International Journal of Molecular Sciences

2024

Jump to: 2023, 2022, 2021

15 pages, 3379 KiB

Open AccessArticle

Effects of Alkaline Extraction pH on Amino Acid Compositions, Protein Secondary Structures, Thermal Stability, and Functionalities of Brewer’s Spent Grain Proteins

by Kunn Hadinoto, Jordy Kim-Ung Ling, Siyu Pu and The-Thien Tran

Int. J. Mol. Sci. 2024, 25(12), 6369; https://doi.org/10.3390/ijms25126369 - 8 Jun 2024

Cited by 1 | Viewed by 1127

Abstract

A high alkaline pH was previously demonstrated to enhance the extraction yield of brewer’s spent grains (BSG) proteins. The effects of extraction pH beyond the extraction yield, however, has not been investigated before. The present work examined the effects of extraction pH (pH [...] Read more.

A high alkaline pH was previously demonstrated to enhance the extraction yield of brewer’s spent grains (BSG) proteins. The effects of extraction pH beyond the extraction yield, however, has not been investigated before. The present work examined the effects of extraction pH (pH 8–12) on BSG proteins’ (1) amino acid compositions, (2) secondary structures, (3) thermal stability, and (4) functionalities (i.e., water/oil holding capacity, emulsifying, and foaming properties). The ideal extraction temperature (60 °C) and BSG-to-solvent ratio (1:20 w/v) for maximizing the extraction yield were first determined to set the conditions for the pH effect study. The results showed that a higher extraction pH led to more balanced compositions between hydrophilic and hydrophobic amino acids and higher proportions of random coils structures indicating increased protein unfolding. This led to superior emulsifying properties of the extracted proteins with more than twofold improvement between pH 8 and a pH larger than 10. The extraction pH, nevertheless, had minimal impact on the water/oil holding capacity, foaming properties, and thermal denaturation propensity of the proteins. The present work demonstrated that a high alkaline pH at pH 11–12 was indeed ideal for both maximizing the extraction yield (37–46 wt.%) and proteins’ functionalities. Full article

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18 pages, 17051 KiB

Open AccessArticle

Proanthocyanidins Ameliorate LPS-Inhibited Osteogenesis of PDLSCs by Restoring Lysine Lactylation

by Yaxin Wu, Xiangyao Wang, Yuxiao Zhang, Zhihao Wen, Yuanyuan Li, Kehan Zhang, Nuerlan Gosar, Qilin Li, Jing Mao and Shiqiang Gong

Int. J. Mol. Sci. 2024, 25(5), 2947; https://doi.org/10.3390/ijms25052947 - 3 Mar 2024

Cited by 2 | Viewed by 1845

Abstract

Periodontitis is a bacteria-induced inflammatory disease characterized by the progressive destruction of periodontal supporting tissues. Periodontal ligament stem cells (PDLSCs) are capable of differentiating into osteoblasts, which is an important stem cell source for endogenous periodontal tissue regeneration. Lysine lactylation (Kla) is a [...] Read more.

Periodontitis is a bacteria-induced inflammatory disease characterized by the progressive destruction of periodontal supporting tissues. Periodontal ligament stem cells (PDLSCs) are capable of differentiating into osteoblasts, which is an important stem cell source for endogenous periodontal tissue regeneration. Lysine lactylation (Kla) is a novel post-translational modification of proteins that is recently thought to be associated with osteogenic differentiation. Here, we found that lactylation levels are reduced both in the periodontal tissue of rats with periodontitis and lipopolysaccharide (LPS)-stimulated human PDLSCs. Proanthocyanidins were able to promote the osteogenesis of inflamed PDLSCs by restoring lactylation levels. Mechanistically, proanthocyanidins increased lactate production and restored the lactylation levels of PDLSCs, which recovered osteogenesis of inflamed PDLSCs via the Wnt/β-catenin pathway. These results provide evidence on how epigenetic regulation by pharmacological agents influence the osteogenic phenotype of stem cells and the process of periodontal tissue repair. Our current study highlights the valuable potential of natural product proanthocyanidins in the regenerative engineering of periodontal tissues. Full article

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26 pages, 2591 KiB

Open AccessReview

Fluorescence-Based Protein Stability Monitoring—A Review

by Negin Gooran and Kari Kopra

Int. J. Mol. Sci. 2024, 25(3), 1764; https://doi.org/10.3390/ijms25031764 - 1 Feb 2024

Cited by 6 | Viewed by 5556

Abstract

Proteins are large biomolecules with a specific structure that is composed of one or more long amino acid chains. Correct protein structures are directly linked to their correct function, and many environmental factors can have either positive or negative effects on this structure. [...] Read more.

Proteins are large biomolecules with a specific structure that is composed of one or more long amino acid chains. Correct protein structures are directly linked to their correct function, and many environmental factors can have either positive or negative effects on this structure. Thus, there is a clear need for methods enabling the study of proteins, their correct folding, and components affecting protein stability. There is a significant number of label-free methods to study protein stability. In this review, we provide a general overview of these methods, but the main focus is on fluorescence-based low-instrument and -expertise-demand techniques. Different aspects related to thermal shift assays (TSAs), also called differential scanning fluorimetry (DSF) or ThermoFluor, are introduced and compared to isothermal chemical denaturation (ICD). Finally, we discuss the challenges and comparative aspects related to these methods, as well as future opportunities and assay development directions. Full article

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17 pages, 1507 KiB

Open AccessArticle

Preparative and Catalytic Properties of Mo^VI Mononuclear and Metallosupramolecular Coordination Assemblies Bearing Hydrazonato Ligands

by Mirna Mandarić, Edi Topić, Dominique Agustin, Jana Pisk and Višnja Vrdoljak

Int. J. Mol. Sci. 2024, 25(3), 1503; https://doi.org/10.3390/ijms25031503 - 25 Jan 2024

Cited by 1 | Viewed by 1051

Abstract

A series of polynuclear, dinuclear, and mononuclear Mo(VI) complexes were synthesized with the hydrazonato ligands derived from 5-methoxysalicylaldehyde and the corresponding hydrazides (isonicotinic hydrazide (H₂L¹), nicotinic hydrazide (H₂L²), 2-aminobenzhydrazide (H₂L³), or [...] Read more.

A series of polynuclear, dinuclear, and mononuclear Mo(VI) complexes were synthesized with the hydrazonato ligands derived from 5-methoxysalicylaldehyde and the corresponding hydrazides (isonicotinic hydrazide (H₂L¹), nicotinic hydrazide (H₂L²), 2-aminobenzhydrazide (H₂L³), or 4-aminobenzhydrazide (H₂L⁴)). The metallosupramolecular compounds obtained from non-coordinating solvents, [MoO₂(L^1,2)]_n (1 and 2) and [MoO₂(L^3,4)]₂ (3 and 4), formed infinite structures and metallacycles, respectively. By blocking two coordination sites with cis-dioxo ligands, the molybdenum centers have three coordination sites occupied by the ONO donor atoms from the rigid hydrazone ligands and one by the N atom of pyridyl or amine-functionalized ligand subcomponents from the neighboring Mo building units. The reaction in methanol afforded the mononuclear analogs [MoO₂(L^1-4)(MeOH)] (1a–4a) with additional monodentate MeOH ligands. All isolated complexes were tested as catalysts for cyclooctene epoxidation using tert-butyl hydroperoxide (TBHP) as an oxidant in water. The impact of the structure and ligand lability on the catalytic efficiency in homogeneous cyclooctene epoxidation was elucidated based on theoretical considerations. Thus, dinuclear assemblies exhibited better catalytic activity than mononuclear or polynuclear complexes. Full article

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25 pages, 4415 KiB

Open AccessArticle

Functionalization of Bacterial Cellulose with the Antimicrobial Peptide KR-12 via Chimerical Cellulose-Binding Peptides

by Elizabeth M. van Zyl and Jeannine M. Coburn

Int. J. Mol. Sci. 2024, 25(3), 1462; https://doi.org/10.3390/ijms25031462 - 25 Jan 2024

Cited by 2 | Viewed by 1771

Abstract

Bacterial-derived cellulose (BC) has been studied as a promising material for biomedical applications, including wound care, due to its biocompatibility, water-holding capacity, liquid/gas permeability, and handleability properties. Although BC has been studied as a dressing material for cutaneous wounds, to date, BC inherently [...] Read more.

