Pub Date : 2023-07-18DOI: 10.2174/2211550112666230718162643
A. Ponizovskiy, Alexander V. Plochov
The paper presents the results of experiments on the purification of air contaminated with S. aureus, as well as the destruction of yeast under the action of cold nonequilibrium plasma of a nanosecond streamer corona discharge. It is shown that plasma is an effective means for destroying both bacteria in the air and biological objects on the surface. The main parameters of the nanosecond streamer corona discharge and their relationship with the operating time of the active plasma components were determined. It was experimentally established that the inactivation time of 80% of S. aureus bacteria with a concentration of 2.1∙104 KOE m-3 was 0.4 s with a specific energy of 28 J∙l-1. The results of measurements of the dependence of the yeast destruction degree on the yeast size, the time of direct exposure to the nanosecond streamer corona discharge, active elements of cold nonequilibrium plasma, and third-party ultraviolet radiation are presented. A comparison of the results of air disinfection experiments with data on yeast destruction shows that the latter can be used for rapid analysis of the effects of low-temperature plasma on other biological objects.
本文介绍了纳秒流光电晕放电冷非平衡等离子体对金黄色葡萄球菌污染空气的净化和对酵母的破坏实验结果。结果表明，等离子体是一种既能杀灭空气中的细菌又能杀灭表面生物的有效手段。确定了纳秒流光电晕放电的主要参数及其与活性等离子体组分工作时间的关系。实验证实，80%的金黄色葡萄球菌在2.1∙104 KOE m-3浓度下失活时间为0.4 s，比能为28 J∙l-1。给出了酵母破坏程度与酵母大小、直接暴露于纳秒流光电晕放电时间、冷非平衡等离子体活性元素和第三方紫外线辐射的关系的测量结果。空气消毒实验结果与酵母破坏数据的比较表明，后者可用于低温等离子体对其他生物物体的影响的快速分析。
{"title":"Cold Non-Equilibrium Plasma As A Tool For Air Disinfection And Destruction Of Biological Objects","authors":"A. Ponizovskiy, Alexander V. Plochov","doi":"10.2174/2211550112666230718162643","DOIUrl":"https://doi.org/10.2174/2211550112666230718162643","url":null,"abstract":"\u0000\u0000The paper presents the results of experiments on the purification of air contaminated with S. aureus, as well as the destruction of yeast under the action of cold nonequilibrium plasma of a nanosecond streamer corona discharge. It is shown that plasma is an effective means for destroying both bacteria in the air and biological objects on the surface. The main parameters of the nanosecond streamer corona discharge and their relationship with the operating time of the active plasma components were determined. It was experimentally established that the inactivation time of 80% of S. aureus bacteria with a concentration of 2.1∙104 KOE m-3 was 0.4 s with a specific energy of 28 J∙l-1. The results of measurements of the dependence of the yeast destruction degree on the yeast size, the time of direct exposure to the nanosecond streamer corona discharge, active elements of cold nonequilibrium plasma, and third-party ultraviolet radiation are presented. A comparison of the results of air disinfection experiments with data on yeast destruction shows that the latter can be used for rapid analysis of the effects of low-temperature plasma on other biological objects.\u0000","PeriodicalId":10850,"journal":{"name":"Current Biotechnology","volume":"31 2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90090542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The control of the Covid-19 epidemic depends on designing a novel, effective vaccine against it. Currently, available vaccines cannot provide complete protection against various mutants of Covid-19. The present investigation aimed to design a new multi-epitope vaccine by using in silico tools. In the present study, the spike-glycoprotein was targeted, desirably stimulating both B and T-cell lymphocytes, providing effective and safe responses in the host immune system. The desired vaccine has been found to possess 448 amino acids of spike glycoprotein. The prognosticated epitopes included 10 CTL, 4 linear B-cells, and 14 HTL, including the 128 amino acid sequence of 50S ribosomal protein adjuvant joined by GPGPG and AAY linkers on the N terminus of linear B-cell, HTL, and CTL epitopes, and the C-terminal joined with HHHHHH (6HIS) linker, indicating stability for vaccine structure. The molecular docking has revealed the protein-protein restricting communication be-tween the immunization construct and the TLR-3-resistant receptor. The vaccine has been de-veloped through selected epitopes, an adjuvant, and an additional epitope. Docking assays with toll-like receptor 3 have been run on a three-dimensional structural model of the vaccine to gauge its immunological potency. Our findings support the hypothesis that our vaccination will activate TLR-mediated downstream immune pathways by aggressively interacting with the innate receptor. The results suggest that the proposed chimeric peptide could initiate an efficient and safe immune response against Covid-19. The proposed vaccine has been proven safe in all critical parameters.
