Enzyme data and metabolic information: BRENDA, a resource for research in biology, biochemistry, and medicine

Examination of intrinsic sulfonamide resistance in Bacillus anthracis: A novel assay for dihydropteroate synthase

“…A range of k cat values from 0.004 s −1 to 15.6 s −1 has been reported for the synthases from different organisms, while K pABA values are in the range of 0.5 µM to 3.8 µM, and K DHP-PP values in the range of 1.4 µM to 30 µM (BRENDA -The Comprehensive Enzyme Information System -www.brenda-enzymes.info) [17]. Kinetic parameters of the DHPS from B. anthracis, which are reported for the first time in this paper, are generally within the range reported for enzymes from other organisms.…”

Examination of intrinsic sulfonamide resistance in Bacillus anthracis: A novel assay for dihydropteroate synthase

“…A range of k cat values from 0.004 s −1 to 15.6 s −1 has been reported for the synthases from different organisms, while K pABA values are in the range of 0.5 µM to 3.8 µM, and K DHP-PP values in the range of 1.4 µM to 30 µM (BRENDA -The Comprehensive Enzyme Information System -www.brenda-enzymes.info) [17]. Kinetic parameters of the DHPS from B. anthracis, which are reported for the first time in this paper, are generally within the range reported for enzymes from other organisms.…”

Traces matter: Targeted optimization of monoclonal antibody N‐glycosylation based on/by implementing automated high‐throughput trace element screening

“…Schematic experiment strategy for parallel optimization of cell culture performance and mAb glycan formation. Production cell cultivations are designed as biphasic processes, starting with an initial growth phase to generate biomass, followed by a subsequent production phase to form the main amount of the intended product (a) Generic mAb N‐glycan structure (b) The iterative screening and optimization approach and used information sources (BRENDA database 31 and the literature) are shown with respective experimental aim, details on tested clones and number of parallel cultivations. DoE, Design of Experiments; GlcNAc, N‐acetylglucosamine; IgG, immunoglobulin G; mAb, monoclonal antibody; NANA, N‐acetylneuraminic acid…”

“…The in‐house developed automated MTP‐based cell culture system was used to run a classical fractional factorial DoE fed‐batch experiment investigating 13 trace elemental ions (Table S4) selected as putative candidates obtained from previous trace element building block screening, from the literature data 23 , and BRENDA 31 database (Table 1). Trace element ions known to be essential in N‐glycosylation process like manganese were included as well as those with unknown contribution but known to leach from metal or glass parts from the equipment like molybdenum, bromine, iodine, rubidium, and zirconium.…”

Population FBA predicts metabolic phenotypes in yeast

“…After censoring proteomics data to remove unreliable distributions, we believe we have good quality of protein copy number distributions. As for the kinetic capacity, we rely primarily on the BRENDA database [ 56 , 57 ]. The BRENDA database often contains several sets of kinetic parameters for a given reaction.…”

Examination of intrinsic sulfonamide resistance in Bacillus anthracis: A novel assay for dihydropteroate synthase

“…A range of k cat values from 0.004 s −1 to 15.6 s −1 has been reported for the synthases from different organisms, while K pABA values are in the range of 0.5 µM to 3.8 µM, and K DHP-PP values in the range of 1.4 µM to 30 µM (BRENDA -The Comprehensive Enzyme Information System -www.brenda-enzymes.info) [17]. Kinetic parameters of the DHPS from B. anthracis, which are reported for the first time in this paper, are generally within the range reported for enzymes from other organisms.…”

Traces matter: Targeted optimization of monoclonal antibody N‐glycosylation based on/by implementing automated high‐throughput trace element screening

“…Schematic experiment strategy for parallel optimization of cell culture performance and mAb glycan formation. Production cell cultivations are designed as biphasic processes, starting with an initial growth phase to generate biomass, followed by a subsequent production phase to form the main amount of the intended product (a) Generic mAb N‐glycan structure (b) The iterative screening and optimization approach and used information sources (BRENDA database 31 and the literature) are shown with respective experimental aim, details on tested clones and number of parallel cultivations. DoE, Design of Experiments; GlcNAc, N‐acetylglucosamine; IgG, immunoglobulin G; mAb, monoclonal antibody; NANA, N‐acetylneuraminic acid…”

“…The in‐house developed automated MTP‐based cell culture system was used to run a classical fractional factorial DoE fed‐batch experiment investigating 13 trace elemental ions (Table S4) selected as putative candidates obtained from previous trace element building block screening, from the literature data 23 , and BRENDA 31 database (Table 1). Trace element ions known to be essential in N‐glycosylation process like manganese were included as well as those with unknown contribution but known to leach from metal or glass parts from the equipment like molybdenum, bromine, iodine, rubidium, and zirconium.…”

Population FBA predicts metabolic phenotypes in yeast

“…After censoring proteomics data to remove unreliable distributions, we believe we have good quality of protein copy number distributions. As for the kinetic capacity, we rely primarily on the BRENDA database [ 56 , 57 ]. The BRENDA database often contains several sets of kinetic parameters for a given reaction.…”

Examination of intrinsic sulfonamide resistance in Bacillus anthracis: A novel assay for dihydropteroate synthase

“…A range of k cat values from 0.004 s −1 to 15.6 s −1 has been reported for the synthases from different organisms, while K pABA values are in the range of 0.5 µM to 3.8 µM, and K DHP-PP values in the range of 1.4 µM to 30 µM (BRENDA -The Comprehensive Enzyme Information System -www.brenda-enzymes.info) [17]. Kinetic parameters of the DHPS from B. anthracis, which are reported for the first time in this paper, are generally within the range reported for enzymes from other organisms.…”

Traces matter: Targeted optimization of monoclonal antibody N‐glycosylation based on/by implementing automated high‐throughput trace element screening

“…Schematic experiment strategy for parallel optimization of cell culture performance and mAb glycan formation. Production cell cultivations are designed as biphasic processes, starting with an initial growth phase to generate biomass, followed by a subsequent production phase to form the main amount of the intended product (a) Generic mAb N‐glycan structure (b) The iterative screening and optimization approach and used information sources (BRENDA database 31 and the literature) are shown with respective experimental aim, details on tested clones and number of parallel cultivations. DoE, Design of Experiments; GlcNAc, N‐acetylglucosamine; IgG, immunoglobulin G; mAb, monoclonal antibody; NANA, N‐acetylneuraminic acid…”

“…The in‐house developed automated MTP‐based cell culture system was used to run a classical fractional factorial DoE fed‐batch experiment investigating 13 trace elemental ions (Table S4) selected as putative candidates obtained from previous trace element building block screening, from the literature data 23 , and BRENDA 31 database (Table 1). Trace element ions known to be essential in N‐glycosylation process like manganese were included as well as those with unknown contribution but known to leach from metal or glass parts from the equipment like molybdenum, bromine, iodine, rubidium, and zirconium.…”

Population FBA predicts metabolic phenotypes in yeast

“…After censoring proteomics data to remove unreliable distributions, we believe we have good quality of protein copy number distributions. As for the kinetic capacity, we rely primarily on the BRENDA database [ 56 , 57 ]. The BRENDA database often contains several sets of kinetic parameters for a given reaction.…”