Special Issue "2020 Feature Papers by Biomolecules’ Editorial Board Members"

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

Deadline for manuscript submissions: closed (31 December 2020).

Special Issue Editor

Dr. Vladimir N. Uversky
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Guest Editor
Molecular Medicine, University of South Florida, Tampa, USA
Interests: intrinsically disordered proteins; protein folding; protein misfolding; partially folded proteins; protein aggregation; protein structure; protein function; protein stability; protein biophysics; protein bioinformatics; conformational diseases; protein–ligand interactions; protein–protein interactions; liquid-liquid phase transitions
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Special Issue Information

Dear Colleagues,

It is our pleasure to announce that we are continuing here a successful initiative started last year by representing a Special Issue of Biomolecules that incorporates papers submitted exclusively by its Editorial Board Members (EBMs). By signifying different areas of research on biomolecules conducted in the laboratories of the journal’s EBMs, this Special Issue introduces Biomolecules as a first-class platform for reporting scientific data. With this Special Issue, we also want to celebrate the ranking of Biomolecules in the ‘Biochemistry & Molecular Biology’ category at 58 of 298 (80.70%, Q1), based on our first official impact factor of 4.694. This is a great achievement, which was earned through many years of hard work, dedication, and commitment from our EBMs.

Authors can submit their manuscripts online at www.mdpi.com by registering and logging in the following website: https://susy.mdpi.com/user/login. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the Special Issue website.

Dr. Vladimir N. Uversky
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 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. 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 2000 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.

Published Papers (10 papers)

