aggregation of FUS was considered to be the cause of those diseases, especially via its prion-like domains (PrLDs), which are rich in glutamine and asparagine residues. Lately, a nonfibrillar self-assembling phenomenon, liquid–liquid phase separation (LLPS), was observed in FUS, and studies of its functions, mechanism, and mutual transformation with pathogenic amyloid have been emerging. This review summarizes recent studies on FUS self-assembling, including both aggregation and LLPS as well as their relationship with the pathology of ALS, FTLD, and other neurodegenerative diseases. Full article
(This article belongs to the Special Issue Recent Advances in Self-Assembled Peptides)
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21 pages, 10165 KiB  
Review
Using Self-Assembling Peptides to Integrate Biomolecules into Functional Supramolecular Biomaterials
by Renjie Liu and Gregory A. Hudalla
Molecules 2019, 24(8), 1450; https://doi.org/10.3390/molecules24081450 - 12 Apr 2019
Cited by 34 | Viewed by 6131
Abstract
Throughout nature, self-assembly gives rise to functional supramolecular biomaterials that can perform complex tasks with extraordinary efficiency and specificity. Inspired by these examples, self-assembly is increasingly used to fabricate synthetic supramolecular biomaterials for diverse applications in biomedicine and biotechnology. Peptides are particularly attractive [...] Read more.
Throughout nature, self-assembly gives rise to functional supramolecular biomaterials that can perform complex tasks with extraordinary efficiency and specificity. Inspired by these examples, self-assembly is increasingly used to fabricate synthetic supramolecular biomaterials for diverse applications in biomedicine and biotechnology. Peptides are particularly attractive as building blocks for these materials because they are based on naturally derived amino acids that are biocompatible and biodegradable; they can be synthesized using scalable and cost-effective methods, and their sequence can be tailored to encode formation of diverse architectures. To endow synthetic supramolecular biomaterials with functional capabilities, it is now commonplace to conjugate self-assembling building blocks to molecules having a desired functional property, such as selective recognition of a cell surface receptor or soluble protein, antigenicity, or enzymatic activity. This review surveys recent advances in using self-assembling peptides as handles to incorporate biologically active molecules into supramolecular biomaterials. Particular emphasis is placed on examples of functional nanofibers, nanovesicles, and other nano-scale structures that are fabricated by linking self-assembling peptides to proteins and carbohydrates. Collectively, this review highlights the enormous potential of these approaches to create supramolecular biomaterials with sophisticated functional capabilities that can be finely tuned to meet the needs of downstream applications. Full article
(This article belongs to the Special Issue Recent Advances in Self-Assembled Peptides)
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