V. Fedchenko, A. Kaloshin, S. Kaloshina, A. Kopylov, A. E. Medvedev
Renalase (RNLS) is a flavoprotein; its N-terminal peptide (amino acid residues 1-17) performs various important functions. Inside cells, it is involved in the Rossmann fold formation (residues 2-35), which is necessary for the binding of the FAD cofactor and the manifestation of the enzymatic activity of RNLS as a FAD-dependent oxidoreductase (EC 1.6.3.5). When RNLS is secreted into the extracellular space, this peptide is cleaved off, and the resulting truncated extracellular RNLS can no longer bind FAD and, therefore, numerous effects described in the literature are carried out by non-catalytic mechanisms. In this work, we have investigated the sensitivity to trypsinolysis of two recombinant forms of human RNLS expressed in prokaryotic cells: (a) full-length RNLS containing the FAD cofactor; (b) a truncated RNLS lacking the 1-17 N-terminal peptide (truncatedRNLS, tRNLS) unable to bind the FAD cofactor. Trypsin (1 unit/20 μL of medium) effectively cleaved both forms of renalase (RNLS and tRNLS). When exposed to a lower concentration of trypsin (0.1 U/20 μL of medium), full length RNLS was more trypsin resistant than tRNLS. We suggest that the different sensitivity of RNLS and tRNLS is apparently determined by the presence of the FAD cofactor in the full-length recombinant protein, which contributes to the formation of a spatial structure that is more resistant to the action of certain proteases.
{"title":"The Study of Sensitivity to Proteolysis of Full-length and Truncated Forms of Recombinant Human Renalase Expressed in the Prokaryotic System","authors":"V. Fedchenko, A. Kaloshin, S. Kaloshina, A. Kopylov, A. E. Medvedev","doi":"10.18097/bmcrm00164","DOIUrl":"https://doi.org/10.18097/bmcrm00164","url":null,"abstract":"Renalase (RNLS) is a flavoprotein; its N-terminal peptide (amino acid residues 1-17) performs various important functions. Inside cells, it is involved in the Rossmann fold formation (residues 2-35), which is necessary for the binding of the FAD cofactor and the manifestation of the enzymatic activity of RNLS as a FAD-dependent oxidoreductase (EC 1.6.3.5). When RNLS is secreted into the extracellular space, this peptide is cleaved off, and the resulting truncated extracellular RNLS can no longer bind FAD and, therefore, numerous effects described in the literature are carried out by non-catalytic mechanisms. In this work, we have investigated the sensitivity to trypsinolysis of two recombinant forms of human RNLS expressed in prokaryotic cells: (a) full-length RNLS containing the FAD cofactor; (b) a truncated RNLS lacking the 1-17 N-terminal peptide (truncatedRNLS, tRNLS) unable to bind the FAD cofactor. Trypsin (1 unit/20 μL of medium) effectively cleaved both forms of renalase (RNLS and tRNLS). When exposed to a lower concentration of trypsin (0.1 U/20 μL of medium), full length RNLS was more trypsin resistant than tRNLS. We suggest that the different sensitivity of RNLS and tRNLS is apparently determined by the presence of the FAD cofactor in the full-length recombinant protein, which contributes to the formation of a spatial structure that is more resistant to the action of certain proteases.","PeriodicalId":286037,"journal":{"name":"Biomedical Chemistry: Research and Methods","volume":"32 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132211044","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}
A general predictive model for assessing the inhibition constant (Ki) value of human acetylcholine muscarinic receptors M1-M5 by potential ligands has been constructed. We used information on the three-dimensional structure of human M1, M2, M4, and M5 receptors, as well as a model of the M3 receptor constructed according to homology based on the structure of the rat M3 receptor. A set of complexes of known inhibitors with the target receptor constructed by means of molecular docking, was selected using an additional option: the coincidence of the spatial position of 4 pharmacophore points of a tested inhibitor and tiotropium, for which the position in the crystal structure was known. For five types of M receptors 199 complexes with known Ki values were selected. Based on the data obtained during molecular dynamics simulation of these complexes by means of the MM-PBSA/MM-GBSA methods, their energy characteristics were calculated. They were used as independent variables in linear regression equations for pKi value prediction. The R2 prediction for the generalized equation was 0.7, and the mean prediction error was 0.55 logarithmic units with a range for pKi=4.7.
