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Khoder RM, Zhang L, Yin T, Liu R, You J, Wang L, Huang Q, Ma H. Gelling properties of acid-induced tofu (soybean curd): Effects of acid type and nano-fish bone. J Food Sci 2024. [PMID: 38591333 DOI: 10.1111/1750-3841.17067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/10/2024]
Abstract
The effects of different types of acid coagulants and nano fish bone (NFB) additives on the characteristics of tofu were investigated using texture analyzers, SEM, FT-IR, and other techniques. The breaking force and penetration distance, in descending order, were found in the tofu induced by glucono-d-lactone (GDL) (180.27 g and 0.75 cm), citric acid (152.90 g and 0.74 cm), lactic acid (123.33 g and 0.73 cm), and acetic acid (69.84 g and 0.58 cm), respectively. The syneresis of these tofu samples was in the reverse order (35.00, 35.66, 39.66, and 44.50%). Lightness and whiteness were not significantly different among the different samples. Regardless of the acid type, the soluble calcium content in the soybean milk was significantly increased after adding NFB. As a result, the breaking force and penetration distance of all tofu samples increased significantly, but the syneresis decreased. Compared with tofu coagulated by other acids, GDL tofu formed a more uniform and dense gel network maintained by the highest intermolecular forces (especially hydrophobic interactions). Regarding the secondary structure, the lowest percentage of α-helix (22.72%) and, correspondingly, the highest β-sheet (48.32%) and random coil (18.81%) were noticed in the GDL tofu. The effects of NFB on the tofu characteristics can be explained by the changes in the gel network, intermolecular forces, and secondary structure, which were in line with the acid type. The characteristics of acid-induced tofu can be most synergistically improved by coagulation with GDL and NFB.
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Affiliation(s)
- Ramy M Khoder
- College of Food Science and Technology/National R&D Branch Center for Conventional Freshwater Fish Processing (Wuhan), Huazhong Agricultural University, Wuhan, P. R. China
- Faculty of Agriculture, Benha University, Benha, Egypt
| | | | - Tao Yin
- College of Food Science and Technology/National R&D Branch Center for Conventional Freshwater Fish Processing (Wuhan), Huazhong Agricultural University, Wuhan, P. R. China
| | - Ru Liu
- College of Food Science and Technology/National R&D Branch Center for Conventional Freshwater Fish Processing (Wuhan), Huazhong Agricultural University, Wuhan, P. R. China
| | - Juan You
- College of Food Science and Technology/National R&D Branch Center for Conventional Freshwater Fish Processing (Wuhan), Huazhong Agricultural University, Wuhan, P. R. China
| | - Lan Wang
- Institute of Agricultural Products Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan, P. R. China
| | - Qilin Huang
- College of Food Science and Technology/National R&D Branch Center for Conventional Freshwater Fish Processing (Wuhan), Huazhong Agricultural University, Wuhan, P. R. China
| | - Huawei Ma
- Engineering Research Center of Processing & Storage of Characteristic and Advantage Aquatic Products from Guangxi, Guangxi Academy of Fishery Science, Nanning, Guangxi, China
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Ye H, Zhang Y, Wang L, Ban J, Wei Y, Fan F, Guo B. Dynamic Study on Water State and Water Migration during Gluten-Starch Model Dough Development under Different Gluten Protein Contents. Foods 2024; 13:996. [PMID: 38611302 PMCID: PMC11012212 DOI: 10.3390/foods13070996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/20/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
Mixing is crucial for dough quality. The gluten content influences water migration in dough development and properties, leading to quality changes in dough-based products. Understanding how the gluten protein content influences water migration during dough development is necessary for dough processing. A compound flour with different gluten protein contents (GPCs, 10-26%, w/w) was used to study the dough farinograph parameters and water migration during dough development. According to the farinograph test of the gluten-starch model dough, the GPC increases the water absorption and the strength of the dough. Water migration was determined via low-field nuclear magnetic resonance (LF-NMR). With the increase in GPC, the gluten protein increases the binding ability of strongly bound water and promotes the transformation of weakly bound water. However, inappropriate GPC (10% and 26%, w/w) results in the release of free water, which is caused by damage to the gluten network according to the microstructure result. Moreover, the changes in proteins' secondary structures are related to the migration of weakly bound water. Therefore, weakly bound water plays an important role in dough development. Overall, these results provide a theoretical basis for the optimization of dough processing.
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Affiliation(s)
- Haoxuan Ye
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Comprehensive Utilization Laboratory of Cereal and Oil Processing, Ministry of Agriculture and Rural, Beijing 100193, China; (H.Y.); (Y.Z.); (Y.W.)
- Department of Food Science and Engineering, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Yingquan Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Comprehensive Utilization Laboratory of Cereal and Oil Processing, Ministry of Agriculture and Rural, Beijing 100193, China; (H.Y.); (Y.Z.); (Y.W.)
- Institute of Western Agriculture, The Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Lei Wang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Comprehensive Utilization Laboratory of Cereal and Oil Processing, Ministry of Agriculture and Rural, Beijing 100193, China; (H.Y.); (Y.Z.); (Y.W.)
| | - Jinfu Ban
- Shijiazhuang Academy of Agricultural and Forestry Sciences, Shijiazhuang 050041, China;
| | - Yimin Wei
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Comprehensive Utilization Laboratory of Cereal and Oil Processing, Ministry of Agriculture and Rural, Beijing 100193, China; (H.Y.); (Y.Z.); (Y.W.)
| | - Fanghui Fan
- Department of Food Science and Engineering, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Boli Guo
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Comprehensive Utilization Laboratory of Cereal and Oil Processing, Ministry of Agriculture and Rural, Beijing 100193, China; (H.Y.); (Y.Z.); (Y.W.)
- Institute of Western Agriculture, The Chinese Academy of Agricultural Sciences, Changji 831100, China
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Srivastava A, Pandey V, Singh N, Marwal A, Shahid MS, Gaur RK. In silico identification of papaya genome-encoded microRNAs to target begomovirus genes in papaya leaf curl disease. Front Microbiol 2024; 15:1340275. [PMID: 38605706 PMCID: PMC11008722 DOI: 10.3389/fmicb.2024.1340275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/26/2024] [Indexed: 04/13/2024] Open
Abstract
Papaya leaf curl disease (PaLCuD) is widespread and classified in the genus begomovirus (Geminiviridae), disseminated by the vector whitefly Bemisia tabaci. RNA interference (RNAi)-based antiviral innate immunity stands as a pivotal defense mechanism and biological process in limiting viral genomes to manage plant diseases. The current study aims to identify and analyze Carica Papaya locus-derived capa-microRNAs with predicted potential for targeting divergent begomovirus species-encoded mRNAs using a 'four integrative in silico algorithms' approach. This research aims to experimentally activate the RNAi catalytic pathway using in silico-predicted endogenous capa-miRNAs and create papaya varieties capable of assessing potential resistance against begomovirus species and monitoring antiviral capabilities. This study identified 48 predicted papaya locus-derived candidates from 23 miRNA families, which were further investigated for targeting begomovirus genes. Premised all the four algorithms combined, capa-miR5021 was the most anticipated miRNA followed by capa-miR482, capa-miR5658, capa-miR530b, capa-miR3441.2, and capa-miR414 'effective' papaya locus-derived candidate capa-miRNA and respected putative binding sites for targets at the consensus nucleotide position. It was predicted to bind and target mostly to AC1 gene of the complementary strand and the AV1 gene of the virion strand of different begomovirus isolates, which were associated with replication-associated protein and encapsidation, respectively, during PaLCuD. These miRNAs were also found targeting betaC1 gene of betasatellite which were associated with retardation in leaf growth and developmental abnormalities with severe symptoms during begomovirus infection. To validate target prediction accuracy, we created an integrated Circos plot for comprehensive visualization of host-virus interaction. In silico-predicted papaya genome-wide miRNA-mediated begomovirus target gene regulatory network corroborated interactions that permit in vivo analysis, which could provide biological material and valuable evidence, leading to the development of begomovirus-resistant papaya plants. The integrative nature of our research positions it at the forefront of efforts to ensure the sustainable cultivation of papaya, particularly in the face of evolving pathogenic threats. As we move forward, the knowledge gained from this study provides a solid foundation for continued exploration and innovation in the field of papaya virology, and to the best of our knowledge, this study represents a groundbreaking endeavor, undertaken for the first time in the context of PaLCuD research.
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Affiliation(s)
- Aarshi Srivastava
- Department of Biotechnology, Deen Dayal Updhyaya Gorakhpur University, Gorakhpur, India
| | - Vineeta Pandey
- Department of Biotechnology, Deen Dayal Updhyaya Gorakhpur University, Gorakhpur, India
| | - Nupur Singh
- Institute of Agriculture and Natural Sciences, Department of Biotechnology, Deen Dayal Updhyaya Gorakhpur University, Gorakhpur, India
| | - Avinash Marwal
- Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, India
| | - Muhammad Shafiq Shahid
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - R. K. Gaur
- Department of Biotechnology, Deen Dayal Updhyaya Gorakhpur University, Gorakhpur, India
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Liu J, Yang K, Wu D, Gong H, Guo L, Ma J, Sun W. Study on the interaction and gel properties of pork myofibrillar protein with konjac polysaccharides. J Sci Food Agric 2024; 104:2284-2293. [PMID: 37950529 DOI: 10.1002/jsfa.13116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/16/2023] [Accepted: 11/11/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND Natural myofibrillar protein (MP) is sensitive to changes in the microenvironment, such as pH and ionic strength, and therefore can adversely affect the final quality of meat products. The aim of this study was to modify natural MP as well as to improve its functional properties. Therefore, the quality improvement effect of konjac polysaccharides with different concentrations (0, 1.5, 3, 4.5 and 6 g kg-1 protein) on MP gels was investigated. RESULTS With a concentration of konjac polysaccharides of 6 g kg-1 protein, the composite gel obtained exhibited a significant improvement of water binding (water holding capacity increased by 7.71%) and textural performance (strength increased from 29.12 to 37.55 N mm, an increase of 8.43 N mm). Meanwhile, konjac polysaccharides could help to form more disulfide bonds and non-disulfide covalent bonds, which enhanced the crosslinking of MP and maintained the MP gel network structure. Then, with the preservation of α-helix structure (a significant increase of 8.11%), slower protein aggregation and formation of small aggregates, this supported the formation of a fine and homogeneous network structure and allowed a reduction in water mobility. CONCLUSION During the heating process, konjac polysaccharides could absorb the surrounding water and fill the gel system, which resulted in an increase in the water content of the gel network and enhanced the gel-forming ability of the gel. Meanwhile, konjac polysaccharides might inhibit irregular aggregation of proteins and promote the formation of small aggregates, which in turn form a homogeneous and continuous gel matrix by orderly arrangement. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Jingyang Liu
- College of Life Science, Yangtze University, Jingzhou, China
| | - Kun Yang
- College of Life Science, Yangtze University, Jingzhou, China
- Key Laboratory of Meat Processing and Quality Control, MOE, Key Laboratory of Meat Processing, MARA, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Di Wu
- College of Life Science, Yangtze University, Jingzhou, China
| | - Honghong Gong
- College of Life Science, Yangtze University, Jingzhou, China
| | - Linxiao Guo
- College of Marxism, Yangtze University, Jingzhou, China
| | - Jing Ma
- College of Life Science, Yangtze University, Jingzhou, China
| | - Weiqing Sun
- College of Life Science, Yangtze University, Jingzhou, China
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Yin C, Yu L, Feng L, Zhou JT, Du C, Shao X, Cheng Y. Nanotoxicity of two-dimensional nanomaterials on human skin and the structural evolution of keratin protein. Nanotechnology 2024; 35:225101. [PMID: 38387099 DOI: 10.1088/1361-6528/ad2c58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/21/2024] [Indexed: 02/24/2024]
Abstract
Two-dimensional (2D) materials have been increasingly widely used in biomedical and cosmetical products nowadays, yet their safe usage in human body and environment necessitates a comprehensive understanding of their nanotoxicity. In this work, the effect of pristine graphene and graphene oxide (GO) on the adsorption and conformational changes of skin keratin using molecular dynamics simulations. It is found that skin keratin can be absorbed through various noncovalent driving forces, such as van der Waals (vdW) and electrostatics. In the case of GO, the oxygen-containing groups prevent tighter contact between skin keratin and the graphene basal plane through steric effects and electrostatic repulsion. On the other hand, electrostatic attraction and hydrogen bonding enhance their binding affinity to positively charged residues such as lysine and arginine. The secondary structure of skin keratin is better preserved in GO system, suggesting that GO has good biocompatibility. The charged groups on GO surface perform as the hydrogen bond acceptors, which is like to the natural receptors of keratin in this physiological environment. This work contributes to a better knowledge of the nanotoxicity of cutting-edge 2D materials on human health, thereby advancing their potential biological applications.
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Affiliation(s)
- Changji Yin
- Monash Suzhou Research Institute, Monash University, SIP, Suzhou 215000, People's Republic of China
- Department of Materials Science and Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Lei Yu
- Guiyang Maternal and Child Health Care Hospital, Guiyang, Guizhou 550002, People's Republic of China
| | - Lei Feng
- Monash Suzhou Research Institute, Monash University, SIP, Suzhou 215000, People's Republic of China
| | - Joey Tianyi Zhou
- Centre for Frontier AI Research (CFAR), Agency for Science, Technology and Research (A*STAR), Singapore
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Chunbao Du
- Monash Suzhou Research Institute, Monash University, SIP, Suzhou 215000, People's Republic of China
- College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an 710065, People's Republic of China
| | - Xiaoshan Shao
- Guiyang Maternal and Child Health Care Hospital, Guiyang, Guizhou 550002, People's Republic of China
| | - Yuan Cheng
- Monash Suzhou Research Institute, Monash University, SIP, Suzhou 215000, People's Republic of China
- Department of Materials Science and Engineering, Monash University, Clayton, VIC 3800, Australia
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Sato H, Koshoubu J, Inoué S, Kawamura I, Yamagishi A. Multidimensional vibrational circular dichroism for insect wings: Comparison of species. Chirality 2024; 36:e23655. [PMID: 38419363 DOI: 10.1002/chir.23655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/16/2024] [Accepted: 02/02/2024] [Indexed: 03/02/2024]
Abstract
This study reports the microscopic measurements of vibrational circular dichroism (VCD) on four different insect wings using a quantum cascade laser VCD system equipped with microscopic scanning capabilities (named multi-dimensional VCD [MultiD-VCD]). Wing samples, including (i) beetle, Anomala albopilosa (female), (ii) European hornet, Verspa crabro flavofasciata Cameron, 1903 (female), (iii) tiny dragonfly, Nannophya pygmae Rambur, 1842 (male), and (iv) dragonfly, Symetrum gracile Oguma, 1915 (male), were used in this study. Two-dimensional patterns of VCD signals (~10 mm × 10 mm) were obtained at a spatial resolution of 100 μm. Measurements covered the absorption peaks assigned to amides I and II in the range of 1500-1740 cm-1 . The measurements were based on the enhancement of VCD signals for the stereoregular linkage of peptide groups. The patterns were remarkably dependent on the species. In samples (i) and (ii), the wings comprised segregated domains of protein aggregates of different secondary structures. The size of each microdomain was approximately 100 μm. In contrast, no clear VCD spectra were detected in samples (iii) and (iv). One possible reason was that the chain of stereoregular polypeptides was too short to achieve VCD enhancement in samples (iii) and (iv). Notably, the unique features were only observed in the VCD spectra because the IR spectra were nearly the same among the species. The VCD results hinted at the connection of protein microscopic structures with the wing flapping mechanisms of each species.
