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Functional Peptides and Their Interactions: From Molecules to Systems

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A special issue of Biomolecules (ISSN 2218-273X).

Deadline for manuscript submissions: closed (30 October 2022) | Viewed by 14567

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Special Issue Editor

Dr. Mikhail Soloviev

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Guest Editor

Department of Biological Sciences, Royal Holloway University of London, London TW20 0EX, UK
Interests: molecular biomarkers for health monitoring and the early detection of cancers; antigenic epitopes; rational and structure-based engineering of functional polypeptides; analytical biochemistry and analytical methods development
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

It is a great pleasure and an honour to invite you to participate in this Special Issue of Biomolecules. “Functional Peptides and Their Interactions: From Molecules to Systems” is dedicated to publishing original research articles, reviews and short communications addressing all aspects related to the discovery and characterisation of peptides, their biological function and their uses in biology, medicine and biomaterial sciences. We particularly welcome manuscripts focussing on functional and structural aspects of interactions between peptides and other biological molecules, organelles, cells, tissues and systems, including digestive, respiratory, circulatory, endocrine, nervous and immune systems, as well as other biologically relevant entities.

Peptides, being short stretches of amino acids or small proteins, occupy a strategic position between proteins and amino acids. Naturally occurring peptides play fundamental regulatory roles as hormones, cytokines, growth factors, possess many important other regulatory roles and biological functions such as antimicrobial and antiviral properties and may exert antioxidant, antithrombotic and other functional effects. Peptides play important roles in innate and adaptive immune systems, possess important immunomodulatory and cytotoxic functions and are implicated in autoimmunity. Unlike ribosomally synthesised proteins, naturally occurring peptides may originate from either ribosomal or non-ribosomal syntheses, the latter largely limited to bacteria and fungi. Protein processing in eukaryotes and protein degradation provide another ample source of complex peptide pools in cells, tissues and organisms. In addition to traditional recombinant synthesis approaches, peptides may be generated enzymatically by proteolytic digestion of longer polypeptide precursors (top-down approaches) or using solid-phase peptide synthesis (bottom-up approaches). Because of the abundance of synthetic approaches and functional and structural screening tools, studies of peptides offer excellent research opportunities and continue to serve as ample sources of new functional biomolecules including peptide therapeutics.

“Functional Peptides and Their Interactions: From Molecules to Systems” will provide a forum for the peptide community from across the world to communicate the latest developments in functional peptide research at molecular, cellular and systems levels. Please join us in sharing with the scientific community your discoveries and other advances in peptide research, peptide engineering, peptide biotechnology and peptide applications.

Dr. Mikhail Soloviev
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. Biomolecules is an international peer-reviewed open access monthly 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

Peptides
Functional peptides
Peptide–peptide interactions
Peptide–protein interactions
Peptide engineering
Native peptides
Therapeutic peptides
Peptidomics
Proteomics

Published Papers (6 papers)

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Research

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11 pages, 2082 KiB

Open AccessArticle

Screening of EWI-2-Derived Peptides for Targeting Tetraspanin CD81 and Their Effect on Cancer Cell Migration

by Thanawat Suwatthanarak, Kei Usuba, Kotomi Kuroha, Masayoshi Tanaka and Mina Okochi

Biomolecules 2023, 13(3), 510; https://doi.org/10.3390/biom13030510 - 10 Mar 2023

Cited by 3 | Viewed by 1798

Abstract

CD81, a transmembrane protein belonging to the tetraspanin family, has recently been suggested as a therapeutic target for cancers. Here, we screened peptides that bind to the tetraspanin CD81 protein, and evaluated their inhibitory activity in cancer cell migration. To screen for CD81-binding peptides (CD81-BP), a peptide array membrane was prepared from the amino acid sequence of the EWI-2 protein, a major partner of CD81, before binding to fluorescently labeled CD81. As a result, four candidate CD81-BPs were identified and characterized. In particular, the CFMKRLRK peptide (called P152 in this study) was found to be the best candidate that preferentially binds to the extracellular loop of CD81, with an estimated dissociation constant of 0.91 µM. Since CD81 was reported to promote cancer cell migration, an initial step in metastasis, the Boyden chamber assay, was next performed to assess the effect of CD81-BP candidates on the migration of MDA-MB-231 human breast cancer cells. Interestingly, our result indicated that P152 could suppress MDA-MB-231 cell migration at the level comparable to that of an anti-human CD81 antibody (5A6). Thus, we propose these CD81-BPs with the anti-migration property against cancer cells for the development of novel therapeutic strategies. Full article

