Pub Date : 2021-07-26DOI: 10.2174/1570164618666210726161428
Y. Shan, Junjie Shang, Dongfang Zhang, Yinshan Cui, Yi Wang, Jie Zhu, Yongkai Ma, P. Song, K. Qin, X. Ji, Yunlin Wei, Lijun Wu
Amylase used in the market is mostly medium-temperature enzyme or high-temperature enzyme and has poor enzyme activity under low-temperature environment. Acid α-amylase can be used to develop digestion additives in the pharmaceutical and healthcare industries. The amino acid sequence and structural differences among α-amylases obtained from various organisms are high enough to confer interesting biochemical diversity to the enzymes. However, low- temperature (0-50℃) amylase, with an optimum temperature and heat sensitivity, has a greater potential value than medium (50-80℃) and high (80-110℃) temperature amylases. The gene amy48 from encoding extracellular α-amylase in Bacillus subtilis YX48 was successfully cloned into the pET30a (+) vector and expressed in Escherichia coli BL21 (DE3) for biochemical characterization. The molecular weight of α-amylase was 75 kDa. The activity of α-amylase was not affected by Ca2+, and Amy48 had the best activity at pH 5.0 and 37℃. AMY48 has high stability over a narrow pH and temperature range (5.0-8.0 and 30-45℃). Amylase activity was strongly inhibited by Zn2+, Mn2+, Cu2+, and Fe2+ ions, but Na+, K+, and Co2+ ions stimulate its activity slightly. The purified enzyme showed gradually reduced activity in the presence of detergents. However, it was remarkably stable against EDTA and urea.
{"title":"Cloning, Expression and Biochemical Characterization of the Recombinant α-amylase from Bacillus subtilis YX48","authors":"Y. Shan, Junjie Shang, Dongfang Zhang, Yinshan Cui, Yi Wang, Jie Zhu, Yongkai Ma, P. Song, K. Qin, X. Ji, Yunlin Wei, Lijun Wu","doi":"10.2174/1570164618666210726161428","DOIUrl":"https://doi.org/10.2174/1570164618666210726161428","url":null,"abstract":"\u0000\u0000Amylase used in the market is mostly medium-temperature enzyme or high-temperature enzyme and has poor enzyme activity under low-temperature environment. Acid α-amylase can be used to develop digestion additives in the pharmaceutical and healthcare industries. The amino acid sequence and structural differences among α-amylases obtained from various organisms are high enough to confer interesting biochemical diversity to the enzymes. However, low- temperature (0-50℃) amylase, with an optimum temperature and heat sensitivity, has a greater potential value than medium (50-80℃) and high (80-110℃) temperature amylases.\u0000\u0000\u0000\u0000\u0000The gene amy48 from encoding extracellular α-amylase in Bacillus subtilis YX48 was successfully cloned into the pET30a (+) vector and expressed in Escherichia coli BL21 (DE3) for biochemical characterization. \u0000\u0000\u0000\u0000\u0000The molecular weight of α-amylase was 75 kDa. The activity of α-amylase was not affected by Ca2+, and Amy48 had the best activity at pH 5.0 and 37℃. AMY48 has high stability over a narrow pH and temperature range (5.0-8.0 and 30-45℃). Amylase activity was strongly inhibited by Zn2+, Mn2+, Cu2+, and Fe2+ ions, but Na+, K+, and Co2+ ions stimulate its activity slightly. The purified enzyme showed gradually reduced activity in the presence of detergents. However, it was remarkably stable against EDTA and urea. \u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"8 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2021-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90186555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-04-26DOI: 10.2174/1570164618666210426090916
Mukesh Kumar, M. Goswami, S. Nayak, P. Gireesh-Babu, A. Chaudhari
To evaluate the binding affinity and biological potency of gonadotropin releasing hormone analogue (GnRHa) Buserelin (C60H86N16O13) based on in silico and in vivo testing for induced breeding in Clarias magur. Many attempts have been made to induce C. magur but encouraging results have not yet been achieved. Hence, it is the need of the hour to find out more potent analogues or other bio-molecules for induced breeding in C. magur to facilitate sustainable aquaculture. To determine the binding affinity of C. magur GnRH receptor through in silico and its validation for induced breeding of C. magur. Buserelin (C60H86N16O13) was selected as the potential GnRHa after screening several peptides for their binding energy with the C. magur GnRH receptor. The induced breeding trial was set up at ICAR-CIFE Powarkheda Centre, M.P. India, and Buserelin was administered in different doses to the brooders along with the dopamine inhibitor domperidone. The standard treatment with the commercial salmon GnRH (sGnRH) analogue Ovaprim® (Syndel, USA) was used as the control. The 3-D structure of C. magur GnRH receptor was generated using MODELLER software. Molecular docking studies revealed the binding preference of the receptor as chicken (c) GnRH-II > Buserelin > sGnRH > catfish (cf) GnRH > human (m) GnRH. Though Buserelin showed better binding affinity compared to sGnRH, induced breeding experiments with magur showed similar performance of the ligands at the equivalent dose of 20 µg/kg B.W., but the spontaneous release of milt from the males was not obsereved in both the cases. Significantly better reproductive parameters were recorded with Buserelin at the dose of 30 µg/kg B.W. The study revealed that that the GnRHa Buserelin can be used as an effective inducing agent for breeding in C. magur.