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Research

Open AccessArticle
Study of the Cluster Thinning Grape as a Source of Phenolic Compounds and Evaluation of Its Antioxidant Potential
Biomolecules 2021, 11(2), 227; https://doi.org/10.3390/biom11020227 - 05 Feb 2021
Viewed by 228
Abstract
Thinning is a common viticulture practice in warm climates, and it is applied to increase the quality of the harvest. Thinning clusters are usually discarded, and they are considered another oenological industry waste. To valorize this by-product, the phenolic content and antioxidant activity [...] Read more.
Thinning is a common viticulture practice in warm climates, and it is applied to increase the quality of the harvest. Thinning clusters are usually discarded, and they are considered another oenological industry waste. To valorize this by-product, the phenolic content and antioxidant activity of three red varieties (Tempranillo, Cabernet Sauvignon, and Syrah), thinned at three different times between veraison and harvest, were studied: the first at the beginning of the veraison stage, in a low ripening stage; the second in an intermediate ripening stage; and, finally, the third sampling in the highest ripening stage. These by-products showed high values of total phenolic contents (10.66–11.75 mg gallic acid equivalent/g), which is of the same order as or even higher than that found in grape pomace. In thinned grape were identified 24 phenolic compounds, being the flavan-3-ols (catechin and epicatechin) of particular interest, with mean contents ranging from 105.1 to 516.4 mg/kg of thinned grape. Antioxidant activity similar to that of the vintage grape was found. It is concluded that thinned grape is a good source of phenolic compounds. Its content does not depend mainly on the grape variety; however, it has been possible to establish differences based on the maturity stage of the thinning grapes: the intermediate ripeness stage, with a Brix degree in the range of 15–16 for this area, would be the optimum collection time for cluster thinning. In this intermediate ripeness stage, thinning grapes present a higher antioxidant activity and there is also appreciable anthocyanin content, which is not found for the lowest ripeness stage, since these samples present an intermediate composition in all the families of determined phenolic compounds: anthocyanins, flavonols, flavan-3-ols, cinnamic acids, and benzoic acids. It is important to note that the experiments in this study have been carried out with whole tinned grapes, without separating the skin or the seeds. Full article
(This article belongs to the Special Issue 2020 Feature Papers by Biomolecules’ Editorial Board Members)
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Open AccessFeature PaperArticle
NTPDase1 Modulates Smooth Muscle Contraction in Mice Bladder by Regulating Nucleotide Receptor Activation Distinctly in Male and Female
Biomolecules 2021, 11(2), 147; https://doi.org/10.3390/biom11020147 - 23 Jan 2021
Viewed by 401
Abstract
Nucleotides released by smooth muscle cells (SMCs) and by innervating nerve terminals activate specific P2 receptors and modulate bladder contraction. We hypothesized that cell surface enzymes regulate SMC contraction in mice bladder by controlling the concentration of nucleotides. We showed by immunohistochemistry, enzymatic [...] Read more.
Nucleotides released by smooth muscle cells (SMCs) and by innervating nerve terminals activate specific P2 receptors and modulate bladder contraction. We hypothesized that cell surface enzymes regulate SMC contraction in mice bladder by controlling the concentration of nucleotides. We showed by immunohistochemistry, enzymatic histochemistry, and biochemical activities that nucleoside triphosphate diphosphohydrolase-1 (NTPDase1) and ecto-5′-nucleotidase were the major ectonucleotidases expressed by SMCs in the bladder. RT-qPCR revealed that, among the nucleotide receptors, there was higher expression of P2X1, P2Y1, and P2Y6 receptors. Ex vivo, nucleotides induced a more potent contraction of bladder strips isolated from NTPDase1 deficient (Entpd1−/−) mice compared to wild type controls. The strongest responses were obtained with uridine 5′-triphosphate (UTP) and uridine 5′-diphosphate (UDP), suggesting the involvement of P2Y6 receptors, which was confirmed with P2ry6−/− bladder strips. Interestingly, this response was reduced in female bladders. Our results also suggest the participation of P2X1, P2Y2 and/or P2Y4, and P2Y12 in these contractions. A reduced response to the thromboxane analogue U46619 was also observed in wild type, Entpd1−/−, and P2ry6−/− female bladders showing another difference due to sex. In summary, NTPDase1 modulates the activation of nucleotide receptors in mouse bladder SMCs, and contractions induced by P2Y6 receptor activation were weaker in female bladders. Full article
(This article belongs to the Special Issue 2020 Feature Papers by Biomolecules’ Editorial Board Members)
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Open AccessArticle
A New Look at the Purported Health Benefits of Commercial and Natural Clays
Biomolecules 2021, 11(1), 58; https://doi.org/10.3390/biom11010058 - 05 Jan 2021
Viewed by 414
Abstract
Clays attributed to have medicinal properties have been used since prehistoric times and are still used today as complementary medicines, which has given rise to unregulated “bioceutical” clays to treat skin conditions. Recently, clays with antibacterial characteristics have been proposed as alternatives to [...] Read more.