{"title":"Design of a Multi-epitope Vaccine against Covid-19: An In silico Approach","authors":"Deepak Chand Sharma, Kaushal Kishor Mishra, Asheesh Kumar Mishra, Vandita Anand, Anjana Pandey, Savita Budhwar","doi":"10.2174/2211550112666230612153430","DOIUrl":"https://doi.org/10.2174/2211550112666230612153430","url":null,"abstract":"\u0000\u0000The control of the Covid-19 epidemic depends on designing a novel, effective vaccine against it. Currently, available vaccines cannot provide complete protection against various mutants of Covid-19.\u0000\u0000\u0000\u0000The present investigation aimed to design a new multi-epitope vaccine by using in silico tools.\u0000\u0000\u0000\u0000In the present study, the spike-glycoprotein was targeted, desirably stimulating both B and T-cell lymphocytes, providing effective and safe responses in the host immune system. The desired vaccine has been found to possess 448 amino acids of spike glycoprotein. The prognosticated epitopes included 10 CTL, 4 linear B-cells, and 14 HTL, including the 128 amino acid sequence of 50S ribosomal protein adjuvant joined by GPGPG and AAY linkers on the N terminus of linear B-cell, HTL, and CTL epitopes, and the C-terminal joined with HHHHHH (6HIS) linker, indicating stability for vaccine structure.\u0000\u0000\u0000\u0000The molecular docking has revealed the protein-protein restricting communication be-tween the immunization construct and the TLR-3-resistant receptor. The vaccine has been de-veloped through selected epitopes, an adjuvant, and an additional epitope. Docking assays with toll-like receptor 3 have been run on a three-dimensional structural model of the vaccine to gauge its immunological potency. Our findings support the hypothesis that our vaccination will activate TLR-mediated downstream immune pathways by aggressively interacting with the innate receptor.\u0000\u0000\u0000\u0000The results suggest that the proposed chimeric peptide could initiate an efficient and safe immune response against Covid-19. The proposed vaccine has been proven safe in all critical parameters.\u0000","PeriodicalId":10850,"journal":{"name":"Current Biotechnology","volume":"100 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76084002","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-05-05DOI: 10.2174/2211550112666230505105656
B. Ostash
Species within the actinobacterial genus Streptomyces represent one of the most gifted natural chemists in the microbial world. Their specialized metabolites attract the interest of the pharmaceutical industry as a source of novel drugs. A majority of these molecules pose an insurmountable challenge for economically justified production via chemical synthesis. Therefore, submerged fermentation-based isolation of such molecules often remains the only viable way to obtain them. This in turn fuels interest in process development programs aiming to maximize the yield of specialized metabolite per volume unit of fermentation medium. Along with the optimization of the medium and the fermentation mode itself, strain improvement remains an important part of an overall process development endeavor. An improved strain can be generated via application of traditional approaches of selection for random or induced mutants and genomics-enabled genetic engineering methods. Here I focus on a specific class of mutations with the gene rpsL for ribosomal protein S12, which often confer resistance to streptomycin in bacteria and upregulate specialized metabolism in Streptomyces. The review will portray the evolution of our understanding of the mechanisms behind rpsL mutations, as well as how technological advances change the way these mutations are introduced into the genomes of interest.