Bacterial-derived cellulose (BC) has been studied as a promising material for biomedical applications, including wound care, due to its biocompatibility, water-holding capacity, liquid/gas permeability, and handleability properties. Although BC has been studied as a dressing material for cutaneous wounds, to date, BC inherently lacks antibacterial properties. The current research utilizes bifunctional chimeric peptides containing carbohydrate binding peptides (CBP; either a short version or a long version) and an antimicrobial peptide (AMP), KR-12. The secondary structure of the chimeric peptides was evaluated and confirmed that the α-helix structure of KR-12 was retained for both chimeric peptides evaluated (Long-CBP-KR12 and Short-CBP-KR12). Chimeric peptides and their individual components were assessed for cytotoxicity, where only higher concentrations of Short-CBP and longer timepoints of Short-CBP-KR12 exposure exhibited negative effects on metabolic activity, which was attributed to solubility issues. All KR-12-containing peptides exhibited antibacterial activity in solution against Escherichia coli (E. coli) and Pseudomonas aeruginosa (P. aeruginosa). The lipopolysaccharide (LPS) binding capability of the peptides was evaluated and the Short-CBP-KR12 peptide exhibited enhanced LPS-binding capabilities compared to KR-12 alone. Both chimeric peptides were able to bind to BC and were observed to be retained on the surface over a 7-day period. All functionalized materials exhibited no adverse effects on the metabolic activity of both normal human dermal fibroblasts (NHDFs) and human epidermal keratinocyte (HaCaT) epithelial cells. Additionally, the BC tethered chimeric peptides exhibited antibacterial activity against E. coli. Overall, this research outlines the design and evaluation of chimeric CBP-KR12 peptides for developing antimicrobial BC membranes with potential applications in wound care. Full article

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15 pages, 1409 KiB

Open AccessArticle

Reliable Dimerization Energies for Modeling of Supramolecular Junctions

by Jiří Czernek and Jiří Brus

Int. J. Mol. Sci. 2024, 25(1), 602; https://doi.org/10.3390/ijms25010602 - 2 Jan 2024

Cited by 2 | Viewed by 1344

Abstract

Accurate estimates of intermolecular interaction energy, ΔE, are crucial for modeling the properties of organic electronic materials and many other systems. For a diverse set of 50 dimers comprising up to 50 atoms (Set50-50, with 7 of its members being models [...] Read more.

Accurate estimates of intermolecular interaction energy, ΔE, are crucial for modeling the properties of organic electronic materials and many other systems. For a diverse set of 50 dimers comprising up to 50 atoms (Set50-50, with 7 of its members being models of single-stacking junctions), benchmark ΔE data were compiled. They were obtained by the focal-point strategy, which involves computations using the canonical variant of the coupled cluster theory with singles, doubles, and perturbative triples [CCSD(T)] performed while applying a large basis set, along with extrapolations of the respective energy components to the complete basis set (CBS) limit. The resulting ΔE data were used to gauge the performance for the Set50-50 of several density-functional theory (DFT)-based approaches, and of one of the localized variants of the CCSD(T) method. This evaluation revealed that (1) the proposed “silver standard” approach, which employs the localized CCSD(T) method and CBS extrapolations, can be expected to provide accuracy better than two kJ/mol for absolute values of ΔE, and (2) from among the DFT techniques, computationally by far the cheapest approach (termed “ωB97X-3c/vDZP” by its authors) performed remarkably well. These findings are directly applicable in cost-effective yet reliable searches of the potential energy surfaces of noncovalent complexes. Full article

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2023

Jump to: 2024, 2022, 2021

15 pages, 4799 KiB

Open AccessArticle

Computational Investigations on Reaction Mechanisms of the Covalent Inhibitors Ponatinib and Analogs Targeting the Extracellular Signal-Regulated Kinases

by Yafeng Tian, Mi Zhang, Panpan Heng, Hua Hou and Baoshan Wang

Int. J. Mol. Sci. 2023, 24(20), 15223; https://doi.org/10.3390/ijms242015223 - 16 Oct 2023

Cited by 1 | Viewed by 1200

Abstract

As an important cancer therapeutic target, extracellular signal-regulated kinases (ERK) are involved in triggering various cellular responses in tumors. Regulation of the ERK signaling pathway by the small molecular inhibitors is highly desired for the sake of cancer therapy. In contrast to the [...] Read more.

As an important cancer therapeutic target, extracellular signal-regulated kinases (ERK) are involved in triggering various cellular responses in tumors. Regulation of the ERK signaling pathway by the small molecular inhibitors is highly desired for the sake of cancer therapy. In contrast to the routine inhibitors targeting ERKs through long-range non-bonding interactions, Ponatinib, a covalent inhibitor to ERK2 with a macrocyclic structure characterized by the α,β-C=C unsaturated ketone, can form the stable -C(S)-C(H)-type complex via the four-center barrier due to the nucleophilic addition reaction of the thiol group of the Cys166 residue of ERK2 with the C=C double bond of Ponatinib with reaction free-energy barrier of 47.2 kcal/mol. Reaction mechanisms for the covalent binding were calculated using QM/MM methods and molecular dynamics simulations. The interaction modes and the corresponding binding free energies were obtained for the non-covalent and covalent complexation. The binding free energies of the non-covalent and covalent inhibitions are 14.8 kcal/mol and 33.4 kcal/mol, respectively. The mechanistic study stimulated a rational design on the modified Ponatinib structure by substituting the C=C bond with the C=N bond. It was demonstrated that the new compound exhibits better inhibition activity toward ERK2 in term of both thermodynamic and kinetic aspects through the covalent binding with a lower reaction free-energy barrier of 23.1 kcal/mol. The present theoretical work sheds new light on the development of the covalent inhibitors for the regulation of ERKs. Full article

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20 pages, 3342 KiB

Open AccessArticle

Cryopreservation Induces Acetylation of Metabolism-Related Proteins in Boar Sperm

by Malik Ahsan Ali, Ziyue Qin, Shan Dou, Anqi Huang, Yihan Wang, Xiang Yuan, Yan Zhang, Qingyong Ni, Rameesha Azmat and Changjun Zeng

Int. J. Mol. Sci. 2023, 24(13), 10983; https://doi.org/10.3390/ijms241310983 - 1 Jul 2023

Cited by 7 | Viewed by 2209

Abstract

Cryodamage affects the normal physiological functions and survivability of boar sperm during cryopreservation. Lysine acetylation is thought to be an important regulatory mechanism in sperm functions. However, little is known about protein acetylation and its effects on cryotolerance or cryodamage in boar sperm. [...] Read more.

Cryodamage affects the normal physiological functions and survivability of boar sperm during cryopreservation. Lysine acetylation is thought to be an important regulatory mechanism in sperm functions. However, little is known about protein acetylation and its effects on cryotolerance or cryodamage in boar sperm. In this study, the characterization and protein acetylation dynamics of boar sperm during cryopreservation were determined using liquid chromatography–mass spectrometry (LC-MS). A total of 1440 proteins were identified out of 4705 modified proteins, and 2764 quantifiable sites were elucidated. Among the differentially modified sites, 1252 were found to be upregulated compared to 172 downregulated sites in fresh and frozen sperms. Gene ontology indicated that these differentially modified proteins are involved in metabolic processes and catalytic and antioxidant activities, which are involved in pyruvate metabolism, phosphorylation and lysine degradation. In addition, the present study demonstrated that the mRNA and protein expressions of SIRT5, IDH2, MDH2 and LDHC, associated with sperm quality parameters, are downregulated after cryopreservation. In conclusion, cryopreservation induces the acetylation and deacetylation of energy metabolism-related proteins, which may contribute to the post-thawed boar sperm quality parameters. Full article

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12 pages, 2376 KiB

Open AccessArticle

Polylactic-Containing Hyperbranched Polymers through the CuAAC Polymerization of Aromatic AB₂ Monomers

by Aurora Pacini, Andrea Nitti, Marcello Vitale and Dario Pasini

Int. J. Mol. Sci. 2023, 24(8), 7620; https://doi.org/10.3390/ijms24087620 - 21 Apr 2023

Cited by 7 | Viewed by 1962

Abstract

We report on the synthesis and characterization of a novel class of hyperbranched polymers, in which a copper(I)-catalyzed alkyne azide cycloaddition (CuAAC) reaction (the prototypical “click” reaction) is used as the polymerization step. The AB₂ monomers bear two azide functionalities and one [...] Read more.

We report on the synthesis and characterization of a novel class of hyperbranched polymers, in which a copper(I)-catalyzed alkyne azide cycloaddition (CuAAC) reaction (the prototypical “click” reaction) is used as the polymerization step. The AB₂ monomers bear two azide functionalities and one alkyne functionality, which have been installed onto a 1,3,5 trisubstituted benzene aromatic skeleton. This synthesis has been optimized in terms of its purification strategies, with an eye on its scalability for the potential industrial applications of hyperbranched polymers as viscosity modifiers. By taking advantage of the modularity of the synthesis, we have been able to install short polylactic acid fragments as the spacing units between the complementary reactive azide and alkyne functionalities, aiming to introduce elements of biodegradability into the final products. The hyperbranched polymers have been obtained with good molecular weights and degrees of polymerization and branching, testifying to the effectiveness of the synthetic design. Simple experiments on glass surfaces have highlighted the possibility of conducting the polymerizations and the formation of the hyperbranched polymers directly in thin films at room temperature. Full article

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21 pages, 7339 KiB

Open AccessArticle

Selectively Modified Lactose and N-Acetyllactosamine Analogs at Three Key Positions to Afford Effective Galectin-3 Ligands

by Shuay Abdullayev, Priyanka Kadav, Purnima Bandyopadhyay, Francisco Javier Medrano, Gabriel A. Rabinovich, Tarun K. Dam, Antonio Romero and René Roy

Int. J. Mol. Sci. 2023, 24(4), 3718; https://doi.org/10.3390/ijms24043718 - 13 Feb 2023

Cited by 2 | Viewed by 2522

Abstract

Galectins constitute a family of galactose-binding lectins overly expressed in the tumor microenvironment as well as in innate and adaptive immune cells, in inflammatory diseases. Lactose ((β-D-galactopyranosyl)-(1→4)-β-D-glucopyranose, Lac) and N-Acetyllactosamine (2-acetamido-2-deoxy-4-O-β-D-galactopyranosyl-D-glucopyranose, LacNAc) have been widely exploited as ligands for a [...] Read more.

