Biomolecules

17 pages, 3938 KiB

Open AccessFeature PaperArticle

Cla4p Kinase Activity Is Down-Regulated by Fus3p during Yeast Mating

by Junwon Kim and Mark D. Rose

Biomolecules 2022, 12(4), 598; https://doi.org/10.3390/biom12040598 - 18 Apr 2022

Cited by 3 | Viewed by 2240

In Saccharomyces cerevisiae, the p21-activated kinase Cla4p regulates polarized morphogenesis and cytokinesis. However, it remains unknown how Cla4p kinase activity is regulated. After pheromone exposure, yeast cells temporally separate the mitotic and mating programs by sequestering Fus2p in the nucleus until cell [...] Read more.

In Saccharomyces cerevisiae, the p21-activated kinase Cla4p regulates polarized morphogenesis and cytokinesis. However, it remains unknown how Cla4p kinase activity is regulated. After pheromone exposure, yeast cells temporally separate the mitotic and mating programs by sequestering Fus2p in the nucleus until cell cycle completion, after which Fus2p exits to facilitate cell fusion. Previously, we showed that sequestration is regulated by two opposing protein kinases, Cla4p and Fus3p. Phosphorylation of Fus2p-S67 by Cla4p promotes nuclear localization by both activating nuclear import and blocking export. During mating, phosphorylation of Fus2p-S85 and Fus2p-S100 by Fus3p promotes nuclear export and blocks import. Here, we find that Cla4p kinase activity is itself down-regulated during mating. Pheromone exposure causes Cla4p hyper-phosphorylation and reduced Fus2p-S67 phosphorylation, dependent on Fus3p. Multiple phosphorylation sites in Cla4p are mating- and/or Fus3p-specific. Of these, Cla4p-S186 phosphorylation reduced the kinase activity of Cla4p, in vitro. A phosphomimetic cla4-S186E mutation caused a strong reduction in Fus2p-S67 phosphorylation and nuclear localization, in vivo. More generally, a non-phosphorylatable mutation, cla4-S186A, caused failure to maintain pheromone arrest and delayed formation of the mating-specific septin morphology. Thus, as cells enter the mating pathway, Fus3p counteracts Cla4p kinase activity to allow proper mating differentiation. Full article

(This article belongs to the Special Issue Transmembrane and Intracellular Signal Transduction Mechanisms: A Themed Issue in Honor of Professor Jeremy Thorner)

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17 pages, 1137 KiB

Open AccessReview

Cerebral Glutamate Regulation and Receptor Changes in Perioperative Neuroinflammation and Cognitive Dysfunction

by Yan Zhang, John-Man-Tak Chu and Gordon-Tin-Chun Wong

Biomolecules 2022, 12(4), 597; https://doi.org/10.3390/biom12040597 - 18 Apr 2022

Cited by 38 | Viewed by 5067

Abstract

Glutamate is the major excitatory neurotransmitter in the central nervous system and is intricately linked to learning and memory. Its activity depends on the expression of AMPA and NMDA receptors and excitatory amino transporters on neurons and glial cells. Glutamate transporters prevent the [...] Read more.

Glutamate is the major excitatory neurotransmitter in the central nervous system and is intricately linked to learning and memory. Its activity depends on the expression of AMPA and NMDA receptors and excitatory amino transporters on neurons and glial cells. Glutamate transporters prevent the excess accumulation of glutamate in synapses, which can lead to aberrant synaptic signaling, excitotoxicity, or cell death. Neuroinflammation can occur acutely after surgical trauma and contributes to the development of perioperative neurocognitive disorders, which are characterized by impairment in multiple cognitive domains. In this review, we aim to examine how glutamate handling and glutamatergic function are affected by neuroinflammation and their contribution to cognitive impairment. We will first summarize the current data regarding glutamate in neurotransmission, its receptors, and their regulation and trafficking. We will then examine the impact of inflammation on glutamate handling and neurotransmission, focusing on changes in glial cells and the effect of cytokines. Finally, we will discuss these changes in the context of perioperative neuroinflammation and the implications they have for perioperative neurocognitive disorders. Full article

(This article belongs to the Special Issue Molecular and Cellular Mechanisms of Neuroinflammation)

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22 pages, 3343 KiB

Open AccessReview

Louis Pasteur: Between Myth and Reality

by Jean-Marc Cavaillon and Sandra Legout

Biomolecules 2022, 12(4), 596; https://doi.org/10.3390/biom12040596 - 18 Apr 2022

Cited by 27 | Viewed by 20935

Abstract

Louis Pasteur is the most internationally known French scientist. He discovered molecular chirality, and he contributed to the understanding of the process of fermentation, helping brewers and winemakers to improve their beverages. He proposed a process, known as pasteurization, for the sterilization of [...] Read more.

Louis Pasteur is the most internationally known French scientist. He discovered molecular chirality, and he contributed to the understanding of the process of fermentation, helping brewers and winemakers to improve their beverages. He proposed a process, known as pasteurization, for the sterilization of wines. He established the germ theory of infectious diseases that allowed Joseph Lister to develop his antiseptic practice in surgery. He solved the problem of silkworm disease, although he had refuted the idea of Antoine Béchamp, who first considered it was a microbial infection. He created four vaccines (fowl cholera, anthrax, pig erysipelas, and rabies) in the paths of his precursors, Henri Toussaint (anthrax vaccine) and Pierre Victor Galtier (rabies vaccine). He generalized the word “vaccination” coined by Richard Dunning, Edward Jenner’s friend. Robert Koch, his most famous opponent, pointed out the great ambiguity of Pasteur’s approach to preparing his vaccines. Analysis of his laboratory notebooks has allowed historians to discern the differences between the legend built by his hagiographers and reality. In this review, we revisit his career, his undeniable achievements, and tell the truth about a hero who made every effort to build his own fame. Full article

(This article belongs to the Special Issue Theme Issue Honoring Scientist Louis Pasteur on His 200th Birthday)

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21 pages, 1977 KiB

Open AccessArticle

The Influence of Heterochronic Non-Myeloablative Bone Marrow Transplantation on the Immune System, Frailty, General Health, and Longevity of Aged Murine Recipients

by Katerina Jazbec, Mojca Jež, Urban Švajger, Boštjan Smrekar, Simona Miceska, Uroš Rajčevič, Mojca Justin, Janja Završnik, Tadej Malovrh, Tanja Švara, Mitja Gombač, Živa Ramšak and Primož Rožman

Biomolecules 2022, 12(4), 595; https://doi.org/10.3390/biom12040595 - 18 Apr 2022

Cited by 2 | Viewed by 3014

Abstract

The stem cell theory of aging postulates that stem cells become inefficient at maintaining the original functions of the tissues. We, therefore, hypothesized that transplanting young bone marrow (BM) to old recipients would lead to rejuvenating effects on immunity, followed by improved general [...] Read more.

