Nonlinear impact of electrolyte solutions on protein dynamics
Chembiochem. 2024 Feb 23:e202400057. doi: 10.1002/cbic.202400057. Online ahead of print.ABSTRACTHalophilic organisms have adapted to multi-molar salt concentrations, their cytoplasmic proteins functioning despite stronger attraction between hydrophobic groups. These proteins, of interest in biotechnology because of decreasing fresh-water resources, have excess acidic amino acids. It has been suggested that conformational fluctuations -- critical for protein function -- decrease in the presence of a stronger hydrophobic effect, and that an acidic proteome would counteract this decrease. However, our understanding of the sal...
Source: Chembiochem - February 23, 2024 Category: Biochemistry Authors: Hosein Geraili Daronkola Benedikt Soeldner Himanshu Singh Rasmus Linser Ana Vila Verde Source Type: research
Development of an Enzyme Cascade System for the Synthesis of Enantiomerically Pure D-Amino Acids Utilizing Ancestral L-Amino Acid Oxidase
This study focuses on establishing an enzymatic cascade system capable of converting various L-amino acids into their D-isomers. The system integrates four enzymes: ancestral L-amino acid oxidase (AncLAAO-N4), D-amino acid dehydrogenase (DAADH), D-glucose dehydrogenase (GDH), and catalase. AncLAAO-N4 initiates the process by converting L-amino acids to corresponding keto acids, which are then stereo-selectively aminated to D-amino acids by DAADH using NADPH and NH4Cl. Concurrently, any generated H2O2 is decomposed into O2 and H2O by catalase, while GDH regenerates NADPH from D-glucose. Optimization of reaction conditions a...
Source: Chembiochem - February 22, 2024 Category: Biochemistry Authors: Hayato Araseki Narumi Sugishima Chisuga Taichi Shogo Nakano Source Type: research
DNA Logic Gates Integrated on DNA Substrates in Molecular Computing
Chembiochem. 2024 Feb 22:e202400080. doi: 10.1002/cbic.202400080. Online ahead of print.ABSTRACTDue to nucleic acid's programmability, it is possible to realize DNA structures with computing functions, and thus a new generation of molecular computers is evolving to solve biological and medical problems. Pioneered by Milan Stojanovic, Boolean DNA logic gates created the foundation for the development of DNA computers. Similar to electronic computers, the field is evolving towards integrating DNA logic gates and circuits by positioning them on substrates to increase circuit density and minimize gate distance and undesired cr...
Source: Chembiochem - February 22, 2024 Category: Biochemistry Authors: Andrea Bardales Viktor Smirnov Katherine Taylor Dmitry Kolpashchikov Source Type: research
Mushroom Tyrosinase: Six Isoenzymes Catalyzing Distinct Reactions
Chembiochem. 2024 Feb 22:e202400050. doi: 10.1002/cbic.202400050. Online ahead of print.ABSTRACT"Mushroom tyrosinase" from the common button mushroom is the most frequently used source of tyrosinase activity, both for basic and applied research. Here, the complete tyrosinase family from Agaricus bisporus var. bisporus (abPPO1-6) was cloned from mRNA and expressed heterologously using a single protocol. All six isoenzymes accept a wide range of phenolic and catecholic substrates, but display pronounced differences in their specificity and enzymatic reaction rate. AbPPO3 ignores γ-l-glutaminyl-4-hydroxybenzene (GHB), a natu...
Source: Chembiochem - February 22, 2024 Category: Biochemistry Authors: Matthias Pretzler Annette Rompel Source Type: research
Modifications of Protein-Bound Substrates by Trans-Acting Enzymes in Natural Products Biosynthesis
Chembiochem. 2024 Feb 22:e202400056. doi: 10.1002/cbic.202400056. Online ahead of print.ABSTRACTEnzymatic modifications of small molecules are a common phenomenon in natural product biosynthesis, leading to the production of diverse bioactive compounds. In polyketide biosynthesis, modifications commonly take place after the completion of the polyketide backbone assembly by the polyketide synthases and the mature products are released from the acyl-carrier protein (ACP). However, exceptions to this rule appear to be widespread, as on-line hydroxylation, methyl transfer, and cyclization during polyketide assembly process are...