{"title":"Ribosomal Protein S12 and Its Effects on Specialized Metabolism of Streptomyces Bacteria","authors":"B. Ostash","doi":"10.2174/2211550112666230505105656","DOIUrl":"https://doi.org/10.2174/2211550112666230505105656","url":null,"abstract":"\u0000\u0000Species within the actinobacterial genus Streptomyces represent one of the most gifted natural chemists in the microbial world. Their specialized metabolites attract the interest of the pharmaceutical industry as a source of novel drugs. A majority of these molecules pose an insurmountable challenge for economically justified production via chemical synthesis. Therefore, submerged fermentation-based isolation of such molecules often remains the only viable way to obtain them. This in turn fuels interest in process development programs aiming to maximize the yield of specialized metabolite per volume unit of fermentation medium. Along with the optimization of the medium and the fermentation mode itself, strain improvement remains an important part of an overall process development endeavor. An improved strain can be generated via application of traditional approaches of selection for random or induced mutants and genomics-enabled genetic engineering methods. Here I focus on a specific class of mutations with the gene rpsL for ribosomal protein S12, which often confer resistance to streptomycin in bacteria and upregulate specialized metabolism in Streptomyces. The review will portray the evolution of our understanding of the mechanisms behind rpsL mutations, as well as how technological advances change the way these mutations are introduced into the genomes of interest.\u0000","PeriodicalId":10850,"journal":{"name":"Current Biotechnology","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90842028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-05-03DOI: 10.2174/2211550112666230503142402
A. Dilmaghani, Babak Elyasi Far, Fereydoun Sajadi, H. Nazemiyeh, Elnaz Mehdizadeh Aghdam
Lipase is one of the most well-known and essential biocatalysts in the detergent, food, and pharmaceutical industries. Microbial lipase sources such as yeasts are applicable due to their stability in harsh conditions. In this study, the effect of temperature, initial pH, and incubation time were investigated to improve the extracellular lipase production by yeast, named Zygoascus hellenicus strain MZ_574439 T. Strain MZ_574439 T has already been isolated and registered from Iran. In the current project, strain MZ_574439 T with 99% similarity to Z. hellenicus was isolated from water samples. Our findings showed that the isolated strain has a remarkable difference from its close phylogenetic species in the production of lipase and can produce extracellular lipase up to 7.2 U/ml while the Z. hellenicus has no ability of lipase production. The isolated strain was not able to produce other hydrolytic enzymes. The enzyme activity results showed that the best activity for the isolated lipase is pH= 7 and 37 °C. The best stability condition for the enzyme occurs at 50 °C and pH =7. From the current study, it can be concluded that Z. hellenicus produces lipase. The lipase enzyme production was optimized with different physiological conditions. Yeast extract could be a better source for maximum lipase production.
{"title":"Study of hydrolytic enzymes activity and stability of the isolated yeast close to Zygoascus hellenicus","authors":"A. Dilmaghani, Babak Elyasi Far, Fereydoun Sajadi, H. Nazemiyeh, Elnaz Mehdizadeh Aghdam","doi":"10.2174/2211550112666230503142402","DOIUrl":"https://doi.org/10.2174/2211550112666230503142402","url":null,"abstract":"\u0000\u0000Lipase is one of the most well-known and essential biocatalysts in the detergent, food, and pharmaceutical industries. Microbial lipase sources such as yeasts are applicable due to their stability in harsh conditions.\u0000\u0000\u0000\u0000In this study, the effect of temperature, initial pH, and incubation time were investigated to improve the extracellular lipase production by yeast, named Zygoascus hellenicus strain MZ_574439 T.\u0000\u0000\u0000\u0000Strain MZ_574439 T has already been isolated and registered from Iran. In the current project, strain MZ_574439 T with 99% similarity to Z. hellenicus was isolated from water samples.\u0000\u0000\u0000\u0000Our findings showed that the isolated strain has a remarkable difference from its close phylogenetic species in the production of lipase and can produce extracellular lipase up to 7.2 U/ml while the Z. hellenicus has no ability of lipase production. The isolated strain was not able to produce other hydrolytic enzymes. The enzyme activity results showed that the best activity for the isolated lipase is pH= 7 and 37 °C. The best stability condition for the enzyme occurs at 50 °C and pH =7.\u0000\u0000\u0000\u0000From the current study, it can be concluded that Z. hellenicus produces lipase. The lipase enzyme production was optimized with different physiological conditions. Yeast extract could be a better source for maximum lipase production.\u0000","PeriodicalId":10850,"journal":{"name":"Current Biotechnology","volume":"432 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82871408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-04-19DOI: 10.2174/2211550112666230419110914
K. K. Sadasivuni, M. Geetha, S. Al-Máadeed, Asan G.A. Muthalif, S. M. S, Mizaj Shabil Sha
Regular blood cholesterol control is an integral part of healthcare for detecting cardiovascular issues immediately. Existing procedures are mostly intrusive and necessitate the collection of blood samples. Furthermore, because of the danger of infection, bruising, and/or haematoma, this measurement method may not be appropriate for continuous or regular examinations. As a result, an alternate option is required, which is known as the noninvasive (NI) approach that does not necessitate the collection of blood samples. Because NI approaches give painless and precise answers, they can be used in place of intrusive procedures. This review article includes a comprehensive investigation on NI methodologies and various NI approaches for detecting cholesterol in the bloodstream. It is important to note that medical system possibilities are changing due to the algorithms for NI techniques, which ultimately project the need for patient monitoring via the internet of medical things (IoMT) and artificial intelligence (AI).