The stem cell theory of aging postulates that stem cells become inefficient at maintaining the original functions of the tissues. We, therefore, hypothesized that transplanting young bone marrow (BM) to old recipients would lead to rejuvenating effects on immunity, followed by improved general health, decreased frailty, and possibly life span extension. We developed a murine model of non-myeloablative heterochronic BM transplantation in which old female BALB/c mice at 14, 16, and 18(19) months of age received altogether 125.1 ± 15.6 million nucleated BM cells from young male donors aged 7–13 weeks. At 21 months, donor chimerism was determined, and the immune system’s innate and adaptive arms were analyzed. Mice were then observed for general health and frailty until spontaneous death, when their lifespan, post-mortem examinations, and histopathological changes were recorded. The results showed that the old mice developed on average 18.7 ± 9.6% donor chimerism in the BM and showed certain improvements in their innate and adaptive arms of the immune system, such as favorable counts of neutrophils in the spleen and BM, central memory Th cells, effector/effector memory Th and Tc cells in the spleen, and B1a and B1b cells in the peritoneal cavity. Borderline enhanced lymphocyte proliferation capacity was also seen. The frailty parameters, pathomorphological results, and life spans did not differ significantly in the transplanted vs. control group of mice. In conclusion, although several favorable effects are obtained in our heterochronic non-myeloablative transplantation model, additional optimization is needed for better rejuvenation effects. Full article

(This article belongs to the Special Issue Stem and Progenitor Cells: Self-Renewal, Commitment and Differentiation – Conceptual and Practical Aspects)

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15 pages, 3056 KiB

Open AccessEditor’s ChoiceArticle

Molecular Recognition of Proteins through Quantitative Force Maps at Single Molecule Level

by Carlos Marcuello, Rocío de Miguel and Anabel Lostao

Biomolecules 2022, 12(4), 594; https://doi.org/10.3390/biom12040594 - 18 Apr 2022

Cited by 25 | Viewed by 3428

Abstract

Intermittent jumping force is an operational atomic-force microscopy mode that produces simultaneous topography and tip-sample maximum-adhesion images based on force spectroscopy. In this work, the operation conditions have been implemented scanning in a repulsive regime and applying very low forces, thus avoiding unspecific [...] Read more.

Intermittent jumping force is an operational atomic-force microscopy mode that produces simultaneous topography and tip-sample maximum-adhesion images based on force spectroscopy. In this work, the operation conditions have been implemented scanning in a repulsive regime and applying very low forces, thus avoiding unspecific tip-sample forces. Remarkably, adhesion images give only specific rupture events, becoming qualitative and quantitative molecular recognition maps obtained at reasonably fast rates, which is a great advantage compared to the force–volume modes. This procedure has been used to go further in discriminating between two similar protein molecules, avidin and streptavidin, in hybrid samples. The adhesion maps generated scanning with biotinylated probes showed features identified as avidin molecules, in the range of 40–80 pN; meanwhile, streptavidin molecules rendered 120–170 pN at the selected working conditions. The gathered results evidence that repulsive jumping force mode applying very small forces allows the identification of biomolecules through the specific rupture forces of the complexes and could serve to identify receptors on membranes or samples or be applied to design ultrasensitive detection technologies. Full article

(This article belongs to the Special Issue Single-Molecule Protein Dynamics)

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1 pages, 156 KiB

Open AccessCorrection

Correction: Hashmi et al. Hydrogen Sulphide Treatment Prevents Renal Ischemia-Reperfusion Injury by Inhibiting the Expression of ICAM-1 and NF-kB Concentration in Normotensive and Hypertensive Rats. Biomolecules 2021, 11, 1549

by Syed F. Hashmi, Hassaan Anwer Rathore, Munavvar A. Sattar, Edward J. Johns, Chee-Yuen Gan, Tan Yong Chia and Ashfaq Ahmad

Biomolecules 2022, 12(4), 593; https://doi.org/10.3390/biom12040593 - 18 Apr 2022

Cited by 1 | Viewed by 1516

Abstract

In the published publication [...] Full article

(This article belongs to the Special Issue Hydrogen Sulfide and Polysulfides, Endogenous Mammalian Transmitters——Honorary Special Issue Commemorating the Work of Prof. Hideo Kimura)

15 pages, 6963 KiB

Open AccessArticle

Identification of Intrinsically Disordered Proteins and Regions in a Non-Model Insect Species Ostrinia nubilalis (Hbn.)

by Miloš Avramov, Éva Schád, Ágnes Révész, Lilla Turiák, Iva Uzelac, Ágnes Tantos, László Drahos and Željko D. Popović

Biomolecules 2022, 12(4), 592; https://doi.org/10.3390/biom12040592 - 18 Apr 2022

Cited by 4 | Viewed by 2884

Abstract

Research in previous decades has shown that intrinsically disordered proteins (IDPs) and regions in proteins (IDRs) are as ubiquitous as highly ordered proteins. Despite this, research on IDPs and IDRs still has many gaps left to fill. Here, we present an approach that [...] Read more.

Research in previous decades has shown that intrinsically disordered proteins (IDPs) and regions in proteins (IDRs) are as ubiquitous as highly ordered proteins. Despite this, research on IDPs and IDRs still has many gaps left to fill. Here, we present an approach that combines wet lab methods with bioinformatics tools to identify and analyze intrinsically disordered proteins in a non-model insect species that is cold-hardy. Due to their known resilience to the effects of extreme temperatures, these proteins likely play important roles in this insect’s adaptive mechanisms to sub-zero temperatures. The approach involves IDP enrichment by sample heating and double-digestion of proteins, followed by peptide and protein identification. Next, proteins are bioinformatically analyzed for disorder content, presence of long disordered regions, amino acid composition, and processes they are involved in. Finally, IDP detection is validated with an in-house 2D PAGE. In total, 608 unique proteins were identified, with 39 being mostly disordered, 100 partially disordered, 95 nearly ordered, and 374 ordered. One-third contain at least one long disordered segment. Functional information was available for only 90 proteins with intrinsic disorders out of 312 characterized proteins. Around half of the 90 proteins are cytoskeletal elements or involved in translational processes. Full article

(This article belongs to the Special Issue Physics of Protein Folding, Misfolding, and Intrinsic Disorder: A Themed Issue in Honour of Professor Vladimir Uversky on the Occasion of His 60th Birthday)

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14 pages, 1564 KiB

Open AccessEditor’s ChoiceReview

Aquaporin-4 in Neuromyelitis Optica Spectrum Disorders: A Target of Autoimmunity in the Central Nervous System

by Yoichiro Abe and Masato Yasui

Biomolecules 2022, 12(4), 591; https://doi.org/10.3390/biom12040591 - 17 Apr 2022

Cited by 18 | Viewed by 4594

Abstract

Since the discovery of a specific autoantibody in patients with neuromyelitis optica spectrum disorder (NMOSD) in 2004, the water channel aquaporin-4 (AQP4) has attracted attention as a target of autoimmune diseases of the central nervous system. In NMOSD, the autoantibody (NMO-IgG) binds to [...] Read more.

Since the discovery of a specific autoantibody in patients with neuromyelitis optica spectrum disorder (NMOSD) in 2004, the water channel aquaporin-4 (AQP4) has attracted attention as a target of autoimmune diseases of the central nervous system. In NMOSD, the autoantibody (NMO-IgG) binds to the extracellular loops of AQP4 as expressed in perivascular astrocytic end-feet and disrupts astrocytes in a complement-dependent manner. NMO-IgG is an excellent marker for distinguishing the disease from other inflammatory demyelinating diseases, such as multiple sclerosis. The unique higher-order structure of AQP4—called orthogonal arrays of particles (OAPs)—as well as its subcellular localization may play a crucial role in the pathogenesis of the disease. Recent studies have also demonstrated complement-independent cytotoxic effects of NMO-IgG. Antibody-induced endocytosis of AQP4 has been suggested to be involved in this mechanism. This review focuses on the binding properties of antibodies that recognize the extracellular region of AQP4 and the characteristics of AQP4 that are implicated in the pathogenesis of NMOSD. Full article

(This article belongs to the Special Issue Aquaporins in the CNS–in Honor of the 30th Anniversary of the Discovery of Aquaporins)

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10 pages, 2771 KiB

Open AccessArticle

Rapid Assay for the Therapeutic Drug Monitoring of Edoxaban

by Md Abdur Rashid, Saiqa Muneer, Yahya Alhamhoom and Nazrul Islam

Biomolecules 2022, 12(4), 590; https://doi.org/10.3390/biom12040590 - 17 Apr 2022

Cited by 5 | Viewed by 3010

Abstract

Edoxaban is a direct oral anticoagulant (DOAC) that has been recently indicated for the treatment of pulmonary embolism (PE) in SARS-CoV-2 infections. Due to its pharmacokinetic variability and a narrow therapeutic index, the safe administration of the drug requires its therapeutic drug monitoring [...] Read more.