{"title":"Evaluation of the Binding Affinity of a Gonadotropin-Releasing Hormone Analogue (GnRH-a) Buserelin through In Silico and In Vivo testing in Clarias magur","authors":"Mukesh Kumar, M. Goswami, S. Nayak, P. Gireesh-Babu, A. Chaudhari","doi":"10.2174/1570164618666210426090916","DOIUrl":"https://doi.org/10.2174/1570164618666210426090916","url":null,"abstract":"To evaluate the binding affinity and biological potency of gonadotropin releasing hormone analogue (GnRHa) Buserelin (C60H86N16O13) based on in silico and in vivo testing for induced breeding in Clarias magur. Many attempts have been made to induce C. magur but encouraging results have not yet been achieved. Hence, it is the need of the hour to find out more potent analogues or other bio-molecules for induced breeding in C. magur to facilitate sustainable aquaculture. To determine the binding affinity of C. magur GnRH receptor through in silico and its validation for induced breeding of C. magur. Buserelin (C60H86N16O13) was selected as the potential GnRHa after screening several peptides for their binding energy with the C. magur GnRH receptor. The induced breeding trial was set up at ICAR-CIFE Powarkheda Centre, M.P. India, and Buserelin was administered in different doses to the brooders along with the dopamine inhibitor domperidone. The standard treatment with the commercial salmon GnRH (sGnRH) analogue Ovaprim® (Syndel, USA) was used as the control. The 3-D structure of C. magur GnRH receptor was generated using MODELLER software. Molecular docking studies revealed the binding preference of the receptor as chicken (c) GnRH-II > Buserelin > sGnRH > catfish (cf) GnRH > human (m) GnRH. Though Buserelin showed better binding affinity compared to sGnRH, induced breeding experiments with magur showed similar performance of the ligands at the equivalent dose of 20 µg/kg B.W., but the spontaneous release of milt from the males was not obsereved in both the cases. Significantly better reproductive parameters were recorded with Buserelin at the dose of 30 µg/kg B.W. The study revealed that that the GnRHa Buserelin can be used as an effective inducing agent for breeding in C. magur.","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"60 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2021-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90814550","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-04-23DOI: 10.2174/1570164618666210423131625
S. Fatima, Fareeha Arshad, Samreen Amani
Heavy metals and metalloids like arsenic, cadmium, mercury acts as denaturing agent for biomolecules. They interfere with protein’s physiological activity by forming a complex with the protein’s side chain or removing the essential metal ions from metalloproteins and replacing them. Protein aggregation is an extensive phenomenon in a cell and is linked with various pathological conditions. In this study, we aim to prove that proteins are highly susceptible to arsenite toxicity by arsenite-induced protein aggregation; and that naringin reduces the aggregation effect. Several biophysical techniques were employed to study the protein aggregation due to arsenite and its prevention by naringin. Through our experiments, the results showed that aggregation induced by arsenite was reduced in the presence of naringin at twice the concentration of arsenite. In conclusion, our study showed that naringin plays a protective role during HSA aggregation due to arsenite.