(This article belongs to the Special Issue Functional Peptides and Their Interactions: From Molecules to Systems)

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21 pages, 2296 KiB

Open AccessEditor’s ChoiceArticle

Targeting of the Interleukin-13 Receptor (IL-13R)α2 Expressing Prostate Cancer by a Novel Hybrid Lytic Peptide

by Riaz Jannoo, Zhidao Xia, Paula E. Row and Venkateswarlu Kanamarlapudi

Biomolecules 2023, 13(2), 356; https://doi.org/10.3390/biom13020356 - 12 Feb 2023

Cited by 2 | Viewed by 1598

Abstract

The IL-13Rα2 cell surface receptor is highly expressed in tumours such as prostate cancer. In this report, we evaluated the hypothesis that prostate cancer cells with enhanced IL-13Rα2 expression are a suitable target for the hybrid lytic peptide (Pep-1-Phor21) peptide, which is generated by fusing the IL-13Rα2 specific ligand (Pep-1) and a cell membrane disrupting lytic peptide (Phor21). The expression of IL-13Rα2 mRNA and protein in prostate cancer tissues and cell lines was assessed via real-time PCR (RT-PCR) and immunoblotting. The effect of Pep-1-Phor21 on the viability of prostate cancer cells grown in monolayers (2D) and microtissue spheroids (3D) was assessed via CellTox green cytotoxic assay. IL-13Rα2 expression and Pep-1-Phor21-mediated killing were also determined in the cells treated with epigenetic regulators (Trichostatin A (TSA) and 5-aza-2 deoxycytidine (5-Aza-dC)). The hybrid lytic peptide cytotoxic activity correlated with the expression of IL-13Rα2 in prostate cancer cell lines cultured as monolayers (2D) or 3D spheroids. In addition, TSA or 5-Aza-dC treatment of prostate cancer cells, particularly those with low expression of IL-13Rα2, enhanced the cells’ sensitivity to the lytic peptide by increasing IL-13Rα2 expression. These results demonstrate that the Pep-1-Phor21 hybrid lytic peptide has potent and selective anticancer properties against IL-13Rα2-expressing prostate cancer cells. Full article

(This article belongs to the Special Issue Functional Peptides and Their Interactions: From Molecules to Systems)

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16 pages, 7327 KiB

Open AccessArticle

Effects of Calcium Ions on the Antimicrobial Activity of Gramicidin A

by Shang-Ting Fang, Shu-Hsiang Huang, Chin-Hao Yang, Jen-Wen Liou, Hemalatha Mani and Yi-Cheng Chen

Biomolecules 2022, 12(12), 1799; https://doi.org/10.3390/biom12121799 - 1 Dec 2022

Cited by 2 | Viewed by 1200

Abstract

Gramicidin A (gA) is a linear antimicrobial peptide that can form a channel and specifically conduct monovalent cations such as H⁺ across the lipid membrane. The antimicrobial activity of gA is associated with the formation of hydroxyl free radicals and the imbalance of NADH metabolism, possibly a consequence caused by the conductance of cations. The ion conductivity of gramicidin A can be blocked by Ca²⁺ ions. However, the effect of Ca²⁺ ions on the antimicrobial activity of gA is unclear. To unveil the role of Ca²⁺ ions, we examined the effect of Ca²⁺ ions on the antimicrobial activity of gramicidin A against Staphylococcus aureus (S. aureus). Results showed that the antimicrobial mechanism of gA and antimicrobial activity by Ca²⁺ ions are concentration-dependent. At the low gA concentration (≤1 μM), the antimicrobial mechanism of gA is mainly associated with the hydroxyl free radical formation and NADH metabolic imbalance. Under this mode, Ca²⁺ ions can significantly inhibit the hydroxyl free radical formation and NADH metabolic imbalance. On the other hand, at high gA concentration (≥5 μM), gramicidin A acts more likely as a detergent. Gramicidin A not only causes an increase in hydroxyl free radical levels and NAD⁺/NADH ratios but also induces the destruction of the lipid membrane composition. At this condition, Ca²⁺ ions can no longer reduce the gA antimicrobial activity but rather enhance the bacterial killing ability of gramicidin A. Full article

(This article belongs to the Special Issue Functional Peptides and Their Interactions: From Molecules to Systems)