Edoxaban is a direct oral anticoagulant (DOAC) that has been recently indicated for the treatment of pulmonary embolism (PE) in SARS-CoV-2 infections. Due to its pharmacokinetic variability and a narrow therapeutic index, the safe administration of the drug requires its therapeutic drug monitoring (TDM) in patients receiving the treatment. In this work, we present a label-free method for the TDM of edoxaban by surface enhanced Raman spectroscopy (SERS). The new method utilises the thiol chemistry of the drug to chemisorb its molecules onto a highly sensitive SERS substrate. This leads to the formation of efficient hotspots and a strong signal enhancement of the drug Raman bands, thus negating the need for a Raman reporter for its SERS quantification. The standard samples were run with a concentration range of 1.4 × 10⁻⁴ M to 10⁻¹² M using a mobile phase comprising of methanol/acetonitrile (85:15 v/v) at 291 nm followed by the good linearity of R² = 0.997. The lowest limit of quantification (LOQ) by the SERS method was experimentally determined to be 10⁻¹² M, whereas LOQ for HPLC-UV was 4.5 × 10⁻⁷ M, respectively. The new method was used directly and in a simple HPLC-SERS assembly to detect the drug in aqueous solutions and in spiked human blood plasma down to 1 pM. Therefore, the SERS method has strong potential for the rapid screening of the drug at pathology labs and points of care. Full article

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20 pages, 4683 KiB

Open AccessArticle

3D Printed Cell Culture Chamber for Testing the Effect of Pump-Based Chronic Drug Delivery on Inner Ear Tissue

by Jana Schwieger, Anna Sophie Frisch, Thomas S. Rau, Thomas Lenarz, Silke Hügl and Verena Scheper

Biomolecules 2022, 12(4), 589; https://doi.org/10.3390/biom12040589 - 17 Apr 2022

Cited by 4 | Viewed by 3025

Abstract

Cochlear hair cell damage and spiral ganglion neuron (SGN) degeneration are the main causes of sensory neural hearing loss. Cochlear implants (CIs) can replace the function of the hair cells and stimulate the SGNs electrically. The condition of the SGNs and their spatial [...] Read more.

Cochlear hair cell damage and spiral ganglion neuron (SGN) degeneration are the main causes of sensory neural hearing loss. Cochlear implants (CIs) can replace the function of the hair cells and stimulate the SGNs electrically. The condition of the SGNs and their spatial distance to the CI are key factors for CI-functionality. For a better performance, a high number of neurons and a closer contact to the electrode are intended. Neurotrophic factors are able to enhance SGN survival and neurite outgrowth, and thereby might optimize the electrode-nerve interaction. This would require chronic factor treatment, which is not yet established for the inner ear. Investigations on chronic drug delivery to SGNs could benefit from an appropriate in vitro model. Thus, an inner ear inspired Neurite Outgrowth Chamber (NOC), which allows the incorporation of a mini-osmotic pump for long-term drug delivery, was designed and three-dimensionally printed. The NOC’s function was validated using spiral ganglion explants treated with ciliary neurotrophic factor, neurotrophin-3, or control fluid released via pumps over two weeks. The NOC proved to be suitable for explant cultivation and observation of pump-based drug delivery over the examined period, with neurotrophin-3 significantly increasing neurite outgrowth compared to the other groups. Full article

(This article belongs to the Special Issue Inner Ear Therapeutics)

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16 pages, 2600 KiB

Open AccessArticle

Early Application of Ipsilateral Cathodal-tDCS in a Mouse Model of Brain Ischemia Results in Functional Improvement and Perilesional Microglia Modulation

by Laura Cherchi, Daniela Anni, Mario Buffelli and Marco Cambiaghi

Biomolecules 2022, 12(4), 588; https://doi.org/10.3390/biom12040588 - 17 Apr 2022

Cited by 9 | Viewed by 3101

Abstract

Early stroke therapeutic approaches rely on limited options, further characterized by a narrow therapeutic time window. In this context, the application of transcranial direct current stimulation (tDCS) in the acute phases after brain ischemia is emerging as a promising non-invasive tool. Despite the [...] Read more.

Early stroke therapeutic approaches rely on limited options, further characterized by a narrow therapeutic time window. In this context, the application of transcranial direct current stimulation (tDCS) in the acute phases after brain ischemia is emerging as a promising non-invasive tool. Despite the wide clinical application of tDCS, the cellular mechanisms underlying its positive effects are still poorly understood. Here, we explored the effects of cathodal tDCS (C-tDCS) 6 h after focal forelimb M1 ischemia in Cx3CR1^GFP/+ mice. C-tDCS improved motor functionality of the affected forelimb, as assessed by the cylinder and foot-fault tests at 48 h, though not changing the ischemic volume. In parallel, histological analysis showed that motor recovery is associated with decreased microglial cell density in the area surrounding the ischemic core, while astrocytes were not affected. Deeper analysis of microglia morphology within the perilesional area revealed a shift toward a more ramified healthier state, with increased processes’ complexity and a less phagocytic anti-inflammatory activity. Taken together, our findings suggest a positive role for early C-tDCS after ischemia, which is able to modulate microglia phenotype and morphology in parallel to motor recovery. Full article

(This article belongs to the Special Issue Key Advances in Brain Stimulation)

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17 pages, 4877 KiB

Open AccessArticle

Expression of Beta-Catenin, Cadherins and P-Runx2 in Fibro-Osseous Lesions of the Jaw: Tissue Microarray Study

by Giuseppe Pannone, Riccardo Nocini, Angela Santoro, Francesca Spirito, Pier Francesco Nocini, Silvana Papagerakis, Renny T. Franceschi, Marina Di Domenico, Angelina Di Carlo, Nana Danelia and Lorenzo Lo Muzio

Biomolecules 2022, 12(4), 587; https://doi.org/10.3390/biom12040587 - 16 Apr 2022

Cited by 4 | Viewed by 3131

Abstract

Fibrous dysplasia (FD) and hyperparathyroidism-jaw tumor syndrome (HPT-JT) are well-characterized benign bone fibro-osseous lesions. The intracellular mechanism leading to excessive deposition of fibrous tissue and alteration of differentiation processes leading to osteomalacia have not yet been fully clarified. Tissue Microarray (TMA)-based immunohistochemical expression [...] Read more.