Galectins constitute a family of galactose-binding lectins overly expressed in the tumor microenvironment as well as in innate and adaptive immune cells, in inflammatory diseases. Lactose ((β-D-galactopyranosyl)-(1→4)-β-D-glucopyranose, Lac) and N-Acetyllactosamine (2-acetamido-2-deoxy-4-O-β-D-galactopyranosyl-D-glucopyranose, LacNAc) have been widely exploited as ligands for a wide range of galectins, sometimes with modest selectivity. Even though several chemical modifications at single positions of the sugar rings have been applied to these ligands, very few examples combined the simultaneous modifications at key positions known to increase both affinity and selectivity. We report herein combined modifications at the anomeric position, C-2, and O-3′ of each of the two sugars, resulting in a 3′-O-sulfated LacNAc analog having a Kd of 14.7 µM against human Gal-3 as measured by isothermal titration calorimetry (ITC). This represents a six-fold increase in affinity when compared to methyl β-D-lactoside having a Kd of 91 µM. The three best compounds contained sulfate groups at the O-3′ position of the galactoside moieties, which were perfectly in line with the observed highly cationic character of the human Gal-3 binding site shown by the co-crystal of one of the best candidates of the LacNAc series. Full article

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17 pages, 2182 KiB

Open AccessArticle

NMR Study on Laccase Polymerization of Kraft Lignin Using Different Enzymes Source

by David Ibarra, Luisa García-Fuentevilla, Gabriela Domínguez, Raquel Martín-Sampedro, Manuel Hernández, María E. Arias, José I. Santos and María E. Eugenio

Int. J. Mol. Sci. 2023, 24(3), 2359; https://doi.org/10.3390/ijms24032359 - 25 Jan 2023

Cited by 7 | Viewed by 2741

Abstract

The usage of laccases is a sustainable and environmentally friendly approach to modifying the Kraft lignin structure for use in certain applications. However, the inherent structure of Kraft lignin, as well as that resulting from laccase modification, still presents challenges for fundamental comprehension [...] Read more.

The usage of laccases is a sustainable and environmentally friendly approach to modifying the Kraft lignin structure for use in certain applications. However, the inherent structure of Kraft lignin, as well as that resulting from laccase modification, still presents challenges for fundamental comprehension and successful lignin valorization. In this study, bacterial and fungal laccases were employed to modify eucalypt Kraft lignin. To evaluate the type and range of the chemical and structural changes of laccase-treated lignins, different NMR techniques, including solution ¹H and 2D NMR (heteronuclear single quantum correlation (HSQC)), and solid-state ¹³C NMR, were applied. Size exclusion chromatography and infrared spectroscopy were also used. Interestingly, HSQC analysis showed substantial changes in the oxygenated aliphatic region of lignins, showing an almost complete absence of signals corresponding to side-chains due to laccase depolymerization. Simultaneously, a significant loss of aromatic signals was observed by HSQC and ¹H NMR, which was attributed to a deprotonation of the lignin benzenic rings due to polymerization/condensation by laccase reactions. Then, condensed structures, such as α-5′, 5-5′, and 4-O-5′, were detected by HSQC and ¹³C NMR, supporting the increment in molecular weight, as well as the phenolic content reduction determined in lignins. Full article

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2022

Jump to: 2024, 2023, 2021

15 pages, 2335 KiB

Open AccessArticle

Employing Engineered Enolase Promoter for Efficient Expression of Thermomyces lanuginosus Lipase in Yarrowia lipolytica via a Self-Excisable Vector

by Liangcheng Jiao, Wenjuan Li, Yunchong Li, Qinghua Zhou, Mengqin Zhu, Guowei Zhao, Houjin Zhang and Yunjun Yan

Int. J. Mol. Sci. 2023, 24(1), 719; https://doi.org/10.3390/ijms24010719 - 31 Dec 2022

Cited by 8 | Viewed by 2315

Abstract

Yarrowia lipolytica is progressively being employed as a workhouse for recombinant protein expression. Here, we expanded the molecular toolbox by engineering the enolase promoter (pENO) and developed a new self-excisable vector, and based on this, a combined strategy was employed to enhance the [...] Read more.

Yarrowia lipolytica is progressively being employed as a workhouse for recombinant protein expression. Here, we expanded the molecular toolbox by engineering the enolase promoter (pENO) and developed a new self-excisable vector, and based on this, a combined strategy was employed to enhance the expression of Thermomyces lanuginosus lipase (TLL) in Y. lipolytica. The strength of 11 truncated enolase promoters of different length was first identified using eGFP as a reporter. Seven of the truncated promoters were selected to examine their ability for driving TLL expression. Then, a series of enolase promoters with higher activities were developed by upstream fusing of different copies of UAS1B, and the recombinant strain Po1f/hp16e₁₀₀-tll harboring the optimal promoter hp16e₁₀₀ obtained a TLL activity of 447 U/mL. Additionally, a new self-excisable vector was developed based on a Cre/loxP recombination system, which achieved efficient markerless integration in Y. lipolytica. Subsequently, strains harboring one to four copies of the tll gene were constructed using this tool, with the three-copy strain Po1f/3tll showing the highest activity of 579 U/mL. The activity of Po1f/3tll was then increased to 720 U/mL by optimizing the shaking flask fermentation parameters. Moreover, the folding-related proteins Hac1, Pdi, and Kar2 were employed to further enhance TLL expression, and the TLL activity of the optimal recombinant strain Po1f/3tll-hac1-pdi-kar2 reached 1197 U/mL. By using this combined strategy, TLL activity was enhanced by approximately 39.9-fold compared to the initial strain. Thus, the new vector and the combined strategy could be a useful tool to engineer Y. lipolytica for high-level expression of heterologous protein. Full article

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11 pages, 1948 KiB

Open AccessArticle

Effects of Biochar and Nitrogen Application on Rice Biomass Saccharification, Bioethanol Yield and Cell Wall Polymers Features

by Izhar Ali, Muhammad Adnan, Anas Iqbal, Saif Ullah, Muhammad Rafiullah Khan, Pengli Yuan, Hua Zhang, Jamal Nasar, Minghua Gu and Ligeng Jiang

Int. J. Mol. Sci. 2022, 23(21), 13635; https://doi.org/10.3390/ijms232113635 - 7 Nov 2022

Cited by 3 | Viewed by 1777

Abstract

Rice is a major food crop that produces abundant biomass wastes for biofuels. To improve rice biomass and yield, nitrogen (N) fertilizer is excessively used, which is not eco-friendly. Alternatively, biochar (B) application is favored to improve rice biomass and yield under low [...] Read more.

Rice is a major food crop that produces abundant biomass wastes for biofuels. To improve rice biomass and yield, nitrogen (N) fertilizer is excessively used, which is not eco-friendly. Alternatively, biochar (B) application is favored to improve rice biomass and yield under low chemical fertilizers. To minimize the reliance on N fertilizer, we applied four B levels (0, 10, 20, and 30 t B ha⁻¹) combined with two N rates (low-135 and high-180 kg ha⁻¹) to improve biomass yield. Results showed that compared to control, the combined B at 20–30 t ha⁻¹ with low N application significantly improved plant dry matter and arabinose (Ara%), while decreasing cellulose crystallinity (Crl), degree of polymerization (DP), and the ratio of xylose/arabinose (Xyl/Ara), resulting in high hexoses (% cellulose) and bioethanol yield (% dry matter). We concluded that B coupled with N can alter cell wall polymer features in paddy rice resulting in high biomass saccharification and bioethanol production. Full article

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15 pages, 2715 KiB

Open AccessArticle

Reaction of Corroles with Sarcosine and Paraformaldehyde: A New Facet of Corrole Chemistry

by Joana F. B. Barata, Paula S. S. Lacerda, Maria Graça P. M. S. Neves, José A. S. Cavaleiro, Catarina I. V. Ramos, Augusto C. Tomé, Paulo E. Abreu and Alberto A. C. C. Pais

Int. J. Mol. Sci. 2022, 23(21), 13581; https://doi.org/10.3390/ijms232113581 - 5 Nov 2022

Viewed by 1708

Abstract

Details on the unexpected formation of two new (dimethylamino)methyl corrole isomers from the reaction of 5,10,15-tris(pentafluorophenyl)corrolatogallium(III) with sarcosine and paraformaldehyde are presented. Semi-empirical calculations on possible mechanism pathways seem to indicate that the new compounds are probably formed through a Mannich-type reaction. The [...] Read more.