{"title":"Arsenite induced conformational changes and aggregation in human serum albumin (HSA) and its prevention by naringin","authors":"S. Fatima, Fareeha Arshad, Samreen Amani","doi":"10.2174/1570164618666210423131625","DOIUrl":"https://doi.org/10.2174/1570164618666210423131625","url":null,"abstract":"\u0000\u0000Heavy metals and metalloids like arsenic, cadmium, mercury acts as denaturing agent for biomolecules. They interfere with protein’s physiological activity by forming a complex with the protein’s side chain or removing the essential metal ions from metalloproteins and replacing them. Protein aggregation is an extensive phenomenon in a cell and is linked with various pathological conditions. \u0000\u0000\u0000\u0000In this study, we aim to prove that proteins are highly susceptible to arsenite toxicity by arsenite-induced protein aggregation; and that naringin reduces the aggregation effect.\u0000\u0000\u0000\u0000\u0000 Several biophysical techniques were employed to study the protein aggregation due to arsenite and its prevention by naringin.\u0000\u0000\u0000\u0000 Through our experiments, the results showed that aggregation induced by arsenite was reduced in the presence of naringin at twice the concentration of arsenite.\u0000\u0000\u0000\u0000In conclusion, our study showed that naringin plays a protective role during HSA aggregation due to arsenite.\u0000\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"161 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2021-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75396211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-04-13DOI: 10.2174/1570164618666210413105907
Xiang Yu, Xiaoyun Zhao, Yongqing Yang, Zhen Li
Soil salinity is a major issue that seriously affects plant growth and cultivated land utilization. Salt tolerance is one of the most fundamental biological processes that ensures plants survival. SOS2 is one of the most important components of the Salt Overly Sensitive (SOS) signaling pathway, which maintains plant ion homeostasis under salt stress. The SOS2-related signaling pathways remain incompletely exploited especially at the proteomics level. In this paper, proteins potentially interacting with and regulated by SOS2 in Arabidopsis were identified. The proteomes of Arabidopsis Wild Type (WT) and SOS2-deficient mutant (sos2-2) exposed to 100 mM NaCl for 6 h were compared, proteins were identified using data-independent acquisition-based quantitative proteomics strategy. A total of 7470 proteins were identified and quantified, 372 Differentially Expressed Proteins (DEP) were detected between WT and sos2-2 mutant under normal condition and 179 DEPs were identified under salt treatment. Functional analysis showed that the DEPs were mainly involved in protein binding and catalytic activity. Among the DEPs under salt stress, the protein expressions of AVP1, Photosystem II reaction center protein A, B, C, and stress-responsive protein (KIN2) were significantly up-regulated. LHCA1, LHCA2, LHCA4, ATPD and ATPE were significantly down-regulated. These proteins were involved in biological processes including: stress response, photosynthesis, transport and heat shock. These results revealed complexity of the functions of SOS2 in maintaining intracellular homeostasis, in addition to its function in sodium homeostasis. Plant salt resistance is not independent but closely related to metabolic processes including photosystem, ATP synthase, transport and other stress resistances.
土壤盐分是严重影响植物生长和耕地利用的重要问题。耐盐性是保证植物生存的最基本的生物过程之一。SOS2是盐过度敏感(Salt oversensitive, SOS)信号通路的重要组成部分，在盐胁迫下维持植物离子稳态。特别是在蛋白质组学水平上，sos2相关的信号通路仍未被完全利用。本文鉴定了拟南芥中可能与SOS2相互作用并受其调控的蛋白。将拟南芥野生型(WT)和sos2缺陷突变体(sos2-2)在100 mM NaCl处理6 h后的蛋白质组学进行比较，采用数据独立获取的定量蛋白质组学策略对蛋白质进行鉴定。共鉴定并定量了7470个蛋白，其中正常条件下WT与sos2-2突变体之间检测到372个差异表达蛋白(DEP)，盐处理下检测到179个差异表达蛋白(DEP)。功能分析表明，DEPs主要参与蛋白质结合和催化活性。盐胁迫下的DEPs中，AVP1、光系统II反应中心蛋白A、B、C和应激响应蛋白(KIN2)的表达量显著上调。LHCA1、LHCA2、LHCA4、ATPD、ATPE显著下调。这些蛋白参与了胁迫反应、光合作用、运输和热休克等生物过程。这些结果揭示了SOS2在维持细胞内稳态方面的复杂功能，以及它在钠稳态方面的功能。植物的耐盐性不是独立的，而是与光系统、ATP合酶、转运等代谢过程密切相关。
{"title":"Quantitative Proteomics Reveals SOS2-related Proteins in Arabidopsis under Salt Stress","authors":"Xiang Yu, Xiaoyun Zhao, Yongqing Yang, Zhen Li","doi":"10.2174/1570164618666210413105907","DOIUrl":"https://doi.org/10.2174/1570164618666210413105907","url":null,"abstract":"\u0000\u0000Soil salinity is a major issue that seriously affects plant growth and cultivated land utilization. Salt tolerance is one of the most fundamental biological processes that ensures plants survival. SOS2 is one of the most important components of the Salt Overly Sensitive (SOS) signaling pathway, which maintains plant ion homeostasis under salt stress. The SOS2-related signaling pathways remain incompletely exploited especially at the proteomics level.\u0000\u0000\u0000\u0000In this paper, proteins potentially interacting with and regulated by SOS2 in Arabidopsis were identified.\u0000\u0000\u0000\u0000The proteomes of Arabidopsis Wild Type (WT) and SOS2-deficient mutant (sos2-2) exposed to 100 mM NaCl for 6 h were compared, proteins were identified using data-independent acquisition-based quantitative proteomics strategy.