Fibrous dysplasia (FD) and hyperparathyroidism-jaw tumor syndrome (HPT-JT) are well-characterized benign bone fibro-osseous lesions. The intracellular mechanism leading to excessive deposition of fibrous tissue and alteration of differentiation processes leading to osteomalacia have not yet been fully clarified. Tissue Microarray (TMA)-based immunohistochemical expression of β-catenin, CK-AE1/AE3, Ki-67, cadherins and P-Runx2 were analyzed in archival samples from nine patients affected by FD and HPT-JT and in seven controls, with the aim of elucidating the contribution of these molecules (β-catenin, cadherins and P-Runx2) in the osteoblast differentiation pathway. β-catenin was strongly upregulated in FD, showing a hyper-cellulated pattern, while it was faintly expressed in bone tumors associated with HPT-JT. Furthermore, the loss of expression of OB-cadherin in osteoblast lineage in FD was accompanied by N-cadherin and P-cadherin upregulation (p < 0.05), while E-cadherin showed a minor role in these pathological processes. P-Runx2 showed over-expression in six out of eight cases of FD and stained moderately positive in the rimming lining osteoblasts in HPT-JT syndrome. β-catenin plays a central role in fibrous tissue proliferation and accompanies the lack of differentiation of osteoblast precursors in mature osteoblasts in FD. The study showed that the combined evaluation of the histological characteristics and the histochemical and immunohistochemical profile of key molecules involved in osteoblast differentiation are useful in the diagnosis, classification and therapeutic management of fibrous-osseous lesions. Full article

(This article belongs to the Special Issue Biomarkers in Oral Diseases)

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14 pages, 3086 KiB

Open AccessArticle

Integrative Gene Expression and Metabolic Analysis Tool IgemRNA

by Kristina Grausa, Ivars Mozga, Karlis Pleiko and Agris Pentjuss

Biomolecules 2022, 12(4), 586; https://doi.org/10.3390/biom12040586 - 16 Apr 2022

Cited by 2 | Viewed by 3135

Abstract

Genome-scale metabolic modeling is widely used to study the impact of metabolism on the phenotype of different organisms. While substrate modeling reflects the potential distribution of carbon and other chemical elements within the model, the additional use of omics data, e.g., transcriptome, has [...] Read more.

Genome-scale metabolic modeling is widely used to study the impact of metabolism on the phenotype of different organisms. While substrate modeling reflects the potential distribution of carbon and other chemical elements within the model, the additional use of omics data, e.g., transcriptome, has implications when researching the genotype–phenotype responses to environmental changes. Several algorithms for transcriptome analysis using genome-scale metabolic modeling have been proposed. Still, they are restricted to specific objectives and conditions and lack flexibility, have software compatibility issues, and require advanced user skills. We classified previously published algorithms, summarized transcriptome pre-processing, integration, and analysis methods, and implemented them in the newly developed transcriptome analysis tool IgemRNA, which (1) has a user-friendly graphical interface, (2) tackles compatibility issues by combining previous data input and pre-processing algorithms in MATLAB, and (3) introduces novel algorithms for the automatic comparison of different transcriptome datasets with or without Cobra Toolbox 3.0 optimization algorithms. We used publicly available transcriptome datasets from Saccharomyces cerevisiae BY4741 and H4-S47D strains for validation. We found that IgemRNA provides a means for transcriptome and environmental data validation on biochemical network topology since the biomass function varies for different phenotypes. Our tool can detect problematic reaction constraints. Full article

(This article belongs to the Special Issue Computational Biology for Metabolic Modelling and Pathway Design)

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12 pages, 1587 KiB

Open AccessArticle

The Fibrinogen-like Domain of ANGPTL3 Facilitates Lipolysis in 3T3-L1 Cells by Activating the Intracellular Erk Pathway

by Simone Bini, Valeria Pecce, Alessia Di Costanzo, Luca Polito, Ameneh Ghadiri, Ilenia Minicocci, Federica Tambaro, Stella Covino, Marcello Arca and Laura D’Erasmo

Biomolecules 2022, 12(4), 585; https://doi.org/10.3390/biom12040585 - 16 Apr 2022

Cited by 10 | Viewed by 2789

Abstract

Background: ANGPTL3 stimulates lipolysis in adipocytes, but the underlying molecular mechanism is yet unknown. The C-terminal fibrinogen-like domain of ANGPTL3 (ANGPTL3-Fld) activates the AKT pathway in endothelial cells. Hence, we evaluated whether ANGPTL3-Fld stimulates lipolysis in adipocytes through the MAPK kinase pathway. Materials [...] Read more.

Background: ANGPTL3 stimulates lipolysis in adipocytes, but the underlying molecular mechanism is yet unknown. The C-terminal fibrinogen-like domain of ANGPTL3 (ANGPTL3-Fld) activates the AKT pathway in endothelial cells. Hence, we evaluated whether ANGPTL3-Fld stimulates lipolysis in adipocytes through the MAPK kinase pathway. Materials and Methods: 3T3-L1 adipocytes were treated with isoproterenol (ISO), ANGPTL3-Fld, or both. Lipolysis was evaluated through the release of free fatty acids (FFAs) in the culture medium. The activation status of intracellular kinases was evaluated with and without the inhibition of the BRAF–ERK arm of the MAPK pathway. Results: ANGPTL3-Fld alone was not able to activate lipolysis, while the combination of ANGPTL3-Fld and ISO determined a 10-fold enrichment of the FFA concentration in the culture medium with an incremental effect (twofold) when compared with ISO alone. ANGPTL3-Fld alone inhibited hormone-sensitive lipase (HSL), whereas the treatment with ISO induced the activation of HSL. The net balance of ANGPTL3-Fld and ISO cotreatment resulted in HSL activation. The results indicate that ANGPTL3-Fld generated an intracellular activation signal involving the MAPK–ERK pathway, possibly through the PDGFRβ—PLCγ-AMPK axis. Conclusion: ANGPTL3-Fld appears to act as a facilitator of lipolysis in adipocytes, and this effect was driven by a signal mediated by a pathway that is different from the canonical β-adrenergic stimulus. Full article

(This article belongs to the Special Issue Emerging Circulating Biomarkers in Atherosclerosis: From Molecular Mechanisms to Therapeutic Strategies)

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12 pages, 2224 KiB

Open AccessArticle

Synthesis and Effect of Conformationally Locked Carbocyclic Guanine Nucleotides on Dynamin

by Kiran S. Toti, John R. Jimah, Veronica Salmaso, Jenny E. Hinshaw and Kenneth A. Jacobson

Biomolecules 2022, 12(4), 584; https://doi.org/10.3390/biom12040584 - 16 Apr 2022

Cited by 1 | Viewed by 2839

Abstract

Guanine nucleotides can flip between a North and South conformation in the ribose moiety. To test the enzymatic activity of GTPases bound to nucleotides in the two conformations, we generated methanocarba guanine nucleotides in the North or South envelope conformations, i.e., (N)-GTP and [...] Read more.