{"title":"Generalized predictive model of estimation of inhibition of muscarinic receptors M1-M5","authors":"A. Mikurova, Vladlen S. Skvortsov, V. Grigoryev","doi":"10.18097/bmcrm00129","DOIUrl":"https://doi.org/10.18097/bmcrm00129","url":null,"abstract":"A general predictive model for assessing the inhibition constant (Ki) value of human acetylcholine muscarinic receptors M1-M5 by potential ligands has been constructed. We used information on the three-dimensional structure of human M1, M2, M4, and M5 receptors, as well as a model of the M3 receptor constructed according to homology based on the structure of the rat M3 receptor. A set of complexes of known inhibitors with the target receptor constructed by means of molecular docking, was selected using an additional option: the coincidence of the spatial position of 4 pharmacophore points of a tested inhibitor and tiotropium, for which the position in the crystal structure was known. For five types of M receptors 199 complexes with known Ki values were selected. Based on the data obtained during molecular dynamics simulation of these complexes by means of the MM-PBSA/MM-GBSA methods, their energy characteristics were calculated. They were used as independent variables in linear regression equations for pKi value prediction. The R2 prediction for the generalized equation was 0.7, and the mean prediction error was 0.55 logarithmic units with a range for pKi=4.7.","PeriodicalId":286037,"journal":{"name":"Biomedical Chemistry: Research and Methods","volume":"185 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115380245","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}
A. Kuzikov, R. Masamrekh, T. Filippova, V. Shumyantseva
The review deals with the electrochemical methods for determination of metabolites of cytochromes P450 catalyzed reactions. We have focused on the electrochemical determination of metabolites of drugs and some endogenous compounds. We have reviewed bielectrode systems for determination of cytochrome P450 activity, where one electrode serves as a matrix for enzyme immobilization and a source of electrons for heme iron ion reduction and initialization of the catalytic reaction towards a substrate and the second one is being used for quantification of the products formed by their electrochemical oxidation. Such systems allow one to elude additional steps of separation of reaction substrates and products. The review also includes discussion of the ways to increase the analytical sensitivity and decrease the limit of detection of the investigated metabolites by chemical modification of electrodes. We demonstrate the possibilities of these systems for cytochrome P450 kinetics analysis and the perspectives of their further improvement, such as increasing the sensitivity of metabolite electrochemical determination by modern electrode modificators, including carbon-based, and construction of devices for automatic monitoring of the products.
{"title":"Electrochemical Analysis of Metabolites as a Method for Cytochromes P450 Activity Determination","authors":"A. Kuzikov, R. Masamrekh, T. Filippova, V. Shumyantseva","doi":"10.18097/bmcrm00176","DOIUrl":"https://doi.org/10.18097/bmcrm00176","url":null,"abstract":"The review deals with the electrochemical methods for determination of metabolites of cytochromes P450 catalyzed reactions. We have focused on the electrochemical determination of metabolites of drugs and some endogenous compounds. We have reviewed bielectrode systems for determination of cytochrome P450 activity, where one electrode serves as a matrix for enzyme immobilization and a source of electrons for heme iron ion reduction and initialization of the catalytic reaction towards a substrate and the second one is being used for quantification of the products formed by their electrochemical oxidation. Such systems allow one to elude additional steps of separation of reaction substrates and products. The review also includes discussion of the ways to increase the analytical sensitivity and decrease the limit of detection of the investigated metabolites by chemical modification of electrodes. We demonstrate the possibilities of these systems for cytochrome P450 kinetics analysis and the perspectives of their further improvement, such as increasing the sensitivity of metabolite electrochemical determination by modern electrode modificators, including carbon-based, and construction of devices for automatic monitoring of the products.","PeriodicalId":286037,"journal":{"name":"Biomedical Chemistry: Research and Methods","volume":"95 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122479710","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 type I collagen was studied in samples of two types of osteoplastic materials produced in the Biotech Research Institute of the Samara State Medical University using immunoblotting. The demineralized samples used in the work were compact bone powder and crushed material of human cancellous bone tissue. Collagen and its polypeptides were separated in a 5% polyacrylamide gel with 3.6 M urea according to the method of Hayashi and Nagai (1979). The advantage of the method is the separation under these conditions of type I and III collagen, as well as the α1(I) and α2(I) chains of type I collagen. Immunoblotting was carried out by diffusion method according to the method of Towbin et al. (1979) using nitrocellulose membranes (Santa Cruz, USA). Primary goat polyclonal antibodies to denatured collagen, 1:500 dilution (Millipore) were used. Peroxidase-conjugated secondary antibodies (mouse vs. goat), 1:80000 dilution (Sigma) were used also. It has been established that the bulk of the compact bone protein is localized between the α1- and α2-fractions of collagen. In samples of cancellous bone tissue, a molecular reduction of the protein is noted. Protein macromolecules with a gradually decreasing molecular weight and low molecular weight polypeptides migrating in the gel with a wide front up to the indicator line are detected. Due to the low specificity of osteoblast integrins in regenerating bone tissue, collagen polypeptides, as well as protein molecules retained in implants, can act as inducers of synthetic processes occurring in osteoblast nuclei. Protein fragmentation products in the implant can act as signaling molecules that trigger cascades of enzymatic reactions and intracellular signaling pathways.