\u0000\u0000\u0000\u0000A total of 7470 proteins were identified and quantified, 372 Differentially Expressed Proteins (DEP) were detected between WT and sos2-2 mutant under normal condition and 179 DEPs were identified under salt treatment. Functional analysis showed that the DEPs were mainly involved in protein binding and catalytic activity. Among the DEPs under salt stress, the protein expressions of AVP1, Photosystem II reaction center protein A, B, C, and stress-responsive protein (KIN2) were significantly up-regulated. LHCA1, LHCA2, LHCA4, ATPD and ATPE were significantly down-regulated. These proteins were involved in biological processes including: stress response, photosynthesis, transport and heat shock.\u0000\u0000\u0000\u0000These results revealed complexity of the functions of SOS2 in maintaining intracellular homeostasis, in addition to its function in sodium homeostasis. Plant salt resistance is not independent but closely related to metabolic processes including photosystem, ATP synthase, transport and other stress resistances.\u0000\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"47 1 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2021-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90052976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-04-13DOI: 10.2174/1570164618666210413111223
Mustafa Ergul, F. Aktan, Yusuf Tutar
The association of a drug with its target protein correlates to its medicinal activity and the microenvironment plays a key role in this association. The key challenge is to identify mutations which unlikely to respond to designed drugs. Hsp70 is an anti-apoptotic factor and tumor cells overexpress Hsp70 to survive against anti-cancer agents. The impact of pathogenic mutations on Hsp70 is unknown. Elucidation of these alterations is essential to understand the molecular switch mechanism. Thus, critical spots on Hsp70 Nucleotide Binding Domain (NBD) are important since mutation-driven sensitivity may be useful in designing innovative inhibitors. ATP, AMP-PNP (non-hydrolyzable analog of ATP) along with commercially available compounds VER-155008 (ATP analog and competitive inhibitor) and MKT-077 (allosteric inhibitor of ADP bound form) were docked to Hsp70 NBD structure in silico to identify critical amino acids of inhibition mechanism. Site-directed mutagenesis of the determined critical residues along with ATP hydrolysis and luciferase refolding were performed. Wild-type and mutant Hsp70s were compared to determine the effect on protein functions in the presence or the absence of inhibitors. This study identified three mutants that have a loss of function for Hsp70, which may alter the drug inhibition activity as oncogenic cells have multiple mutations. Two commercial inhibitors employed here that mimic ATP and ADP states respectively are not affected by these mutational perturbations and displayed effective interference for Hsp70 functions. Designing inhibitors by considering these critical residues may improve drug design and increase drug efficiency.
{"title":"Critical Residues in HSP70 Nucleotide Binding Domain for Challenges in Drug Design","authors":"Mustafa Ergul, F. Aktan, Yusuf Tutar","doi":"10.2174/1570164618666210413111223","DOIUrl":"https://doi.org/10.2174/1570164618666210413111223","url":null,"abstract":"\u0000\u0000The association of a drug with its target protein correlates to its medicinal activity and the microenvironment plays a key role in this association. The key challenge is to identify mutations which unlikely to respond to designed drugs. \u0000\u0000\u0000\u0000 Hsp70 is an anti-apoptotic factor and tumor cells overexpress Hsp70 to survive against anti-cancer agents. The impact of pathogenic mutations on Hsp70 is unknown. Elucidation of these alterations is essential to understand the molecular switch mechanism. Thus, critical spots on Hsp70 Nucleotide Binding Domain (NBD) are important since mutation-driven sensitivity may be useful in designing innovative inhibitors. \u0000\u0000\u0000\u0000ATP, AMP-PNP (non-hydrolyzable analog of ATP) along with commercially available compounds VER-155008 (ATP analog and competitive inhibitor) and MKT-077 (allosteric inhibitor of ADP bound form) were docked to Hsp70 NBD structure in silico to identify critical amino acids of inhibition mechanism. Site-directed mutagenesis of the determined critical residues along with ATP hydrolysis and luciferase refolding were performed. Wild-type and mutant Hsp70s were compared to determine the effect on protein functions in the presence or the absence of inhibitors.\u0000\u0000\u0000\u0000This study identified three mutants that have a loss of function for Hsp70, which may alter the drug inhibition activity as oncogenic cells have multiple mutations. \u0000\u0000\u0000\u0000Two commercial inhibitors employed here that mimic ATP and ADP states respectively are not affected by these mutational perturbations and displayed effective interference for Hsp70 functions. Designing inhibitors by considering these critical residues may improve drug design and increase drug efficiency.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"13 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2021-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89402095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-04-02DOI: 10.2174/1570164618666210402152159
Burak Yazgan, O. Ozcelik, A. Ayar, Gülin Renda, Tuba Yıldırım