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Affiliation(s)
- Hisako Sato
- Faculty of Science, Ehime University, Matsuyama, Japan
| | | | - Sayako Inoué
- Geodynamics Research Center, Ehime University, Matsuyama, Japan
| | - Izuru Kawamura
- Graduate School of Engineering Science, Yokohama National University, Yokohama, Japan
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Li S, Zhang Y, Chen J. Backbone interactions and secondary structures in phase separation of disordered proteins. Biochem Soc Trans 2024; 52:319-329. [PMID: 38348795 DOI: 10.1042/bst20230618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/29/2024]
Abstract
Intrinsically disordered proteins (IDPs) are one of the major drivers behind the formation and characteristics of biomolecular condensates. Due to their inherent flexibility, the backbones of IDPs are significantly exposed, rendering them highly influential and susceptible to biomolecular phase separation. In densely packed condensates, exposed backbones have a heightened capacity to interact with neighboring protein chains, which might lead to strong coupling between the secondary structures and phase separation and further modulate the subsequent transitions of the condensates, such as aging and fibrillization. In this mini-review, we provide an overview of backbone-mediated interactions and secondary structures within biomolecular condensates to underscore the importance of protein backbones in phase separation. We further focus on recent advances in experimental techniques and molecular dynamics simulation methods for probing and exploring the roles of backbone interactions and secondary structures in biomolecular phase separation involving IDPs.
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Affiliation(s)
- Shanlong Li
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - Yumeng Zhang
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, U.S.A
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Chorostecki U, Saus E, Gabaldón T. Probing RNA structural landscapes across Candida yeast genomes. Front Microbiol 2024; 15:1362067. [PMID: 38468856 PMCID: PMC10926079 DOI: 10.3389/fmicb.2024.1362067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024] Open
Abstract
Understanding the intricate roles of RNA molecules in virulence and host-pathogen interactions can provide valuable insights into combatting infections and improving human health. Although much progress has been achieved in understanding transcriptional regulation during host-pathogen interactions in diverse species, more is needed to know about the structure of pathogen RNAs. This is particularly true for fungal pathogens, including pathogenic yeasts of the Candida genus, which are the leading cause of hospital-acquired fungal infections. Our work addresses the gap between RNA structure and their biology by employing genome-wide structure probing to comprehensively explore the structural landscape of mRNAs and long non-coding RNAs (lncRNAs) in the four major Candida pathogens. Specifically focusing on mRNA, we observe a robust correlation between sequence conservation and structural characteristics in orthologous transcripts, significantly when sequence identity exceeds 50%, highlighting structural feature conservation among closely related species. We investigate the impact of single nucleotide polymorphisms (SNPs) on mRNA secondary structure. SNPs within 5' untranslated regions (UTRs) tend to occur in less structured positions, suggesting structural constraints influencing transcript regulation. Furthermore, we compare the structural properties of coding regions and UTRs, noting that coding regions are generally more structured than UTRs, consistent with similar trends in other species. Additionally, we provide the first experimental characterization of lncRNA structures in Candida species. Most lncRNAs form independent subdomains, similar to human lncRNAs. Notably, we identify hairpin-like structures in lncRNAs, a feature known to be functionally significant. Comparing hairpin prevalence between lncRNAs and protein-coding genes, we find enrichment in lncRNAs across Candida species, humans, and Arabidopsis thaliana, suggesting a conserved role for these structures. In summary, our study offers valuable insights into the interplay between RNA sequence, structure, and function in Candida pathogens, with implications for gene expression regulation and potential therapeutic strategies against Candida infections.
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Affiliation(s)
- Uciel Chorostecki
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Barcelona, Spain
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ester Saus
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- ICREA, Barcelona, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
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9
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Jia R, Yang Y, Liao G, Wu H, Yang C, Wang G. Flavor Characteristics of Umami Peptides from Wuding Chicken Revealed by Molecular Dynamics Simulation. J Agric Food Chem 2024; 72:3673-3682. [PMID: 38290215 DOI: 10.1021/acs.jafc.3c08348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Wuding chicken is famous for its delicious meat, and HLEEEIK, LDDALR, and ELY were jointly extracted from different processing stages of Wuding chicken. However, whether these peptides can be used as umami supplements is unclear. The sensory evaluation tests were used to study the taste characteristics. The secondary structure of the peptides and their interaction with T1R1/T1R3 were predicted by the circular dichroism spectrum and molecular dynamics simulation. The umami threshold was 0.03125 to 0.06250 mg/mL, all of which could increase umami, saltiness, sweetness, and mask bitterness. Compared with HLEEEIK, the frequency of umami active fragments and the improvement rate of the umami score of EEE increased by 133.35% and 40.09%, respectively. Peptides were dominated by umami taste according to sensory analysis, among which EE-3 (3.18) has the highest umami intensity followed by LR-4 (2.58), HK-7 (2.13), and EY-3 (1.82). The main secondary structure of umami peptides was β-folding, and Tyr74, Arg323, Arg272, and Gln35 were the key amino acid residues for binding of umami peptides to the receptor. This study further elucidated that the umami intensity of the peptides could be altered by changing the sequence composition of the peptides, which enhanced our understanding of the complex flavor properties of umami peptides.
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Affiliation(s)
- Rong Jia
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Yuan Yang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Guozhou Liao
- Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Hongyan Wu
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Chunfang Yang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Guiying Wang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Livestock Product Processing and Engineering Technology Research Center of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
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Pereira RN, Rodrigues R, Avelar Z, Leite AC, Leal R, Pereira RS, Vicente A. Electrical Fields in the Processing of Protein-Based Foods. Foods 2024; 13:577. [PMID: 38397554 PMCID: PMC10887823 DOI: 10.3390/foods13040577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Electric field-based technologies offer interesting perspectives which include controlled heat dissipation (via the ohmic heating effect) and the influence of electrical variables (e.g., electroporation). These factors collectively provide an opportunity to modify the functional and technological properties of numerous food proteins, including ones from emergent plant- and microbial-based sources. Currently, numerous scientific studies are underway, contributing to the emerging body of knowledge about the effects on protein properties. In this review, "Electric Field Processing" acknowledges the broader range of technologies that fall under the umbrella of using the direct passage of electrical current in food material, giving particular focus to the ones that are industrially implemented. The structural and biological effects of electric field processing (thermal and non-thermal) on protein fractions from various sources will be addressed. For a more comprehensive contextualization of the significance of these effects, both conventional and alternative protein sources, along with their respective ingredients, will be introduced initially.
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Affiliation(s)
- Ricardo N. Pereira
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (R.N.P.); (R.R.); (Z.A.); (A.C.L.); (R.L.); (R.S.P.)
- LABBELS—Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Rui Rodrigues
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (R.N.P.); (R.R.); (Z.A.); (A.C.L.); (R.L.); (R.S.P.)
- LABBELS—Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Zita Avelar
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (R.N.P.); (R.R.); (Z.A.); (A.C.L.); (R.L.); (R.S.P.)
| | - Ana Catarina Leite
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (R.N.P.); (R.R.); (Z.A.); (A.C.L.); (R.L.); (R.S.P.)
| | - Rita Leal
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (R.N.P.); (R.R.); (Z.A.); (A.C.L.); (R.L.); (R.S.P.)
| | - Ricardo S. Pereira
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (R.N.P.); (R.R.); (Z.A.); (A.C.L.); (R.L.); (R.S.P.)
| | - António Vicente
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (R.N.P.); (R.R.); (Z.A.); (A.C.L.); (R.L.); (R.S.P.)
- LABBELS—Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
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11
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Sumikawa T, Nakakido M, Matsunaga R, Kuroda D, Nagatoishi S, Tsumoto K. Generation of antibodies to an extracellular region of the transporters Glut1/Glut4 by immunization with a designed antigen. J Biol Chem 2024; 300:105640. [PMID: 38199569 PMCID: PMC10862009 DOI: 10.1016/j.jbc.2024.105640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/14/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024] Open
Abstract
Monoclonal antibodies are one of the fastest growing class of drugs. Nevertheless, relatively few biologics target multispanning membrane proteins because of technical challenges. To target relatively small extracellular regions of multiple membrane-spanning proteins, synthetic peptides, which are composed of amino acids corresponding to an extracellular region of a membrane protein, are often utilized in antibody discovery. However, antibodies to these peptides often do not recognize parental membrane proteins. In this study, we designed fusion proteins in which an extracellular helix of the membrane protein glucose transporter 1 (Glut1) was grafted onto the scaffold protein Adhiron. In the initial design, the grafted fragment did not form a helical conformation. Molecular dynamics simulations of full-length Glut1 suggested the importance of intramolecular interactions formed by surrounding residues in the formation of the helical conformation. A fusion protein designed to maintain such intramolecular interactions did form the desired helical conformation in the grafted region. We then immunized an alpaca with the designed fusion protein and obtained VHH (variable region of heavy-chain antibodies) using the phage display method. The binding of these VHH antibodies to the recombinant Glut1 protein was evaluated by surface plasmon resonance, and their binding to Glut1 on the cell membrane was further validated by flow cytometry. Furthermore, we also succeeded in the generation of a VHH against another integral membrane protein, glucose transporter 4 (Glut4) with the same strategy. These illustrates that our combined biochemical and computational approach can be applied to designing other novel fusion proteins for generating site-specific antibodies.
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Affiliation(s)
- Taichi Sumikawa
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Makoto Nakakido
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Ryo Matsunaga
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan; Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Satoru Nagatoishi
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan; Laboratory of Medical Proteomics, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan; Laboratory of Medical Proteomics, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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12
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Wu K, Li Y, Chen J. Effect of pH on the Structure, Functional Properties and Rheological Properties of Collagen from Greenfin Horse-Faced Filefish ( Thamnaconus septentrionalis) Skin. Mar Drugs 2024; 22:45. [PMID: 38248670 PMCID: PMC10817565 DOI: 10.3390/md22010045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/06/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
Collagen is an important biopolymer widely used in food, cosmetics and biomedical applications. Understanding the effect of pH on the structure and properties of collagen is beneficial for its further processing and exploitation. In this study, greenfin horse-faced filefish skin collagen (GHSC) was prepared and identified as a type I collagen. We systematically investigated the effect of pH on the structural, functional and rheological properties of GHSC. Scanning electron microscopy showed that the collagen morphology changed from an ordered stacked sheet structure to a rough silk-like structure as pH increased. Gaussian-fitted Fourier infrared spectroscopy results of the collagen revealed that it unfolded with increasing pH. Moreover, the ordered structure was reduced, and random coils became the dominant conformation. Its β-sheet and random coil contents increased from 18.43 ± 0.08 and 33.62 ± 0.17 to 19.72 ± 0.02 and 39.53 ± 1.03%, respectively, with increasing pH. α-helices and β-turns decreased from 35.00 ± 0.26 and 12.95 ± 0.01 to 29.39 ± 0.92 and 11.36 ± 0.10%, respectively. The increase in β-sheets and random coils allowed the pI-treated collagen to exhibit maximum water contact angle. The emulsification and foaming properties decreased and then increased with increasing pH in a V-shape. The increased net surface charge and β-sheets in collagen benefited its emulsification and foaming properties. The rheological results showed that the protoprotein exhibited shear-thinning properties in all pH ranges. The collagen solutions showed liquid-like behaviour in low-pH (2, 4) solutions and solid-like behaviour in high-pH (6, 7.83 and 10) solutions. Moreover, the frequency-dependent properties of the storage modulus (G') and loss modulus (G″) of the collagen solutions weakened with increasing pH. Collagen has considerable frequency-dependent properties of G' and G″ at low pH (2, 4). Thus, the importance of collagen raw material preparation for subsequent processing was emphasised, which may provide new insights into applying collagen-based materials in food, biomaterials and tissue engineering.
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Affiliation(s)
| | | | - Junde Chen
- Technical Innovation Center for Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; (K.W.); (Y.L.)
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13
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Li J, Tan YS, Verma CS. Dissecting the geometric and hydrophobic constraints of stapled peptides. Proteins 2024. [PMID: 38196284 DOI: 10.1002/prot.26662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/01/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
Stapled peptides are a promising class of molecules with potential as highly specific probes of protein-protein interactions and as therapeutics. Hydrocarbon stapling affects the peptide properties through the interplay of two factors: enhancing the overall hydrophobicity and constraining the conformational flexibility. By constructing a series of virtual peptides, we study the role of each factor in modulating the structural properties of a hydrocarbon-stapled peptide PM2, which has been shown to enter cells, engage its target Mouse Double Minute 2 (MDM2), and activate p53. Hamiltonian replica exchange molecular dynamics (HREMD) simulations suggest that hydrocarbon stapling favors helical populations of PM2 through a combination of the geometric constraints and the enhanced hydrophobicity of the peptide. To further understand the conformational landscape of the stapled peptides along the binding pathway, we performed HREMD simulations by restraining the peptide at different distances from MDM2. When the peptide approaches MDM2, the binding pocket undergoes dehydration which appears to be greater in the presence of the stapled peptide compared with the linear peptide. In the binding pocket, the helicity of the stapled peptide is increased due to the favorable interactions between the peptide residues as well as the staple and the microenvironment of the binding pocket, contributing to enhanced affinity. The dissection of the multifaceted mechanism of hydrocarbon stapling into individual factors not only deepens fundamental understanding of peptide stapling, but also provides guidelines for the design of new stapled peptides.