Details on the unexpected formation of two new (dimethylamino)methyl corrole isomers from the reaction of 5,10,15-tris(pentafluorophenyl)corrolatogallium(III) with sarcosine and paraformaldehyde are presented. Semi-empirical calculations on possible mechanism pathways seem to indicate that the new compounds are probably formed through a Mannich-type reaction. The extension of the protocol to the free-base 5,10,15-tris(pentafluorophenyl)corrole afforded an unexpected new seven-membered ring corrole derivative, confirming the peculiar behavior of corroles towards known reactions when compared to the well-behaved porphyrin counterparts. Full article

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12 pages, 2256 KiB

Open AccessArticle

In Situ Growth of Nanosilver on Fabric for Flexible Stretchable Electrodes

by Qingwei Liao, Yuxiang Yin, Jingxin Zhang, Wei Si, Wei Hou and Lei Qin

Int. J. Mol. Sci. 2022, 23(21), 13236; https://doi.org/10.3390/ijms232113236 - 31 Oct 2022

Cited by 7 | Viewed by 2037

Abstract

Flexible sensing can disruptively change the physical form of traditional electronic devices to achieve flexibility in information acquisition, processing, transmission, display, and even energy, and it is a core technology for a new generation of the industrial internet. Fabric is naturally flexible and [...] Read more.

Flexible sensing can disruptively change the physical form of traditional electronic devices to achieve flexibility in information acquisition, processing, transmission, display, and even energy, and it is a core technology for a new generation of the industrial internet. Fabric is naturally flexible and stretchable, and its knitted ability makes it flexibility and stretchability even more adjustable. However, fabric needs to be electrically conductive to be used for flexible sensing, which allows it to carry a variety of circuits. The dip-coating technique is a common method for preparing conductive fabrics, which are made conductive by attaching conductive fillers to the fabrics. However, the adhesion of the conductive fillers on the surface of such conductive fabrics is weak, and the conductive property will decay rapidly because the conductive filler falls off after repeated stretching, limiting the lifespan of flexible electronic devices based on conductive fabric. We chose multifunctional nanosilver as a conductive filler, and we increased the adhesion of nanosilver to fabric fiber by making nanosilver grow in situ and cover the fiber, so as to obtain conductive fabric with good conductivity. This conductive fabric has a minimum square resistance of 9 Ω/sq and has better electrical conductivity and more stable electrical properties than the conductive fabric prepared using the dip-coating process, and its square resistance did not increase significantlyafter 60 stretches. Full article

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11 pages, 1180 KiB

Open AccessArticle

Chiral Discrimination Mechanisms by Silylated-Acetylated Cyclodextrins: Superficial Interactions vs. Inclusion

by Federica Balzano, Gloria Uccello-Barretta, Giuseppe Sicoli, Letizia Vanni, Alessandra Recchimurzo and Federica Aiello

Int. J. Mol. Sci. 2022, 23(21), 13169; https://doi.org/10.3390/ijms232113169 - 29 Oct 2022

Cited by 3 | Viewed by 1720

Abstract

Cyclodextrin derivatives constitute a powerful class of auxiliary agents for the discrimination of apolar chiral substrates. Both host–guest inclusion phenomena and interactions with the derivatizing groups located on the surface of the macrocycle could drive the enantiodiscrimination; thus, it is important to understand [...] Read more.

Cyclodextrin derivatives constitute a powerful class of auxiliary agents for the discrimination of apolar chiral substrates. Both host–guest inclusion phenomena and interactions with the derivatizing groups located on the surface of the macrocycle could drive the enantiodiscrimination; thus, it is important to understand the role that these processes play in the rational design of new chiral selectors. The purpose of this study is to compare via nuclear magnetic resonance (NMR) spectroscopy the efficiency of silylated-acetylated α-, β-, and γ-cyclodextrins in the chiral discrimination of 1,1,1,3,3-pentafluoro-2-(fluoromethoxy)-3-methoxypropane (compound B) and methyl 2-chloropropionate (MCP). NMR DOSY (Diffusion Ordered SpectroscopY) experiments were conducted for the determination of the bound molar fractions and the association constants, whereas ROESY (Rotating-frame Overhauser Enhancement SpectroscopY) measurements provided information on the hosts’ conformation and on the interaction phenomena with the guests. Compound B, endowed with fluorinated moieties, is not deeply included due to attractive Si-F interactions occurring at the external surface of the cyclodextrins. Therefore, a low selectivity toward the size of cyclodextrin cavity is found. By contrast, enantiodiscrimination of MCP relies on the optimal fitting between the size of the guest and that of the cyclodextrin cavity. Full article

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16 pages, 3244 KiB

Open AccessArticle

Aphid BCR4 Structure and Activity Uncover a New Defensin Peptide Superfamily

by Karine Loth, Nicolas Parisot, Françoise Paquet, Hugo Terrasson, Catherine Sivignon, Isabelle Rahioui, Mélanie Ribeiro Lopes, Karen Gaget, Gabrielle Duport, Agnès F. Delmas, Vincent Aucagne, Abdelaziz Heddi, Federica Calevro and Pedro da Silva

Int. J. Mol. Sci. 2022, 23(20), 12480; https://doi.org/10.3390/ijms232012480 - 18 Oct 2022

Cited by 4 | Viewed by 2400

Abstract

Aphids (Hemiptera: Aphidoidea) are among the most detrimental insects for agricultural plants, and their management is a great challenge in agronomical research. A new class of proteins, called Bacteriocyte-specific Cysteine-Rich (BCR) peptides, provides an alternative to chemical insecticides for pest control. BCRs were [...] Read more.

Aphids (Hemiptera: Aphidoidea) are among the most detrimental insects for agricultural plants, and their management is a great challenge in agronomical research. A new class of proteins, called Bacteriocyte-specific Cysteine-Rich (BCR) peptides, provides an alternative to chemical insecticides for pest control. BCRs were initially identified in the pea aphid Acyrthosiphon pisum. They are small disulfide bond-rich proteins expressed exclusively in aphid bacteriocytes, the insect cells that host intracellular symbiotic bacteria. Here, we show that one of the A. pisum BCRs, BCR4, displays prominent insecticidal activity against the pea aphid, impairing insect survival and nymphal growth, providing evidence for its potential use as a new biopesticide. Our comparative genomics and phylogenetic analyses indicate that BCRs are restricted to the aphid lineage. The 3D structure of BCR4 reveals that this peptide belongs to an as-yet-unknown structural class of peptides and defines a new superfamily of defensins. Full article

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11 pages, 1107 KiB

Open AccessArticle

First Report on the Streptococcus gallolyticus (S. bovis Biotype I) DSM 13808 Exopolysaccharide Structure

by Anna Maciejewska, Czeslaw Lugowski and Jolanta Lukasiewicz

Int. J. Mol. Sci. 2022, 23(19), 11797; https://doi.org/10.3390/ijms231911797 - 5 Oct 2022

Cited by 2 | Viewed by 2255

Abstract

Streptococcus gallolyticus subspecies gallolyticus, known as Streptococcus bovis biotype I, is a facultative pathogen causing bacteraemia, infective endocarditis and sepsis that has been linked with colorectal cancer (CRC), but this correlation is still unclear. Bacterial surface structures, such as the major sugar [...] Read more.

Streptococcus gallolyticus subspecies gallolyticus, known as Streptococcus bovis biotype I, is a facultative pathogen causing bacteraemia, infective endocarditis and sepsis that has been linked with colorectal cancer (CRC), but this correlation is still unclear. Bacterial surface structures, such as the major sugar antigens exposed to the outside of the microorganism, are potential virulence factors. One of the primary sugar antigens loosely attached to the cell surface is the biofilm component, exopolysaccharide (EPS). EPSs of S. bovis are poorly characterized molecules. Until now, only one S. macedonicus Sc136 EPS structure was known to the entire S. bovis group. The S. gallolyticus DSM 13808 EPS was investigated by chemical analysis, mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy. The hexasaccharide repeating unit of the EPS, containing four Glc, two Rha residues and one phosphate group, has been described “ →6)-α-d-Glcp-(1→3)-β-l-Rhap-(1→4)-β-d-Glcp-(1→3)-[β-d-Glcp-(1→2)]-α-l-Rhap-(1→2)-α-d-Glcp-(1→P→”. Full article

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13 pages, 2951 KiB

Open AccessArticle

Sunscreen Ingredient Octocrylene’s Potency to Disrupt Vitamin D Synthesis

by Sayed Aliul Hasan Abdi, Amena Ali, Shabihul Fatma Sayed, Sumathi Nagarajan, Abutahir, Prawez Alam and Abuzer Ali

Int. J. Mol. Sci. 2022, 23(17), 10154; https://doi.org/10.3390/ijms231710154 - 5 Sep 2022

Cited by 7 | Viewed by 3789

Abstract

Octocrylene is a widely used ingredient in sunscreen products, and it has been observed that the use of sunscreen has been increasing over the last few decades. In this paper, we investigated the way in which sunscreen’s ingredient octocrylene may disrupt normal vitamin [...] Read more.