Iris taochia is an endemic plant in Turkey. Iris species has many biological effects such as antibacterial, antiinflammatory, antioxidant and anticancer properties. Apoptosis is a programmed cell death and this mechanism regulates the death of cancer cells. The aim of our work is to investigate how the Iris taochia extracts affect the apoptotic activity in the MCF7 cells. Cytotoxic dose and cell viability is determined by the MTT assay. Bad, Bax, Bcl-2, Bcl-W, Bid, Bim, Caspase 3, Caspase 8, CD40, CD40L, cIAP-2, CytoC, DR6, Fas, FasL, HSP27, HSP60, HSP70, HTRA, IGF-I, IGF-II, IGFBP-1, IGFBP-2, IGFBP-3, IGFBP-4, IGFBP-5, IGFBP-6, IGF-1sR, Livin, p21, p27, p53, SMAC, Survivin, sTNF-R1, sTNF-R2, TNF-α, TNF-β, TRAILR-1, TRAILR-2, TRAILR-3, TRAILR-4 and XIAP proteins were measured by the membrane array kit. Iris taochia extracts exhibited significant cytotoxic effects on MCF7 cells and IC50 values ranging from 1.56 to 100 μg/mL. Our results indicate that MeOH extract of Iris taochia in MCF7 cells may be a regulator of cell death proteins, cell cycle and growth factors. DCM and EtOH extracts of Iris taochia have a limited effect on MCF7 cells. Especially, HSPs, which play a significant role in chemoresistance downregulating DCM and EtOH extracts of Iris taochia, whereas ligands and receptors of extrinsic apoptotic pathway are upregulated by these extracts. This is the first study to investigate the cytotoxic and apoptotic effect of Iris taochia extracts on MCF7 cells. Results also showed that Iris taochia reduced cell viability and induced apoptotic pathways as a potential regulator of cancer cell death.
{"title":"Cytotoxic and Apoptotic Effect of Iris taochia Plant Extracts on Human Breast Cancer (MCF-7) Cells","authors":"Burak Yazgan, O. Ozcelik, A. Ayar, Gülin Renda, Tuba Yıldırım","doi":"10.2174/1570164618666210402152159","DOIUrl":"https://doi.org/10.2174/1570164618666210402152159","url":null,"abstract":"\u0000\u0000Iris taochia is an endemic plant in Turkey. Iris species has many biological effects such as antibacterial, antiinflammatory, antioxidant \u0000and anticancer properties. Apoptosis is a programmed cell death and this mechanism regulates the death of cancer cells. \u0000\u0000\u0000\u0000The aim of our work is to investigate how the Iris taochia extracts affect the apoptotic activity in the MCF7 cells. \u0000\u0000\u0000\u0000Cytotoxic dose and cell viability is determined by the MTT assay. Bad, Bax, Bcl-2, Bcl-W, Bid, Bim, Caspase 3, Caspase 8, CD40, CD40L, cIAP-2, CytoC, DR6, Fas, FasL, HSP27, HSP60, HSP70, HTRA, IGF-I, IGF-II, IGFBP-1, IGFBP-2, IGFBP-3, IGFBP-4, IGFBP-5, IGFBP-6, IGF-1sR, Livin, p21, p27, p53, SMAC, Survivin, sTNF-R1, sTNF-R2, TNF-α, TNF-β, TRAILR-1, TRAILR-2, TRAILR-3, TRAILR-4 and XIAP proteins were measured by the membrane array kit.\u0000\u0000\u0000\u0000Iris taochia extracts exhibited significant cytotoxic effects on MCF7 cells and IC50 values ranging from 1.56 to 100 μg/mL. Our results indicate that MeOH extract of Iris taochia in MCF7 cells may be a regulator of cell death proteins, cell cycle and growth factors. DCM and EtOH extracts of Iris taochia have a limited effect on MCF7 cells. Especially, HSPs, which play a significant role in chemoresistance downregulating DCM and EtOH extracts of Iris taochia, whereas ligands and receptors of extrinsic apoptotic pathway are upregulated by these extracts.\u0000\u0000\u0000\u0000This is the first study to investigate the cytotoxic and apoptotic effect of Iris taochia extracts on MCF7 cells. Results also showed that Iris taochia reduced cell viability and induced apoptotic pathways as a potential regulator of cancer cell death.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"38 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2021-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77651414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-03-31DOI: 10.2174/1570164617999200529122637
B. Jabbar, Batcho Agossa Anicet, M. Sarwar, B. Rashid, S. Hassan, T. Husnain
Exploring molecular mechanism of abiotic stress tolerance in plants is needed to overcome the deterioration of yield and quality of crop plants to meet the food security challenges of the growing population. MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate target gene expression for modulating plant growth, development, and response to different stresses. Agave belonging to CAM plants’ has remarkable tolerance to extreme conditions of drought and heat; however, molecular mechanisms underlying this excellence are yet to explore. This study applies comparative genomics approach on available Transcriptome (RNA- Seq) data of Agave deserti to identify potential miRNAs, and miRNA targets. Transcriptome datasets consisting of 128,869 Agave contigs was processed to create local database, for nucleotide homology analysis with 6,028 non-redundant plant miRNAs as query sequences. Protein coding sequences were removed, and potential pre-miRNA sequences were tested for stability analysis based on a variety of factors, including but not limited to %G+C content and minimum free energy (-ΔG), as a filter to remove pseudo pre-miRNAs. This study identified 30 unique miRNAs of Agave deserti harboring 14 different categories of precursors. Phylogenetic analysis revealed evolutionary relationship between newly identified pre-miRNAs with corresponding pre-miRNA homologues. Target genes of miRNAs were predicted subsequently, and possible functions were defined by functional annotation analysis. The results of this study will pave the way for further research, exploring the molecular mechanisms in Agave deserti and the role of miRNAs in gene regulation under abiotic stresses.