Guanine nucleotides can flip between a North and South conformation in the ribose moiety. To test the enzymatic activity of GTPases bound to nucleotides in the two conformations, we generated methanocarba guanine nucleotides in the North or South envelope conformations, i.e., (N)-GTP and (S)-GTP, respectively. With dynamin as a model system, we examined the effects of (N)-GTP and (S)-GTP on dynamin-mediated membrane constriction, an activity essential for endocytosis. Dynamin membrane constriction and fission activity are dependent on GTP binding and hydrolysis, but the effect of the conformational state of the GTP nucleotide on dynamin activity is not known. After reconstituting dynamin-mediated lipid tubulation and membrane constriction in vitro, we observed via cryo-electron microscopy (cryo-EM) that (N)-GTP, but not (S)-GTP, enables the constriction of dynamin-decorated lipid tubules. These findings suggest that the activity of dynamin is dependent on the conformational state of the GTP nucleotide. However, a survey of nucleotide ribose conformations associated with dynamin structures in nature shows almost exclusively the (S)-conformation. The explanation for this mismatch of (N) vs. (S) required for GTP analogues in a dynamin-mediated process will be addressed in future studies. Full article

(This article belongs to the Special Issue Pharmacology of Purinergic Receptors—Honorary Special Issue Dedicated to Prof. Pier Andrea Borea)

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13 pages, 4312 KiB

Open AccessArticle

Exacerbation of Elastase-Induced Emphysema via Increased Oxidative Stress in Metallothionein-Knockout Mice

by Ken Ichiro Tanaka, Sachie Shiota, Okina Sakakibara, Mikako Shimoda, Ayaka Takafuji, Misaki Takabatake, Yoshito Kadota, Takashige Kawakami, Shinya Suzuki and Masahiro Kawahara

Biomolecules 2022, 12(4), 583; https://doi.org/10.3390/biom12040583 - 15 Apr 2022

Cited by 8 | Viewed by 2677

Abstract

Although the pathogenesis of chronic obstructive pulmonary disease (COPD) is not yet fully understood, recent studies suggest that the disruption of the intracellular balance of oxidative (such as reactive oxygen species (ROS)) and antioxidant molecules plays an important role in COPD development and [...] Read more.

Although the pathogenesis of chronic obstructive pulmonary disease (COPD) is not yet fully understood, recent studies suggest that the disruption of the intracellular balance of oxidative (such as reactive oxygen species (ROS)) and antioxidant molecules plays an important role in COPD development and progression. Metallothionein is an endogenous metal-binding protein with reported ROS scavenging activity. Although there have been many publications on the protective effects of metallothionein in the kidney and liver, its role in COPD models such as elastase- or cigarette smoke (CS)-induced lung injury is unknown. Thus, in the present study, we analyzed the elastase-induced lung injury model using metallothionein-knockout (MT-KO; MT-1 and -2 gene deletion) mice. The expression of MT-1 and MT-2 in the lungs of MT-KO mice was markedly lower compared with that in the lungs of wildtype (WT) mice. Porcine pancreatic elastase (PPE)-induced lung injury (alveolar enlargement and respiratory impairment) was significantly exacerbated in MT-KO mice compared with WT mice. Additionally, PPE-induced increases in the number of inflammatory cells, inflammatory cytokines, and cell death in lung tissue were significantly more pronounced in MT-KO mice compared with WT mice. Finally, using an in vivo imaging system, we also found that PPE-induced ROS production in the lungs was enhanced in MT-KO mice compared with WT mice. These results suggest that metallothionein may act as an inhibitor against elastase-induced lung injury by suppressing ROS production. These results suggest that metallothionein protein, or compounds that can induce metallothionein, could be useful in the treatment of COPD. Full article

(This article belongs to the Special Issue Zinc in Health and Disease Conditions)

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25 pages, 2770 KiB

Open AccessReview

“Malancha” [Alternanthera philoxeroides (Mart.) Griseb.]: A Potential Therapeutic Option against Viral Diseases

by Lutfun Nahar, Sushmita Nath and Satyajit D. Sarker

Biomolecules 2022, 12(4), 582; https://doi.org/10.3390/biom12040582 - 14 Apr 2022

Cited by 5 | Viewed by 3417

Abstract

Alternanthera philoxeroides (Mart.) Griseb., commonly known as “Alligator weed” in English, and “Malancha” in Bengali, is a leafy vegetable from the family Amaranthaceae A. L. de Jussieu. This species is native to China, particularly to the provinces around the Yangtze River, other Far [...] Read more.

Alternanthera philoxeroides (Mart.) Griseb., commonly known as “Alligator weed” in English, and “Malancha” in Bengali, is a leafy vegetable from the family Amaranthaceae A. L. de Jussieu. This species is native to China, particularly to the provinces around the Yangtze River, other Far East and South-East Asian countries, and countries from other continents (e.g., South America). This plant also grows in certain areas in Australia, New Zealand, and the USA. While in Bangladesh the leaves of this plant are consumed as a vegetable, in China, this plant has been used widely as a traditional remedy for the treatment of various viral diseases (e.g., measles, influenza, and haemorrhagic fever). Flavonoids and saponins are the two largest groups of phytochemicals produced by this plant, and the antiviral property of this plant and its compounds has been studied extensively. This review article reviews all published literature on this plant and critically appraises its phytochemical profile linking to biomolecular interactions and therapeutic potential, particularly, against viral diseases. Full article

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19 pages, 940 KiB

Open AccessEditor’s ChoiceReview

Potential Effects of Natural H₂S-Donors in Hypertension Management

by Eugenia Piragine, Valentina Citi, Kim Lawson, Vincenzo Calderone and Alma Martelli

Biomolecules 2022, 12(4), 581; https://doi.org/10.3390/biom12040581 - 14 Apr 2022

Cited by 19 | Viewed by 3745

Abstract

After the discovery of hydrogen sulfide (H₂S) in the central nervous system by Abe and Kimura in 1996, the physiopathological role of H₂S has been widely investigated in several systems such as the cardiovascular. In particular, H₂S [...] Read more.

After the discovery of hydrogen sulfide (H₂S) in the central nervous system by Abe and Kimura in 1996, the physiopathological role of H₂S has been widely investigated in several systems such as the cardiovascular. In particular, H₂S plays a pivotal role in the control of vascular tone, exhibiting mechanisms of action able to induce vasodilation: for instance, activation of potassium channels (KATP and Kv7) and inhibition of 5-phosphodiesterase (5-PDE). These findings paved the way for the research of natural and synthetic exogenous H₂S-donors (i.e., molecules able to release H₂S) in order to have new tools for the management of hypertension. In this scenario, some natural molecules derived from Alliaceae (i.e., garlic) and Brassicaceae (i.e., rocket or broccoli) botanical families show the profile of slow H₂S-donors able to mimic the endogenous production of this gasotransmitter and therefore can be viewed as interesting potential tools for management of hypertension or pre-hypertension. In this article, the preclinical and clinical impacts of these natural H₂S-donors on hypertension and vascular integrity have been reviewed in order to give a complete panorama of their potential use for the management of hypertension and related vascular diseases. Full article

(This article belongs to the Special Issue Hydrogen Sulfide and Polysulfides, Endogenous Mammalian Transmitters——Honorary Special Issue Commemorating the Work of Prof. Hideo Kimura)

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15 pages, 986 KiB

Open AccessReview

Effects of Glucose Metabolism, Lipid Metabolism, and Glutamine Metabolism on Tumor Microenvironment and Clinical Implications

by Longfei Zhu, Xuanyu Zhu and Yan Wu

Biomolecules 2022, 12(4), 580; https://doi.org/10.3390/biom12040580 - 14 Apr 2022

Cited by 58 | Viewed by 8002

Abstract

In recent years, an increasingly more in depth understanding of tumor metabolism in tumorigenesis, tumor growth, metastasis, and prognosis has been achieved. The broad heterogeneity in tumor tissue is the critical factor affecting the outcome of tumor treatment. Metabolic heterogeneity is not only [...] Read more.

