Dynamic lid domain of Chloroflexus aurantiacus Malonyl-CoA reductase controls the reaction
Biochimie. 2023 Nov 10:S0300-9084(23)00304-8. doi: 10.1016/j.biochi.2023.11.003. Online ahead of print.ABSTRACTMalonyl-Coenzyme A Reductase (MCR) in Chloroflexus aurantiacus, a characteristic enzyme of the 3-hydroxypropionate (3-HP) cycle, catalyses the reduction of malonyl-CoA to 3-HP. MCR is a bi-functional enzyme; in the first step, malonyl-CoA is reduced to the free intermediate malonate semialdehyde by the C-terminal region of MCR, and this is further reduced to 3-HP by the N-terminal region of MCR. Here we present the crystal structures of both N-terminal and C-terminal regions of the MCR from C. aurantiacus. A catal...
Source: Biochimie - November 12, 2023 Category: Biochemistry Authors: Burak V Kabasakal Charles A R Cotton James W Murray Source Type: research

Dynamic lid domain of Chloroflexus aurantiacus Malonyl-CoA reductase controls the reaction
Biochimie. 2023 Nov 10:S0300-9084(23)00304-8. doi: 10.1016/j.biochi.2023.11.003. Online ahead of print.ABSTRACTMalonyl-Coenzyme A Reductase (MCR) in Chloroflexus aurantiacus, a characteristic enzyme of the 3-hydroxypropionate (3-HP) cycle, catalyses the reduction of malonyl-CoA to 3-HP. MCR is a bi-functional enzyme; in the first step, malonyl-CoA is reduced to the free intermediate malonate semialdehyde by the C-terminal region of MCR, and this is further reduced to 3-HP by the N-terminal region of MCR. Here we present the crystal structures of both N-terminal and C-terminal regions of the MCR from C. aurantiacus. A catal...
Source: Biochimie - November 12, 2023 Category: Biochemistry Authors: Burak V Kabasakal Charles A R Cotton James W Murray Source Type: research

Small molecular exogenous modulators of active forms of MMPs
Biochimie. 2023 Nov 7:S0300-9084(23)00292-4. doi: 10.1016/j.biochi.2023.10.021. Online ahead of print.ABSTRACTMatrix metalloproteinases (MMPs) are endopeptidases, and their activity depends on calcium and zinc metal ions. These enzymes are expressed originally in zymogenic form, where the active site of proteins is closed by a prodomain which is removed during activation. A homeostatic balance of their activity is primarily regulated by a 'cysteine switch' located on a consensus sequence of the prodomain and natural endogenous inhibitors, called tissue inhibitors of metalloproteinases (TIMPs). Breakage of this homeostasis ...
Source: Biochimie - November 9, 2023 Category: Biochemistry Authors: Ish Kumar Melissa Silva Dinesh A Choudhary Syeda F Ali Raymond Rusak Paulina Cotzomi Suzanne Wiecek Iwon Sato Rinat Khundoker Bora Donmez Samantha Gabriel Monica Bobila Mihaela D Leonida Christian Traba Source Type: research

Small molecular exogenous modulators of active forms of MMPs
Biochimie. 2023 Nov 7:S0300-9084(23)00292-4. doi: 10.1016/j.biochi.2023.10.021. Online ahead of print.ABSTRACTMatrix metalloproteinases (MMPs) are endopeptidases, and their activity depends on calcium and zinc metal ions. These enzymes are expressed originally in zymogenic form, where the active site of proteins is closed by a prodomain which is removed during activation. A homeostatic balance of their activity is primarily regulated by a 'cysteine switch' located on a consensus sequence of the prodomain and natural endogenous inhibitors, called tissue inhibitors of metalloproteinases (TIMPs). Breakage of this homeostasis ...
Source: Biochimie - November 9, 2023 Category: Biochemistry Authors: Ish Kumar Melissa Silva Dinesh A Choudhary Syeda F Ali Raymond Rusak Paulina Cotzomi Suzanne Wiecek Iwon Sato Rinat Khundoker Bora Donmez Samantha Gabriel Monica Bobila Mihaela D Leonida Christian Traba Source Type: research

Small molecular exogenous modulators of active forms of MMPs
Biochimie. 2023 Nov 7:S0300-9084(23)00292-4. doi: 10.1016/j.biochi.2023.10.021. Online ahead of print.ABSTRACTMatrix metalloproteinases (MMPs) are endopeptidases, and their activity depends on calcium and zinc metal ions. These enzymes are expressed originally in zymogenic form, where the active site of proteins is closed by a prodomain which is removed during activation. A homeostatic balance of their activity is primarily regulated by a 'cysteine switch' located on a consensus sequence of the prodomain and natural endogenous inhibitors, called tissue inhibitors of metalloproteinases (TIMPs). Breakage of this homeostasis ...
Source: Biochimie - November 9, 2023 Category: Biochemistry Authors: Ish Kumar Melissa Silva Dinesh A Choudhary Syeda F Ali Raymond Rusak Paulina Cotzomi Suzanne Wiecek Iwon Sato Rinat Khundoker Bora Donmez Samantha Gabriel Monica Bobila Mihaela D Leonida Christian Traba Source Type: research