{"title":"RNA-Seq Data Analysis Unveils Potential Conserved Micro-RNAs in Agave Deserti","authors":"B. Jabbar, Batcho Agossa Anicet, M. Sarwar, B. Rashid, S. Hassan, T. Husnain","doi":"10.2174/1570164617999200529122637","DOIUrl":"https://doi.org/10.2174/1570164617999200529122637","url":null,"abstract":"\u0000\u0000Exploring molecular mechanism of abiotic stress tolerance in plants is needed to\u0000overcome the deterioration of yield and quality of crop plants to meet the food security challenges\u0000of the growing population.\u0000\u0000\u0000\u0000MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate target\u0000gene expression for modulating plant growth, development, and response to different stresses.\u0000Agave belonging to CAM plants’ has remarkable tolerance to extreme conditions of drought and\u0000heat; however, molecular mechanisms underlying this excellence are yet to explore.\u0000\u0000\u0000\u0000This study applies comparative genomics approach on available Transcriptome (RNA-\u0000Seq) data of Agave deserti to identify potential miRNAs, and miRNA targets.\u0000\u0000\u0000\u0000Transcriptome datasets consisting of 128,869 Agave contigs was processed to create local\u0000database, for nucleotide homology analysis with 6,028 non-redundant plant miRNAs as query\u0000sequences. Protein coding sequences were removed, and potential pre-miRNA sequences were tested\u0000for stability analysis based on a variety of factors, including but not limited to %G+C content\u0000and minimum free energy (-ΔG), as a filter to remove pseudo pre-miRNAs.\u0000\u0000\u0000\u0000This study identified 30 unique miRNAs of Agave deserti harboring 14 different categories\u0000of precursors. Phylogenetic analysis revealed evolutionary relationship between newly identified\u0000pre-miRNAs with corresponding pre-miRNA homologues. Target genes of miRNAs were\u0000predicted subsequently, and possible functions were defined by functional annotation analysis.\u0000\u0000\u0000\u0000The results of this study will pave the way for further research, exploring the molecular\u0000mechanisms in Agave deserti and the role of miRNAs in gene regulation under abiotic stresses.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"40 1","pages":"248-263"},"PeriodicalIF":0.8,"publicationDate":"2021-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85044840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-02-23DOI: 10.2174/1570164618666210223160742
A. Basak, S. Basak
Self-attachment of proteins leading to the formation of highly insoluble protein oligomers and aggregates has become an important focus of research owing to its diverse implications in pathophysiology and diseases. This has become a more frequent phenomenon in most neurological and neurodegenerative diseases as well as in dementia. In recent years such event of protein aggregation has linked to other disease conditions, disorders or adverse health conditions. Interestingly, aggregation of protein also plays role in development, growth or metabolism. Most often physiological proteins are initially bio-synthesised in native or nascent geometrical forms or conformations but later they undergo specific folding pattern and thereby acquire a stable configuration that is biologically relevant and active. It is highly important that these proteins remain in their biologically active configuration in order to exert their functional properties. Any alteration or change to this structural configuration can be detrimental to their specific functions and may cause pathological consequences leading to the onset of diseases or disorders. Several factors such as the action of chaperones, binding partners, physiological metal ions, pH level, temperature, ionic strength, interfacial exposure (solid-liquid, liquid-liquid, gas-liquid), mutation and post translational modification, chemical changes, interaction with small molecules such as lipids, hormones, etc. and solvent environment have been either identified or proposed as important factors in conferring the ultimate status of protein structure and configuration. Among many misfolding protein conformations, self-assembly or aggregation is the most significant. It leads to the formation of highly oligomeric self-aggregates that precipitate and interfere with many biochemical processes with serious pathological consequences. The most common implication of protein aggregation leading to the formation of deposits / plaques of various morphological types is the onset of neurological and neurodegenerative diseases that include Alzheimer’s, Parkinson’s, Huntington, ALS (Amyotrophic Lateral Sclerosis), CJD (Creutzfeldt Jakob Dementia), Prion diseases, Amyloidosis and other forms of dementia. However increasingly studies revealed that protein aggregation may also be associated with other diseases such as cancer, type 2 diabetes, renal, corneal and cardiovascular diseases. Protein aggregation diseases are now considered as part of “Proteinopathy” which refers to conditions where proteins become structurally abnormal or fail to fold into stable normal configurations. In this review, we reflect on various aspects of protein self-aggregation, potential underlying causes, mechanism, role of secondary structures, pathological consequences and possible intervention strategies as reported in published literatures.
