Pub Date : 2018-10-24DOI: 10.15226/2376-4589/4/1/00130
Z. Hua
The microspheres constituted by proteinoids synthesized from Fox’s simulation experiments. They had peptide bond structure and weak catalysis, as well as proliferated themselves. Such microspheres were believed the models for primitive life. Due to lack of metabolism and self-reproduction, the microspheres could not meet requirements of life. Thus, how microspheres could evolve into primitive life remain unsolved mysteries. The microspheres were supposed a dissipative structure and the processes of absorption and hydrolysis could be balanced to maintain their stability by consuming proteinoids. Proteinoid molecules differed in their life spans, which were mainly determined by their multi-space structures. Consequently, molecule selection and retention could occur spontaneously in microspheres and lead to a more organized and stabilized structure of the whole microsphere with time through dissipative process. More complex chain network of chemical reactions could happen in microspheres because the proteinoid with complex, ordered multi-space structure and relatively high catalytic activity would retain. In such microspheres, nucleotides could produce and further aggregate into RNA. The synthesis of real proteins could take place with RNA as the template catalyzed by proteinoids or RNA inside microspheres. When template-based protein molecules replaced the proteinoid inside the microspheres, a protein-based self-catalyzed network of chemical reactions could take place. It is plausible if Fox’s proteinoids microspheres is to dawn on a dissipative structure, then molecule selection could occur spontaneously by “dissipative” proteinoids, and the microspheres would acquire catalytic activity due to preserved the proteinoid with a large molecular weight and relatively complex and ordered multi-space structure, and relatively high catalytic activity. Thus the microspheres would spontaneously go to self-organizing, and evolve into primitive life.
{"title":"On the Origin of Life: A Possible Way from Fox's Microspheres into Primitive Life","authors":"Z. Hua","doi":"10.15226/2376-4589/4/1/00130","DOIUrl":"https://doi.org/10.15226/2376-4589/4/1/00130","url":null,"abstract":"The microspheres constituted by proteinoids synthesized from Fox’s simulation experiments. They had peptide bond structure and weak catalysis, as well as proliferated themselves. Such microspheres were believed the models for primitive life. Due to lack of metabolism and self-reproduction, the microspheres could not meet requirements of life. Thus, how microspheres could evolve into primitive life remain unsolved mysteries. The microspheres were supposed a dissipative structure and the processes of absorption and hydrolysis could be balanced to maintain their stability by consuming proteinoids. Proteinoid molecules differed in their life spans, which were mainly determined by their multi-space structures. Consequently, molecule selection and retention could occur spontaneously in microspheres and lead to a more organized and stabilized structure of the whole microsphere with time through dissipative process. More complex chain network of chemical reactions could happen in microspheres because the proteinoid with complex, ordered multi-space structure and relatively high catalytic activity would retain. In such microspheres, nucleotides could produce and further aggregate into RNA. The synthesis of real proteins could take place with RNA as the template catalyzed by proteinoids or RNA inside microspheres. When template-based protein molecules replaced the proteinoid inside the microspheres, a protein-based self-catalyzed network of chemical reactions could take place. It is plausible if Fox’s proteinoids microspheres is to dawn on a dissipative structure, then molecule selection could occur spontaneously by “dissipative” proteinoids, and the microspheres would acquire catalytic activity due to preserved the proteinoid with a large molecular weight and relatively complex and ordered multi-space structure, and relatively high catalytic activity. Thus the microspheres would spontaneously go to self-organizing, and evolve into primitive life.","PeriodicalId":90972,"journal":{"name":"SOJ biochemistry","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45019304","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 : 2018-10-01DOI: 10.15226/2376-4589/4/1/00129
N. A. El-Baky, M. Sharaf, E. Amer, Hoda Reda Kholef, Mohamed Zakaria Hussain, A. Amara
Recently, a protocol for ghost cells preparations was introduced. It was given the name sponge-like protocol: Procaryotes, eucaryotes and virus were turned to ghost cells using such protocol. In this study, with slight modifications, Aspergillus niger ghost cells were prepared using the same protocol. Both the Minimum Inhibitory Concentration (MIC) and the minimum growth concentration (MGC) values for H2O2, NaOH, NaHCO3 and SDS against A. niger were determined. Five different randomization experiments were conducted instead of the full Plackett–Burman design. During the ghost preparation steps, the released Protein and DNA were measured spectrophotometrically at 280nm and 260nm, respectively. The quality of the prepared ghost cells were evaluated during the preparation steps using light microscope. Transmission electron microscope was used for evaluating the final steps. Protein and DNA electrophoresis were conducted to evaluate the quality of the released protein and DNA after each randomization experiment. The data obtained prove correct evacuation of the fungal cells from their cytoplasmic content during the successive steps. The study not only introduces a protocol for preparing ghost cells from Aspergillus niger but also enables the isolation of both of protein and DNA. The idea, the concept and the tools used in this study could establish a more sensitive method for protein and DNA isolation using any of four utilized chemical compounds. This proposes the same concept of enzyme-induced cell lysis which is based on minimizing the effect of used chemicals or enzymes. The study recommended extending the benefit of the sponge-like protocol from being a protocol for ghost cells preparation to DNA and protein isolation technique using the same concept.