Source: Chembiochem - February 22, 2024 Category: Biochemistry Authors: Leigh E Skala Benjamin Philmus Taifo Mahmud Source Type: research
Development of an Enzyme Cascade System for the Synthesis of Enantiomerically Pure D-Amino Acids Utilizing Ancestral L-Amino Acid Oxidase
This study focuses on establishing an enzymatic cascade system capable of converting various L-amino acids into their D-isomers. The system integrates four enzymes: ancestral L-amino acid oxidase (AncLAAO-N4), D-amino acid dehydrogenase (DAADH), D-glucose dehydrogenase (GDH), and catalase. AncLAAO-N4 initiates the process by converting L-amino acids to corresponding keto acids, which are then stereo-selectively aminated to D-amino acids by DAADH using NADPH and NH4Cl. Concurrently, any generated H2O2 is decomposed into O2 and H2O by catalase, while GDH regenerates NADPH from D-glucose. Optimization of reaction conditions a...
Source: Chembiochem - February 22, 2024 Category: Biochemistry Authors: Hayato Araseki Narumi Sugishima Chisuga Taichi Shogo Nakano Source Type: research
DNA Logic Gates Integrated on DNA Substrates in Molecular Computing
Chembiochem. 2024 Feb 22:e202400080. doi: 10.1002/cbic.202400080. Online ahead of print.ABSTRACTDue to nucleic acid's programmability, it is possible to realize DNA structures with computing functions, and thus a new generation of molecular computers is evolving to solve biological and medical problems. Pioneered by Milan Stojanovic, Boolean DNA logic gates created the foundation for the development of DNA computers. Similar to electronic computers, the field is evolving towards integrating DNA logic gates and circuits by positioning them on substrates to increase circuit density and minimize gate distance and undesired cr...
Source: Chembiochem - February 22, 2024 Category: Biochemistry Authors: Andrea Bardales Viktor Smirnov Katherine Taylor Dmitry Kolpashchikov Source Type: research
Mushroom Tyrosinase: Six Isoenzymes Catalyzing Distinct Reactions
Chembiochem. 2024 Feb 22:e202400050. doi: 10.1002/cbic.202400050. Online ahead of print.ABSTRACT"Mushroom tyrosinase" from the common button mushroom is the most frequently used source of tyrosinase activity, both for basic and applied research. Here, the complete tyrosinase family from Agaricus bisporus var. bisporus (abPPO1-6) was cloned from mRNA and expressed heterologously using a single protocol. All six isoenzymes accept a wide range of phenolic and catecholic substrates, but display pronounced differences in their specificity and enzymatic reaction rate. AbPPO3 ignores γ-l-glutaminyl-4-hydroxybenzene (GHB), a natu...
Source: Chembiochem - February 22, 2024 Category: Biochemistry Authors: Matthias Pretzler Annette Rompel Source Type: research
Modifications of Protein-Bound Substrates by Trans-Acting Enzymes in Natural Products Biosynthesis
Chembiochem. 2024 Feb 22:e202400056. doi: 10.1002/cbic.202400056. Online ahead of print.ABSTRACTEnzymatic modifications of small molecules are a common phenomenon in natural product biosynthesis, leading to the production of diverse bioactive compounds. In polyketide biosynthesis, modifications commonly take place after the completion of the polyketide backbone assembly by the polyketide synthases and the mature products are released from the acyl-carrier protein (ACP). However, exceptions to this rule appear to be widespread, as on-line hydroxylation, methyl transfer, and cyclization during polyketide assembly process are...
Source: Chembiochem - February 22, 2024 Category: Biochemistry Authors: Leigh E Skala Benjamin Philmus Taifo Mahmud Source Type: research
Engineering A-type Dye-decolorizing Peroxidases by Modification of a Conserved Glutamate Residue
Chembiochem. 2024 Feb 20:e202300872. doi: 10.1002/cbic.202300872. Online ahead of print.ABSTRACTDye-decolorizing peroxidases (DyPs) are recently identified microbial enzymes that have been used in several Biotechnology applications from wastewater treatment to lignin valorization. However, their properties and mechanism of action still have many open questions. Their heme-containing active site is buried by three conserved flexible loops with a putative role in modulating substrate access and enzyme catalysis. Here, we investigated the role of a conserved glutamate residue in stabilizing interactions in loop 2 of A-type Dy...