Clays attributed to have medicinal properties have been used since prehistoric times and are still used today as complementary medicines, which has given rise to unregulated “bioceutical” clays to treat skin conditions. Recently, clays with antibacterial characteristics have been proposed as alternatives to antibiotics, potentially overcoming modern day antibiotic resistance. Clays with suggested antibacterial properties were examined to establish their effects on common wound-infecting bacteria. Geochemical, microscopical, and toxicological characterization of clay particulates, their suspensions and filtered leachates was performed on THP-1 and HaCaT cell lines. Cytoskeletal toxicity, cell proliferation/viability (MTT assays), and migration (scratch wounds) were further evaluated. Clays were assayed for antibacterial efficacy using minimum inhibitory concentration assays. All clays possessed a mineral content with antibacterial potential; however, clay leachates contained insufficient ions to have any antibacterial effects. All clay leachates displayed toxicity towards THP-1 monocytes, while clay suspensions showed less toxicity, suggesting immunogenicity. Reduced clay cytotoxicity on HaCaTs was shown, as many leachates stimulated wound-healing responses. The “Green” clay exhibited antibacterial effects and only in suspension, which was lost upon neutralization. pH and its interaction with clay particle surface charge is more significant than previously understood to emphasize dangers of unregulated marketing and unsubstantiated bioceutical claims. Full article
(This article belongs to the Special Issue 2020 Feature Papers by Biomolecules’ Editorial Board Members)
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Open AccessArticle
Role of Hydrogen Sulfide and 3-Mercaptopyruvate Sulfurtransferase in the Regulation of the Endoplasmic Reticulum Stress Response in Hepatocytes
Biomolecules 2020, 10(12), 1692; https://doi.org/10.3390/biom10121692 - 18 Dec 2020
Cited by 1 | Viewed by 490
Abstract
It is estimated that over 1.5 billion people suffer from various forms of chronic liver disease worldwide. The emerging prevalence of metabolic syndromes and alcohol misuse, along with the lack of disease-modifying agents for the therapy of many severe liver conditions predicts that [...] Read more.
It is estimated that over 1.5 billion people suffer from various forms of chronic liver disease worldwide. The emerging prevalence of metabolic syndromes and alcohol misuse, along with the lack of disease-modifying agents for the therapy of many severe liver conditions predicts that chronic liver disease will continue to be a major problem in the future. Better understanding of the underlying pathogenetic mechanisms and identification of potential therapeutic targets remains a priority. Herein, we explored the potential role of the 3-mercaptopyruvate sulfurtransferase/hydrogen sulfide (H2S) system in the regulation of the endoplasmic reticulum (ER) stress and of its downstream processes in the immortalized hepatic cell line HepG2 in vitro. ER stress suppressed endogenous H2S levels and pharmacological supplementation of H2S with sodium hydrogen sulfide (NaHS) mitigated many aspects of ER stress, culminating in improved cellular bioenergetics and prevention of autophagic arrest, thereby switching cells’ fate towards survival. Genetic silencing of 3-MST or pharmacological inhibition of the key enzymes involved in hepatocyte H2S biosynthesis exacerbated many readouts related to ER-stress or its downstream functional responses. Our findings implicate the 3-MST/H2S system in the intracellular network that governs proteostasis and ER-stress adaptability in hepatocytes and reinforce the therapeutic potential of pharmacological H2S supplementation. Full article
(This article belongs to the Special Issue 2020 Feature Papers by Biomolecules’ Editorial Board Members)
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Open AccessArticle
Insight into the Anticancer Activity of Copper(II) 5-Methylenetrimethylammonium-Thiosemicarbazonates and Their Interaction with Organic Cation Transporters
Biomolecules 2020, 10(9), 1213; https://doi.org/10.3390/biom10091213 - 20 Aug 2020
Cited by 1 | Viewed by 884
Abstract
A series of four water-soluble salicylaldehyde thiosemicarbazones with a positively charged trimethylammonium moiety ([H2LR]Cl, R = H, Me, Et, Ph) and four copper(II) complexes [Cu(HLR)Cl]Cl (14) were synthesised with the aim to study [...] Read more.
A series of four water-soluble salicylaldehyde thiosemicarbazones with a positively charged trimethylammonium moiety ([H2LR]Cl, R = H, Me, Et, Ph) and four copper(II) complexes [Cu(HLR)Cl]Cl (14) were synthesised with the aim to study (i) their antiproliferative activity in cancer cells and, (ii) for the first time for thiosemicarbazones, the interaction with membrane transport proteins, specifically organic cation transporters OCT1–3. The compounds were comprehensively characterised by analytical, spectroscopic and X-ray diffraction methods. The highest cytotoxic effect was observed in the neuroblastoma cell line SH-5YSY after 24 h exposure and follows the rank order: 3 > 2 > 4 > cisplatin > 1 >> [H2LR]Cl. The copper(II) complexes showed marked interaction with OCT1–3, comparable to that of well-known OCT inhibitors (decynium 22, prazosin and corticosterone) in the cell-based radiotracer uptake assays. The work paves the way for the development of more potent and selective anticancer drugs and/or OCT inhibitors. Full article
(This article belongs to the Special Issue 2020 Feature Papers by Biomolecules’ Editorial Board Members)
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Open AccessArticle