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Affiliation(s)
- Jianguo Li
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Singapore Eye Research Institute, Singapore, Singapore
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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14
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Zareie AR, Dabral P, Verma SC. G-Quadruplexes in the Regulation of Viral Gene Expressions and Their Impacts on Controlling Infection. Pathogens 2024; 13:60. [PMID: 38251367 PMCID: PMC10819198 DOI: 10.3390/pathogens13010060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid structures that play significant roles in regulating various biological processes, including replication, transcription, translation, and recombination. Recent studies have identified G4s in the genomes of several viruses, such as herpes viruses, hepatitis viruses, and human coronaviruses. These structures are implicated in regulating viral transcription, replication, and virion production, influencing viral infectivity and pathogenesis. G4-stabilizing ligands, like TMPyP4, PhenDC3, and BRACO19, show potential antiviral properties by targeting and stabilizing G4 structures, inhibiting essential viral life-cycle processes. This review delves into the existing literature on G4's involvement in viral regulation, emphasizing specific G4-stabilizing ligands. While progress has been made in understanding how these ligands regulate viruses, further research is needed to elucidate the mechanisms through which G4s impact viral processes. More research is necessary to develop G4-stabilizing ligands as novel antiviral agents. The increasing body of literature underscores the importance of G4s in viral biology and the development of innovative therapeutic strategies against viral infections. Despite some ligands' known regulatory effects on viruses, a deeper comprehension of the multifaceted impact of G4s on viral processes is essential. This review advocates for intensified research to unravel the intricate relationship between G4s and viral processes, paving the way for novel antiviral treatments.
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Affiliation(s)
| | | | - Subhash C. Verma
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, 1664 N Virginia Street, Reno, NV 89557, USA; (A.R.Z.); (P.D.)
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15
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Bonvin E, Personne H, Paschoud T, Reusser J, Gan BH, Luscher A, Köhler T, van Delden C, Reymond JL. Antimicrobial Peptide-Peptoid Hybrids with and without Membrane Disruption. ACS Infect Dis 2023; 9:2593-2606. [PMID: 38062792 PMCID: PMC10714400 DOI: 10.1021/acsinfecdis.3c00421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023]
Abstract
Among synthetic analogues of antimicrobial peptides (AMPs) under investigation to address antimicrobial resistance, peptoids (N-alkylated oligoglycines) have been reported to act both by membrane disruption and on intracellular targets. Here we gradually introduced peptoid units into the membrane-disruptive undecapeptide KKLLKLLKLLL to test a possible transition toward intracellular targeting. We found that selected hybrids containing up to five peptoid units retained the parent AMP's α-helical folding, membrane disruption, and antimicrobial effects against Gram-negative bacteria including multidrug-resistant (MDR) strains of Pseudomonas aeruginosa and Klebsiella pneumoniae while showing reduced hemolysis and cell toxicities. Furthermore, some hybrids containing as few as three peptoid units as well as the full peptoid lost folding, membrane disruption, hemolysis, and cytotoxicity but displayed strong antibacterial activity under dilute medium conditions typical for proline-rich antimicrobial peptides (PrAMPs), pointing to intracellular targeting. These findings parallel previous reports that partially helical amphiphilic peptoids are privileged oligomers for antibiotic development.
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Affiliation(s)
- Etienne Bonvin
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Hippolyte Personne
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Thierry Paschoud
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Jérémie Reusser
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Bee-Ha Gan
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Alexandre Luscher
- Department
of Microbiology and Molecular Medicine, University of Geneva, CH-1211 Geneva, Switzerland
- Service of
Infectious Diseases, University Hospital
of Geneva, CH-1211 Geneva, Switzerland
| | - Thilo Köhler
- Department
of Microbiology and Molecular Medicine, University of Geneva, CH-1211 Geneva, Switzerland
- Service of
Infectious Diseases, University Hospital
of Geneva, CH-1211 Geneva, Switzerland
| | - Christian van Delden
- Department
of Microbiology and Molecular Medicine, University of Geneva, CH-1211 Geneva, Switzerland
- Service of
Infectious Diseases, University Hospital
of Geneva, CH-1211 Geneva, Switzerland
| | - Jean-Louis Reymond
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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16
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Zahraee H, Arab SS, Khoshbin Z, Bozorgmehr MR. A comprehensive computer simulation insight into inhibitory mechanisms of EGCG and NQTrp ligands on amyloid-beta assemblies as the Alzheimer's disease insignia. J Biomol Struct Dyn 2023; 41:10830-10839. [PMID: 36576270 DOI: 10.1080/07391102.2022.2158939] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/10/2022] [Indexed: 12/29/2022]
Abstract
Amyloid-β peptide with predominant presence in the senile plaques is the most common agent for Alzheimer's disease (AD) incidence. Assembly of the amyloid-β(1-42) (Aβ1-42) isoform is known as the main reason for the AD appearance. Epigallocatechin gallate (EGCG) and 1,4-naphthoquinone-2-yl-L-tryptophan (NQTrp) are two small molecules that inhibit the formation of the Aβ1-42 fibrils. The present study provides molecular insight to clarify the inhibitory mechanisms of the EGCG and NQTrp ligands on the Aβ1-42 assemblies by using molecular dynamics (MD) simulation. Hence, nine different Aβ1-42-containing systems including the monomer, dimer, and hexamer of Aβ1-42 considering each of them in a media with no ligands, in the presence of one EGCG ligand, and in the presence of one EGCG ligand were studied with a simulation time of 1 µs for each system. The precise investigation of the peptide-ligand distance, conformational factor (Pi), solvent accessible surface area (SASA), dictionary of secondary structure (DSSP), and Lys28-Ala42 salt bridge analyses confirmed that the hydroxyl-rich structure of the EGCG ligand applied its inhibitory effect on the aggregation of the peptides indirectly by involving water molecules. While the hydroxyl-free structure of the NQTrp ligand exposed its inhibitory effect through a direct interaction with the Aβ1-42 peptides. Besides, reduced density gradient (RDG) analysis clarified the hydrogen bonding interactions as the dominant ones for the peptide-EGCG systems, and also, steric and van der Waals interactions for the peptide-NQTrp systems.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hamed Zahraee
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Zahra Khoshbin
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
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17
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Nasaev SS, Mukanov AR, Kuznetsov II, Veselovsky AV. AliNA - a deep learning program for RNA secondary structure prediction. Mol Inform 2023; 42:e202300113. [PMID: 37710142 DOI: 10.1002/minf.202300113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/16/2023]
Abstract
Nowadays there are numerous discovered natural RNA variations participating in different cellular processes and artificial RNA, e. g., aptamers, riboswitches. One of the required tasks in the investigation of their functions and mechanism of influence on cells and interaction with targets is the prediction of RNA secondary structures. The classic thermodynamic-based prediction algorithms do not consider the specificity of biological folding and deep learning methods that were designed to resolve this issue suffer from homology-based methods problems. Herein, we present a method for RNA secondary structure prediction based on deep learning - AliNA (ALIgned Nucleic Acids). Our method successfully predicts secondary structures for non-homologous to train-data RNA families thanks to usage of the data augmentation techniques. Augmentation extends existing datasets with easily-accessible simulated data. The proposed method shows a high quality of prediction across different benchmarks including pseudoknots. The method is available on GitHub for free (https://github.com/Arty40m/AliNA).
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Affiliation(s)
- Shamsudin S Nasaev
- Institute of Biomedical Chemistry, 10, Pogodinskaya str., 119121, Moscow, Russia
| | - Artem R Mukanov
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, 18, Kremlyovskaya str., 420008, Kazan, Russia
| | - Ivan I Kuznetsov
- Moscow University of Finance and Law, 10 block 1, Serpuhovsky val str., 115191, Moscow, Russia
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18
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Dowling RC, Carroll GT, Kirschman DL, Masthay MB, Mammana A. Circular dichroism and UV-Vis detection of UV-induced damage to nucleic acids. Chirality 2023; 35:973-982. [PMID: 37503965 DOI: 10.1002/chir.23612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/26/2023] [Accepted: 07/05/2023] [Indexed: 07/29/2023]
Abstract
In this report, we demonstrate that CD spectroscopy can be used as a tool to detect changes to DNA upon irradiation with UV light. We follow the spectroscopic response of DNA samples irradiated at selected exposure times with both CD and UV-Vis spectroscopy. We analyzed four different nucleic acids to evaluate the effect of the sequence on photodegradation. Only one polymer, calf thymus DNA, was a natural nucleic acid and contained all four nucleobases. The other three were synthetic polymers and contained only one type of base pair: poly (deoxyadenylic-deoxythymidylic) acid [poly (dA-dT)2 ] and poly (deoxyadenylic acid) · poly (deoxythymidylic acid) [poly (dA) · poly (dT)], which contained only adenine and thymine; poly (deoxyguanylic-deoxycytidylic) acid [poly (dG-dC)2 ], which contained only guanine and cytosine. CD and UV-Vis spectra showed sequence dependent changes. In particular, poly (dA) · poly (dT) undergoes changes more rapidly than the other sequences investigated. The CD spectrum of poly (dA) · poly (dT) gradually undergoes an inversion, suggesting a change in helicity, before disappearing due to the unfolding of the double strand.
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Affiliation(s)
- Reed C Dowling
- Department of Chemistry, University of Dayton, Dayton, Ohio, USA
| | | | | | - Mark B Masthay
- Department of Chemistry, University of Dayton, Dayton, Ohio, USA
| | - Angela Mammana
- Department of Chemistry, University of Dayton, Dayton, Ohio, USA
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19
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Welc-Stanowska R, Kłosok K, Nawrocka A. Insight into Organization of Gliadin and Glutenin Extracted from Gluten Modified by Phenolic Acids. Molecules 2023; 28:7790. [PMID: 38067520 PMCID: PMC10708489 DOI: 10.3390/molecules28237790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/16/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
The changes in the secondary structure of individual gluten protein fractions (gliadin and glutenin) caused by the supplementation of model dough with eight phenolic acids were analysed. Gliadins and glutenins were extracted from gluten samples obtained from overmixed dough. The changes in the gliadin secondary structure depended on the amount of phenolic acid added to the dough. Higher acid concentrations (0.1% and 0.2%) led to a significant reduction in the amount of α-helices and to the formation of aggregates, non-ordered secondary structures, and antiparallel β-sheets. After the addition of acids at a lower concentration (0.05%), the disaggregation of pseudo-β-sheet structures and the formation of β-turns, hydrogen-bonded β-turns, and antiparallel β-sheets were detected. In the case of glutenin, most of the phenolic acids induced the formation of intermolecular hydrogen bonds between the polypeptide chains, leading to glutenin aggregation. When phenolic acids were added at a concentration of 0.05%, the process of protein folding and regular secondary structure formation was also observed. In this system, antiparallel β-sheets and β-turns were created at the expense of pseudo-β-sheets.
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Affiliation(s)
- Renata Welc-Stanowska
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland; (K.K.); (A.N.)
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20
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Nie Y, Zhang Y, Wu J. The Secondary Structure of Potato Spindle Tuber Viroid Determines Its Infectivity in Nicotiana benthamiana. Viruses 2023; 15:2307. [PMID: 38140547 PMCID: PMC10748084 DOI: 10.3390/v15122307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
The function of RNAs is determined by their structure. However, studying the relationship between RNA structure and function often requires altering RNA sequences to modify the structures, which leads to the neglect of the importance of RNA sequences themselves. In our research, we utilized potato spindle tuber viroid (PSTVd), a circular-form non-coding infectious RNA, as a model with which to investigate the role of a specific rod-like structure in RNA function. By generating linear RNA transcripts with different start sites, we established 12 PSTVd forms with different secondary structures while maintaining the same sequence. The RNA secondary structures were predicted using the mfold tool and validated through native PAGE gel electrophoresis after in vitro RNA folding. Analysis using plant infection assays revealed that the formation of a correct rod-like structure is crucial for the successful infection of PSTVd. Interestingly, the inability of PSTVd forms with non-rod-like structures to infect plants could be partially compensated by increasing the amount of linear viroid RNA transcripts, suggesting the existence of additional RNA secondary structures, such as the correct rod-like structure, alongside the dominant structure in the RNA inoculum of these forms. Our study demonstrates the critical role of RNA secondary structures in determining the function of infectious RNAs.
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Affiliation(s)
| | | | - Jian Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (Y.N.); (Y.Z.)
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21
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Luo L, Deng Y, Liu G, Zhou P, Zhao Z, Li P, Zhang M. Enhancing Solubility and Reducing Thermal Aggregation in Pea Proteins through Protein Glutaminase-Mediated Deamidation. Foods 2023; 12:4130. [PMID: 38002188 PMCID: PMC10670925 DOI: 10.3390/foods12224130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
The limited solubility and stability of pea proteins hinder their utilization in liquid formulations. In this study, protein glutaminase (PG) was employed to modify pea protein isolates (PPIs) and obtain deamidated PPI with varying degrees of deamidation (DD, 10-25%). The solubility and thermal stability of these deamidated PPI samples were assessed, and a comprehensive analysis, including SDS-PAGE, zeta potential, FTIR, surface hydrophobicity, and intrinsic fluorescence, was conducted to elucidate the mechanism behind the improvement in their functional properties. The results reveal that PG modification greatly enhances the solubility and heat stability of PPI, with the most notable improvements observed at higher DD (>20%). PG modification increases the net charge of PPI, leading to the unfolding and extension of the protein structures, thus exposing more hydrophobic groups. These structural changes are particularly pronounced when DD exceeds 20%. This increased electrostatic repulsion between carboxyl groups would promote protein unfolding, enhancing interactions with water and hindering the aggregation of unfolded protein in the presence of salts at elevated temperatures (supported by high-performance size exclusion chromatography and transmission electron microscopy). Accordingly, PG-mediated deamidation shows promise in enhancing the functional properties of PPI.