Octocrylene is a widely used ingredient in sunscreen products, and it has been observed that the use of sunscreen has been increasing over the last few decades. In this paper, we investigated the way in which sunscreen’s ingredient octocrylene may disrupt normal vitamin D synthesis pathway, resulting in an imbalance in vitamin D levels in the body. The key techniques used for this insilico investigation were molecular docking, molecular dynamic (MD) simulation, and MMPBSA-based assessment. Vitamin D abnormalities have become very common in human health. Unknown exposure to chemicals may be one of the important risk factors. In molecular docking analysis, octocrylene exhibited a binding energy of −11.52 kcal/mol with vitamin D binding protein (1KXP) and −11.71 for the calcitriol native ligand. Octocrylene had a binding potency of −11.152 kcal/mol with the vitamin D receptor (1DB1), and calcitriol had a binding potency of −8.73 kcal/mol. In addition, octocrylene has shown binding energy of −8.96 kcal/mol with CYP2R1, and the calcitriol binding energy was −10.36 kcal/mol. Regarding stability, the root-mean-square deviation (RMSD), the root-mean-square fluctuation (RMSF), the radius of gyration, hydrogen bonding, and the solvent-accessible surface area (SASA) exhibited that octocrylene has a stable binding pattern similar to calcitriol. These findings revealed that incessant exposure to octocrylene may disrupt normal vitamin D synthesis. Full article

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10 pages, 260 KiB

Open AccessArticle

The Detectability of the Viral RNA in Blood and Cerebrospinal Fluid of Patients with Tick-Borne Encephalitis

by Sambor Grygorczuk, Justyna Dunaj-Małyszko, Piotr Czupryna, Artur Sulik, Kacper Toczyłowski, Agnieszka Siemieniako-Werszko, Agnieszka Żebrowska, Sławomir Pancewicz and Anna Moniuszko-Malinowska

Int. J. Mol. Sci. 2022, 23(16), 9332; https://doi.org/10.3390/ijms23169332 - 19 Aug 2022

Cited by 8 | Viewed by 1784

Abstract

Background: The detection rate of viral RNA in tick-borne encephalitis (TBE) is low and variable between studies, and its diagnostic/prognostic potential is not well defined. We attempted to detect RNA of TBE virus (TBEV) in body fluids of TBE patients. Methods: We studied [...] Read more.

Background: The detection rate of viral RNA in tick-borne encephalitis (TBE) is low and variable between studies, and its diagnostic/prognostic potential is not well defined. We attempted to detect RNA of TBE virus (TBEV) in body fluids of TBE patients. Methods: We studied 98 adults and 12 children with TBEV infection, stratified by the disease phase and presentation. EDTA blood and cerebrospinal fluid (CSF) samples were obtained upon hospital admission. RNA was extracted from freshly obtained plasma, concentrated leukocyte-enriched CSF, and whole blood samples, and real time PCR was performed with a Rotor-Gene Q thermocycler. Results: TBEV RNA was detected in (1) plasma of one (of the two studied) adult patients with an abortive infection, (2) plasma of two (of the two studied) adults in the peripheral phase of TBE, and (3) plasma and blood of an adult in the neurologic phase of TBE presenting as meningoencephalomyelitis. No CSF samples were TBEV RNA-positive. Conclusions: The detection of TBEV RNA in blood might be diagnostic in the peripheral phase of TBE. The lack of TBEV RNA in the CSF cellular fraction speaks against TBEV influx into the central nervous system with infiltrating leukocytes and is consistent with a relatively low intrathecal viral burden. Full article

20 pages, 27527 KiB

Open AccessReview

Cartilage Oligomeric Matrix Protein, Diseases, and Therapeutic Opportunities

by Jiarui Cui and Jiaming Zhang

Int. J. Mol. Sci. 2022, 23(16), 9253; https://doi.org/10.3390/ijms23169253 - 17 Aug 2022

Cited by 21 | Viewed by 6528

Abstract

Cartilage oligomeric matrix protein (COMP) is an extracellular matrix (ECM) glycoprotein that is critical for collagen assembly and ECM stability. Mutations of COMP cause endoplasmic reticulum stress and chondrocyte apoptosis, resulting in rare skeleton diseases. The bouquet-like structure of COMP allows it to [...] Read more.

Cartilage oligomeric matrix protein (COMP) is an extracellular matrix (ECM) glycoprotein that is critical for collagen assembly and ECM stability. Mutations of COMP cause endoplasmic reticulum stress and chondrocyte apoptosis, resulting in rare skeleton diseases. The bouquet-like structure of COMP allows it to act as a bridging molecule that regulates cellular phenotype and function. COMP is able to interact with many other ECM components and binds directly to a variety of cellular receptors and growth factors. The roles of COMP in other skeleton diseases, such as osteoarthritis, have been implied. As a well-established biochemical marker, COMP indicates cartilage turnover associated with destruction. Recent exciting achievements indicate its involvement in other diseases, such as malignancy, cardiovascular diseases, and tissue fibrosis. Here, we review the basic concepts of COMP and summarize its novel functions in the regulation of signaling events. These findings renew our understanding that COMP has a notable function in cell behavior and disease progression as a signaling regulator. Interestingly, COMP shows distinct functions in different diseases. Targeting COMP in malignancy may withdraw its beneficial effects on the vascular system and induce or aggravate cardiovascular diseases. COMP supplementation is a promising treatment for OA and aortic aneurysms while it may induce tissue fibrosis or cancer metastasis. Full article

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36 pages, 4865 KiB

Open AccessReview

Cellulose-Based Nanomaterials Advance Biomedicine: A Review

by Hani Nasser Abdelhamid and Aji P. Mathew

Int. J. Mol. Sci. 2022, 23(10), 5405; https://doi.org/10.3390/ijms23105405 - 12 May 2022

Cited by 66 | Viewed by 6374

Abstract

There are various biomaterials, but none fulfills all requirements. Cellulose biopolymers have advanced biomedicine to satisfy high market demand and circumvent many ecological concerns. This review aims to present an overview of cellulose knowledge and technical biomedical applications such as antibacterial agents, antifouling, [...] Read more.

There are various biomaterials, but none fulfills all requirements. Cellulose biopolymers have advanced biomedicine to satisfy high market demand and circumvent many ecological concerns. This review aims to present an overview of cellulose knowledge and technical biomedical applications such as antibacterial agents, antifouling, wound healing, drug delivery, tissue engineering, and bone regeneration. It includes an extensive bibliography of recent research findings from fundamental and applied investigations. Cellulose-based materials are tailorable to obtain suitable chemical, mechanical, and physical properties required for biomedical applications. The chemical structure of cellulose allows modifications and simple conjugation with several materials, including nanoparticles, without tedious efforts. They render the applications cheap, biocompatible, biodegradable, and easy to shape and process. Full article

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14 pages, 6078 KiB

Open AccessArticle

Structural Insights into Iron Ions Accumulation in Dps Nanocage

by Yury Chesnokov, Andrey Mozhaev, Roman Kamyshinsky, Alexander Gordienko and Liubov Dadinova

Int. J. Mol. Sci. 2022, 23(10), 5313; https://doi.org/10.3390/ijms23105313 - 10 May 2022

Cited by 5 | Viewed by 2359

Abstract

Dps (DNA-binding protein from starved cells) is well known for the structural protection of bacterial DNA by the formation of highly ordered intracellular assemblies under stress conditions. Moreover, this ferritin-like protein can perform fast oxidation of ferrous ions and subsequently accumulate clusters of [...] Read more.

Dps (DNA-binding protein from starved cells) is well known for the structural protection of bacterial DNA by the formation of highly ordered intracellular assemblies under stress conditions. Moreover, this ferritin-like protein can perform fast oxidation of ferrous ions and subsequently accumulate clusters of ferric ions in its nanocages, thus providing the bacterium with physical and chemical protection. Here, cryo-electron microscopy was used to study the accumulation of iron ions in the nanocage of a Dps protein from Escherichia coli. We demonstrate that Fe²⁺ concentration in the solution and incubation time have an insignificant effect on the volume and the morphology of iron minerals formed in Dps nanocages. However, an increase in the Fe²⁺ level leads to an increase in the proportion of larger clusters and the clusters themselves are composed of discrete ~1–1.5 nm subunits. Full article

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21 pages, 7562 KiB

Open AccessArticle

Microrheological Phenomenon and Mechanical Properties of High-Aspect-Ratio Microgroove Injection Moulding of Kaolin/PP Composites

by Yan Lou, Xiangwei Zhou, Dongyue Zhang and Fengyu Cheng

Int. J. Mol. Sci. 2022, 23(9), 4944; https://doi.org/10.3390/ijms23094944 - 29 Apr 2022

Cited by 3 | Viewed by 1677

Abstract

The microrheological phenomenon of kaolin-filled polypropylene (kaolin/PP) composites was investigated for the first time. The microviscosity of kaolin/PP composites was studied by changing the melt temperature and shear rate. Then, injection moulding experiments of rectangular microgrooves with different aspect ratios using kaolin/PP composites [...] Read more.