{"title":"Futuristic Approach to Cholesterol Detection by Utilizing Non-invasive\u0000Techniques","authors":"K. K. Sadasivuni, M. Geetha, S. Al-Máadeed, Asan G.A. Muthalif, S. M. S, Mizaj Shabil Sha","doi":"10.2174/2211550112666230419110914","DOIUrl":"https://doi.org/10.2174/2211550112666230419110914","url":null,"abstract":"\u0000\u0000Regular blood cholesterol control is an integral part of healthcare for detecting cardiovascular issues immediately. Existing procedures are mostly intrusive and necessitate the collection\u0000of blood samples. Furthermore, because of the danger of infection, bruising, and/or haematoma, this\u0000measurement method may not be appropriate for continuous or regular examinations. As a result, an\u0000alternate option is required, which is known as the noninvasive (NI) approach that does not necessitate the collection of blood samples. Because NI approaches give painless and precise answers, they\u0000can be used in place of intrusive procedures. This review article includes a comprehensive investigation on NI methodologies and various NI approaches for detecting cholesterol in the bloodstream.\u0000It is important to note that medical system possibilities are changing due to the algorithms for NI\u0000techniques, which ultimately project the need for patient monitoring via the internet of medical\u0000things (IoMT) and artificial intelligence (AI).\u0000","PeriodicalId":10850,"journal":{"name":"Current Biotechnology","volume":"141 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76801160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-04-17DOI: 10.2174/2211550112666230417100541
Richu Singla, M. Arora, P. Bansal
Ribonucleic acid (RNA) and its types have emerged as master regulators of biological processes and expanded knowledge regarding the role of RNA in the gene expression inside the cell have dramatically changed the therapeutic strategies in the past few years. RNA has become a focus for developing novel therapeutic schemes and hence RNA-based therapies, particularly in viral diseases have become more enthralling and promising. It is due to the fact that RNA offers various advantages in disease management as it can be edited and customized in its various forms such as secondary and tertiary structures. Principles and mechanisms regarding RNA therapeutics are well described in volumes, however, the information regarding long-awaited RNA-based drug development and potential hurdles as well as barriers in the way is still scattered. In this regard, these agents are required to overcome a plethora of barriers such as stability of drug targets, immunogenicity, adequate binding, targeted delivery, etc. to become effective drugs. Most of the trials are changing their way from in-vitro to in-vivo studies and it is not far away when RNA-based therapeutics will find their way from bench to bedside. In this communication, the authors give a brief review of important recent advances in above said domains of miRNA therapeutics.