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Affiliation(s)
- Lijuan Luo
- Sericultural & Agri-Food Research Institute Guangdong Academy of Agricultural Sciences, Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou 510610, China; (L.L.)
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuanyuan Deng
- Sericultural & Agri-Food Research Institute Guangdong Academy of Agricultural Sciences, Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou 510610, China; (L.L.)
| | - Guang Liu
- Sericultural & Agri-Food Research Institute Guangdong Academy of Agricultural Sciences, Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou 510610, China; (L.L.)
| | - Pengfei Zhou
- Sericultural & Agri-Food Research Institute Guangdong Academy of Agricultural Sciences, Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou 510610, China; (L.L.)
| | - Zhihao Zhao
- Sericultural & Agri-Food Research Institute Guangdong Academy of Agricultural Sciences, Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou 510610, China; (L.L.)
| | - Ping Li
- Sericultural & Agri-Food Research Institute Guangdong Academy of Agricultural Sciences, Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou 510610, China; (L.L.)
| | - Mingwei Zhang
- Sericultural & Agri-Food Research Institute Guangdong Academy of Agricultural Sciences, Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou 510610, China; (L.L.)
- Food Laboratory of Zhongyuan, Luohe 462300, China
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Kumashiro M, Matsuo K. Characterization of membrane-interaction mechanisms of proteins using vacuum-ultraviolet circular dichroism spectroscopy. Chirality 2023; 35:826-837. [PMID: 37418251 DOI: 10.1002/chir.23607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/30/2023] [Accepted: 06/21/2023] [Indexed: 07/08/2023]
Abstract
Protein-membrane interactions play an important role in various biological phenomena, such as material transport, demyelinating diseases, and antimicrobial activity. We combined vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy with theoretical (e.g., molecular dynamics and neural networks) and polarization experimental (e.g., linear dichroism and fluorescence anisotropy) methods to characterize the membrane interaction mechanisms of three soluble proteins (or peptides). α1 -Acid glycoprotein has the drug-binding ability, but the combination of VUVCD and neural-network method revealed that the membrane interaction causes the extension of helix in the N-terminal region, which reduces the binding ability. Myelin basic protein (MBP) is an essential component of the myelin sheath with a multi-layered structure. Molecular dynamics simulations using a VUVCD-guided system showed that MBP forms two amphiphilic and three non-amphiphilic helices as membrane interaction sites. These multivalent interactions may allow MBP to interact with two opposing membrane leaflets, contributing to the formation of a multi-layered myelin structure. The antimicrobial peptide magainin 2 interacts with the bacterial membrane, causing damage to its structure. VUVCD analysis revealed that the M2 peptides assemble in the membrane and turn into oligomers with a β-strand structure. Linear dichroism and fluorescence anisotropy suggested that the oligomers are inserted into the hydrophobic core of the membrane, disrupting the bacterial membrane. Overall, our findings demonstrate that VUVCD and its combination with theoretical and polarization experimental methods pave the way for unraveling the molecular mechanisms of biological phenomena related to protein-membrane interactions.
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Affiliation(s)
- Munehiro Kumashiro
- Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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23
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Rosenberg AA, Yehishalom N, Marx A, Bronstein AM. An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units. Proc Natl Acad Sci U S A 2023; 120:e2301064120. [PMID: 37878722 PMCID: PMC10623034 DOI: 10.1073/pnas.2301064120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 08/24/2023] [Indexed: 10/27/2023] Open
Abstract
Protein structure, both at the global and local level, dictates function. Proteins fold from chains of amino acids, forming secondary structures, α-helices and β-strands, that, at least for globular proteins, subsequently fold into a three-dimensional structure. Here, we show that a Ramachandran-type plot focusing on the two dihedral angles separated by the peptide bond, and entirely contained within an amino acid pair, defines a local structural unit. We further demonstrate the usefulness of this cross-peptide-bond Ramachandran plot by showing that it captures β-turn conformations in coil regions, that traditional Ramachandran plot outliers fall into occupied regions of our plot, and that thermophilic proteins prefer specific amino acid pair conformations. Further, we demonstrate experimentally that the effect of a point mutation on backbone conformation and protein stability depends on the amino acid pair context, i.e., the identity of the adjacent amino acid, in a manner predictable by our method.
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Affiliation(s)
- Aviv A. Rosenberg
- Department of Computer Science, Technion–Israel Institute of Technology, Haifa32000, Israel
| | - Nitsan Yehishalom
- Faculty of Biology, Technion–Israel Institute of Technology, Haifa32000, Israel
| | - Ailie Marx
- Department of Computer Science, Technion–Israel Institute of Technology, Haifa32000, Israel
| | - Alex M. Bronstein
- Department of Computer Science, Technion–Israel Institute of Technology, Haifa32000, Israel
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24
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Contardo I, Guzmán F, Enrione J. Conformational and Structural Changes in Chickpea Proteins Caused by Simulated Salivary Alterations in the Elderly. Foods 2023; 12:3668. [PMID: 37835321 PMCID: PMC10572786 DOI: 10.3390/foods12193668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The impact of salivary alterations on chickpea protein structure in the elderly has not been well documented. This study aimed to understand the role of simulated salivary alterations in the conformational properties and secondary structure of the chickpea protein isolate (CPI). Whey protein isolate (WPI) was used as the reference. Protein dispersions (10%) were subjected to in vitro oral processing under simulated salivary conditions in both the elderly and adult subjects. Proteins and their oral counterparts were characterized in terms of their composition, charge, size, solubility, water absorption, molecular weight (MW), and secondary structure (Circular Dichroism and Raman spectroscopy). Under condition of simulated oral digestion in the elderly population, the ordered secondary protein structure was significantly affected, decreasing α-helix by ~36% and ~29% in CPI and WPI compared to the control (adult) population, respectively. An increase in the unordered random coil state was observed. These results could be attributed to an increase in electrolytes in the salivary composition. The structure of CPI is more stable than that of WPI because of its higher MW, more rigid structure, less charged surface, and different amino acid compositions. This study is meaningful in understanding how alterations in the elderly oral system affect protein conformation and is expected to improve the understanding of plant-based protein digestibility.
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Affiliation(s)
- Ingrid Contardo
- Biopolymer Research and Engineering Laboratory (BiopREL), School of Nutrition and Dietetics, Faculty of Medicine, Universidad de los Andes, Chile, Monseñor Álvaro del Portillo 12.455, Las Condes, Santiago 7620086, Chile;
- Centro de Investigación e Innovación Biomédica (CIIB), Universidad de los Andes, Chile, Monseñor Álvaro del Portillo 12.455, Las Condes, Santiago 7620086, Chile
| | - Fanny Guzmán
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile;
| | - Javier Enrione
- Biopolymer Research and Engineering Laboratory (BiopREL), School of Nutrition and Dietetics, Faculty of Medicine, Universidad de los Andes, Chile, Monseñor Álvaro del Portillo 12.455, Las Condes, Santiago 7620086, Chile;
- Centro de Investigación e Innovación Biomédica (CIIB), Universidad de los Andes, Chile, Monseñor Álvaro del Portillo 12.455, Las Condes, Santiago 7620086, Chile
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25
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Okamoto S, Echigoya Y, Tago A, Segawa T, Sato Y, Itou T. Antiviral Efficacy of RNase H-Dependent Gapmer Antisense Oligonucleotides against Japanese Encephalitis Virus. Int J Mol Sci 2023; 24:14846. [PMID: 37834294 PMCID: PMC10573891 DOI: 10.3390/ijms241914846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/23/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
RNase H-dependent gapmer antisense oligonucleotides (ASOs) are a promising therapeutic approach via sequence-specific binding to and degrading target RNAs. However, the efficacy and mechanism of antiviral gapmer ASOs have remained unclear. Here, we investigated the inhibitory effects of gapmer ASOs containing locked nucleic acids (LNA gapmers) on proliferating a mosquito-borne flavivirus, Japanese encephalitis virus (JEV), with high mortality. We designed several LNA gapmers targeting the 3' untranslated region of JEV genomic RNAs. In vitro screening by plaque assay using Vero cells revealed that LNA gapmers targeting a stem-loop region effectively inhibit JEV proliferation. Cell-based and RNA cleavage assays using mismatched LNA gapmers exhibited an underlying mechanism where the inhibition of viral production results from JEV RNA degradation by LNA gapmers in a sequence- and modification-dependent manner. Encouragingly, LNA gapmers potently inhibited the proliferation of five JEV strains of predominant genotypes I and III in human neuroblastoma cells without apparent cytotoxicity. Database searching showed a low possibility of off-target binding of our LNA gapmers to human RNAs. The target viral RNA sequence conservation observed here highlighted their broad-spectrum antiviral potential against different JEV genotypes/strains. This work will facilitate the development of an antiviral LNA gapmer therapy for JEV and other flavivirus infections.
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Affiliation(s)
- Shunsuke Okamoto
- Laboratory of Preventive Veterinary Medicine and Animal Health, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan; (S.O.); (T.S.); (T.I.)
- Nihon University Veterinary Research Center, Fujisawa, Kanagawa 252-0880, Japan; (A.T.); (Y.S.)
| | - Yusuke Echigoya
- Nihon University Veterinary Research Center, Fujisawa, Kanagawa 252-0880, Japan; (A.T.); (Y.S.)
- Laboratory of Biomedical Science, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Ayaka Tago
- Nihon University Veterinary Research Center, Fujisawa, Kanagawa 252-0880, Japan; (A.T.); (Y.S.)
- Laboratory of Biomedical Science, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Takao Segawa
- Laboratory of Preventive Veterinary Medicine and Animal Health, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan; (S.O.); (T.S.); (T.I.)
- Nihon University Veterinary Research Center, Fujisawa, Kanagawa 252-0880, Japan; (A.T.); (Y.S.)
| | - Yukita Sato
- Nihon University Veterinary Research Center, Fujisawa, Kanagawa 252-0880, Japan; (A.T.); (Y.S.)
- Laboratory of Biomedical Science, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Takuya Itou
- Laboratory of Preventive Veterinary Medicine and Animal Health, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan; (S.O.); (T.S.); (T.I.)
- Nihon University Veterinary Research Center, Fujisawa, Kanagawa 252-0880, Japan; (A.T.); (Y.S.)
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Zhang J, Ji S, Zhou G, Cui P, Miao L, Chen Y, Lyu F, Ding Y. Effect of pulsed light on myofibrillar protein of large yellow croaker (Pseudosciaena crocea) during refrigerated storage. J Food Sci 2023; 88:4097-4107. [PMID: 37589300 DOI: 10.1111/1750-3841.16626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 08/18/2023]
Abstract
This study mainly evaluated the effect of different energies of pulsed light (PL) treatment (100, 200, 300, 400, and 500 J/pulse) on myofibrillar protein (MP) of large yellow croaker during refrigerated storage. The results showed that PL treatment would cause a certain degree of oxidation to the MP of large yellow croaker at the initial stage, which showed that the total sulfhydryl content of the protein decreased, the carbonyl content and the average particle size increased, and the β-sheet to β-turn transformation, the tertiary structure of the protein unfolds, and the hydrophobic groups were exposed, causing the reduction of intrinsic fluorescence intensity. However, subsequent storage studies found that PL treatment could slow down the oxidation rate of MP. The decrease rate of total sulfhydryl content and the increase rate of carbonyl content in the 300 J/pulse group were both reduced by about 1.7 times compared with the control group. At the same time, the PL treatment with this intensity could also better protect the secondary structure, tertiary structure, and microstructure of MP. This study provided theoretical basis and reference for analyzing the quality change rule and mechanism of large yellow croaker during refrigerated storage after PL treatment. Studies have shown that PL treatment can reduce the adverse changes of MP in large yellow croaker during cold storage.
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Affiliation(s)
- Jianyou Zhang
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Hangzhou, China
- National R&D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Shengqiang Ji
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Hangzhou, China
- National R&D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, China
| | - Guangcheng Zhou
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Hangzhou, China
- National R&D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, China
| | - Pengbo Cui
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Hangzhou, China
- National R&D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Li Miao
- China Certification & Inspection Group Zhejiang Co., Ltd, Hangzhou, China
| | - Yutong Chen
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Hangzhou, China
- National R&D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, China
| | - Fei Lyu
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Hangzhou, China
- National R&D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Yuting Ding
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Hangzhou, China
- National R&D Branch Center for Pelagic Aquatic Products Processing (Hangzhou), Hangzhou, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
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27
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Xu X, Wang Z, Li M, Su Y, Zhang Q, Zhang S, Hu J. Reconstructed Hierarchically Structured Keratin Fibers with Shape-Memory Features Based on Reversible Secondary-Structure Transformation. Adv Mater 2023; 35:e2304725. [PMID: 37417728 DOI: 10.1002/adma.202304725] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/27/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
Biocompatible and biodegradable shape-memory polymers have gained popularity as smart materials, offering a wide range of applications and environmental benefits. Herein, the possibility of fabricating regenerated water-triggered shape-memory keratin fibers from wool and cellulose in a more effective and environmentally friendly manner is investigated. The regenerated keratin fibers exhibit comparable shape-memory performance to other hydration-responsive materials, with a shape-fixity ratio of 94.8 ± 2.15% and a shape-recovery rate of 81.4 ± 3.84%. Owing to their well-preserved secondary structure and cross-linking network, keratin fibers exhibit outstanding water-stability and wet stretchability, with a maximum tensile strain of 362 ± 15.9%. In this system, the reconfiguration of the protein secondary structure between α-helix and β-sheet is investigated as the fundamental actuation mechanism in response to hydration. This responsiveness is studied under force loading and unloading along the fiber axis. Hydrogen bonds act as the "switches" clicked by water molecules to trigger the shape-memory effect, while disulfide bonds and cellulose nanocrystals play the role of "net-points" to maintain the permanent shape of the material. Water-triggered shape-memory keratin fibers are manipulable and exhibit potential in the fabrication of textile actuators, which may be applied in smart apparel and programmable biomedical devices.