Evaluation of the effect of dimethyl fumarate on human bone marrow-derived mesenchymal stem cells using bottom-up proteomics
In this study, we treated bone marrow-derived MSCs with DMF and evaluated their proteome using bottom-up proteomics. The MSCs were exposed to 10 μM DMF for 24 h, followed by lysis with an SDS solution, digestion with trypsin using an s-trap column, and analysis using nanoLC-MS/MS, which identified 2262 proteins with confidence. Bioinformatic analysis of the identified proteins revealed 47 upregulated proteins and 81 downregulated proteins upon DMF treatment. Pathway enrichment analysis suggested a possible decrease in autophagy and a decrease in the activity of the TCA cycle, while indicating a potential increase in proli...
Source: Biochimie - November 6, 2023 Category: Biochemistry Authors: Maryam Adelipour Hyojin Hwang Dokyung Kwon Kee K Kim Jeong Hee Moon David M Lubman Jeongkwon Kim Source Type: research

Optimizing expression, purification, structural and functional assessments of a novel dimeric incretin (GLP-1cpGLP-1)
In this study, a new dimeric GLP-1 analogue (GLP-1cpGLP-1) was designed by inserting human insulin C-peptide (CP) in the middle of a dimer of [Gly8] GLP-1 (7-36). Then, the dimeric incretin (GLP-1cpGLP-1) was ligated to human αB-crystallin (αB-Cry) to create a hybrid protein, abbreviated as αB-GLP-1cpGLP-1. The constructed gene was well expressed in the bacterial host system. After specific chemical release from the hybrid protein, the dimeric incretin was purified by size exclusion chromatography (SEC). Finally, the RP-HPLC analysis indicated a purity of >99 % for the dimeric incretin. The secondary structure assess...
Source: Biochimie - November 6, 2023 Category: Biochemistry Authors: Rawayh Albaghlany Mohammad Bagher Shahsavani Masaru Hoshino Ali Akbar Moosavi-Movahedi Younes Ghasemi Reza Yousefi Source Type: research

Evaluation of the effect of dimethyl fumarate on human bone marrow-derived mesenchymal stem cells using bottom-up proteomics
In this study, we treated bone marrow-derived MSCs with DMF and evaluated their proteome using bottom-up proteomics. The MSCs were exposed to 10 μM DMF for 24 h, followed by lysis with an SDS solution, digestion with trypsin using an s-trap column, and analysis using nanoLC-MS/MS, which identified 2262 proteins with confidence. Bioinformatic analysis of the identified proteins revealed 47 upregulated proteins and 81 downregulated proteins upon DMF treatment. Pathway enrichment analysis suggested a possible decrease in autophagy and a decrease in the activity of the TCA cycle, while indicating a potential increase in proli...
Source: Biochimie - November 6, 2023 Category: Biochemistry Authors: Maryam Adelipour Hyojin Hwang Dokyung Kwon Kee K Kim Jeong Hee Moon David M Lubman Jeongkwon Kim Source Type: research

Optimizing expression, purification, structural and functional assessments of a novel dimeric incretin (GLP-1cpGLP-1)
In this study, a new dimeric GLP-1 analogue (GLP-1cpGLP-1) was designed by inserting human insulin C-peptide (CP) in the middle of a dimer of [Gly8] GLP-1 (7-36). Then, the dimeric incretin (GLP-1cpGLP-1) was ligated to human αB-crystallin (αB-Cry) to create a hybrid protein, abbreviated as αB-GLP-1cpGLP-1. The constructed gene was well expressed in the bacterial host system. After specific chemical release from the hybrid protein, the dimeric incretin was purified by size exclusion chromatography (SEC). Finally, the RP-HPLC analysis indicated a purity of >99 % for the dimeric incretin. The secondary structure assess...
Source: Biochimie - November 6, 2023 Category: Biochemistry Authors: Rawayh Albaghlany Mohammad Bagher Shahsavani Masaru Hoshino Ali Akbar Moosavi-Movahedi Younes Ghasemi Reza Yousefi Source Type: research

Evaluation of the effect of dimethyl fumarate on human bone marrow-derived mesenchymal stem cells using bottom-up proteomics
In this study, we treated bone marrow-derived MSCs with DMF and evaluated their proteome using bottom-up proteomics. The MSCs were exposed to 10 μM DMF for 24 h, followed by lysis with an SDS solution, digestion with trypsin using an s-trap column, and analysis using nanoLC-MS/MS, which identified 2262 proteins with confidence. Bioinformatic analysis of the identified proteins revealed 47 upregulated proteins and 81 downregulated proteins upon DMF treatment. Pathway enrichment analysis suggested a possible decrease in autophagy and a decrease in the activity of the TCA cycle, while indicating a potential increase in proli...
Source: Biochimie - November 6, 2023 Category: Biochemistry Authors: Maryam Adelipour Hyojin Hwang Dokyung Kwon Kee K Kim Jeong Hee Moon David M Lubman Jeongkwon Kim Source Type: research