In recent years, an increasingly more in depth understanding of tumor metabolism in tumorigenesis, tumor growth, metastasis, and prognosis has been achieved. The broad heterogeneity in tumor tissue is the critical factor affecting the outcome of tumor treatment. Metabolic heterogeneity is not only found in tumor cells but also in their surrounding immune and stromal cells; for example, many suppressor cells, such as tumor-associated macrophages (TAMs), myeloid-derived suppressor cells (MDSCs), and tumor-associated T-lymphocytes. Abnormalities in metabolism often lead to short survival or resistance to antitumor therapy, e.g., chemotherapy, radiotherapy, targeted therapy, and immunotherapy. Using the metabolic characteristics of the tumor microenvironment to identify and treat cancer has become a great research hotspot. This review systematically addresses the impacts of metabolism on tumor cells and effector cells and represents recent research advances of metabolic effects on other cells in the tumor microenvironment. Finally, we introduce some applications of metabolic features in clinical oncology. Full article

(This article belongs to the Collection Molecular Biology: Feature Papers)

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18 pages, 4417 KiB

Open AccessArticle

IntroSpect: Motif-Guided Immunopeptidome Database Building Tool to Improve the Sensitivity of HLA I Binding Peptide Identification by Mass Spectrometry

by Le Zhang, Geng Liu, Guixue Hou, Haitao Xiang, Xi Zhang, Ying Huang, Xiuqing Zhang, Bo Li and Leo J. Lee

Biomolecules 2022, 12(4), 579; https://doi.org/10.3390/biom12040579 - 14 Apr 2022

Cited by 5 | Viewed by 2921

Abstract

Although database search tools originally developed for shotgun proteome have been widely used in immunopeptidomic mass spectrometry identifications, they have been reported to achieve undesirably low sensitivities or high false positive rates as a result of the hugely inflated search space caused by [...] Read more.

Although database search tools originally developed for shotgun proteome have been widely used in immunopeptidomic mass spectrometry identifications, they have been reported to achieve undesirably low sensitivities or high false positive rates as a result of the hugely inflated search space caused by the lack of specific enzymic digestions in immunopeptidome. To overcome such a problem, we developed a motif-guided immunopeptidome database building tool named IntroSpect, which is designed to first learn the peptide motifs from high confidence hits in the initial search, and then build a targeted database for refined search. Evaluated on 18 representative HLA class I datasets, IntroSpect can improve the sensitivity by an average of 76%, compared to conventional searches with unspecific digestions, while maintaining a very high level of accuracy (~96%), as confirmed by synthetic validation experiments. A distinct advantage of IntroSpect is that it does not depend on any external HLA data, so that it performs equally well on both well-studied and poorly-studied HLA types, unlike the previously developed method SpectMHC. We have also designed IntroSpect to keep a global FDR that can be conveniently controlled, similar to a conventional database search. Finally, we demonstrate the practical value of IntroSpect by discovering neoepitopes from MS data directly, an important application in cancer immunotherapies. IntroSpect is freely available to download and use. Full article

(This article belongs to the Section Bioinformatics and Systems Biology)

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16 pages, 926 KiB

Open AccessReview

Insulin Receptors and Insulin Action in the Heart: The Effects of Left Ventricular Assist Devices

by Konstantina Pantazi, Eleni Karlafti, Alexandra Bekiaridou, Matthaios Didagelos, Antonios Ziakas and Triantafyllos Didangelos

Biomolecules 2022, 12(4), 578; https://doi.org/10.3390/biom12040578 - 14 Apr 2022

Cited by 7 | Viewed by 2809

Abstract

This year, 2022, marks the 100th anniversary of the isolation of human insulin and its administration to patients suffering from diabetes mellitus (DM). Insulin exerts many effects on the human body, including the cardiac tissue. The pathways implicated include the PKB/Akt signaling pathway, [...] Read more.

This year, 2022, marks the 100th anniversary of the isolation of human insulin and its administration to patients suffering from diabetes mellitus (DM). Insulin exerts many effects on the human body, including the cardiac tissue. The pathways implicated include the PKB/Akt signaling pathway, the Janus kinase, and the mitogen-activated protein kinase pathway and lead to normal cardiac growth, vascular smooth muscle regulation, and cardiac contractility. This review aims to summarize the existing knowledge and provide new insights on insulin pathways of cardiac tissue, along with the role of left ventricular assist devices on insulin regulation and cardiac function. Full article

(This article belongs to the Special Issue 100th Anniversary of Insulin: Insulin Receptor Signaling in Health and Disease)

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17 pages, 5465 KiB

Open AccessArticle

The Ribosome Is the Ultimate Receptor for Trypsin Modulating Oostatic Factor (TMOF)

by Dov Borovsky, Pierre Rougé and Robert G. Shatters, Jr.

Biomolecules 2022, 12(4), 577; https://doi.org/10.3390/biom12040577 - 14 Apr 2022

Cited by 4 | Viewed by 2183

Abstract

Aedes aegypti Trypsin Modulating Oostatic Factor (AeaTMOF). a mosquito decapeptide that controls trypsin biosynthesis in female and larval mosquitoes. enters the gut epithelial cells of female mosquitoes using ABC-tmfA receptor/importer. To study the ultimate targeted receptor after AeaTMOF [...] Read more.

Aedes aegypti Trypsin Modulating Oostatic Factor (AeaTMOF). a mosquito decapeptide that controls trypsin biosynthesis in female and larval mosquitoes. enters the gut epithelial cells of female mosquitoes using ABC-tmfA receptor/importer. To study the ultimate targeted receptor after AeaTMOF enters the cell, AeaTMOF was incubated in vitro with either Escherichia coli or Spodoptera frugiperda protein-expressing extracts containing 70S and 80S ribosomes, respectively. The effect of AeaTMOF on luciferase biosynthesis in vitro using 70S ribosomes was compared with that of oncocin112 (1–13), a ribosome-binding antibacterial peptide. The IC₅₀ of 1 μM and 2 μM, respectively, for both peptides was determined. Incubation with a protein-expressing system and S. frugiperda 80S ribosomes determined an IC₅₀ of 1.8 μM for Aedes aegypti larval late trypsin biosynthesis. Incubation of purified E. coli ribosome with increasing concentration of AeaTMOF shows that the binding of AeaTMOF to the bacterial ribosome exhibits a high affinity (K_D = 23 ± 3.4 nM, B_max = 0.553 ± 0.023 pmol/μg ribosome and K_assoc = 4.3 × 10⁷ M⁻¹). Molecular modeling and docking experiments show that AeaTMOF binds bacterial and Drosophila ribosome (50S and 60S, respectively) at the entrance of the ribosome exit tunnel, blocking the tRNA entrance and preventing protein biosynthesis. Recombinant E. coli cells that express only ABC-tmfA importer are inhibited by AeaTMOF but not by oncocin112 (1–13). These results suggest that the ribosome is the ultimate targeted receptor of AeaTMOF. Full article

(This article belongs to the Special Issue Insect Receptors: Biochemical, Physiological and Molecular Studies)

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16 pages, 1275 KiB

Open AccessReview

by Ankit Srivastava, Parvez Alam and Byron Caughey

Biomolecules 2022, 12(4), 576; https://doi.org/10.3390/biom12040576 - 14 Apr 2022

Cited by 19 | Viewed by 6647

Abstract

Various disease-associated forms or strains of α-synuclein (αSyn^D) can spread and accumulate in a prion-like fashion during synucleinopathies such as Parkinson’s disease (PD), Lewy body dementia (DLB), and multiple system atrophy (MSA). This capacity for self-propagation has enabled the development of [...] Read more.