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17 pages, 3979 KiB

Open AccessArticle

Molecular Characterization of Kunitz-Type Protease Inhibitors from Blister Beetles (Coleoptera, Meloidae)

by Emiliano Fratini, Marianna Nicoletta Rossi, Lucrezia Spagoni, Alessandra Riccieri, Emiliano Mancini, Fabio Polticelli, Marco Alberto Bologna, Paolo Mariottini and Manuela Cervelli

Biomolecules 2022, 12(7), 988; https://doi.org/10.3390/biom12070988 - 15 Jul 2022

Cited by 1 | Viewed by 2004

Abstract

Protease inhibitors are widely studied since the unrestricted activity of proteases can cause extensive organ lesions. In particular, elastase activity is involved in the pathophysiology of acute lung injury, for example during SARS-CoV-2 infection, while serine proteases and thrombin-like proteases are involved in the development and/or pathology of the nervous system. Natural protease inhibitors have the advantage to be reversible and with few side effects and thus are increasingly considered as new drugs. Kunitz-type protease inhibitors (KTPIs), reported in the venom of various organisms, such as wasps, spiders, scorpions, and snakes, have been studied for their potent anticoagulant activity and widespread protease inhibitor activity. Putative KTPI anticoagulants have been identified in transcriptomic resources obtained for two blister beetle species, Lydus trimaculatus and Mylabris variabilis. The KTPIs of L. trimaculatus and M. variabilis were characterized by combined transcriptomic and bioinformatics methodologies. The full-length mRNA sequences were divided on the base of the sequence of the active sites of the putative proteins. In silico protein structure analyses of each group of translational products show the biochemical features of the active sites and the potential protease targets. Validation of these genes is the first step for considering these molecules as new drugs for use in medicine. Full article

(This article belongs to the Special Issue Functional Peptides and Their Interactions: From Molecules to Systems)

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Review

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20 pages, 2896 KiB

Open AccessFeature PaperReview

SNARE Modulators and SNARE Mimetic Peptides

by Mikhail Khvotchev and Mikhail Soloviev

Biomolecules 2022, 12(12), 1779; https://doi.org/10.3390/biom12121779 - 29 Nov 2022

Cited by 4 | Viewed by 2601

Abstract

The soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptor (SNARE) proteins play a central role in most forms of intracellular membrane trafficking, a key process that allows for membrane and biocargo shuffling between multiple compartments within the cell and extracellular environment. The structural organization of SNARE proteins is relatively simple, with several intrinsically disordered and folded elements (e.g., SNARE motif, N-terminal domain, transmembrane region) that interact with other SNAREs, SNARE-regulating proteins and biological membranes. In this review, we discuss recent advances in the development of functional peptides that can modify SNARE-binding interfaces and modulate SNARE function. The ability of the relatively short SNARE motif to assemble spontaneously into stable coiled coil tetrahelical bundles has inspired the development of reduced SNARE-mimetic systems that use peptides for biological membrane fusion and for making large supramolecular protein complexes. We evaluate two such systems, based on peptide-nucleic acids (PNAs) and coiled coil peptides. We also review how the self-assembly of SNARE motifs can be exploited to drive on-demand assembly of complex re-engineered polypeptides. Full article

(This article belongs to the Special Issue Functional Peptides and Their Interactions: From Molecules to Systems)

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18 pages, 816 KiB

Open AccessReview

Bioactive Peptides and Proteins from Wasp Venoms

by Lei Luo, Peter Muiruri Kamau and Ren Lai

Biomolecules 2022, 12(4), 527; https://doi.org/10.3390/biom12040527 - 30 Mar 2022

Cited by 9 | Viewed by 4240

Abstract

Wasps, members of the order Hymenoptera, use their venom for predation and defense. Accordingly, their venoms contain various constituents acting on the circulatory, immune and nervous systems. Wasp venom possesses many allergens, enzymes, bioactive peptides, amino acids, biogenic amines, and volatile matters. In particular, some peptides show potent antimicrobial, anti-inflammatory, antitumor, and anticoagulant activity. Additionally, proteinous components from wasp venoms can cause tissue damage or allergic reactions in organisms. These bioactive peptides and proteins involved in wasp predation and defense may be potential sources of lead pharmaceutically active molecules. In this review, we focus on the advances in bioactive peptides and protein from the venom of wasps and their biological effects, as well as the allergic reactions and immunotherapy induced by the wasp venom. Full article

(This article belongs to the Special Issue Functional Peptides and Their Interactions: From Molecules to Systems)

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