{"title":"Protein and DNA Isolation from Aspergillus Niger as well as Ghost Cells Formation","authors":"N. A. El-Baky, M. Sharaf, E. Amer, Hoda Reda Kholef, Mohamed Zakaria Hussain, A. Amara","doi":"10.15226/2376-4589/4/1/00129","DOIUrl":"https://doi.org/10.15226/2376-4589/4/1/00129","url":null,"abstract":"Recently, a protocol for ghost cells preparations was introduced. It was given the name sponge-like protocol: Procaryotes, eucaryotes and virus were turned to ghost cells using such protocol. In this study, with slight modifications, Aspergillus niger ghost cells were prepared using the same protocol. Both the Minimum Inhibitory Concentration (MIC) and the minimum growth concentration (MGC) values for H2O2, NaOH, NaHCO3 and SDS against A. niger were determined. Five different randomization experiments were conducted instead of the full Plackett–Burman design. During the ghost preparation steps, the released Protein and DNA were measured spectrophotometrically at 280nm and 260nm, respectively. The quality of the prepared ghost cells were evaluated during the preparation steps using light microscope. Transmission electron microscope was used for evaluating the final steps. Protein and DNA electrophoresis were conducted to evaluate the quality of the released protein and DNA after each randomization experiment. The data obtained prove correct evacuation of the fungal cells from their cytoplasmic content during the successive steps. The study not only introduces a protocol for preparing ghost cells from Aspergillus niger but also enables the isolation of both of protein and DNA. The idea, the concept and the tools used in this study could establish a more sensitive method for protein and DNA isolation using any of four utilized chemical compounds. This proposes the same concept of enzyme-induced cell lysis which is based on minimizing the effect of used chemicals or enzymes. The study recommended extending the benefit of the sponge-like protocol from being a protocol for ghost cells preparation to DNA and protein isolation technique using the same concept.","PeriodicalId":90972,"journal":{"name":"SOJ biochemistry","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47313046","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 : 2018-06-12DOI: 10.15226/2376-4589/4/1/00128
N. Abd El-Baky
Considering the superior biological activities of Camel Lactoferrin (cLf) over lactoferrin from other animal species; which we previously confirmed and continuing the analysis of antimicrobial effectiveness of cLf; we started in previous studies, the current study aimed to formulate a protein-fatty acid complex of cLf and Oleic Acid (OA) and to compare it’s in vitro antimicrobial activities against different pathogens with those of a similar Bovine Lactoferrin (bLf)-OA complex. Antimicrobial activity of these complexes was evaluated by agar disc diffusion method, broth microdilution assay, and ELISAestimating Lf and its complexes binding to bacterial outer membrane proteins. Agar disc diffusion assay results revealed that inhibitory activity of both free cLf and cLf-OA against 13 test pathogens (Methicillin-Resistant Staphylococcus Aureus (MRSA), Staphylococcus aureus, Bacillus cereus, Escherichia coli, Salmonella typhi, Shigella sonnei, Klebsiella pneumonia, Pseudomonas aeruginosa, Proteus vulgaris, Serratia marcescens, Candida albicans, Aspergillus niger, and Aspergillus flavus) noticeably exceeded that of corresponding bLf and bLf-OA. Additionally, free OA exhibited antimicrobial activity against MRSA, S. aureus, B. cereus, and C. albicans and to a lesser extent against E. coli, K. pneumonia as well as A. niger and A. flavus. Consequently, synergy was evident between cLf/bLf and OA (mostly higher in case of cLf) in prepared complexes against MRSA, S. aureus, B. cereus, and C. albicans. cLf-OA demonstrated 4 times lower Minimum Inhibitory Concentration (MIC) values against MRSA, B. cereus, and C. albicans than bLf-OA; indicating more superiority in case of cLf-OA than free cLf that showed only twice the activity of bLf. ELISA signals confirmed binding of biotinylated cLf/bLf and cLf/bLf-OA to bacterial membrane proteins. This study proves that cLf obtains enhanced antimicrobial activities after complex formation with fatty acids such as OA even than its free form which has already superior activity than other Lf species; thus this complex may be used as a cure of various microbial infections.