The microrheological phenomenon of kaolin-filled polypropylene (kaolin/PP) composites was investigated for the first time. The microviscosity of kaolin/PP composites was studied by changing the melt temperature and shear rate. Then, injection moulding experiments of rectangular microgrooves with different aspect ratios using kaolin/PP composites and mechanical property tests of the samples were carried out. The results showed that with increasing kaolin content, the microviscosity of the kaolin/PP composites gradually increases. The shear rate had the greatest influence on the microviscosity, and the kaolin content had the least influence. When the aspect ratio of rectangular microgrooves is small, with an increasing kaolin content, the microgroove filling rate increases, and the microstructured sample geometric shape replication effect is good; however, when the aspect ratio reaches 10:1, the microgroove filling rate decreases with an increasing kaolin content. The microstructured sample geometric shape replication effect is also poor, and size effects appear. Different factors control the microrheological morphology of composites with different aspect ratios, including the shear deformation and viscous flow of composites. The increase in kaolin content leads to a decrease in the friction coefficient and an increase in the wear resistance of the composites. We concluded that the best composite formulation for kaolin/PP composites in microinjection is the 7KL/PP composite with 7% kaolin. When the aspect ratio is 5:1, the reproduction of the microstructured sample geometry is the best, and the comprehensive mechanical properties of the sample are the best. Full article

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28 pages, 1775 KiB

Open AccessReview

Deep Eutectic Solvent as Green Solvent in Extraction of Biological Macromolecules: A Review

by Jordy Kim Ung Ling and Kunn Hadinoto

Int. J. Mol. Sci. 2022, 23(6), 3381; https://doi.org/10.3390/ijms23063381 - 21 Mar 2022

Cited by 92 | Viewed by 11950

Abstract

Greater awareness of environmental sustainability has driven many industries to transition from using synthetic organic solvents to greener solvents in their manufacturing. Deep eutectic solvents (DESs) have emerged as a highly promising category of green solvents with well-demonstrated and wide-ranging applications, including their [...] Read more.

Greater awareness of environmental sustainability has driven many industries to transition from using synthetic organic solvents to greener solvents in their manufacturing. Deep eutectic solvents (DESs) have emerged as a highly promising category of green solvents with well-demonstrated and wide-ranging applications, including their use as a solvent in extraction of small-molecule bioactive compounds for food and pharmaceutical applications. The use of DES as an extraction solvent of biological macromolecules, on the other hand, has not been as extensively studied. Thereby, the feasibility of employing DES for biomacromolecule extraction has not been well elucidated. To bridge this gap, this review provides an overview of DES with an emphasis on its unique physicochemical properties that make it an attractive green solvent (e.g., non-toxicity, biodegradability, ease of preparation, renewable, tailorable properties). Recent advances in DES extraction of three classes of biomacromolecules—i.e., proteins, carbohydrates, and lipids—were discussed and future research needs were identified. The importance of DES’s properties—particularly its viscosity, polarity, molar ratio of DES components, and water addition—on the DES extraction’s performance were discussed. Not unlike the findings from DES extraction of bioactive small molecules, DES extraction of biomacromolecules was concluded to be generally superior to extraction using synthetic organic solvents. Full article

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36 pages, 11232 KiB

Open AccessArticle

Interactions between Nanoclay, CTAB and Linear/Star Shaped Polymers

by Elżbieta Grządka, Ewelina Godek, Grzegorz Słowik, Agnieszka Kowalczuk, Jakub Matusiak and Urszula Maciołek

Int. J. Mol. Sci. 2022, 23(6), 3051; https://doi.org/10.3390/ijms23063051 - 11 Mar 2022

Cited by 3 | Viewed by 2885

Abstract

The influence of star-shaped (PAA-SS) and linear polyacrylic acid (PAA) with different molecular weights (high—PAA-HMW and low—PAA-LMW) on the structure of the adsorption layer, adsorption amount, electrokinetic and stabilizing properties of the PAA/CTAB/nanoclay suspensions was studied. The properties of the systems containing one [...] Read more.

The influence of star-shaped (PAA-SS) and linear polyacrylic acid (PAA) with different molecular weights (high—PAA-HMW and low—PAA-LMW) on the structure of the adsorption layer, adsorption amount, electrokinetic and stabilizing properties of the PAA/CTAB/nanoclay suspensions was studied. The properties of the systems containing one of these polymers, the cationic surfactant—hexadecyltrimethylammonium bromide (CTAB) and the surface-modified nanoclay (N-SM) were analyzed using the following techniques: BET, CHN, FT-IR, ED-XRF, XRD, HRTEM, UV-Vis, tensiometry and zeta potential measurements. It was proved that PAA could be used as an effective stabilizer of N-SM. Moreover, the addition of CTAB caused a significant increase in the stability of the systems but decreased the adsorption of PAA on the N-SM surface and changed the structure of the adsorption layers. The largest stability was observed in the PAA-HMW/CTAB system. The PAA polymers and PAA/CTAB complexes adsorbed, especially on the clay surface, influenced the primary distribution of the layered sheets but kept the same basal d-spacing. The adsorption of PAA and the PAA/CTAB complexes took place mainly at the plate edges and on the contact space between the sheets. The obtained results will be used for the preparation of the PAA/CTAB/nanoclay composite for water purification. Full article

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33 pages, 4045 KiB

Open AccessReview

Recent Advances in Copper-Based Solid Heterogeneous Catalysts for Azide–Alkyne Cycloaddition Reactions

by Noura Aflak, Hicham Ben El Ayouchia, Lahoucine Bahsis, Hafid Anane, Miguel Julve and Salah-Eddine Stiriba

Int. J. Mol. Sci. 2022, 23(4), 2383; https://doi.org/10.3390/ijms23042383 - 21 Feb 2022

Cited by 40 | Viewed by 5620

Abstract

The copper(I)-catalyzed azide−alkyne cycloaddition (CuAAC) reaction is considered to be the most representative ligation process within the context of the “click chemistry” concept. This CuAAC reaction, which yields compounds containing a 1,2,3-triazole core, has become relevant in the construction of biologically complex systems, [...] Read more.

The copper(I)-catalyzed azide−alkyne cycloaddition (CuAAC) reaction is considered to be the most representative ligation process within the context of the “click chemistry” concept. This CuAAC reaction, which yields compounds containing a 1,2,3-triazole core, has become relevant in the construction of biologically complex systems, bioconjugation strategies, and supramolecular and material sciences. Although many CuAAC reactions are performed under homogenous conditions, heterogenous copper-based catalytic systems are gaining exponential interest, relying on the easy removal, recovery, and reusability of catalytically copper species. The present review covers the most recently developed copper-containing heterogenous solid catalytic systems that use solid inorganic/organic hybrid supports, and which have been used in promoting CuAAC reactions. Due to the demand for 1,2,3-triazoles as non-classical bioisosteres and as framework-based drugs, the CuAAC reaction promoted by solid heterogenous catalysts has greatly improved the recovery and removal of copper species, usually by simple filtration. In so doing, the solving of the toxicity issue regarding copper particles in compounds of biological interest has been achieved. This protocol is also expected to produce a practical chemical process for accessing such compounds on an industrial scale. Full article

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14 pages, 2205 KiB

Open AccessArticle

Impact of Collagen Crosslinking on Dislocated Human Shoulder Capsules—Effect on Structural and Mechanical Properties

by Pauline Cornette, Ilhem Lilia Jaabar, Vincent Dupres, Jean-David Werthel, Francis Berenbaum, Xavier Houard, Jessem Landoulsi and Geoffroy Nourissat

Int. J. Mol. Sci. 2022, 23(4), 2297; https://doi.org/10.3390/ijms23042297 - 18 Feb 2022

Cited by 4 | Viewed by 1912

Abstract

Classical treatments of shoulder instability are associated with recurrence. To determine whether the modification of the capsule properties may be an alternative procedure, the effect of crosslinking treatment on the structure and mechanical properties of diseased human shoulder capsules was investigated. Joint capsules [...] Read more.