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Affiliation(s)
- Xiaoyun Xu
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong SAR, 999077, China
| | - Zhuang Wang
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong SAR, 999077, China
| | - Min Li
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong SAR, 999077, China
| | - Yupei Su
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong SAR, 999077, China
| | - Qi Zhang
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong SAR, 999077, China
| | - Shuai Zhang
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong SAR, 999077, China
| | - Jinlian Hu
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong SAR, 999077, China
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28
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Le N, Chand A, Braun E, Keyes C, Wu Q, Kim K. Interactions between Quantum Dots and G-Actin. Int J Mol Sci 2023; 24:14760. [PMID: 37834208 PMCID: PMC10572542 DOI: 10.3390/ijms241914760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/16/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Quantum dots (QDs) are a type of nanoparticle with excellent optical properties, suitable for many optical-based biomedical applications. However, the potential of quantum dots to be used in clinical settings is limited by their toxicity. As such, much effort has been invested to examine the mechanism of QDs' toxicity. Yet, the current literature mainly focuses on ROS- and apoptosis-mediated cell death induced by QDs, which overlooks other aspects of QDs' toxicity. Thus, our study aimed to provide another way by which QDs negatively impact cellular processes by investigating the possibility of protein structure and function modification upon direct interaction. Through shotgun proteomics, we identified a number of QD-binding proteins, which are functionally associated with essential cellular processes and components, such as transcription, translation, vesicular trafficking, and the actin cytoskeleton. Among these proteins, we chose to closely examine the interaction between quantum dots and actin, as actin is one of the most abundant proteins in cells and plays crucial roles in cellular processes and structural maintenance. We found that CdSe/ZnS QDs spontaneously bind to G-actin in vitro, causing a static quenching of G-actin's intrinsic fluorescence. Furthermore, we found that this interaction favors the formation of a QD-actin complex with a binding ratio of 1:2.5. Finally, we also found that CdSe/ZnS QDs alter the secondary structure of G-actin, which may affect G-actin's function and properties. Overall, our study provides an in-depth mechanistic examination of the impact of CdSe/ZnS QDs on G-actin, proposing that direct interaction is another aspect of QDs' toxicity.
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Affiliation(s)
- Nhi Le
- Department of Biology, Missouri State University, Springfield, MO 65897, USA; (N.L.); (A.C.); (E.B.)
| | - Abhishu Chand
- Department of Biology, Missouri State University, Springfield, MO 65897, USA; (N.L.); (A.C.); (E.B.)
| | - Emma Braun
- Department of Biology, Missouri State University, Springfield, MO 65897, USA; (N.L.); (A.C.); (E.B.)
| | - Chloe Keyes
- Jordan Valley Innovation Center, Springfield, MO 65806, USA; (C.K.); (Q.W.)
| | - Qihua Wu
- Jordan Valley Innovation Center, Springfield, MO 65806, USA; (C.K.); (Q.W.)
| | - Kyoungtae Kim
- Department of Biology, Missouri State University, Springfield, MO 65897, USA; (N.L.); (A.C.); (E.B.)
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29
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Vargas-Rosales P, D’Addio A, Zhang Y, Caflisch A. Disrupting Dimeric β-Amyloid by Electric Fields. ACS Phys Chem Au 2023; 3:456-466. [PMID: 37780539 PMCID: PMC10540290 DOI: 10.1021/acsphyschemau.3c00021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/26/2023] [Accepted: 06/26/2023] [Indexed: 10/03/2023]
Abstract
The early oligomers of the amyloid Aβ peptide are implicated in Alzheimer's disease, but their transient nature complicates the characterization of their structure and toxicity. Here, we investigate the stability of the minimal toxic species, i.e., β-amyloid dimers, in the presence of an oscillating electric field. We first use deep learning (AlphaFold-multimer) for generating initial models of Aβ42 dimers. The flexibility and secondary structure content of the models are then analyzed by multiple runs of molecular dynamics (MD). Structurally stable models are similar to ensemble representatives from microsecond-long MD sampling. Finally, we employ the validated model as the starting structure of MD simulations in the presence of an external oscillating electric field and observe a fast decay of β-sheet content at high field strengths. Control simulations using the helical dimer of the 42-residue leucine zipper peptide show higher structural stability than the Aβ42 dimer. The simulation results provide evidence that an external electric field (oscillating at 1 GHz) can disrupt amyloid oligomers which should be further investigated by experiments with brain organoids in vitro and eventually in vivo.
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Affiliation(s)
| | - Alessio D’Addio
- Department of Biochemistry, University of Zurich, CH-8057 Zürich, Switzerland
| | - Yang Zhang
- Department of Biochemistry, University of Zurich, CH-8057 Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, CH-8057 Zürich, Switzerland
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30
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Martins C, Diharce J, Nadaradjane AA, de Brevern AG. Evaluation of the Potential Impact of In Silico Humanization on V HH Dynamics. Int J Mol Sci 2023; 24:14586. [PMID: 37834033 PMCID: PMC10572902 DOI: 10.3390/ijms241914586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/14/2023] [Accepted: 09/16/2023] [Indexed: 10/15/2023] Open
Abstract
Camelids have the peculiarity of having classical antibodies composed of heavy and light chains as well as single-chain antibodies. They have lost their light chains and one heavy-chain domain. This evolutionary feature means that their terminal heavy-chain domain, VH, called VHH here, has no partner and forms an independent domain. The VHH is small and easy to express alone; it retains thermodynamic and interaction properties. Consequently, VHHs have garnered significant interest from both biotechnological and pharmaceutical perspectives. However, due to their origin in camelids, they cannot be used directly on humans. A humanization step is needed before a possible use. However, changes, even in the constant parts of the antibodies, can lead to a loss of quality. A dedicated tool, Llamanade, has recently been made available to the scientific community. In a previous paper, we already showed the different types of VHH dynamics. Here, we have selected a representative VHH and tested two humanization hypotheses to accurately assess the potential impact of these changes. This example shows that despite the non-negligible change (1/10th of residues) brought about by humanization, the effect is not drastic, and the humanized VHH retains conformational properties quite similar to those of the camelid VHH.
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Affiliation(s)
- Carla Martins
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-75014 Paris, France; (C.M.); (J.D.)
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-97715 Saint Denis Messag, France
| | - Julien Diharce
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-75014 Paris, France; (C.M.); (J.D.)
| | - Aravindan Arun Nadaradjane
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-97715 Saint Denis Messag, France
| | - Alexandre G. de Brevern
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-75014 Paris, France; (C.M.); (J.D.)
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-97715 Saint Denis Messag, France
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31
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Zavatski S, Dubkov S, Gromov D, Bandarenka H. Comparative Study of SERS-Spectra of NQ21 Peptide on Silver Particles and in Gold-Coated "Nanovoids". Biosensors (Basel) 2023; 13:895. [PMID: 37754129 PMCID: PMC10526949 DOI: 10.3390/bios13090895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/21/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023]
Abstract
The NQ21 peptide has relatively recently attracted attention in the biomedical sphere due to its prospects for facilitating the engineering of the HIV1 vaccine and ELISA test. Today, there is still a need for a reliable and fast methodology that reveals the secondary structure of this analyte at the low concentrations conventionally used in vaccines and immunological assays. The present research determined the differences between the surface-enhanced Raman scattering (SERS) spectra of NQ21 peptide molecules adsorbed on solid SERS-active substrates depending on their geometry and composition. The ultimate goal of our research was to propose an algorithm and SERS-active material for structural analysis of peptides. Phosphate buffer solutions of the 30 µg/mL NQ21 peptide at different pH levels were used for the SERS measurements, with silver particles on mesoporous silicon and gold-coated "nanovoids" in macroporous silicon. The SERS analysis of the NQ21 peptide was carried out by collecting the SERS spectra maps. The map assessment with an originally developed algorithm resulted in defining the effect of the substrate on the secondary structure of the analyte molecules. Silver particles are recommended for peptide detection if it is not urgent to precisely reveal all the characteristic bands, because they provide greater enhancement but are accompanied by analyte destruction. If the goal is to carefully study the secondary structure and composition of the peptide, it is better to use SERS-active gold-coated "nanovoids". Objective results can be obtained by collecting at least three 15 × 15 maps of the SERS spectra of a given peptide on substrates from different batches.
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Affiliation(s)
- Siarhei Zavatski
- Applied Plasmonic Laboratory, Belarusian State University of Informatics and Radioelectronics, 220013 Minsk, Belarus;
| | - Sergey Dubkov
- Institute of Advanced Materials and Technologies, National Research University of Electronic Technology, Moscow 124498, Russia; (S.D.)
| | - Dmitry Gromov
- Institute of Advanced Materials and Technologies, National Research University of Electronic Technology, Moscow 124498, Russia; (S.D.)
- Institute for Bionic Technologies and Engineering, I.M. Sechenov First Moscow State Medical University, Moscow 119435, Russia
| | - Hanna Bandarenka
- Applied Plasmonic Laboratory, Belarusian State University of Informatics and Radioelectronics, 220013 Minsk, Belarus;
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Carvajal-Mena N, Tabilo-Munizaga G, Saldaña MDA, Pérez-Won M, Herrera-Lavados C, Lemus-Mondaca R, Moreno-Osorio L. Three-Dimensional Printing Parameter Optimization for Salmon Gelatin Gels Using Artificial Neural Networks and Response Surface Methodology: Influence on Physicochemical and Digestibility Properties. Gels 2023; 9:766. [PMID: 37754446 PMCID: PMC10530252 DOI: 10.3390/gels9090766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023] Open
Abstract
This study aimed to optimize the 3D printing parameters of salmon gelatin gels (SGG) using artificial neural networks with the genetic algorithm (ANN-GA) and response surface methodology (RSM). In addition, the influence of the optimal parameters obtained using the two different methodologies was evaluated for the physicochemical and digestibility properties of the printed SGG (PSGG). The ANN-GA had a better fit (R2 = 99.98%) with the experimental conditions of the 3D printing process than the RSM (R2 = 93.99%). The extrusion speed was the most influential parameter according to both methodologies. The optimal values of the printing parameters for the SGG were 0.70 mm for the nozzle diameter, 0.5 mm for the nozzle height, and 24 mm/s for the extrusion speed. Gel thermal properties showed that the optimal 3D printing conditions affected denaturation temperature and enthalpy, improving digestibility from 46.93% (SGG) to 51.52% (PSGG). The secondary gel structures showed that the β-turn structure was the most resistant to enzymatic hydrolysis, while the intermolecular β-sheet was the most labile. This study validated two optimization methodologies to achieve optimal 3D printing parameters of salmon gelatin gels, with improved physicochemical and digestibility properties for use as transporters to incorporate high value nutrients to the body.
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Affiliation(s)
- Nailín Carvajal-Mena
- Department of Food Engineering, Universidad del Bío-Bío, Avenida Andrés Bello 720, Chillán 3780000, Chile; (N.C.-M.); (M.P.-W.); (C.H.-L.)
| | - Gipsy Tabilo-Munizaga
- Department of Food Engineering, Universidad del Bío-Bío, Avenida Andrés Bello 720, Chillán 3780000, Chile; (N.C.-M.); (M.P.-W.); (C.H.-L.)
| | - Marleny D. A. Saldaña
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada;
| | - Mario Pérez-Won
- Department of Food Engineering, Universidad del Bío-Bío, Avenida Andrés Bello 720, Chillán 3780000, Chile; (N.C.-M.); (M.P.-W.); (C.H.-L.)
| | - Carolina Herrera-Lavados
- Department of Food Engineering, Universidad del Bío-Bío, Avenida Andrés Bello 720, Chillán 3780000, Chile; (N.C.-M.); (M.P.-W.); (C.H.-L.)
| | - Roberto Lemus-Mondaca
- Department of Food Science and Chemical Technology, Universidad de Chile, Santos Dumont 964, Santiago 8330015, Chile;
| | - Luis Moreno-Osorio
- Department of Basic Sciences, Universidad del Bío-Bío, Avenida Andrés Bello 720, Chillán 3780000, Chile;
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Mendivil A, Ramírez R, Morin J, Ramirez JL, Siccha-Ramirez R, Britzke R, Rivera F, Ampuero A, Oliveros N, Congrains C. Comparative Mitogenome Analysis of Two Native Apple Snail Species (Ampullariidae, Pomacea) from Peruvian Amazon. Genes (Basel) 2023; 14:1769. [PMID: 37761909 PMCID: PMC10531094 DOI: 10.3390/genes14091769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/22/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Apple snails of the genus Pomacea Perry, 1810 (Mollusca: Caenogastropoda: Ampullariidae) are native to the Neotropics and exhibit high species diversity, holding cultural and ecological significance as an important protein source in Peru. However, most genetic studies in Pomacea have focused mostly on invasive species, especially in Southeast Asia, where they are considered important pests. In this study, we assembled and annotated the mitochondrial genomes of two Pomacea species native to the Peruvian Amazon: Pomacea reevei Ampuero & Ramírez, 2023 and Pomacea aulanieri (Deville & Hupé, 1850). The mitogenomes of P. reevei and P. aulanieri comprise 15,660 and 16,096 bp, respectively, and contain the typical 37 genes of the animal mitochondria with a large control region of 292 bp in P. reevei and 524 bp in P. aulanieri-which fall within the range of what is currently known in Pomacea. Comparisons with previously published mitogenomes in Pomacea revealed differences in the overlapping of adjacent genes, the size of certain protein-coding genes (PCGs) and the secondary structure of some tRNAs that are consistent with the phylogenetic relationships between these species. These findings provide valuable insights into the systematics and genomics of the genus Pomacea.
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Affiliation(s)
- Alejandro Mendivil
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Carlos Germán Amezaga 375, Lima 15081, Peru; (A.M.); (J.L.R.); (R.S.-R.); (R.B.); (F.R.); (N.O.)
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima 15046, Peru
| | - Rina Ramírez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Carlos Germán Amezaga 375, Lima 15081, Peru; (A.M.); (J.L.R.); (R.S.-R.); (R.B.); (F.R.); (N.O.)
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima 15046, Peru
| | - Jaime Morin
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Carlos Germán Amezaga 375, Lima 15081, Peru; (A.M.); (J.L.R.); (R.S.-R.); (R.B.); (F.R.); (N.O.)
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima 15046, Peru
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Erlings Skakkes gate 47B, 7012 Trondheim, Norway; (J.M.)
| | - Jorge L. Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Carlos Germán Amezaga 375, Lima 15081, Peru; (A.M.); (J.L.R.); (R.S.-R.); (R.B.); (F.R.); (N.O.)