在萨马拉国立医科大学生物技术研究所生产的两种骨塑材料样品中，使用免疫印迹法研究了I型胶原蛋白。工作中使用的脱矿样品是致密骨粉和人类松质骨组织的粉碎材料。按照Hayashi和Nagai(1979)的方法，在含有3.6 M尿素的5%聚丙烯酰胺凝胶中分离胶原蛋白及其多肽。该方法的优点是在这些条件下分离了I型和III型胶原，以及I型胶原的α1(I)和α2(I)链。参照Towbin et al.(1979)使用硝化纤维素膜(Santa Cruz, USA)的方法，采用扩散法进行免疫印迹。山羊变性胶原蛋白多克隆抗体，1:500稀释(Millipore)。还使用过氧化物酶偶联二抗(小鼠对山羊)，1:8000稀释(Sigma)。已经确定，大部分致密骨蛋白位于胶原蛋白的α1-和α2组分之间。在松质骨组织样本中，发现了蛋白质的分子减少。检测到分子量逐渐减小的蛋白质大分子和低分子量多肽在凝胶中以宽前向指示线迁移。由于成骨细胞整合素在再生骨组织中的特异性较低，胶原多肽以及植入物中保留的蛋白质分子可作为成骨细胞核合成过程的诱导剂。植入物中的蛋白质碎片化产物可以作为信号分子，触发酶促反应级联和细胞内信号通路。
{"title":"The Study of Type I Collagen by Immunoblotting in Samples of Bone-Plastic Biomaterials","authors":"T. Medvedeva, L. Volova, L. N. Kulagina","doi":"10.18097/bmcrm00189","DOIUrl":"https://doi.org/10.18097/bmcrm00189","url":null,"abstract":"The type I collagen was studied in samples of two types of osteoplastic materials produced in the Biotech Research Institute of the Samara State Medical University using immunoblotting. The demineralized samples used in the work were compact bone powder and crushed material of human cancellous bone tissue. Collagen and its polypeptides were separated in a 5% polyacrylamide gel with 3.6 M urea according to the method of Hayashi and Nagai (1979). The advantage of the method is the separation under these conditions of type I and III collagen, as well as the α1(I) and α2(I) chains of type I collagen. Immunoblotting was carried out by diffusion method according to the method of Towbin et al. (1979) using nitrocellulose membranes (Santa Cruz, USA). Primary goat polyclonal antibodies to denatured collagen, 1:500 dilution (Millipore) were used. Peroxidase-conjugated secondary antibodies (mouse vs. goat), 1:80000 dilution (Sigma) were used also. It has been established that the bulk of the compact bone protein is localized between the α1- and α2-fractions of collagen. In samples of cancellous bone tissue, a molecular reduction of the protein is noted. Protein macromolecules with a gradually decreasing molecular weight and low molecular weight polypeptides migrating in the gel with a wide front up to the indicator line are detected. Due to the low specificity of osteoblast integrins in regenerating bone tissue, collagen polypeptides, as well as protein molecules retained in implants, can act as inducers of synthetic processes occurring in osteoblast nuclei. Protein fragmentation products in the implant can act as signaling molecules that trigger cascades of enzymatic reactions and intracellular signaling pathways.","PeriodicalId":286037,"journal":{"name":"Biomedical Chemistry: Research and Methods","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130203936","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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