Classical treatments of shoulder instability are associated with recurrence. To determine whether the modification of the capsule properties may be an alternative procedure, the effect of crosslinking treatment on the structure and mechanical properties of diseased human shoulder capsules was investigated. Joint capsules harvested from patients during shoulder surgery (n = 5) were treated or not with UV and/or riboflavin (0.1%, 1.0% and 2.5%). The structure and the mechanical properties of the capsules were determined by atomic force microscopy. The effect of treatments on cell death was investigated. Collagen fibrils were well-aligned and adjacent to each other with a D-periodicity of 66.9 ± 3.2 nm and a diameter of 71.8 ± 15.4 nm in control untreated capsules. No effect of treatments was observed on the organization of the collagen fibrils nor on their intrinsic characteristics, including D-periodicity or their mean diameter. The treatments also did not induce cell death. In contrast, UV + 2.5% riboflavin induced capsule stiffness, as revealed by the increased Young’s modulus values (p < 0.0001 for each patient). Our results showed that the crosslinking procedure changed the biomechanics of diseased capsules, while keeping their structural organisation unchanged at the single fibril level. The UV/riboflavin crosslinking procedure may be a promising way to preserve the functions of collagen-based tissues and tune their elasticity for clinically relevant treatments. Full article

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23 pages, 5994 KiB

Open AccessReview

Cell Cycle-Dependent Transcription: The Cyclin Dependent Kinase Cdk1 Is a Direct Regulator of Basal Transcription Machineries

by Jorrit M. Enserink and Pierre Chymkowitch

Int. J. Mol. Sci. 2022, 23(3), 1293; https://doi.org/10.3390/ijms23031293 - 24 Jan 2022

Cited by 33 | Viewed by 5720

Abstract

The cyclin-dependent kinase Cdk1 is best known for its function as master regulator of the cell cycle. It phosphorylates several key proteins to control progression through the different phases of the cell cycle. However, studies conducted several decades ago with mammalian cells revealed [...] Read more.

The cyclin-dependent kinase Cdk1 is best known for its function as master regulator of the cell cycle. It phosphorylates several key proteins to control progression through the different phases of the cell cycle. However, studies conducted several decades ago with mammalian cells revealed that Cdk1 also directly regulates the basal transcription machinery, most notably RNA polymerase II. More recent studies in the budding yeast Saccharomyces cerevisiae have revisited this function of Cdk1 and also revealed that Cdk1 directly controls RNA polymerase III activity. These studies have also provided novel insight into the physiological relevance of this process. For instance, cell cycle-stage-dependent activity of these complexes may be important for meeting the increased demand for various proteins involved in housekeeping, metabolism, and protein synthesis. Recent work also indicates that direct regulation of the RNA polymerase II machinery promotes cell cycle entry. Here, we provide an overview of the regulation of basal transcription by Cdk1, and we hypothesize that the original function of the primordial cell-cycle CDK was to regulate RNAPII and that it later evolved into specialized kinases that govern various aspects of the transcription machinery and the cell cycle. Full article

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17 pages, 2860 KiB

Open AccessArticle

Molecular Evolution of Tubulins in Diatoms

by Kirill V. Khabudaev, Darya P. Petrova, Yekaterina D. Bedoshvili, Yelena V. Likhoshway and Mikhail A. Grachev

Int. J. Mol. Sci. 2022, 23(2), 618; https://doi.org/10.3390/ijms23020618 - 6 Jan 2022

Cited by 5 | Viewed by 2487

Abstract

Microtubules are formed by α- and β-tubulin heterodimers nucleated with γ-tubulin. Tubulins are conserved eukaryotic proteins. Previously, it was shown that microtubules are involved in diatom silica frustule morphogenesis. Diatom frustules are varied, and their morphology is species-specific. Despite the attractiveness of the [...] Read more.

Microtubules are formed by α- and β-tubulin heterodimers nucleated with γ-tubulin. Tubulins are conserved eukaryotic proteins. Previously, it was shown that microtubules are involved in diatom silica frustule morphogenesis. Diatom frustules are varied, and their morphology is species-specific. Despite the attractiveness of the problem of elucidating the molecular mechanisms of genetically programmed morphogenesis, the structure and evolution of diatom tubulins have not been studied previously. Based on available genomic and transcriptome data, we analyzed the phylogeny of the predicted amino acid sequences of diatom α-, β- and γ-tubulins and identified five groups for α-tubulins, six for β-tubulins and four for γ-tubulins. We identified characteristic amino acids of each of these groups and also analyzed possible posttranslational modification sites of diatom tubulins. According to our results, we assumed what changes occurred in the diatom tubulin structures during their evolution. We also identified which tubulin groups are inherent in large diatom taxa. The similarity between the evolution of diatom tubulins and the evolution of diatoms suggests that molecular changes in α-, β- and γ-tubulins could be one of the factors in the formation of a high morphological diversity of diatoms. Full article

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2021

Jump to: 2024, 2023, 2022

21 pages, 4365 KiB

Open AccessArticle

Sustainable Bioactive Packaging Based on Thermoplastic Starch and Microalgae

by Anna Martina Tedeschi, Fabrizio Di Caprio, Antonella Piozzi, Francesca Pagnanelli and Iolanda Francolini

Int. J. Mol. Sci. 2022, 23(1), 178; https://doi.org/10.3390/ijms23010178 - 24 Dec 2021

Cited by 16 | Viewed by 4716

Abstract

This study combines the use of corn starch and Tetradesmus obliquus microalgae for the production of antioxidant starch films as flexible packaging material. Starch was plasticized with glycerol and blended with 1 w% polyallylamine chosen as an agent to modify the film physical [...] Read more.

This study combines the use of corn starch and Tetradesmus obliquus microalgae for the production of antioxidant starch films as flexible packaging material. Starch was plasticized with glycerol and blended with 1 w% polyallylamine chosen as an agent to modify the film physical properties. The addition of polyallylamine improved film water stability and water vapor transmission rate as well as mechanical stiffness and tenacity. The dried Tetradesmus obliquus microalgae, which showed an EC₅₀ value of 2.8 mg/mg DPPH (2.2-Diphenyl-1-picrylhydrazyl radical), was then used as antioxidant filler. The addition of microalgae provided the films with good antioxidant activity, which increased with microalgae content increasing. To our knowledge, this is the first study reporting the development of sustainable bioactive packaging films composed of almost 100% starch, and follows the European union’s goals on plastics strategy concerning the promotion of bio-based, compostable plastics and the setting up of approaches to prevent food waste with a simple plastic packaging. Full article

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24 pages, 9915 KiB

Open AccessReview

Enzymatic Approach in Calcium Phosphate Biomineralization: A Contribution to Reconcile the Physicochemical with the Physiological View

by Clément Guibert and Jessem Landoulsi

Int. J. Mol. Sci. 2021, 22(23), 12957; https://doi.org/10.3390/ijms222312957 - 30 Nov 2021

Cited by 15 | Viewed by 3501

Abstract

Biomineralization is the process by which organisms produce hard inorganic matter from soft tissues with outstanding control of mineral deposition in time and space. For this purpose, organisms deploy a sophisticated “toolkit” that has resulted in significant evolutionary innovations, for which calcium phosphate [...] Read more.

Biomineralization is the process by which organisms produce hard inorganic matter from soft tissues with outstanding control of mineral deposition in time and space. For this purpose, organisms deploy a sophisticated “toolkit” that has resulted in significant evolutionary innovations, for which calcium phosphate (CaP) is the biomineral selected for the skeleton of vertebrates. While CaP mineral formation in aqueous media can be investigated by studying thermodynamics and kinetics of phase transitions in supersaturated solutions, biogenic mineralization requires coping with the inherent complexity of biological systems. This mainly includes compartmentalization and homeostatic processes used by organisms to regulate key physiological factors, including temperature, pH and ion concentration. A detailed analysis of the literature shows the emergence of two main views describing the mechanism of CaP biomineralization. The first one, more dedicated to the study of in vivo systems and supported by researchers in physiology, often involves matrix vesicles (MVs). The second one, more investigated by the physicochemistry community, involves collagen intrafibrillar mineralization particularly through in vitro acellular models. Herein, we show that there is an obvious need in the biological systems to control both where and when the mineral forms through an in-depth survey of the mechanism of CaP mineralization. This necessity could gather both communities of physiologists and physicochemists under a common interest for an enzymatic approach to better describe CaP biomineralization. Both homogeneous and heterogeneous enzymatic catalyses are conceivable for these systems, and a few preliminary promising results on CaP mineralization for both types of enzymatic catalysis are reported in this work. Through them, we aim to describe the relevance of our point of view and the likely findings that could be obtained when adding an enzymatic approach to the already rich and creative research field dealing with CaP mineralization. This complementary approach could lead to a better understanding of the biomineralization mechanism and inspire the biomimetic design of new materials. Full article

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23 pages, 6473 KiB

Open AccessArticle

Novel Hybrid Polymer Composites Based on Anthraquinone and Eco-Friendly Dyes with Potential for Use in Intelligent Packaging Materials

by Anna Masek, Angelika Plota, Julia Chrzastowska and Małgorzata Piotrowska

Int. J. Mol. Sci. 2021, 22(22), 12524; https://doi.org/10.3390/ijms222212524 - 20 Nov 2021

Cited by 4 | Viewed by 2866

Abstract

This study aimed to present the influence of bio-based and anthraquinone dyes and their combinations on the optical properties of ethylene-propylene (EPM) composites after thermo-oxidative and climatic aging. Therefore, the chosen polymer was filled with a natural, plant-origin flavonoid—quercetin, and with two commercial [...] Read more.