{"title":"Differential Antimicrobial Effectiveness of Camel Lactoferrin-Oleic Acid and Bovine Lactoferrin-Oleic Acid Complexes against Several Pathogens","authors":"N. Abd El-Baky","doi":"10.15226/2376-4589/4/1/00128","DOIUrl":"https://doi.org/10.15226/2376-4589/4/1/00128","url":null,"abstract":"Considering the superior biological activities of Camel Lactoferrin (cLf) over lactoferrin from other animal species; which we previously confirmed and continuing the analysis of antimicrobial effectiveness of cLf; we started in previous studies, the current study aimed to formulate a protein-fatty acid complex of cLf and Oleic Acid (OA) and to compare it’s in vitro antimicrobial activities against different pathogens with those of a similar Bovine Lactoferrin (bLf)-OA complex. Antimicrobial activity of these complexes was evaluated by agar disc diffusion method, broth microdilution assay, and ELISAestimating Lf and its complexes binding to bacterial outer membrane proteins. Agar disc diffusion assay results revealed that inhibitory activity of both free cLf and cLf-OA against 13 test pathogens (Methicillin-Resistant Staphylococcus Aureus (MRSA), Staphylococcus aureus, Bacillus cereus, Escherichia coli, Salmonella typhi, Shigella sonnei, Klebsiella pneumonia, Pseudomonas aeruginosa, Proteus vulgaris, Serratia marcescens, Candida albicans, Aspergillus niger, and Aspergillus flavus) noticeably exceeded that of corresponding bLf and bLf-OA. Additionally, free OA exhibited antimicrobial activity against MRSA, S. aureus, B. cereus, and C. albicans and to a lesser extent against E. coli, K. pneumonia as well as A. niger and A. flavus. Consequently, synergy was evident between cLf/bLf and OA (mostly higher in case of cLf) in prepared complexes against MRSA, S. aureus, B. cereus, and C. albicans. cLf-OA demonstrated 4 times lower Minimum Inhibitory Concentration (MIC) values against MRSA, B. cereus, and C. albicans than bLf-OA; indicating more superiority in case of cLf-OA than free cLf that showed only twice the activity of bLf. ELISA signals confirmed binding of biotinylated cLf/bLf and cLf/bLf-OA to bacterial membrane proteins. This study proves that cLf obtains enhanced antimicrobial activities after complex formation with fatty acids such as OA even than its free form which has already superior activity than other Lf species; thus this complex may be used as a cure of various microbial infections.","PeriodicalId":90972,"journal":{"name":"SOJ biochemistry","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67332761","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 : 2014-01-01DOI: 10.15226/2376-4589/1/1/00103
Megan N Sandberg, Jordan A Greco, Nicole L Wagner, Tabitha L Amora, Lavoisier A Ramos, Min-Hsuan Chen, Barry E Knox, Robert R Birge
Three active-site components in rhodopsin play a key role in the stability and function of the protein: 1) the counter-ion residues which stabilize the protonated Schiff base, 2) water molecules, and 3) the hydrogen-bonding network. The ionizable residue Glu-181, which is involved in an extended hydrogen-bonding network with Ser-186, Tyr-268, Tyr-192, and key water molecules within the active site of rhodopsin, has been shown to be involved in a complex counter-ion switch mechanism with Glu-113 during the photobleaching sequence of the protein. Herein, we examine the photobleaching sequence of the E181Q rhodopsin mutant by using cryogenic UV-visible spectroscopy to further elucidate the role of Glu-181 during photoactivation of the protein. We find that lower temperatures are required to trap the early photostationary states of the E181Q mutant compared to native rhodopsin. Additionally, a Blue Shifted Intermediate (BSI, λmax = 498 nm, 100 K) is observed after the