Free-Radical-Mediated Formation of Trans-Cardiolipin Isomers, Analytical Approaches for Lipidomics and Consequences of the Structural Organization of Membranes
Biomolecules 2020, 10(8), 1189; https://doi.org/10.3390/biom10081189 - 15 Aug 2020
Viewed by 925
Abstract
Free-radical-mediated processes, such as peroxidation, isomerization and hydrogenation affecting fatty acid integrity and biological functions, have a trans-disciplinary relevance. Cardiolipins (CL, (1,3-diphosphatidyl-sn-glycerol)) and tetra-linoleoyl-CL are complex phospholipids, exclusively present in the Inner Mitochondrial Membrane (IMM) lipids, where they maintain membrane integrity [...] Read more.
Free-radical-mediated processes, such as peroxidation, isomerization and hydrogenation affecting fatty acid integrity and biological functions, have a trans-disciplinary relevance. Cardiolipins (CL, (1,3-diphosphatidyl-sn-glycerol)) and tetra-linoleoyl-CL are complex phospholipids, exclusively present in the Inner Mitochondrial Membrane (IMM) lipids, where they maintain membrane integrity and regulate enzyme functionalities. Peroxidation pathways and fatty acid remodeling are known causes of mitochondrial disfunctions and pathologies, including cancer. Free-radical-mediated isomerization with the change of the cis CL into geometrical trans isomers is an unknown process with possible consequences on the supramolecular membrane lipid organization. Here, the formation of mono-trans CL (MT-CL) and other trans CL isomers (T-CL) is reported using CL from bovine heart mitochondria and thiyl radicals generated by UV-photolysis from 2-mercaptoethanol. Analytical approaches for CL isomer separation and identification via 1H/13C NMR are provided, together with the chemical study of CL derivatization to fatty acid methyl esters (FAME), useful for lipidomics and metabolomics research. Kinetics information of the radical chain isomerization process was obtained using γ-irradiation conditions. The CL isomerization affected the structural organization of membranes, as tested by the reduction in unilamellar liposome diameter, and accompanied the well-known process of oxidative consumption induced by Fenton reagents. These results highlight a potential new molecular modification pathway of mitochondrial lipids with wide applications to membrane functions and biological consequences. Full article
(This article belongs to the Special Issue 2020 Feature Papers by Biomolecules’ Editorial Board Members)
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Open AccessFeature PaperArticle
Attenuation of Inflammatory Symptoms by Icariside B2 in Carrageenan and LPS-Induced Inflammation Models via Regulation of MAPK/NF-κB Signaling Cascades
Biomolecules 2020, 10(7), 1037; https://doi.org/10.3390/biom10071037 - 11 Jul 2020
Viewed by 785
Abstract
Prolonged inflammatory responses can lead to the development of several chronic diseases, such as autoimmune disorders and the development of natural therapeutic agents is required. A murine model was used to assess the anti-inflammatory effects of the megastigmane glucoside, icariside B2 (ICSB), and [...] Read more.
Prolonged inflammatory responses can lead to the development of several chronic diseases, such as autoimmune disorders and the development of natural therapeutic agents is required. A murine model was used to assess the anti-inflammatory effects of the megastigmane glucoside, icariside B2 (ICSB), and the assessment was carried out in vitro, and in vivo. The in vitro anti-inflammatory effects of ICSB were tested using LPS-stimulated BV2 cells, and the protein expression levels of inflammatory genes and cytokines were assessed. Mice were subcutaneously injected with 1% carrageenan (CA) to induce acute phase inflammation in the paw. Inflammation was assessed by measuring paw volumes hourly; subsequently, the mice were euthanized and the right hind paw skin was expunged and processed for reverse transcription-polymerase chain reaction (RT-PCR) and Western blot analyses. ICSB inhibits LPS-stimulated nitric oxide (NO) and prostaglandin E2 (PGE2) generation by reducing the expression of inducible NO synthase (iNOS) and cyclooxygenase 2 (COX-2). ICSB also inhibits the COX-2 enzyme with an IC50 value of 7.80 ± 0.26 µM. Molecular docking analysis revealed that ICSB had a strong binding affinity with both murine and human COX-2 proteins with binding energies of −8 kcal/mol and −7.4 kcal/mol, respectively. ICSB also reduces the manifestation of pro-inflammatory cytokines, such as TNF-α, IL-6, and IL-1β, at their transcriptional and translational level. ICSB hinders inhibitory protein κBα (IκBα) phosphorylation, thereby terminating the nuclear factor kappa-light-chain-enhancer of activated B cell (NF-κB) nuclear translocation. ICSB also represses the mitogen-activated protein kinases (MAPKs) signaling pathways. ICSB (50 mg/kg) showed an anti-edema effect in CA-induced mice and suppressed the CA-induced increases in iNOS and COX-2 protein levels. ICSB attenuated inflammatory responses by downregulating NF-κB expression through interference with extracellular signal-regulated kinase (ERK) and p38 phosphorylation, and by modulating the expression levels of iNOS, COX-2, TNF-α, IL-1β, and IL-6. Full article
(This article belongs to the Special Issue 2020 Feature Papers by Biomolecules’ Editorial Board Members)
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Open AccessArticle
PSIONplusm Server for Accurate Multi-Label Prediction of Ion Channels and Their Types
Biomolecules 2020, 10(6), 876; https://doi.org/10.3390/biom10060876 - 07 Jun 2020
Viewed by 614
Abstract