Optimizing expression, purification, structural and functional assessments of a novel dimeric incretin (GLP-1cpGLP-1)
In this study, a new dimeric GLP-1 analogue (GLP-1cpGLP-1) was designed by inserting human insulin C-peptide (CP) in the middle of a dimer of [Gly8] GLP-1 (7-36). Then, the dimeric incretin (GLP-1cpGLP-1) was ligated to human αB-crystallin (αB-Cry) to create a hybrid protein, abbreviated as αB-GLP-1cpGLP-1. The constructed gene was well expressed in the bacterial host system. After specific chemical release from the hybrid protein, the dimeric incretin was purified by size exclusion chromatography (SEC). Finally, the RP-HPLC analysis indicated a purity of >99 % for the dimeric incretin. The secondary structure assess...
Source: Biochimie - November 6, 2023 Category: Biochemistry Authors: Rawayh Albaghlany Mohammad Bagher Shahsavani Masaru Hoshino Ali Akbar Moosavi-Movahedi Younes Ghasemi Reza Yousefi Source Type: research

Evaluation of the effect of dimethyl fumarate on human bone marrow-derived mesenchymal stem cells using bottom-up proteomics
In this study, we treated bone marrow-derived MSCs with DMF and evaluated their proteome using bottom-up proteomics. The MSCs were exposed to 10 μM DMF for 24 h, followed by lysis with an SDS solution, digestion with trypsin using an s-trap column, and analysis using nanoLC-MS/MS, which identified 2262 proteins with confidence. Bioinformatic analysis of the identified proteins revealed 47 upregulated proteins and 81 downregulated proteins upon DMF treatment. Pathway enrichment analysis suggested a possible decrease in autophagy and a decrease in the activity of the TCA cycle, while indicating a potential increase in proli...
Source: Biochimie - November 6, 2023 Category: Biochemistry Authors: Maryam Adelipour Hyojin Hwang Dokyung Kwon Kee K Kim Jeong Hee Moon David M Lubman Jeongkwon Kim Source Type: research

Optimizing expression, purification, structural and functional assessments of a novel dimeric incretin (GLP-1cpGLP-1)
In this study, a new dimeric GLP-1 analogue (GLP-1cpGLP-1) was designed by inserting human insulin C-peptide (CP) in the middle of a dimer of [Gly8] GLP-1 (7-36). Then, the dimeric incretin (GLP-1cpGLP-1) was ligated to human αB-crystallin (αB-Cry) to create a hybrid protein, abbreviated as αB-GLP-1cpGLP-1. The constructed gene was well expressed in the bacterial host system. After specific chemical release from the hybrid protein, the dimeric incretin was purified by size exclusion chromatography (SEC). Finally, the RP-HPLC analysis indicated a purity of >99 % for the dimeric incretin. The secondary structure assess...
Source: Biochimie - November 6, 2023 Category: Biochemistry Authors: Rawayh Albaghlany Mohammad Bagher Shahsavani Masaru Hoshino Ali Akbar Moosavi-Movahedi Younes Ghasemi Reza Yousefi Source Type: research

Study of the structure-function relationship of formate dehydrogenase- an important enzyme for Staphylococcus aureus biofilms by rational design
Biochimie. 2023 Nov 2:S0300-9084(23)00287-0. doi: 10.1016/j.biochi.2023.10.016. Online ahead of print.ABSTRACTNAD+-dependent formate dehydrogenase (FDH, EC 1.2.1.2) from the bacterium Staphylococcus aureus (SauFDH) plays an important role in the vital activity of this bacterium, especially in the form of biofilms. Understanding its mechanism and structure-function relationship can help to find special inhibitors of this enzyme, which can be used as medicines against staphylococci. The gene encoding SauFDH was successfully cloned and expressed in our laboratory. This enzyme has the highest kcat value among the described FDH...
Source: Biochimie - November 4, 2023 Category: Biochemistry Authors: TatyanaS Iurchenko Seseg B Bolotova Anastasia A Loginova Ivan S Kargov Denis L Atroshenko Svyatoslav S Savin Evgenii V Pometun Vladimir I Tishkov Anastasia A Pometun Source Type: research

Study of the structure-function relationship of formate dehydrogenase- an important enzyme for Staphylococcus aureus biofilms by rational design
Biochimie. 2023 Nov 2:S0300-9084(23)00287-0. doi: 10.1016/j.biochi.2023.10.016. Online ahead of print.ABSTRACTNAD+-dependent formate dehydrogenase (FDH, EC 1.2.1.2) from the bacterium Staphylococcus aureus (SauFDH) plays an important role in the vital activity of this bacterium, especially in the form of biofilms. Understanding its mechanism and structure-function relationship can help to find special inhibitors of this enzyme, which can be used as medicines against staphylococci. The gene encoding SauFDH was successfully cloned and expressed in our laboratory. This enzyme has the highest kcat value among the described FDH...
Source: Biochimie - November 4, 2023 Category: Biochemistry Authors: TatyanaS Iurchenko Seseg B Bolotova Anastasia A Loginova Ivan S Kargov Denis L Atroshenko Svyatoslav S Savin Evgenii V Pometun Vladimir I Tishkov Anastasia A Pometun Source Type: research