formation of E181Q Bathorhodopsin (Batho, λmax = 556 nm, 10 K) but prior to formation of E181Q Lumirhodopsin (Lumi, λmax = 506 nm, 220 K). A potential energy diagram of the observed photointermediates suggests the E181Q Batho intermediate has an enthalpy value 7.99 KJ/mol higher than E181Q BSI, whereas in rhodopsin, the BSI is 10.02 KJ/mol higher in enthalpy than Batho. Thus, the Batho to BSI transition is enthalpically driven in E181Q and entropically driven in native rhodopsin. We conclude that the substitution of Glu-181 with Gln-181 results in a significant perturbation of the hydrogen-bonding network within the active site of rhodopsin. In addition, the removal of a key electrostatic interaction between the chromophore and the protein destabilizes the protein in both the dark state and Batho intermediate conformations while having a stabilizing effect on the BSI conformation. The observed destabilization upon this substitution further supports that Glu-181 is negatively charged in the early intermediates of the photobleaching sequence of rhodopsin.
{"title":"Low-Temperature Trapping of Photointermediates of the Rhodopsin E181Q Mutant.","authors":"Megan N Sandberg, Jordan A Greco, Nicole L Wagner, Tabitha L Amora, Lavoisier A Ramos, Min-Hsuan Chen, Barry E Knox, Robert R Birge","doi":"10.15226/2376-4589/1/1/00103","DOIUrl":"https://doi.org/10.15226/2376-4589/1/1/00103","url":null,"abstract":"<p><p>Three active-site components in rhodopsin play a key role in the stability and function of the protein: 1) the counter-ion residues which stabilize the protonated Schiff base, 2) water molecules, and 3) the hydrogen-bonding network. The ionizable residue Glu-181, which is involved in an extended hydrogen-bonding network with Ser-186, Tyr-268, Tyr-192, and key water molecules within the active site of rhodopsin, has been shown to be involved in a complex counter-ion switch mechanism with Glu-113 during the photobleaching sequence of the protein. Herein, we examine the photobleaching sequence of the E181Q rhodopsin mutant by using cryogenic UV-visible spectroscopy to further elucidate the role of Glu-181 during photoactivation of the protein. We find that lower temperatures are required to trap the early photostationary states of the E181Q mutant compared to native rhodopsin. Additionally, a Blue Shifted Intermediate (BSI, λ<sub>max</sub> = 498 nm, 100 K) is observed after the formation of E181Q Bathorhodopsin (Batho, λ<sub>max</sub> = 556 nm, 10 K) but prior to formation of E181Q Lumirhodopsin (Lumi, λ<sub>max</sub> = 506 nm, 220 K). A potential energy diagram of the observed photointermediates suggests the E181Q Batho intermediate has an enthalpy value 7.99 KJ/mol higher than E181Q BSI, whereas in rhodopsin, the BSI is 10.02 KJ/mol higher in enthalpy than Batho. Thus, the Batho to BSI transition is enthalpically driven in E181Q and entropically driven in native rhodopsin. We conclude that the substitution of Glu-181 with Gln-181 results in a significant perturbation of the hydrogen-bonding network within the active site of rhodopsin. In addition, the removal of a key electrostatic interaction between the chromophore and the protein destabilizes the protein in both the dark state and Batho intermediate conformations while having a stabilizing effect on the BSI conformation. The observed destabilization upon this substitution further supports that Glu-181 is negatively charged in the early intermediates of the photobleaching sequence of rhodopsin.</p>","PeriodicalId":90972,"journal":{"name":"SOJ biochemistry","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4301618/pdf/nihms649943.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33003111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：