{"title":"RNA-based Therapeutics: Master Regulator for Bioengineering Systems in\u0000Medicine World","authors":"Richu Singla, M. Arora, P. Bansal","doi":"10.2174/2211550112666230417100541","DOIUrl":"https://doi.org/10.2174/2211550112666230417100541","url":null,"abstract":"\u0000\u0000Ribonucleic acid (RNA) and its types have emerged as master regulators of biological\u0000processes and expanded knowledge regarding the role of RNA in the gene expression inside the cell\u0000have dramatically changed the therapeutic strategies in the past few years. RNA has become a focus\u0000for developing novel therapeutic schemes and hence RNA-based therapies, particularly in viral diseases have become more enthralling and promising. It is due to the fact that RNA offers various advantages in disease management as it can be edited and customized in its various forms such as secondary and tertiary structures. Principles and mechanisms regarding RNA therapeutics are well described in volumes, however, the information regarding long-awaited RNA-based drug development and potential hurdles as well as barriers in the way is still scattered. In this regard, these agents\u0000are required to overcome a plethora of barriers such as stability of drug targets, immunogenicity,\u0000adequate binding, targeted delivery, etc. to become effective drugs. Most of the trials are changing\u0000their way from in-vitro to in-vivo studies and it is not far away when RNA-based therapeutics will\u0000find their way from bench to bedside. In this communication, the authors give a brief review of important recent advances in above said domains of miRNA therapeutics.\u0000","PeriodicalId":10850,"journal":{"name":"Current Biotechnology","volume":"41 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90551217","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-04-07DOI: 10.2174/2211550112666230407101119
M. Choura
Intrinsically Disordered Proteins (IDPs) are natively unstructured proteins. Interestingly, IDPs are ubiquitous and play key roles in cellular and protein functions. While IDPs are studied in some proteomes, many remain to be uncovered. Here, I have explored the first large-scale study of IDPs in T. turgidum. Additionally, a comparative analysis of T. turgidum and T. aestivum IDPs was performed for highlighting the disorder use in each species. The data indicated that the T.turgidum proteome is significantly more disordered than the T. aestivum proteome. Gene ontology analysis revealed that IDPs in T. turgidum are mainly catalytic and binding proteins involved in the regulation of cellular and metabolic processes.
{"title":"Proteome-Wide analysis of protein disorder in Durum wheat","authors":"M. Choura","doi":"10.2174/2211550112666230407101119","DOIUrl":"https://doi.org/10.2174/2211550112666230407101119","url":null,"abstract":"\u0000\u0000Intrinsically Disordered Proteins (IDPs) are natively unstructured proteins. Interestingly, IDPs are ubiquitous and play key roles in cellular and protein functions. While IDPs are studied in some proteomes, many remain to be uncovered.\u0000\u0000\u0000\u0000Here, I have explored the first large-scale study of IDPs in T. turgidum. Additionally, a comparative analysis of T. turgidum and T. aestivum IDPs was performed for highlighting the disorder use in each species.\u0000\u0000\u0000\u0000The data indicated that the T.turgidum proteome is significantly more disordered than the T. aestivum proteome.\u0000\u0000\u0000\u0000Gene ontology analysis revealed that IDPs in T. turgidum are mainly catalytic and binding proteins involved in the regulation of cellular and metabolic processes.\u0000","PeriodicalId":10850,"journal":{"name":"Current Biotechnology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87467573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-31DOI: 10.2174/2211550112666230331104839
V. S. Mattaparthi, P. Borah