This study aimed to present the influence of bio-based and anthraquinone dyes and their combinations on the optical properties of ethylene-propylene (EPM) composites after thermo-oxidative and climatic aging. Therefore, the chosen polymer was filled with a natural, plant-origin flavonoid—quercetin, and with two commercial anthraquinone dyes (C.I. Solvent Yellow 163 and C.I. Solvent Red 207). The manufactured polymer composites were subjected to accelerated aging tests: weathering and thermo-oxidation, respectively. Examination of the materials’ properties indicated that the combination of synthetic and natural dyes can result in better resistance to oxidizing agents and higher thermal stability of ethylene-propylene products. Moreover, color change of quercetin-containing samples due to exposure to simulated atmospheric conditions could be a promising solution for use as aging indicators in intelligent packaging materials that will inform about the ongoing degradation process. Another interesting finding is that these samples exhibited good fungistatic activity against Candida albicans yeast and Aspergillus niger mold. Overall, this novel solution based on hybrid polymer composites containing natural and commercial dyes is a more environmentally friendly alternative to traditional materials used in the plastic packaging industry with better and more desirable properties. Full article

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14 pages, 3022 KiB

Open AccessArticle

SARS-CoV-2 Variants, RBD Mutations, Binding Affinity, and Antibody Escape

by Lin Yang, Jiacheng Li, Shuai Guo, Chengyu Hou, Chenchen Liao, Liping Shi, Xiaoliang Ma, Shenda Jiang, Bing Zheng, Yi Fang, Lin Ye and Xiaodong He

Int. J. Mol. Sci. 2021, 22(22), 12114; https://doi.org/10.3390/ijms222212114 - 9 Nov 2021

Cited by 23 | Viewed by 4749

Abstract

Since 2020, the receptor-binding domain (RBD) of the spike protein of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been constantly mutating, producing most of the notable missense mutations in the context of “variants of concern”, probably in response to the [...] Read more.

Since 2020, the receptor-binding domain (RBD) of the spike protein of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been constantly mutating, producing most of the notable missense mutations in the context of “variants of concern”, probably in response to the vaccine-driven alteration of immune profiles of the human population. The Delta variant, in particular, has become the most prevalent variant of the epidemic, and it is spreading in countries with the highest vaccination rates, causing the world to face the risk of a new wave of the contagion. Understanding the physical mechanism responsible for the mutation-induced changes in the RBD’s binding affinity, its transmissibility, and its capacity to escape vaccine-induced immunity is the “urgent challenge” in the development of preventive measures, vaccines, and therapeutic antibodies against the coronavirus disease 2019 (COVID-19) pandemic. In this study, entropy–enthalpy compensation and the Gibbs free energy change were used to analyze the impact of the RBD mutations on the binding affinity of SARS-CoV-2 variants with the receptor angiotensin converting enzyme 2 (ACE2) and existing antibodies. Through the analysis, we found that the existing mutations have already covered almost all possible detrimental mutations that could result in an increase of transmissibility, and that a possible mutation in amino-acid position 498 of the RBD can potentially enhance its binding affinity. A new calculation method for the binding energies of protein–protein complexes is proposed based on the entropy–enthalpy compensation rule. All known structures of RBD–antibody complexes and the RBD–ACE2 complex comply with the entropy–enthalpy compensation rule in providing the driving force behind the spontaneous protein–protein docking. The variant-induced risk of breakthrough infections in vaccinated people is attributed to the L452R mutation’s reduction of the binding affinity of many antibodies. Mutations reversing the hydrophobic or hydrophilic performance of residues in the spike RBD potentially cause breakthrough infections of coronaviruses due to the changes in geometric complementarity in the entropy–enthalpy compensations between antibodies and the virus at the binding sites. Full article

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26 pages, 11388 KiB

Open AccessArticle

Co-Immobilization of Rhizopus oryzae and Candida rugosa Lipases onto mMWCNTs@4-arm-PEG-NH₂—A Novel Magnetic Nanotube–Polyethylene Glycol Amine Composite—And Its Applications for Biodiesel Production

by Saadiah A. Abdulmalek, Kai Li, Jianhua Wang, Michael Kidane Ghide and Yunjun Yan

Int. J. Mol. Sci. 2021, 22(21), 11956; https://doi.org/10.3390/ijms222111956 - 4 Nov 2021

Cited by 20 | Viewed by 2634

Abstract

This article describes the successful synthesis of a novel nanocomposite of superparamagnetic multi-walled nanotubes with a four-arm polyethylene glycol amine polymer (mMWCNTs@4-arm-PEG-NH₂). This composite was then employed as a support for the covalent co-immobilization of Rhizopus oryzae and Candida rugosa lipases [...] Read more.

This article describes the successful synthesis of a novel nanocomposite of superparamagnetic multi-walled nanotubes with a four-arm polyethylene glycol amine polymer (mMWCNTs@4-arm-PEG-NH₂). This composite was then employed as a support for the covalent co-immobilization of Rhizopus oryzae and Candida rugosa lipases under appropriate conditions. The co-immobilized lipases (CIL-mMWCNTs@4-arm-PEG-NH₂) exhibited maximum specific activity of 99.626U/mg protein, which was 34.5-fold superior to that of free ROL, and its thermal stability was greatly improved. Most significantly, CIL-mMWCNTs@4-arm-PEG-NH₂ was used to prepare biodiesel from waste cooking oil under ultrasound conditions, and within 120 min, the biodiesel conversion rate reached 97.64%. This was due to the synergy effect between ROL and CRL and the ultrasound-assisted enzymatic process, resulting in an increased biodiesel yield in a short reaction time. Moreover, after ten reuse cycles, the co-immobilized lipases still retained a biodiesel yield of over 78.55%, exhibiting excellent operational stability that is attractive for practical applications. Consequently, the combined use of a novel designed carrier, the co-immobilized lipases with synergy effect, and the ultrasound-assisted enzymatic reaction exhibited potential prospects for future applications in biodiesel production and various industrial applications. Full article

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20 pages, 3116 KiB

Open AccessReview

Encapsulation of Plant Biocontrol Bacteria with Alginate as a Main Polymer Material

by Roohallah Saberi Riseh, Yury A. Skorik, Vijay Kumar Thakur, Mojde Moradi Pour, Elahe Tamanadar and Shahnaz Shahidi Noghabi

Int. J. Mol. Sci. 2021, 22(20), 11165; https://doi.org/10.3390/ijms222011165 - 16 Oct 2021

Cited by 133 | Viewed by 9156

Abstract

One of the most favored trends in modern agriculture is biological control. However, many reports show that survival of biocontrol bacteria is poor in host plants. Providing biocontrol agents with protection by encapsulation within external coatings has therefore become a popular idea. Various [...] Read more.

One of the most favored trends in modern agriculture is biological control. However, many reports show that survival of biocontrol bacteria is poor in host plants. Providing biocontrol agents with protection by encapsulation within external coatings has therefore become a popular idea. Various techniques, including extrusion, spray drying, and emulsion, have been introduced for encapsulation of biocontrol bacteria. One commonly used biopolymer for this type of microencapsulation is alginate, a biopolymer extracted from seaweed. Recent progress has resulted in the production of alginate-based microcapsules that meet key bacterial encapsulation requirements, including biocompatibility, biodegradability, and support of long-term survival and function. However, more studies are needed regarding the effect of encapsulation on protective bacteria and their targeted release in organic crop production systems. Most importantly, the efficacy of alginate use for the encapsulation of biocontrol bacteria in pest and disease management requires further verification. Achieving a new formulation based on biodegradable polymers can have significant effects on increasing the quantity and quality of agricultural products. Full article

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18 pages, 4200 KiB

Open AccessArticle

Free Radical-Mediated Protein Radical Formation in Differentiating Monocytes

by Ankush Prasad, Renuka Ramalingam Manoharan, Michaela Sedlářová and Pavel Pospíšil

Int. J. Mol. Sci. 2021, 22(18), 9963; https://doi.org/10.3390/ijms22189963 - 15 Sep 2021

Cited by 11 | Viewed by 2599

Abstract

Free radical-mediated activation of inflammatory macrophages remains ambiguous with its limitation to study within biological systems. U-937 and HL-60 cell lines serve as a well-defined model system known to differentiate into either macrophages or dendritic cells in response to various chemical stimuli linked [...] Read more.

Free radical-mediated activation of inflammatory macrophages remains ambiguous with its limitation to study within biological systems. U-937 and HL-60 cell lines serve as a well-defined model system known to differentiate into either macrophages or dendritic cells in response to various chemical stimuli linked with reactive oxygen species (ROS) production. Our present work utilizes phorbol 12-myristate-13-acetate (PMA) as a stimulant, and factors such as concentration and incubation time were considered to achieve optimized differentiation conditions. ROS formation likely hydroxyl radical (HO^●) was confirmed by electron paramagnetic resonance (EPR) spectroscopy combined with confocal laser scanning microscopy (CLSM). In particular, U-937 cells were utilized further to identify proteins undergoing oxidation by ROS using anti-DMPO (5,5-dimethyl-1-pyrroline N-oxide) antibodies. Additionally, the expression pattern of NADPH Oxidase 4 (NOX4) in relation to induction with PMA was monitored to correlate the pattern of ROS generated. Utilizing macrophages as a model system, findings from the present study provide a valuable source for expanding the knowledge of differentiation and protein expression dynamics. Full article

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