蛋白质的自附着导致高度不溶性蛋白质寡聚物和聚集体的形成，由于其在病理生理学和疾病中的多种意义，已成为研究的重要焦点。这在大多数神经和神经退行性疾病以及痴呆症中已经成为一种更常见的现象。近年来，这种蛋白质聚集事件与其他疾病、失调或不良健康状况有关。有趣的是，蛋白质的聚集也在发育、生长或代谢中发挥作用。大多数情况下，生理蛋白最初以天然或新生的几何形式或构象进行生物合成，但后来它们经历了特定的折叠模式，从而获得了具有生物学相关性和活性的稳定构型。为了发挥其功能特性，这些蛋白质保持其生物活性结构是非常重要的。这种结构构型的任何改变或改变都可能损害它们的特定功能，并可能引起病理后果，导致疾病或失调的发作。伴侣、结合伙伴、生理金属离子、pH值、温度、离子强度、界面暴露(固-液、液-液、气-液)、突变和翻译后修饰、化学变化、与小分子(如脂类、激素等)的相互作用以及溶剂环境等因素已被确定或提出为决定蛋白质结构和构型最终状态的重要因素。在许多错误折叠的蛋白质构象中，自组装或聚集是最重要的。它导致形成高度低聚的自聚集体，沉淀并干扰许多生化过程，造成严重的病理后果。蛋白质聚集导致各种形态类型的沉积物/斑块形成的最常见含义是神经和神经退行性疾病的发病，包括阿尔茨海默氏症、帕金森氏症、亨廷顿氏症、肌萎缩性侧索硬化症(ALS)、克雅氏痴呆症(Creutzfeldt Jakob Dementia)、朊病毒病、淀粉样变性和其他形式的痴呆症。然而，越来越多的研究表明，蛋白质聚集也可能与其他疾病有关，如癌症、2型糖尿病、肾脏、角膜和心血管疾病。蛋白质聚集性疾病现在被认为是“蛋白质病”的一部分，“蛋白质病”指的是蛋白质在结构上异常或无法折叠成稳定的正常构型的情况。在这篇综述中，我们反思了蛋白质自聚集的各个方面，潜在的潜在原因，机制，二级结构的作用，病理后果和可能的干预策略，已发表的文献报道。
{"title":"Protein aggregation and self assembly in Health and Disease","authors":"A. Basak, S. Basak","doi":"10.2174/1570164618666210223160742","DOIUrl":"https://doi.org/10.2174/1570164618666210223160742","url":null,"abstract":"\u0000\u0000Self-attachment of proteins leading to the formation of highly insoluble protein oligomers and aggregates has become an important focus of research owing to its diverse implications in pathophysiology and diseases. This has become a more frequent phenomenon in most neurological and neurodegenerative diseases as well as in dementia. In recent years such event of protein aggregation has linked to other disease conditions, disorders or adverse health conditions. Interestingly, aggregation of protein also plays role in development, growth or metabolism. Most often physiological proteins are initially bio-synthesised in native or nascent geometrical forms or conformations but later they undergo specific folding pattern and thereby acquire a stable configuration that is biologically relevant and active. It is highly important that these proteins remain in their biologically active configuration in order to exert their functional properties. Any alteration or change to this structural configuration can be detrimental to their specific functions and may cause pathological consequences leading to the onset of diseases or disorders. Several factors such as the action of chaperones, binding partners, physiological metal ions, pH level, temperature, ionic strength, interfacial exposure (solid-liquid, liquid-liquid, gas-liquid), mutation and post translational modification, chemical changes, interaction with small molecules such as lipids, hormones, etc. and solvent environment have been either identified or proposed as important factors in conferring the ultimate status of protein structure and configuration. \u0000Among many misfolding protein conformations, self-assembly or aggregation is the most significant. It leads to the formation of highly oligomeric self-aggregates that precipitate and interfere with many biochemical processes with serious pathological consequences. The most common implication of protein aggregation leading to the formation of deposits / plaques of various morphological types is the onset of neurological and neurodegenerative diseases that include Alzheimer’s, Parkinson’s, Huntington, ALS (Amyotrophic Lateral Sclerosis), CJD (Creutzfeldt Jakob Dementia), Prion diseases, Amyloidosis and other forms of dementia. However increasingly studies revealed that protein aggregation may also be associated with other diseases such as cancer, type 2 diabetes, renal, corneal and cardiovascular diseases. Protein aggregation diseases are now considered as part of “Proteinopathy” which refers to conditions where proteins become structurally abnormal or fail to fold into stable normal configurations. In this review, we reflect on various aspects of protein self-aggregation, potential underlying causes, mechanism, role of secondary structures, pathological consequences and possible intervention strategies as reported in published literatures. \u0000\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"26 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2021-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74040726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-02-18DOI: 10.2174/1570164618666210218141148
Xiaoqing Liu, Zhenyu Yang, Yaoxin Wang, Qi Dai
The fast growing of protein sequencing and protein structure data has promoted the development of the protein structural class prediction. Several prediction methods have been proposed to study protein folding rate, DNA binding sites, as well as reducing the search of conformational space and realizing the prediction of tertiary structure. This paper introduces the current approaches of protein structural class prediction and emphasize their steps from information extraction to classification algorithms.