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima 15046, Peru
| | - Raquel Siccha-Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Carlos Germán Amezaga 375, Lima 15081, Peru; (A.M.); (J.L.R.); (R.S.-R.); (R.B.); (F.R.); (N.O.)
| | - Ricardo Britzke
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Carlos Germán Amezaga 375, Lima 15081, Peru; (A.M.); (J.L.R.); (R.S.-R.); (R.B.); (F.R.); (N.O.)
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima 15046, Peru
| | - Fátima Rivera
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Carlos Germán Amezaga 375, Lima 15081, Peru; (A.M.); (J.L.R.); (R.S.-R.); (R.B.); (F.R.); (N.O.)
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima 15046, Peru
| | - Andre Ampuero
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima 15046, Peru
- Department of Marine Zoology, Senckenberg Research Institute, 60325 Frankfurt am Main, Germany; (A.A.)
| | - Nilda Oliveros
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Carlos Germán Amezaga 375, Lima 15081, Peru; (A.M.); (J.L.R.); (R.S.-R.); (R.B.); (F.R.); (N.O.)
| | - Carlos Congrains
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, HI 96822, USA;
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, HI 96720, USA
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Arnittali M, Rissanou AN, Kefala A, Kokkinidis M, Harmandaris V. Structure of amino acid sequence-reversed wtRop protein: insights from atomistic molecular dynamics simulations. J Biomol Struct Dyn 2023:1-15. [PMID: 37671833 DOI: 10.1080/07391102.2023.2252903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/23/2023] [Indexed: 09/07/2023]
Abstract
This study aims to the investigation of the advantages of designing new proteins presume upon a 'bias' sequence of amino acids, based on the reversed sequence of parent proteins, such as the retro ones. The structural simplicity of wtRop offers a very attractive model system to study these aspects. The current work is based on all-atom Molecular Dynamics (MD) simulations and corresponding experimental evidence on two different types of reversed wtRop protein, one with a fully reversed sequence of amino acids (rRop) and another with a partially reversed sequence (prRop), where only the five residues of the loop region (30ASP-34GLN) were not reversed. The exploration of the structure of the two retro proteins is performed highlighting the similarities and the differences with their parent protein, by employing various measures. Two models have been studied for both reversed proteins, a dimeric and a monomeric with the former one found to be more stable than the latter. Preferable equilibrium structures that the protein molecule can attain are explored, indicating the equilibration pathway. Simulation findings indicate a disruption of the α-helical structure and the appearance of additional secondary structures for both retro proteins. Reduced structural stability compared to their parent protein (wtRop) is also found. A corruption of the hydrophobic core is observed in the dimeric models. Furthermore, the simulations findings are consistent with the experimental characterization of prRop by circular dichroism spectroscopy (CD) which highlights an unstable, highly α-helical protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maria Arnittali
- Computation-Based Science and Technology Research Center, The Cyprus Institute, Nicosia, Cyprus
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology Hellas (FORTH), Heraklion, Greece
- Department of Mathematics and Applied Mathematics, University of Crete, Heraklion, Crete, Greece
| | - Anastassia N Rissanou
- National Hellenic Research Foundation, Theoretical and Physical Chemistry Institute, Athens, Greece
| | - Aikaterini Kefala
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (FORTH), Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (FORTH), Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Vagelis Harmandaris
- Computation-Based Science and Technology Research Center, The Cyprus Institute, Nicosia, Cyprus
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology Hellas (FORTH), Heraklion, Greece
- Department of Mathematics and Applied Mathematics, University of Crete, Heraklion, Crete, Greece
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Jiménez-Gaona Y, Vivanco-Galván O, Cruz D, Armijos-Carrión A, Suárez JP. Compensatory Base Changes in ITS2 Secondary Structure Alignment, Modelling, and Molecular Phylogeny: An Integrated Approach to Improve Species Delimitation in Tulasnella (Basidiomycota). J Fungi (Basel) 2023; 9:894. [PMID: 37755002 PMCID: PMC10532482 DOI: 10.3390/jof9090894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/08/2023] [Accepted: 08/17/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND The delimitation of species of Tulasnella has been extensively studied, mainly at the morphological (sexual and asexual states) and molecular levels-showing ambiguity between them. An integrative species concept that includes characteristics such as molecular, ecology, morphology, and other information is crucial for species delimitation in complex groups such as Tulasnella. OBJECTIVES The aim of this study is to test evolutionary relationships using a combination of alignment-based and alignment-free distance matrices as an alternative molecular tool to traditional methods, and to consider the secondary structures and CBCs from ITS2 (internal transcribed spacer) sequences for species delimitation in Tulasnella. METHODOLOGY Three phylogenetic approaches were plotted: (i) alignment-based, (ii) alignment-free, and (iii) a combination of both distance matrices using the DISTATIS and pvclust libraries from an R package. Finally, the secondary structure consensus was modeled by Mfold, and a CBC analysis was obtained to complement the species delimitation using 4Sale. RESULTS AND CONCLUSIONS The phylogenetic tree results showed delimited monophyletic clades in Tulasnella spp., where all 142 Tulasnella sequences were divided into two main clades A and B and assigned to seven species (T. asymmetrica, T. andina, T. eichleriana ECU6, T. eichleriana ECU4 T. pinicola, T. violea), supported by bootstrap values from 72% to 100%. From the 2D secondary structure alignment, three types of consensus models with helices and loops were obtained. Thus, T. albida belongs to type I; T. eichleriana, T. tomaculum, and T. violea belong to type II; and T. asymmetrica, T. andina, T. pinicola, and T. spp. (GER) belong to type III; each type contains four to six domains, with nine CBCs among these that corroborate different species.
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Affiliation(s)
- Yuliana Jiménez-Gaona
- Departamento de Química, Universidad Técnica Particular de Loja (UTPL), San Cayetano Alto s/n, Loja 1101608, Ecuador
| | - Oscar Vivanco-Galván
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja (UTPL), San Cayetano Alto s/n, Loja 1101608, Ecuador; (O.V.-G.); (D.C.); (J.P.S.)
| | - Darío Cruz
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja (UTPL), San Cayetano Alto s/n, Loja 1101608, Ecuador; (O.V.-G.); (D.C.); (J.P.S.)
| | - Angelo Armijos-Carrión
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL A1B 3X9, Canada;
| | - Juan Pablo Suárez
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja (UTPL), San Cayetano Alto s/n, Loja 1101608, Ecuador; (O.V.-G.); (D.C.); (J.P.S.)
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Ito T, Matsunaga N, Kurashima M, Demizu Y, Misawa T. Enhancing Chemical Stability through Structural Modification of Antimicrobial Peptides with Non-Proteinogenic Amino Acids. Antibiotics (Basel) 2023; 12:1326. [PMID: 37627746 PMCID: PMC10451648 DOI: 10.3390/antibiotics12081326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Multidrug-resistant bacteria (MDRB) remain a significant threat to humanity, resulting in over 1.2 million deaths per year. To combat this problem effectively, the development of therapeutic agents with diverse mechanisms of action is crucial. Antimicrobial peptides (AMPs) have emerged as promising next-generation therapeutics to combat infectious diseases, particularly MDRB. By targeting microbial membranes and inducing lysis, AMPs can effectively inhibit microbial growth, making them less susceptible to the development of resistance. Numerous structural advancements have been made to optimize the efficacy of AMPs. Previously, we developed 17KKV-Aib, a derivative of the Magainin 2 (Mag2) peptide, by incorporating a,a-disubstituted amino acids (dAAs) to modulate its secondary structure. 17KKV-Aib demonstrated potent antimicrobial activity against Gram-positive and Gram-negative bacteria, including multidrug-resistant Pseudomonas aeruginosa (MDRP), with minimal hemolytic activity against human red blood cells. However, 17KKV-Aib faces challenges regarding its susceptibility to digestive enzymes, hindering its potential as an antimicrobial agent. In this study, we designed and synthesized derivatives of 17KKV-Aib, replacing Lys residues with 4-aminopiperidine-4-carboxylic acid (Api), which is a cyclized dAA residue possessing cationic properties on its side chain. We investigated the impact of Api substitution on the secondary structure, antimicrobial activity, hemolytic activity, and resistance to digestive enzymes. Our findings revealed that introducing Api residues preserved the helical structure and antimicrobial activity and enhanced resistance to digestive enzymes, with a slight increase in hemolytic activity.
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Affiliation(s)
- Takahito Ito
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-shi 210-9501, Japan; (T.I.)
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Yokohama 230-0045, Japan
| | - Natsumi Matsunaga
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-shi 210-9501, Japan; (T.I.)
| | - Megumi Kurashima
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-shi 210-9501, Japan; (T.I.)
| | - Yosuke Demizu
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-shi 210-9501, Japan; (T.I.)
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Yokohama 230-0045, Japan
| | - Takashi Misawa
- National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-shi 210-9501, Japan; (T.I.)
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Taha A, Casanova F, Talaikis M, Stankevič V, Žurauskienė N, Šimonis P, Pakštas V, Jurkūnas M, Gomaa MAE, Stirkė A. Effects of Pulsed Electric Field on the Physicochemical and Structural Properties of Micellar Casein. Polymers (Basel) 2023; 15:3311. [PMID: 37571205 PMCID: PMC10422647 DOI: 10.3390/polym15153311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023] Open
Abstract
Pulsed electric field (PEF) as a green processing technology is drawing greater attention due to its eco-friendliness and potential to promote sustainable development goals. In this study, the effects of different electric field strengths (EFS, 0-30 kV/cm) on the structure and physicochemical features of casein micelles (CSMs) were investigated. It was found that the particle sizes of CSMs increased at low EFS (10 kV/cm) but decreased at high EFS (30 kV/cm). The absolute ζ-potential at 30 kV/cm increased from -26.6 (native CSMs) to -29.5 mV. Moreover, it was noticed that PEF treatment leads to changes in the surface hydrophobicity; it slightly increased at low EFS (10 kV/cm) but decreased at EFS > 10 kV/cm. PEF enhanced the protein solubility from 84.9 (native CSMs) to 87.1% (at 10 kV/cm). PEF at low EFS (10 kV/cm) intensified the emission fluorescence spectrum of CSMs, while higher EFS reduced the fluorescence intensity compared to native CSMs. Moreover, the analysis of the Amide Ι region showed that PEF-treated CSMs reduced the α-helix and increased the β-sheet content. Raman spectra confirmed that PEF treatment > 10 kV/cm buried tyrosine (Tyr) residues in a hydrophobic environment. It was also found that PEF treatment mainly induced changes in the disulfide linkages. In conclusion, PEF technology can be employed as an eco-friendly technology to change the structure and physiochemical properties of CSMs; this could improve their techno-functional properties.
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Affiliation(s)
- Ahmed Taha
- State Research Institute Center for Physical Sciences and Technology, Saulėtekio al. 3, LT-10257 Vilnius, Lithuania (A.S.)
| | - Federico Casanova
- Food Production Engineering, National Food Institute, Technical University of Denmark, 2800 Lyngby, Denmark;
| | - Martynas Talaikis
- State Research Institute Center for Physical Sciences and Technology, Saulėtekio al. 3, LT-10257 Vilnius, Lithuania (A.S.)
| | - Voitech Stankevič
- State Research Institute Center for Physical Sciences and Technology, Saulėtekio al. 3, LT-10257 Vilnius, Lithuania (A.S.)
| | - Nerija Žurauskienė
- State Research Institute Center for Physical Sciences and Technology, Saulėtekio al. 3, LT-10257 Vilnius, Lithuania (A.S.)
| | - Povilas Šimonis
- State Research Institute Center for Physical Sciences and Technology, Saulėtekio al. 3, LT-10257 Vilnius, Lithuania (A.S.)
| | - Vidas Pakštas
- State Research Institute Center for Physical Sciences and Technology, Saulėtekio al. 3, LT-10257 Vilnius, Lithuania (A.S.)
| | - Marijus Jurkūnas
- State Research Institute Center for Physical Sciences and Technology, Saulėtekio al. 3, LT-10257 Vilnius, Lithuania (A.S.)
| | - Mohamed A. E. Gomaa
- Department of Food Science, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria 21531, Egypt
| | - Arūnas Stirkė
- State Research Institute Center for Physical Sciences and Technology, Saulėtekio al. 3, LT-10257 Vilnius, Lithuania (A.S.)
- Micro and Nanodevices Laboratory, Institute of Solid State Physics, University of Latvia, Kengaraga Str. 8, LV-1063 Riga, Latvia
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Liu Y, Yang L, Zhao S, Zhao Y, Kang Z, Zhu M, He H, Ma H. Effect of Artemisia sphaerocephala krasch gum on the functional properties of pork batters. J Texture Stud 2023; 54:571-581. [PMID: 36793251 DOI: 10.1111/jtxs.12746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 10/09/2022] [Accepted: 02/06/2023] [Indexed: 02/17/2023]
Abstract
The influence of the incorporation of Artemisia sphaerocephala krasch gum (ASK gum; 0-0.18%) on the water holding capability (WHC), texture, color, rheological property, water distribution, protein conformation and microstructure of pork batters was investigated. The results showed that the cooking yield, WHC and L* value of pork batter gels significantly increased (p < .05) with the increasing incorporation of ASK gum, and the highest value were observed at 0.15%; the a* value decreased significantly (p < .05) and no significance was obtained in b* value (p > .05); the hardness, elasticity, cohesiveness and chewiness increased first and then decreased, and reached the highest value at 0.15%. The rheological results showed that the higher G' value was obtained in pork batters by the incorporation of ASK gum; the low field NMR analysis indicated that ASK gum significantly increased the proportion of P2b and P21 (p < .05) and decreased the proportion of P22 ; Fourier transform infrared spectroscopy (FTIR) indicated that the ASK gum significantly reduced the α-helix content and increased the β-sheet content (p < .05). Scanning electron microscopy results suggested that the incorporation of ASK gum could promote the formation of a more homogeneous and stable microstructure of pork batter gels. Therefore, appropriate incorporation (0.15%) of ASK gum may improve the gel properties of pork batters, and while excessive incorporation (0.18%) could weaken the gel properties.