α-Synuclein has become the main therapeutic target in Parkinson's disease and related Synucleinopathies since the discovery of genetic associations between α-Synuclein and Parkinson's disease risk and the identification of aggregated α-Synuclein as the primary protein constituent of Lewy pathology two decades ago. The two new peptides K84s (FLVWGCLRGSAIGECVVHGGPPSRH) and K102s (FLKRWARSTRWGTASCGGS) have recently been found to significantly reduce the oligomerization and aggregation of α-Synuclein. However, it is still unclear where these peptides interact with α-Synuclein at the moment. To examine the locations where K84s and K102s interact with α-Synuclein. In this investigation, the PEPFOLD3 server was used to generate the 3-D structures of the K84s and K102s peptides. Using the PatchDock web server, the two peptides were docked to the α-Synuclein molecule. After that, 50 ns of Molecular Dynamics (MD) simulations using the Amberff99SBildn force field were performed on the two resulting docked complexes. The two complexes' structure, dynamics, energy profiles, and binding modes were identified through analysis of the respective MD simulation trajectories. By submitting the two complexes' lowest energy structure to the PDBsum website, the interface residues in the two complexes were identified. The per residue energy decomposition (PRED) analysis using the MM-GBSA technique was used to calculate the contributions of each residue in the α-Synuclein of (α-Synuclein-K84s/K102s) complexes to the total binding free energy. The binding of the two peptides with the α-Synuclein was demonstrated to have high binding free energy. The binding free energies of the (α-Synuclein-K84s) and (α-Synuclein-K102s) complexes are -33.61 kcal/mol and -40.88 kcal/mol respectively. Using PDBsum server analysis, it was determined that in the (α-Synuclein-K84s) complex, the residues GLY 25, ALA 29, VAL 49, LEU 38, VAL 40, GLU 28, GLY 47, LYS 32, GLU 35, GLY 36, TYR 39, VAL 48 and VAL 26 (from α-Synuclein) and SER 23, LEU 7, ILE 12, HIS 25, PHE 1, HIS 18, CYS 6, ARG 24, PRO 21 and ARG 8 (from K84s peptide) were identified to be present at the interface. In the (α-Synuclein-K102s) complex, the residues VAL 40, GLY 36, GLU 35, TYR 39, LYS 45, LEU 38, LYS 43, VAL 37, THR 44, VAL 49, VAL 48, and GLU 46 (from α-Synuclein) and ARG 10, GLY 12, GLY 18, SER 15, THR 13, SER 19, TRP 11, ALA 14, CYS 16, ARG 7, ARG 4 and GLY 17 (from K102s peptide) were identified to be present at the interface. The PRED analysis revealed that the residues PHE 1, LEU 7, ILE 12, LEU 2, VAL 3, GLY 5, and PRO 21 of the K84s peptide and residues VAL 48, ALA 29, VAL 40, TYR 39, VAL 49, VAL 26 and GLY 36 of α-Synuclein in the (α-Synuclein-K84s) complex are responsible for the intermolecular interaction. The residues ARG 4, ARG 10, TRP 11, ALA 14, SER 15, CYS 16 and SER 19 of the K102s peptide and residues GLU 46, LYS 45, VAL 49, GLU 35, VAL 48, TYR 39, and VAL 40 of α-Synuclein are responsible f
{"title":"Investigation into the Interaction Sites of the K84s and K102s Peptides with α-Synuclein for Understanding the Anti-Aggregation Mechanism: an in silico study","authors":"V. S. Mattaparthi, P. Borah","doi":"10.2174/2211550112666230331104839","DOIUrl":"https://doi.org/10.2174/2211550112666230331104839","url":null,"abstract":"\u0000\u0000α-Synuclein has become the main therapeutic target in Parkinson's disease and related Synucleinopathies since the discovery of genetic associations between α-Synuclein and Parkinson's disease risk and the identification of aggregated α-Synuclein as the primary protein constituent of Lewy pathology two decades ago. The two new peptides K84s (FLVWGCLRGSAIGECVVHGGPPSRH) and K102s (FLKRWARSTRWGTASCGGS) have recently been found to significantly reduce the oligomerization and aggregation of α-Synuclein. However, it is still unclear where these peptides interact with α-Synuclein at the moment.\u0000\u0000\u0000\u0000\u0000To examine the locations where K84s and K102s interact with α-Synuclein.\u0000\u0000\u0000\u0000\u0000In this investigation, the PEPFOLD3 server was used to generate the 3-D structures of the K84s and K102s peptides. Using the PatchDock web server, the two peptides were docked to the α-Synuclein molecule. After that, 50 ns of Molecular Dynamics (MD) simulations using the Amberff99SBildn force field were performed on the two resulting docked complexes. The two complexes' structure, dynamics, energy profiles, and binding modes were identified through analysis of the respective MD simulation trajectories. By submitting the two complexes' lowest energy structure to the PDBsum website, the interface residues in the two complexes were identified. The per residue energy decomposition (PRED) analysis using the MM-GBSA technique was used to calculate the contributions of each residue in the α-Synuclein of (α-Synuclein-K84s/K102s) complexes to the total binding free energy.