Computational prediction of ion channels facilitates the identification of putative ion channels from protein sequences. Several predictors of ion channels and their types were developed in the last quindecennial. While they offer reasonably accurate predictions, they also suffer a few shortcomings including lack [...] Read more.
Computational prediction of ion channels facilitates the identification of putative ion channels from protein sequences. Several predictors of ion channels and their types were developed in the last quindecennial. While they offer reasonably accurate predictions, they also suffer a few shortcomings including lack of availability, parallel prediction mode, single-label prediction (inability to predict multiple channel subtypes), and incomplete scope (inability to predict subtypes of the voltage-gated channels). We developed a first-of-its-kind PSIONplusm method that performs sequential multi-label prediction of ion channels and their subtypes for both voltage-gated and ligand-gated channels. PSIONplusm sequentially combines the outputs produced by three support vector machine-based models from the PSIONplus predictor and is available as a webserver. Empirical tests show that PSIONplusm outperforms current methods for the multi-label prediction of the ion channel subtypes. This includes the existing single-label methods that are available to the users, a naïve multi-label predictor that combines results produced by multiple single-label methods, and methods that make predictions based on sequence alignment and domain annotations. We also found that the current methods (including PSIONplusm) fail to accurately predict a few of the least frequently occurring ion channel subtypes. Thus, new predictors should be developed when a larger quantity of annotated ion channels will be available to train predictive models. Full article
(This article belongs to the Special Issue 2020 Feature Papers by Biomolecules’ Editorial Board Members)
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Open AccessArticle
Viridistratins A−C, Antimicrobial and Cytotoxic Benzo[j]fluoranthenes from Stromata of Annulohypoxylon viridistratum (Hypoxylaceae, Ascomycota)
Biomolecules 2020, 10(5), 805; https://doi.org/10.3390/biom10050805 - 23 May 2020
Cited by 8 | Viewed by 961
Abstract
During the course of our search for novel biologically active metabolites from tropical fungi, we are using chemotaxonomic and taxonomic methodology for the preselection of interesting materials. Recently, three previously undescribed benzo[j]fluoranthenes (13) together with the known [...] Read more.
During the course of our search for novel biologically active metabolites from tropical fungi, we are using chemotaxonomic and taxonomic methodology for the preselection of interesting materials. Recently, three previously undescribed benzo[j]fluoranthenes (13) together with the known derivatives truncatones A and C (4, 5) were isolated from the stromata of the recently described species Annulohypoxylon viridistratum collected in Thailand. Their chemical structures were elucidated by means of spectral methods, including nuclear magnetic resonance (NMR) spectroscopy and high-resolution mass spectrometry (HR-MS). The new compounds, for which we propose the trivial names viridistratins A−C, exhibited weak-to-moderate antimicrobial and cytotoxic activities in cell-based assays. Full article
(This article belongs to the Special Issue 2020 Feature Papers by Biomolecules’ Editorial Board Members)
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Open AccessArticle
The Cytosolic Phospholipase A2α N-Terminal C2 Domain Binds and Oligomerizes on Membranes with Positive Curvature
Biomolecules 2020, 10(4), 647; https://doi.org/10.3390/biom10040647 - 22 Apr 2020
Cited by 1 | Viewed by 1134
Abstract
Group IV phospholipase A2α (cPLA2α) regulates the production of prostaglandins and leukotrienes via the formation of arachidonic acid from membrane phospholipids. The targeting and membrane binding of cPLA2α to the Golgi involves the N-terminal C2 domain, whereas [...] Read more.
Group IV phospholipase A2α (cPLA2α) regulates the production of prostaglandins and leukotrienes via the formation of arachidonic acid from membrane phospholipids. The targeting and membrane binding of cPLA2α to the Golgi involves the N-terminal C2 domain, whereas the catalytic domain produces arachidonic acid. Although most studies of cPLA2α concern its catalytic activity, it is also linked to homeostatic processes involving the generation of vesicles that traffic material from the Golgi to the plasma membrane. Here we investigated how membrane curvature influences the homeostatic role of cPLA2α in vesicular trafficking. The cPLA2α C2 domain is known to induce changes in positive membrane curvature, a process which is dependent on cPLA2α membrane penetration. We showed that cPLA2α undergoes C2 domain-dependent oligomerization on membranes in vitro and in cells. We found that the association of the cPLA2α C2 domain with membranes is limited to membranes with positive curvature, and enhanced C2 domain oligomerization was observed on vesicles ~50 nm in diameter. We demonstrated that the cPLA2α C2 domain localizes to cholesterol enriched Golgi-derived vesicles independently of cPLA2α catalytic activity. Moreover, we demonstrate the C2 domain selectively localizes to lipid droplets whereas the full-length enzyme to a much lesser extent. Our results therefore provide novel insight into the molecular forces that mediate C2 domain-dependent membrane localization in vitro and in cells. Full article
(This article belongs to the Special Issue 2020 Feature Papers by Biomolecules’ Editorial Board Members)
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