Various disease-associated forms or strains of α-synuclein (αSyn^D) can spread and accumulate in a prion-like fashion during synucleinopathies such as Parkinson’s disease (PD), Lewy body dementia (DLB), and multiple system atrophy (MSA). This capacity for self-propagation has enabled the development of seed amplification assays (SAAs) that can detect αSyn^D in clinical samples. Notably, α-synuclein real-time quaking-induced conversion (RT-QuIC) and protein misfolding cyclic amplification (PMCA) assays have evolved as ultrasensitive, specific, and relatively practical methods for detecting αSyn^D in a variety of biospecimens including brain tissue, CSF, skin, and olfactory mucosa from synucleinopathy patients. However, αSyn SAAs still lack concordance in detecting MSA and familial forms of PD/DLB, and the assay parameters show poor correlations with various clinical measures. End-point dilution analysis in αSyn RT-QuIC assays allows for the quantitation of relative amounts of αSyn^D seeding activity that may correlate moderately with clinical measures and levels of other biomarkers. Herein, we review recent advancements in α-synuclein SAAs for detecting αSyn^D and describe in detail the modified Spearman–Karber quantification algorithm used with end-point dilutions. Full article

(This article belongs to the Special Issue Prions and Prion-Like Mechanisms in Disease and Biological Function)

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24 pages, 7894 KiB

Open AccessArticle

Hypoxia Alters the Proteome Profile and Enhances the Angiogenic Potential of Dental Pulp Stem Cell-Derived Exosomes

by Baoyu Li, Xuehong Xian, Xinwei Lin, Luo Huang, Ailin Liang, Hongwei Jiang and Qimei Gong

Biomolecules 2022, 12(4), 575; https://doi.org/10.3390/biom12040575 - 14 Apr 2022

Cited by 19 | Viewed by 3617

Abstract

Dental pulp stem cells (DPSCs) and their exosomes (Exos) are effective treatments for regenerative medicine. Hypoxia was confirmed to improve the angiogenic potential of stem cells. However, the angiogenic effect and mechanism of hypoxia-preconditioned DPSC-Exos are poorly understood. We isolated exosomes from DPSCs [...] Read more.

Dental pulp stem cells (DPSCs) and their exosomes (Exos) are effective treatments for regenerative medicine. Hypoxia was confirmed to improve the angiogenic potential of stem cells. However, the angiogenic effect and mechanism of hypoxia-preconditioned DPSC-Exos are poorly understood. We isolated exosomes from DPSCs under normoxia (Nor-Exos) and hypoxia (Hypo-Exos) and added them to human umbilical vein endothelial cells (HUVECs). HUVEC proliferation, migration and angiogenic capacity were assessed by CCK-8, transwell, tube formation assays, qRT-PCR and Western blot. iTRAQ-based proteomics and bioinformatic analysis were performed to investigate proteome profile differences between Nor-Exos and Hypo-Exos. Western blot, immunofluorescence and immunohistochemistry were used to detect the expression of lysyl oxidase-like 2 (LOXL2) in vitro and in vivo. Finally, we silenced LOXL2 in HUVECs and rescued tube formation with Hypo-Exos. Hypo-Exos enhanced HUVEC proliferation, migration and tube formation in vitro superior to Nor-Exos. The proteomics analysis identified 79 proteins with significantly different expression in Hypo-Exos, among which LOXL2 was verified as being upregulated in hypoxia-preconditioned DPSCs, Hypo-Exos, and inflamed dental pulp. Hypo-Exos partially rescued the inhibitory influence of LOXL2 silence on HUVEC tube formation. In conclusion, hypoxia enhanced the angiogenic potential of DPSCs-Exos and partially altered their proteome profile. LOXL2 is likely involved in Hypo-Exos mediated angiogenesis. Full article

(This article belongs to the Section Bioinformatics and Systems Biology)

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10 pages, 618 KiB

Open AccessReview

Metformin in Differentiated Thyroid Cancer: Molecular Pathways and Its Clinical Implications

by Manuel García-Sáenz, Miry Lobaton-Ginsberg and Aldo Ferreira-Hermosillo

Biomolecules 2022, 12(4), 574; https://doi.org/10.3390/biom12040574 - 14 Apr 2022

Cited by 15 | Viewed by 5013

Abstract

Metformin is a synthetic biguanide that improves insulin sensitivity and reduces hepatic gluconeogenesis. Aside being the first-line therapy for Type 2 Diabetes (T2D), many pleiotropic effects have been discovered in recent years, such as its capacity to reduce cancer risk and tumorigenesis. Although [...] Read more.

Metformin is a synthetic biguanide that improves insulin sensitivity and reduces hepatic gluconeogenesis. Aside being the first-line therapy for Type 2 Diabetes (T2D), many pleiotropic effects have been discovered in recent years, such as its capacity to reduce cancer risk and tumorigenesis. Although widely studied, the effect of metformin on thyroid cancer remains controversial. Potential mechanisms for its growth inhibitory effects have been elucidated in various preclinical studies that involved pathways related to adenosine mono-phosphate-activated protein kinase (AMPK), mammalian target of rapamycin (mTOR), mitochondrial glycerophosphate dehydrogenase (mGPDH), and the nuclear factor κB (NF-κB). Hyperinsulinemia increases cell glucose uptake and oxidative stress, and promotes thyroid cell growth, leading to hyperproliferation, carcinogenesis, and the development of malignant tumors. Furthermore, it has also been related to thyroid nodules size in nodular disease, as well as tumoral size in patients with thyroid cancer. Several clinical studies concluded that metformin might have an important role as an adjuvant therapy to reduce the growth of benign and malignant thyroid neoplasms. This suggests that metformin might be useful for patients with differentiated or poorly differentiated thyroid cancer and metabolic diseases such as insulin resistance or diabetes. Full article

(This article belongs to the Special Issue Metformin and Cancer)

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2 pages, 175 KiB

Open AccessComment

Comment on Chen et al. Dual Blockade of Lactate/GPR81 and PD-1/PD-L1 Pathways Enhances the Anti-Tumor Effects of Metformin. Biomolecules 2021, 11, 1373

by Nicolai Stransky and Stephan M. Huber

Biomolecules 2022, 12(4), 573; https://doi.org/10.3390/biom12040573 - 13 Apr 2022

Cited by 1 | Viewed by 2107

Abstract

In the study of Chen et al. [...] Full article

(This article belongs to the Special Issue Repurposing Drugs for Anti-Cancer Therapy)

15 pages, 4833 KiB

Open AccessArticle

Mutational Effect of Some Major COVID-19 Variants on Binding of the S Protein to ACE2

by Zhendong Li and John Z. H. Zhang

Biomolecules 2022, 12(4), 572; https://doi.org/10.3390/biom12040572 - 13 Apr 2022

Cited by 6 | Viewed by 2708

Abstract

COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has many variants that accelerated the spread of the virus. In this study, we investigated the quantitative effect of some major mutants of the spike protein of SARS-CoV-2 binding to the [...] Read more.

COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has many variants that accelerated the spread of the virus. In this study, we investigated the quantitative effect of some major mutants of the spike protein of SARS-CoV-2 binding to the human angiotensin-converting enzyme 2 (ACE2). These mutations are directly related to the Variant of Concern (VOC) including Alpha, Beta, Gamma, Delta and Omicron. Our calculations show that five major mutations (N501Y, E484K, L452R, T478K and K417N), first reported in Alpha, Beta, Gamma and Delta variants, all increase the binding of the S protein to ACE2 (except K417N), consistent with the experimental findings. We also studied an additional eight mutations of the Omicron variant that are located on the interface of the receptor binding domain (RDB) and have not been reported in other VOCs. Our study showed that most of these mutations (except Y505H and G446S) enhance the binding of the S protein to ACE2. The computational predictions helped explain why the Omicron variant quickly became dominant worldwide. Finally, comparison of several different computational methods for binding free energy calculation of these mutants was made. The alanine scanning method used in the current calculation helped to elucidate the residue-specific interactions responsible for the enhanced binding affinities of the mutants. The results show that the ASGB (alanine scanning with generalized Born) method is an efficient and reliable method for these binding free energy calculations due to mutations. Full article

(This article belongs to the Special Issue State-of-the-Art Biophysics, Biochemistry and Molecular Biology in China)

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11 pages, 1812 KiB

Open AccessArticle

Bacterial Glycocalyx Integrity Impacts Tolerance of Myxococcus xanthus to Antibiotics and Oxidative-Stress Agents

by Fares Saïdi, Razieh Bitazar, Nicholas Y. Bradette and Salim T. Islam

Biomolecules 2022, 12(4), 571; https://doi.org/10.3390/biom12040571 - 12 Apr 2022

Cited by 6 | Viewed by 2772

Abstract

The presence of an exopolysaccharide (EPS) layer surrounding bacterial cells, termed a “glycocalyx”, confers protection against toxic molecules. However, the effect of glycocalyx integrity on the tolerance to such agents is poorly understood. Using a modified disc-diffusion assay, we tested the susceptibility to [...] Read more.

The presence of an exopolysaccharide (EPS) layer surrounding bacterial cells, termed a “glycocalyx”, confers protection against toxic molecules. However, the effect of glycocalyx integrity on the tolerance to such agents is poorly understood. Using a modified disc-diffusion assay, we tested the susceptibility to a panel of antibiotics and oxidative stress-inducing compounds of various mutant strains of the social predatory Gram-negative soil bacterium Myxococcus xanthus; the selected mutants were those that manifest different physical states of their respective EPS glycocalyces. While the overall presence of an EPS layer was indeed beneficial for tolerance, the integrity of this layer was also found to affect the susceptibility of the bacterium to killing; however, this finding was not universal, and instead was dependent on the specific compound tested. Thus, the integrity of the cell-surface EPS glycocalyx plays an important role in the tolerance of M. xanthus to harmful compounds. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Bacterial Multicellularity)

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14 pages, 1669 KiB

Open AccessArticle

Propofol, an Anesthetic Agent, Inhibits HCN Channels through the Allosteric Modulation of the cAMP-Dependent Gating Mechanism

by Morihiro Shimizu, Xinya Mi, Futoshi Toyoda, Akiko Kojima, Wei-Guang Ding, Yutaka Fukushima, Mariko Omatsu-Kanbe, Hirotoshi Kitagawa and Hiroshi Matsuura

Biomolecules 2022, 12(4), 570; https://doi.org/10.3390/biom12040570 - 12 Apr 2022

Cited by 7 | Viewed by 2572

Abstract

Propofol is a broadly used intravenous anesthetic agent that can cause cardiovascular effects, including bradycardia and asystole. A possible mechanism for these effects is slowing cardiac pacemaker activity due to inhibition of the hyperpolarization-activated, cyclic nucleotide-gated (HCN) channels. However, it remains unclear how [...] Read more.

Propofol is a broadly used intravenous anesthetic agent that can cause cardiovascular effects, including bradycardia and asystole. A possible mechanism for these effects is slowing cardiac pacemaker activity due to inhibition of the hyperpolarization-activated, cyclic nucleotide-gated (HCN) channels. However, it remains unclear how propofol affects the allosteric nature of the voltage- and cAMP-dependent gating mechanism in HCN channels. To address this aim, we investigated the effect of propofol on HCN channels (HCN4 and HCN2) in heterologous expression systems using a whole-cell patch clamp technique. The extracellular application of propofol substantially suppressed the maximum current at clinical concentrations. This was accompanied by a hyperpolarizing shift in the voltage dependence of channel opening. These effects were significantly attenuated by intracellular loading of cAMP, even after considering the current modification by cAMP in opposite directions. The differential degree of propofol effects in the presence and absence of cAMP was rationalized by an allosteric gating model for HCN channels, where we assumed that propofol affects allosteric couplings between the pore, voltage-sensor, and cyclic nucleotide-binding domain (CNBD). The model predicted that propofol enhanced autoinhibition of pore opening by unliganded CNBD, which was relieved by the activation of CNBD by cAMP. Taken together, these findings reveal that propofol acts as an allosteric modulator of cAMP-dependent gating in HCN channels, which may help us to better understand the clinical action of this anesthetic drug. Full article

(This article belongs to the Special Issue Molecular Pathogenesis of Cardiac Arrhythmia)

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15 pages, 3486 KiB

Open AccessArticle

Prognostic Value of LINC-ROR (rs1942347) Variant in Patients with Colon Cancer Harboring BRAF Mutation: A Propensity Score-Matched Analysis

by Aly A. M. Shaalan, Sara H. Mokhtar, Hanadi Talal Ahmedah, Amany I. Almars, Eman A. Toraih, Afaf T. Ibrahiem, Manal S. Fawzy and Mai A. Salem

Biomolecules 2022, 12(4), 569; https://doi.org/10.3390/biom12040569 - 12 Apr 2022

Cited by 6 | Viewed by 2410

Abstract

Emerging studies show that long intergenic non-protein coding RNA, regulator of reprogramming (LINC-ROR) is aberrantly expressed in several types of cancer, including colon cancer (CC). LINC-ROR intronic variant rs1942347 may impact gene regulation and disease phenotype. We aimed to explore the [...] Read more.

Emerging studies show that long intergenic non-protein coding RNA, regulator of reprogramming (LINC-ROR) is aberrantly expressed in several types of cancer, including colon cancer (CC). LINC-ROR intronic variant rs1942347 may impact gene regulation and disease phenotype. We aimed to explore the potential association of LINC-ROR (rs1942347) with the clinicopathological features and outcome of CC cases. Archived FFPE (n = 180) CC samples were enrolled. Taq-Man allelic discrimination PCR was used for genotyping in propensity-matched cohorts with/without positive staining for mutant BRAF protein after eliminating confounders bias. The rs1942347*A allele variant was associated with high pathological grade, larger tumor size, distant metastasis, and mortality. Multiple logistic regression analysis adjusted by sex and BRAF mutation showed A/A genotype carriers to have 3 times more risk of early onset of cancer (OR = 3.13, 95%CI = 1.28–7.69, p = 0.034) than T/T genotype carriers. Overall analysis showed that rs1942347*A allele carriers had higher risk of mortality under heterozygote (OR = 2.13, 95%CI = 1.08–4.35, p = 0.003), homozygote (OR = 5.0, 95%CI = 1.69–14.29, p = 0.003), dominant (OR = 3.33, 95%CI = 1.20–9.09, p = 0.003), and recessive (OR = 2.63, 95%CI = 1.37–5.0, p = 0.011) models compared to T/T allele carriers. Stratified analysis by BRAF status revealed that the ancestor T/T allele conferred protection in BRAF mutant CC patients and was associated with a 73–93% reduced risk of mortality under heterozygote/homozygote comparison models. Using Kaplan–Meier curves, carriers of the A/A genotype had shorter survival times than T/T cohorts. The univariate Cox regression model revealed that the A/A genotype was associated with a 3.5 times greater mortality risk than the T/T genotype. However, after adjustment by multiple Cox regression analysis, the risk was insignificant. In conclusion, this is the first study identifying the potential association of the LINC-ROR (rs1942347) variant with CC prognosis. Full article

(This article belongs to the Special Issue The Role of MicroRNAs, Long Non-coding RNAs and Circular RNAs in Cancer Metastasis and Cancer Therapy Resistance)

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