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Affiliation(s)
- Yu Liu
- School of Food Science and Technology, Henan Institute of Science and Technology, Xinxiang, People's Republic of China
- National Pork Processing Technology Research and Development Professional Center, Xinxiang, People's Republic of China
| | - Liu Yang
- School of Food Science and Technology, Henan Institute of Science and Technology, Xinxiang, People's Republic of China
- National Pork Processing Technology Research and Development Professional Center, Xinxiang, People's Republic of China
| | - Shengming Zhao
- School of Food Science and Technology, Henan Institute of Science and Technology, Xinxiang, People's Republic of China
- National Pork Processing Technology Research and Development Professional Center, Xinxiang, People's Republic of China
| | - Yanyan Zhao
- School of Food Science and Technology, Henan Institute of Science and Technology, Xinxiang, People's Republic of China
| | - Zhuangli Kang
- School of Food Science and Technology, Henan Institute of Science and Technology, Xinxiang, People's Republic of China
- National Pork Processing Technology Research and Development Professional Center, Xinxiang, People's Republic of China
| | - Mingming Zhu
- School of Food Science and Technology, Henan Institute of Science and Technology, Xinxiang, People's Republic of China
- National Pork Processing Technology Research and Development Professional Center, Xinxiang, People's Republic of China
| | - Hongju He
- School of Food Science and Technology, Henan Institute of Science and Technology, Xinxiang, People's Republic of China
- National Pork Processing Technology Research and Development Professional Center, Xinxiang, People's Republic of China
| | - Hanjun Ma
- School of Food Science and Technology, Henan Institute of Science and Technology, Xinxiang, People's Republic of China
- National Pork Processing Technology Research and Development Professional Center, Xinxiang, People's Republic of China
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Chira S, Ciocan C, Bica C, Calin GA, Berindan-Neagoe I. Artificial miRNAs derived from miR-181 family members have potential in cancer therapy due to an altered spectrum of target mRNAs. FEBS Lett 2023; 597:1989-2005. [PMID: 37283340 DOI: 10.1002/1873-3468.14673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/08/2023] [Accepted: 05/22/2023] [Indexed: 06/08/2023]
Abstract
miRNAs are a class of noncoding RNAs with gene regulation properties, and they function as key factors in cell homeostasis. The interaction of miRNAs with their target mRNAs is largely considered to rely on sequence complementarity; however, some evidence indicates that mature miRNAs can adopt diverse conformations with implications for their function. Using the oncogenic miR-181 family as a study model, we suggest that a potential relationship between the primary sequence and secondary structure of miRNAs may have an impact on the number and spectrum of targeted cellular transcripts. We further emphasize that specific alterations in miR-181 primary sequences might impose certain constraints on target gene selection compared with the wild-type sequences, leading to the targeting of new transcripts with upregulated function in cancer.
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Affiliation(s)
- Sergiu Chira
- Research Center for Functional Genomics, Biomedicine, and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cristina Ciocan
- Research Center for Functional Genomics, Biomedicine, and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cecilia Bica
- Research Center for Functional Genomics, Biomedicine, and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - George A Calin
- Translational Molecular Pathology, MD Anderson Cancer Center, Texas State University, Houston, TX, USA
- The RNA Interference and Non-codingRNA Center, MD Anderson Cancer Center, Texas State University, Houston, TX, USA
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine, and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
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Xie C, Shi BB, Liu GH, Li SH, Kang ZL. Using Potassium Bicarbonate to Improve the Water-Holding Capacity, Gel and Rheology Characteristics of Reduced-Phosphate Silver Carp Batters. Molecules 2023; 28:5608. [PMID: 37513480 PMCID: PMC10386509 DOI: 10.3390/molecules28145608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
To study the use of partial or total potassium bicarbonate (PBC) to replace sodium tripolyphosphate (STPP) on reduced-phosphate silver carp batters, all the batters were composed of silver carp surimi, pork back fat, ice water, spices, sugar, and sodium chloride. Therein, the sample of T1 contained 4 g/kg STPP; T2 contained 1 g/kg PBC, 3 g/kg STPP; T3 contained 2 g/kg PBC, 2 g/kg STPP; T4 contained 3 g/kg PBC, 1 g/kg STPP; T5 contained 4 g/kg PBC, and they were all produced using a bowl chopper. The changes in pH, whiteness, water- and oil-holding capacity, gel and rheological properties, as well as protein conformation were investigated. The pH, cooking yield, water- and oil-holding capacity, texture properties, and the G' values at 90 °C of the reduced-phosphate silver carp batters with PBC significantly increased (p < 0.05) compared to the sample without PBC. Due to the increasing pH and enhanced ion strength, more β-sheet and β-turns structures were formed. Furthermore, by increasing PBC, the pH significantly increased (p < 0.05) and the cooked silver carp batters became darkened. Meanwhile, more CO2 was generated, which destroyed the gel structure, leading the water- and oil-holding capacity, texture properties, and G' values at 90 °C to be increased and then decreased. Overall, using PBC partial as a substitute of STPP enables reduced-phosphate silver carp batter to have better gel characteristics and water-holding capacity by increasing its pH and changing its rheology characteristic and protein conformation.
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Affiliation(s)
- Chun Xie
- School of Pharmacy, Shangqiu Medical College, Shangqiu 476100, China
| | - Bei-Bei Shi
- School of Pharmacy, Shangqiu Medical College, Shangqiu 476100, China
| | - Guang-Hui Liu
- School of Pharmacy, Shangqiu Medical College, Shangqiu 476100, China
| | - Si-Han Li
- School of Pharmacy, Shangqiu Medical College, Shangqiu 476100, China
| | - Zhuang-Li Kang
- Engineering Research Center for Huaiyang Cuisin of Jiangsu Province, College of Tourism and Culinary, Yangzhou University, Yangzhou 225127, China
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Wu KE, Zou JY, Chang H. Machine learning modeling of RNA structures: methods, challenges and future perspectives. Brief Bioinform 2023; 24:bbad210. [PMID: 37280185 DOI: 10.1093/bib/bbad210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/12/2023] [Accepted: 05/17/2023] [Indexed: 06/08/2023] Open
Abstract
The three-dimensional structure of RNA molecules plays a critical role in a wide range of cellular processes encompassing functions from riboswitches to epigenetic regulation. These RNA structures are incredibly dynamic and can indeed be described aptly as an ensemble of structures that shifts in distribution depending on different cellular conditions. Thus, the computational prediction of RNA structure poses a unique challenge, even as computational protein folding has seen great advances. In this review, we focus on a variety of machine learning-based methods that have been developed to predict RNA molecules' secondary structure, as well as more complex tertiary structures. We survey commonly used modeling strategies, and how many are inspired by or incorporate thermodynamic principles. We discuss the shortcomings that various design decisions entail and propose future directions that could build off these methods to yield more robust, accurate RNA structure predictions.
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Affiliation(s)
- Kevin E Wu
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - James Y Zou
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Chang
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
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Wu J, Xu D, Wei X, Liao W, Li X, Zhuo Z. Characterization of the complete mitochondrial genome of the longhorn beetle, Batocerahorsfieldi (Coleoptera, Cerambycidae) and its phylogenetic analysis with suitable longhorn beetles. Zookeys 2023; 1168:387-402. [PMID: 37448482 PMCID: PMC10336557 DOI: 10.3897/zookeys.1168.105328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Mitochondrial genome analysis is an important tool for studying insect phylogenetics. The longhorn beetle, Batocerahorsfieldi, is a significant pest in timber, economic and protection forests. This study determined the mitochondrial genome of B.horsfieldi and compared it with the mitochondrial genomes of other Cerambycidae with the aim of exploring the phylogenetic status of the pest and the evolutionary relationships among some Cerambycidae subgroups. The complete mitochondrial genome of B.horsfieldi was sequenced by the Illumina HiSeq platform. The mitochondrial genome was aligned and compared with the existing mitochondrial genomes of Batoceralineolata and B.rubus in GenBank (MF521888, MW629558, OM161963, respectively). The secondary structure of transfer RNA (tRNA) was predicted using tRNAScan-SE server v.1.21 and MITOS WebSever. Thirteen protein-coding genes (PCGs) and two ribosomal RNA gene sequences of 21 longhorn beetles, including B.horsfieldi, plus two outgroups, Dryopsernesti (Dryopidae) and Heterocerusparallelus (Heteroceridae), were analyzed. The phylogenetic tree was constructed using maximum likelihood and Bayesian inference methods. In this study, we successfully obtained the complete mitochondrial genome of B.horsfieldi for the first time, which is 15 425 bp in length. It contains 37 genes and an A + T-rich region, arranged in the same order as the recognized ancestor of longhorn beetles. The genome of B.horsfieldi is composed of 33.12% A bases, 41.64% T bases, 12.08% C bases, and 13.16% G bases. The structure, nucleotide composition, and codon usage of the new mitochondrial genome are not significantly different from other longhorn mitochondrial genomes. Phylogenetic analyses revealed that Cerambycidae formed a highly supported single clade, and Vesperidae was either clustered with Cerambycidae or formed a separate clade. Interestingly, B.horsfieldi, B.rubus and B.lineolata were clustered with Monochamus and Anoplophora species in both analyses, with high node support. Additionally, the VesperidaeSpiniphilusspinicornis and Vesperussanzi and the 19 Cerambycidae species formed a sister clade in the Bayesian analysis. Our results have produced new complete mitogenomic data, which will provide information for future phylogenetic and taxonomic research, and provide a foundation for future relevant research.
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Affiliation(s)
- Junhao Wu
- College of Life Science, China West Normal University, Nanchong, 637002, China China West Normal University Nanchong China
| | - Danping Xu
- College of Life Science, China West Normal University, Nanchong, 637002, China China West Normal University Nanchong China
| | - Xinju Wei
- College of Life Science, China West Normal University, Nanchong, 637002, China China West Normal University Nanchong China
| | - Wenkai Liao
- College of Life Science, China West Normal University, Nanchong, 637002, China China West Normal University Nanchong China
| | - Xiushan Li
- College of Life Science, China West Normal University, Nanchong, 637002, China China West Normal University Nanchong China
| | - Zhihang Zhuo
- College of Life Science, China West Normal University, Nanchong, 637002, China China West Normal University Nanchong China
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Zhao T, Pan Y. An evaluation of the effect of hydrofluoric acid (HF) treatment on keratins. J Exp Zool B Mol Dev Evol 2023; 340:377-384. [PMID: 36002950 DOI: 10.1002/jez.b.23173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 06/26/2022] [Accepted: 07/28/2022] [Indexed: 06/09/2023]
Abstract
Hydrofluoric acid (HF) is commonly used in geological and paleontological research to extract organic fossils for morphological and chemical studies. However, during HF treatment, organic matter can also be altered, which raises concerns that HF-treated organic matter may not be representative of the original organic matter. To provide reference data for protein studies on fossils, herein, we use Fourier transform infrared (FTIR) spectroscopy to investigate the effect of HF (21.3 M) treatment on keratins, with treatment durations ranging from 2 to 48 h. Results show that the FTIR spectra of HF-treated samples are overall similar to that of the untreated sample, while curve fitting shows that HF treatment has led to alteration of the secondary structure in all the HF-treated samples and the effect is time-dependent. The 2- and 4-h treatment mainly reduced the content of the random coils, α-helix, and intermolecular β-sheet. From 8h onwards, the content of random coils greatly increased at the expense of other structures. Our results imply that for protein detection in fossils using FTIR spectroscopy, the negative effect of HF treatment is not substantial, as the bands characteristic of proteins, that is, amide A, amide B, amide I, amide II, and amide III, are still present after the 48-h treatment. If the target is a secondary structure, the effect of HF treatment should be considered. When HF treatment is necessary, limiting the treatment duration to less than 4h may be a choice.
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Affiliation(s)
- Tao Zhao
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Centre for Research and Education on Biological Evolution and Environment and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China
| | - Yanhong Pan
- State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Centre for Research and Education on Biological Evolution and Environment and Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, China
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Zhou T, Gilliam NJ, Li S, Spandau S, Osborn RM, Connor S, Anderson CS, Mariani TJ, Thakar J, Dewhurst S, Mathews DH, Huang L, Sun Y. Generation and Functional Analysis of Defective Viral Genomes during SARS-CoV-2 Infection. mBio 2023; 14:e0025023. [PMID: 37074178 PMCID: PMC10294654 DOI: 10.1128/mbio.00250-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/28/2023] [Indexed: 04/20/2023] Open
Abstract
Defective viral genomes (DVGs) have been identified in many RNA viruses as a major factor influencing antiviral immune response and viral pathogenesis. However, the generation and function of DVGs in SARS-CoV-2 infection are less known. In this study, we elucidated DVG generation in SARS-CoV-2 and its relationship with host antiviral immune response. We observed DVGs ubiquitously from transcriptome sequencing (RNA-seq) data sets of in vitro infections and autopsy lung tissues of COVID-19 patients. Four genomic hot spots were identified for DVG recombination, and RNA secondary structures were suggested to mediate DVG formation. Functionally, bulk and single-cell RNA-seq analysis indicated the interferon (IFN) stimulation of SARS-CoV-2 DVGs. We further applied our criteria to the next-generation sequencing (NGS) data set from a published cohort study and observed a significantly higher amount and frequency of DVG in symptomatic patients than those in asymptomatic patients. Finally, we observed exceptionally diverse DVG populations in one immunosuppressive patient up to 140 days after the first positive test of COVID-19, suggesting for the first time an association between DVGs and persistent viral infections in SARS-CoV-2. Together, our findings strongly suggest a critical role of DVGs in modulating host IFN responses and symptom development, calling for further inquiry into the mechanisms of DVG generation and into how DVGs modulate host responses and infection outcome during SARS-CoV-2 infection. IMPORTANCE Defective viral genomes (DVGs) are generated ubiquitously in many RNA viruses, including SARS-CoV-2. Their interference activity to full-length viruses and IFN stimulation provide the potential for them to be used in novel antiviral therapies and vaccine development. SARS-CoV-2 DVGs are generated through the recombination of two discontinuous genomic fragments by viral polymerase complex, and this recombination is also one of the major mechanisms for the emergence of new coronaviruses. Focusing on the generation and function of SARS-CoV-2 DVGs, these studies identify new hot spots for nonhomologous recombination and strongly suggest that the secondary structures within viral genomes mediate the recombination. Furthermore, these studies provide the first evidence for IFN stimulation activity of de novo DVGs during natural SARS-CoV-2 infection. These findings set up the foundation for further mechanism studies of SARS-CoV-2 recombination and provide evidence to harness the immunostimulatory potential of DVGs in the development of a vaccine and antivirals for SARS-CoV-2.