{"title":"Prediction of Protein Structural Classes: Features Extraction to Classification Algorithm","authors":"Xiaoqing Liu, Zhenyu Yang, Yaoxin Wang, Qi Dai","doi":"10.2174/1570164618666210218141148","DOIUrl":"https://doi.org/10.2174/1570164618666210218141148","url":null,"abstract":"\u0000\u0000The fast growing of protein sequencing and protein structure data has promoted the development of the protein structural class prediction. Several prediction methods have been proposed to study protein folding rate, DNA binding sites, as well as reducing the search of conformational space and realizing the prediction of tertiary structure. This paper introduces the current approaches of protein structural class prediction and emphasize their steps from information extraction to classification algorithms.\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"16 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2021-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81812076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-02-12DOI: 10.2174/1570164618666210212123850
C. Polanco, V. Uversky, G. Vargas-Alarcón, T. Buhse, A. Huberman, M. Márquez, Leire Andrés
In the vast variety of viruses known, there is a particular interest in those transmitted to humans and whose ability to disseminate represents a significant public health issue. The present study’s objective is to bioinformatically characterize the proteins of the two main divisions of viruses, RNA-viruses and DNA-viruses. In this work, a set of in-house computational programs was used to calculate the polarity/charge profiles and intrinsic disorder predisposition profiles of the proteins of several groups of viruses representing both types extracted from UniProt database. The efficiency of these computational programs was statistically verified. It was found that the polarity/charge profile of the proteins is, in most cases, an efficient discriminant that allows the re-creation of the taxonomy known for both viral groups. Additionally, the entire set of "reviewed" proteins in UniProt database was analyzed to find proteins with the polarity/charge profiles similar to those obtained for each viral group. This search revealed a substantial number of proteins with such polarity-charge profiles. Polarity/charge profile represents a physicochemical metric, which is easy to calculate, and which can be used to effectively identify viral groups from their protein sequences.
{"title":"Characterization of proteins from putative human DNA and RNA viruses.","authors":"C. Polanco, V. Uversky, G. Vargas-Alarcón, T. Buhse, A. Huberman, M. Márquez, Leire Andrés","doi":"10.2174/1570164618666210212123850","DOIUrl":"https://doi.org/10.2174/1570164618666210212123850","url":null,"abstract":"\u0000\u0000 In the vast variety of viruses known, there is a particular interest in those transmitted to humans and whose ability to disseminate represents a significant public health issue. \u0000\u0000\u0000\u0000 The present study’s objective is to bioinformatically characterize the proteins of the two main divisions of viruses, RNA-viruses and DNA-viruses. \u0000\u0000\u0000\u0000\u0000In this work, a set of in-house computational programs was used to calculate the polarity/charge profiles and intrinsic disorder predisposition profiles of the proteins of several groups of viruses representing both types extracted from UniProt database. The efficiency of these computational programs was statistically verified. \u0000\u0000\u0000\u0000It was found that the polarity/charge profile of the proteins is, in most cases, an efficient discriminant that allows the re-creation of the taxonomy known for both viral groups. Additionally, the entire set of \"reviewed\" proteins in UniProt database was analyzed to find proteins with the polarity/charge profiles similar to those obtained for each viral group. This search revealed a substantial number of proteins with such polarity-charge profiles. \u0000\u0000\u0000\u0000Polarity/charge profile represents a physicochemical metric, which is easy to calculate, and which can be used to effectively identify viral groups from their protein sequences.\u0000\u0000","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"32 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2021-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88856858","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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