Source: Chembiochem - February 20, 2024 Category: Biochemistry Authors: Enik ő Hermann Carolina F Rodrigues L ígia O Martins Clemens Peterbauer Chris Oostenbrink Source Type: research
Engineering A-type Dye-decolorizing Peroxidases by Modification of a Conserved Glutamate Residue
Chembiochem. 2024 Feb 20:e202300872. doi: 10.1002/cbic.202300872. Online ahead of print.ABSTRACTDye-decolorizing peroxidases (DyPs) are recently identified microbial enzymes that have been used in several Biotechnology applications from wastewater treatment to lignin valorization. However, their properties and mechanism of action still have many open questions. Their heme-containing active site is buried by three conserved flexible loops with a putative role in modulating substrate access and enzyme catalysis. Here, we investigated the role of a conserved glutamate residue in stabilizing interactions in loop 2 of A-type Dy...
Source: Chembiochem - February 20, 2024 Category: Biochemistry Authors: Enik ő Hermann Carolina F Rodrigues L ígia O Martins Clemens Peterbauer Chris Oostenbrink Source Type: research
Discovery of a Photoaffinity Probe that Captures the Active Conformation of the Cannabinoid CB2 Receptor
Chembiochem. 2024 Feb 19:e202300785. doi: 10.1002/cbic.202300785. Online ahead of print.ABSTRACTThe cannabinoid receptor type 2 (CB2R) is a G protein-coupled receptor with therapeutic potential for the treatment of inflammatory disorders. Fluorescent probes are desirable to study its receptor localization, expression and occupancy. Previously, we have reported a photoaffinity probe LEI-121 that stabilized the inactive conformation of the CB2R. Here, we report the structure-based design of a novel bifunctional probe that captures the active conformation of the CB2R upon irradiation with light. An alkyne handle was incorpora...
Source: Chembiochem - February 19, 2024 Category: Biochemistry Authors: Laura V de Paus Yu An Antonius P A Janssen Richard J B H N Van den Berg Laura H Heitman Mario Van der Stelt Source Type: research
Functional and Mechanistic Characterization of the 4,5-diepi-Isoishwarane Synthase from the Liverwort Radula lindenbergiana
Chembiochem. 2024 Feb 19:e202400104. doi: 10.1002/cbic.202400104. Online ahead of print.ABSTRACTThe microbial type sesquiterpene synthase RlMTPSL4 from the liverwort Radula lindenbergiana was investigated for its products, showing the formation of several sesquiterpene hydrocarbons. The main product was structurally characterized as the new compound 4,5-diepi-isoishwarane, while the side products included the known hydrocarbons germacrene A, a-selinene, eremophilene and 4,5-diepi-aristolochene. The cyclization mechanism towards 4,5-diepi-isoishwarane catalyzed by RlMTPSL4 was investigated through isotopic labeling experime...
Source: Chembiochem - February 19, 2024 Category: Biochemistry Authors: Houchao Xu Tobias K öllner Feng Chen Jeroen S Dickschat Source Type: research
Discovery of a Photoaffinity Probe that Captures the Active Conformation of the Cannabinoid CB2 Receptor
Chembiochem. 2024 Feb 19:e202300785. doi: 10.1002/cbic.202300785. Online ahead of print.ABSTRACTThe cannabinoid receptor type 2 (CB2R) is a G protein-coupled receptor with therapeutic potential for the treatment of inflammatory disorders. Fluorescent probes are desirable to study its receptor localization, expression and occupancy. Previously, we have reported a photoaffinity probe LEI-121 that stabilized the inactive conformation of the CB2R. Here, we report the structure-based design of a novel bifunctional probe that captures the active conformation of the CB2R upon irradiation with light. An alkyne handle was incorpora...
Source: Chembiochem - February 19, 2024 Category: Biochemistry Authors: Laura V de Paus Yu An Antonius P A Janssen Richard J B H N Van den Berg Laura H Heitman Mario Van der Stelt Source Type: research
Functional and Mechanistic Characterization of the 4,5-diepi-Isoishwarane Synthase from the Liverwort Radula lindenbergiana
Chembiochem. 2024 Feb 19:e202400104. doi: 10.1002/cbic.202400104. Online ahead of print.ABSTRACTThe microbial type sesquiterpene synthase RlMTPSL4 from the liverwort Radula lindenbergiana was investigated for its products, showing the formation of several sesquiterpene hydrocarbons. The main product was structurally characterized as the new compound 4,5-diepi-isoishwarane, while the side products included the known hydrocarbons germacrene A, a-selinene, eremophilene and 4,5-diepi-aristolochene. The cyclization mechanism towards 4,5-diepi-isoishwarane catalyzed by RlMTPSL4 was investigated through isotopic labeling experime...
Source: Chembiochem - February 19, 2024 Category: Biochemistry Authors: Houchao Xu Tobias K öllner Feng Chen Jeroen S Dickschat Source Type: research