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Affiliation(s)
- Terry Zhou
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
| | - Nora J. Gilliam
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
- Medical Scientist Training Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Translational Biomedical Sciences PhD Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Sizhen Li
- School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, Oregon, USA
| | - Simone Spandau
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
| | - Raven M. Osborn
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
- Translational Biomedical Sciences PhD Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Sarah Connor
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester, Rochester, New York, USA
| | - Christopher S. Anderson
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester, Rochester, New York, USA
| | - Thomas J. Mariani
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester, Rochester, New York, USA
| | - Juilee Thakar
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Stephen Dewhurst
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
| | - David H. Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York, USA
| | - Liang Huang
- School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, Oregon, USA
| | - Yan Sun
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
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Hedaya OM, Subbaiah KCV, Jiang F, Xie LH, Wu J, Khor E, Zhu M, Mathews DH, Proschel C, Yao P. Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy. bioRxiv 2023:2023.06.15.545153. [PMID: 37397986 PMCID: PMC10312771 DOI: 10.1101/2023.06.15.545153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Translation of upstream open reading frames (uORFs) typically abrogates translation of main (m)ORFs. The molecular mechanism of uORF regulation in cells is not well understood. Here, we identified a double-stranded RNA (dsRNA) structure residing within the GATA4 uORF that augments uORF translation and inhibits mORF translation. Antisense oligonucleotides (ASOs) that disrupt this dsRNA structure promote mORF translation, while ASOs that base-pair immediately downstream (i.e., forming a bimolecular double-stranded region) of either the uORF or mORF start codon enhance uORF or mORF translation, respectively. Human cardiomyocytes and mice treated with a uORF-enhancing ASO showed reduced cardiac GATA4 protein levels and increased resistance to cardiomyocyte hypertrophy. We further show the general utility of uORF-dsRNA- or mORF- targeting ASO to regulate mORF translation for other mRNAs. Our work demonstrates a regulatory paradigm that controls translational efficiency and a useful strategy to alter protein expression and cellular phenotypes by targeting or generating dsRNA downstream of a uORF or mORF start codon. Bullet points for discoveries dsRNA within GATA4 uORF activates uORF translation and inhibits mORF translation. ASOs that target the dsRNA can either inhibit or enhance GATA4 mORF translation. ASOs can be used to impede hypertrophy in human cardiomyocytes and mouse hearts.uORF- and mORF-targeting ASOs can be used to control translation of multiple mRNAs.
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Affiliation(s)
- Omar M. Hedaya
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Kadiam C. Venkata Subbaiah
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Feng Jiang
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Li Huitong Xie
- Department of Biomedical Genetics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Jiangbin Wu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - EngSoon Khor
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Mingyi Zhu
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - David H. Mathews
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Chris Proschel
- Department of Biomedical Genetics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
| | - Peng Yao
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
- The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642
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Najeh S, Zandi K, Kharma N, Perreault J. Computational design and experimental verification of pseudoknotted ribozymes. RNA 2023; 29:764-776. [PMID: 36868786 PMCID: PMC10187678 DOI: 10.1261/rna.079148.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/27/2022] [Indexed: 05/18/2023]
Abstract
The design of new RNA sequences that retain the function of a model RNA structure is a challenge in bioinformatics because of the structural complexity of these molecules. RNA can fold into its secondary and tertiary structures by forming stem-loops and pseudoknots. A pseudoknot is a set of base pairs between a region within a stem-loop and nucleotides outside of this stem-loop; this motif is very important for numerous functional structures. It is important for any computational design algorithm to take into account these interactions to give a reliable result for any structures that include pseudoknots. In our study, we experimentally validated synthetic ribozymes designed by Enzymer, which implements algorithms allowing for the design of pseudoknots. Enzymer is a program that uses an inverse folding approach to design pseudoknotted RNAs; we used it in this study to design two types of ribozymes. The ribozymes tested were the hammerhead and the glmS, which have a self-cleaving activity that allows them to liberate the new RNA genome copy during rolling-circle replication or to control the expression of the downstream genes, respectively. We demonstrated the efficiency of Enzymer by showing that the pseudoknotted hammerhead and glmS ribozymes sequences it designed were extensively modified compared to wild-type sequences and were still active.
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Affiliation(s)
- Sabrine Najeh
- INRS - Institut Armand-Frappier, Laval, QC H7V 1B7, Canada
| | - Kasra Zandi
- Software Engineering and Computer Science Department, Concordia University, Montreal, Quebec H3G 1M8, Canada
| | - Nawwaf Kharma
- Electrical and Computer Engineering Department, Concordia University, Montreal, Quebec H3G 1M8, Canada
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Qiu M, Wang N, Pend J, Li Y, Li L, Xie X. Ultrasound-assisted reverse micelle extraction and characterization of tea protein from tea residue. J Sci Food Agric 2023; 103:4068-4076. [PMID: 36495023 DOI: 10.1002/jsfa.12381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/21/2022] [Accepted: 12/10/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND In this study, ultrasonic-assisted reverse micelles were used to extract tea protein from tea residues. First, the extraction conditions of ultrasonic power, ionic strength and pH were optimized by response surface methodology. Then, structural comparison of ultrasonic-assisted reverse micelle extraction of tea protein (UARME) and ultrasonic-assisted alkali extraction (UAAE) were performed using scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy and amino acid composition. RESULTS The optimum process conditions were determined as follows: ultrasonic power 300 W, KCl 0.15 mol L-1 , pH 8. The extraction rate was 46.29%, which was close to the theoretical value (46.44%). SEM showed that the protein particles extracted by UARME were smaller than those by UAAE. The results of FTIR spectroscopy showed that the protein extracted by UARME had higher α-helix, β-sheet and β-turn, and the contents were 20%, 62.3% and 17.1%, respectively. The content of random coil was 0%, which was significantly lower than that of alkali extraction, indicating that the secondary structure of protein extracted by UARME was more orderly. By comparing the amino acid composition of the two methods, the amino acid content of tea protein extracted by UARME was significantly higher than that of UAAE. CONCLUSION The biological activity of tea protein is closely related to its structure. Compared with alkali extraction, reverse micelles can better protect the secondary structure of proteins, which is of great significance for studying their functional properties. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Minjian Qiu
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Nannan Wang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Jiamin Pend
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Yan Li
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Lu Li
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Xinan Xie
- College of Food Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, Guangzhou, China
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D'Arco A, Di Fabrizio M, Mancini T, Mosetti R, Macis S, Tranfo G, Della Ventura G, Marcelli A, Petrarca M, Lupi S. Secondary Structures of MERS-CoV, SARS-CoV, and SARS-CoV-2 Spike Proteins Revealed by Infrared Vibrational Spectroscopy. Int J Mol Sci 2023; 24:ijms24119550. [PMID: 37298500 DOI: 10.3390/ijms24119550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/28/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
All coronaviruses are characterized by spike glycoproteins whose S1 subunits contain the receptor binding domain (RBD). The RBD anchors the virus to the host cellular membrane to regulate the virus transmissibility and infectious process. Although the protein/receptor interaction mainly depends on the spike's conformation, particularly on its S1 unit, their secondary structures are poorly known. In this paper, the S1 conformation was investigated for MERS-CoV, SARS-CoV, and SARS-CoV-2 at serological pH by measuring their Amide I infrared absorption bands. The SARS-CoV-2 S1 secondary structure revealed a strong difference compared to those of MERS-CoV and SARS-CoV, with a significant presence of extended β-sheets. Furthermore, the conformation of the SARS-CoV-2 S1 showed a significant change by moving from serological pH to mild acidic and alkaline pH conditions. Both results suggest the capability of infrared spectroscopy to follow the secondary structure adaptation of the SARS-CoV-2 S1 to different environments.
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Affiliation(s)
- Annalisa D'Arco
- Laboratori Nazionali Frascati, National Institute for Nuclear Physics (INFN-LNF), Via E. Fermi 54, 00044 Frascati, Italy
- Department of Physics, University of Rome 'La Sapienza', P.le A. Moro 2, 00185 Rome, Italy
| | - Marta Di Fabrizio
- Laboratory of Biological Electron Microscopy, School of Basic Sciences, Institute of Physics, EPFL & Department of Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, 1015 Lausanne, Switzerland
| | - Tiziana Mancini
- Department of Physics, University of Rome 'La Sapienza', P.le A. Moro 2, 00185 Rome, Italy
| | - Rosanna Mosetti
- Department of Physics, University of Rome 'La Sapienza', P.le A. Moro 2, 00185 Rome, Italy
| | - Salvatore Macis
- Department of Physics, University of Rome 'La Sapienza', P.le A. Moro 2, 00185 Rome, Italy
| | - Giovanna Tranfo
- Department of Occupational and Environmental Medicine, Epidemiology and Hygiene, INAIL, Monte Porzio Catone, 00078 Rome, Italy
| | - Giancarlo Della Ventura
- Laboratori Nazionali Frascati, National Institute for Nuclear Physics (INFN-LNF), Via E. Fermi 54, 00044 Frascati, Italy
- Department of Science, University Rome Tre, Largo San Leonardo Murialdo 1, 00146 Rome, Italy
| | - Augusto Marcelli
- Laboratori Nazionali Frascati, National Institute for Nuclear Physics (INFN-LNF), Via E. Fermi 54, 00044 Frascati, Italy
- Rome International Centre for Materials Science Superstipes, Via dei Sabelli 119A, 00185 Rome, Italy
| | - Massimo Petrarca
- National Institute for Nuclear Physics Section Rome1, P.le A. Moro 2, 00185 Rome, Italy
- Department of Basic and Applied Sciences for Engineering (SBAI), University of Rome 'La Sapienza', Via Scarpa 16, 00161 Rome, Italy
| | - Stefano Lupi
- Department of Physics, University of Rome 'La Sapienza', P.le A. Moro 2, 00185 Rome, Italy
- National Institute for Nuclear Physics Section Rome1, P.le A. Moro 2, 00185 Rome, Italy
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Pandit E, Das L, Das AK, Dolui S, Saha S, Pal U, Mondal A, Chowdhury J, Biswas SC, Maiti NC. Single point mutations at the S129 residue of α-synuclein and their effect on structure, aggregation, and neurotoxicity. Front Chem 2023; 11:1145877. [PMID: 37304685 PMCID: PMC10250651 DOI: 10.3389/fchem.2023.1145877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/10/2023] [Indexed: 06/13/2023] Open
Abstract
Parkinson's disease is an age-related neurological disorder, and the pathology of the disease is linked to different types of aggregates of α-synuclein or alpha-synuclein (aS), which is an intrinsically disordered protein. The C-terminal domain (residues 96-140) of the protein is highly fluctuating and possesses random/disordered coil conformation. Thus, the region plays a significant role in the protein's solubility and stability by an interaction with other parts of the protein. In the current investigation, we examined the structure and aggregation behavior of two artificial single point mutations at a C-terminal residue at position 129 that represent a serine residue in the wild-type human aS (wt aS). Circular Dichroism (CD) and Raman spectroscopy were performed to analyse the secondary structure of the mutated proteins and compare it to the wt aS. Thioflavin T assay and atomic force microscopy imaging helped in understanding the aggregation kinetics and type of aggregates formed. Finally, the cytotoxicity assay gave an idea about the toxicity of the aggregates formed at different stages of incubation due to mutations. Compared to wt aS, the mutants S129A and S129W imparted structural stability and showed enhanced propensity toward the α-helical secondary structure. CD analysis showed proclivity of the mutant proteins toward α-helical conformation. The enhancement of α-helical propensity lengthened the lag phase of fibril formation. The growth rate of β-sheet-rich fibrillation was also reduced. Cytotoxicity tests on SH-SY5Y neuronal cell lines established that the S129A and S129W mutants and their aggregates were potentially less toxic than wt aS. The average survivability rate was ∼40% for cells treated with oligomers (presumably formed after 24 h of incubation of the freshly prepared monomeric protein solution) produced from wt aS and ∼80% for cells treated with oligomers obtained from mutant proteins. The relative structural stability with α-helical propensity of the mutants could be a plausible reason for their slow rate of oligomerization and fibrillation, and this was also the possible reason for reduced toxicity to neuronal cells.
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Affiliation(s)
- Esha Pandit
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
| | - Lopamudra Das
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
| | - Anoy Kumar Das
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Sandip Dolui
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
| | - Saumen Saha
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
| | - Uttam Pal
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
| | - Animesh Mondal
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
| | | | - Subhas C. Biswas
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Nakul C. Maiti
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
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Xian Q, Wang S, Liu Y, Kan S, Zhang W. Structure-Based GC Investigation Sheds New Light on ITS2 Evolution in Corydalis Species. Int J Mol Sci 2023; 24:ijms24097716. [PMID: 37175423 PMCID: PMC10178233 DOI: 10.3390/ijms24097716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Guanine and cytosine (GC) content is a fundamental component of genetic diversity and essential for phylogenetic analyses. However, the GC content of the ribosomal internal transcribed spacer 2 (ITS2) remains unknown, despite the fact that ITS2 is a widely used phylogenetic marker. Here, the ITS2 was high-throughput sequenced from 29 Corydalis species, and their GC contents were comparatively investigated in the context of ITS2's characteristic secondary structure and concerted evolution. Our results showed that the GC contents of ITS2 were 131% higher than those of their adjacent 5.8S regions, suggesting that ITS2 underwent GC-biased evolution. These GCs were distributed in a heterogeneous manner in the ITS2 secondary structure, with the paired regions being 130% larger than the unpaired regions, indicating that GC is chosen for thermodynamic stability. In addition, species with homogeneous ITS2 sequences were always GC-rich, supporting GC-biased gene conversion (gBGC), which occurred with ITS2's concerted evolution. The RNA substitution model inferred also showed a GC preference among base pair transformations, which again supports gBGC. Overall, structurally based GC investigation reveals that ITS2 evolves under structural stability and gBGC selection, significantly increasing its GC content.
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Affiliation(s)
- Qing Xian
- Marine College, Shandong University, Weihai 264209, China
| | - Suyin Wang
- Marine College, Shandong University, Weihai 264209, China
| | - Yanyan Liu
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wei Zhang
- Marine College, Shandong University, Weihai 264209, China
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