\u0000\u0000\u0000\u0000\u0000The binding of the two peptides with the α-Synuclein was demonstrated to have high binding free energy. The binding free energies of the (α-Synuclein-K84s) and (α-Synuclein-K102s) complexes are -33.61 kcal/mol and -40.88 kcal/mol respectively. Using PDBsum server analysis, it was determined that in the (α-Synuclein-K84s) complex, the residues GLY 25, ALA 29, VAL 49, LEU 38, VAL 40, GLU 28, GLY 47, LYS 32, GLU 35, GLY 36, TYR 39, VAL 48 and VAL 26 (from α-Synuclein) and SER 23, LEU 7, ILE 12, HIS 25, PHE 1, HIS 18, CYS 6, ARG 24, PRO 21 and ARG 8 (from K84s peptide) were identified to be present at the interface. In the (α-Synuclein-K102s) complex, the residues VAL 40, GLY 36, GLU 35, TYR 39, LYS 45, LEU 38, LYS 43, VAL 37, THR 44, VAL 49, VAL 48, and GLU 46 (from α-Synuclein) and ARG 10, GLY 12, GLY 18, SER 15, THR 13, SER 19, TRP 11, ALA 14, CYS 16, ARG 7, ARG 4 and GLY 17 (from K102s peptide) were identified to be present at the interface. The PRED analysis revealed that the residues PHE 1, LEU 7, ILE 12, LEU 2, VAL 3, GLY 5, and PRO 21 of the K84s peptide and residues VAL 48, ALA 29, VAL 40, TYR 39, VAL 49, VAL 26 and GLY 36 of α-Synuclein in the (α-Synuclein-K84s) complex are responsible for the intermolecular interaction. The residues ARG 4, ARG 10, TRP 11, ALA 14, SER 15, CYS 16 and SER 19 of the K102s peptide and residues GLU 46, LYS 45, VAL 49, GLU 35, VAL 48, TYR 39, and VAL 40 of α-Synuclein are responsible f","PeriodicalId":10850,"journal":{"name":"Current Biotechnology","volume":"33 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88428907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-09DOI: 10.2174/2211550112666230109165101
Reena Gupta, Apoorva Sood, Manpreet Kaur
Lipases are carboxylic ester hydrolase enzymes, constituting the class of serine hydrolases, requiring no cofactor for their action. They have various substrates and produce glycerol and free fatty acids through the hydrolysis of fats and oils. Owing to their wide applications and the simplicity with which they can be mass-produced, these are a significant group of biotechnologically important enzymes. In addition, lipases have the special characteristic of operating at a lipid/water interface. Present review focuses on the medical and therapeutic use of lipases. These enzymes and their inhibitors have applications with remarkable success for managing or even treating diseases such as cancer, obesity, atherosclerosis, and Alzheimer’s. Lipases have also been used to produce healthier fatty acids and low-fat cheese. The characteristic physicochemical and catalytic properties of enzymes make them ideal for biosensors and digestive aids in individuals with exocrine pancreatic inefficiency. Newer avenues open as deeper and more relevant studies are being conducted on newer lipases.
{"title":"Lipases and their applications in biomedical field","authors":"Reena Gupta, Apoorva Sood, Manpreet Kaur","doi":"10.2174/2211550112666230109165101","DOIUrl":"https://doi.org/10.2174/2211550112666230109165101","url":null,"abstract":"\u0000\u0000Lipases are carboxylic ester hydrolase enzymes, constituting the class of serine hydrolases, requiring no cofactor for their action.\u0000\u0000\u0000\u0000They have various substrates and produce glycerol and free fatty acids through the hydrolysis of fats and oils. Owing to their wide applications and the simplicity with which they can be mass-produced, these are a significant group of biotechnologically important enzymes. In addition, lipases have the special characteristic of operating at a lipid/water interface.\u0000\u0000\u0000\u0000Present review focuses on the medical and therapeutic use of lipases. These enzymes and their inhibitors have applications with remarkable success for managing or even treating diseases such as cancer, obesity, atherosclerosis, and Alzheimer’s. Lipases have also been used to produce healthier fatty acids and low-fat cheese.\u0000\u0000\u0000\u0000The characteristic physicochemical and catalytic properties of enzymes make them ideal for biosensors and digestive aids in individuals with exocrine pancreatic inefficiency. Newer avenues open as deeper and more relevant studies are being conducted on newer lipases.\u0000","PeriodicalId":10850,"journal":{"name":"Current Biotechnology","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80024950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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