Functional and conformational transitions of mevalonate diphosphate decarboxylase from Bacopa monniera

Stress-dependent flexibility of a full-length human monoclonal antibody: Insights from molecular dynamics to support biopharmaceutical development

After several decades of advancements in drug discovery, product development of biopharmaceuticals remains a time- and resource-consuming endeavor. One of the main reasons is associated to the lack of fundamental understanding of conformational dynamics of such biologic entities, and how they respond to various stresses encountered during manufacturing. In this work, we have studied the conformational dynamics of human IgG₁κ b12 monoclonal antibody (mAb) using molecular dynamics simulations. The hundreds of nanoseconds long trajectories reveal that b12 mAb is highly flexible. Its variable domains show greater conformational fluctuations than the constant domains. Additionally, it collapses towards a more globular shape in response to thermal stress, leading to decrease in the total solvent exposed surface area and radius of gyration. This behavior is more pronounced for the deglycosylated b12 mAb, and it appears to correlate with increase in inter-domain contacts between specific regions of the antibody. Conformational fluctuations also cause temporary formation and disruption of hydrophobic and charged patches on the antibody surface, which is particularly important for the prediction of CMC properties during development phases of antibody-based biotherapeutics. The insights gained through these simulations may help the development of biologic drugs, especially with regards to manufacturing processes where antibodies may undergo significant thermal stress.

In silico/computational analysis of mevalonate pyrophosphate decarboxylase gene families in Campanulids

Mevalonate pyrophosphate decarboxylase (MPD) is a key enzyme in terpenoid biosynthesis. MPD plays an important role in the upstream regulation of secondary plant metabolism. However, studies on the MPD gene are relatively very few despite its importance in plant metabolism. Currently, no systematic analysis has been conducted on the MPD gene in plants under the order Apiales, which comprises important medicinal plants such as Panax ginseng and Panax notoginseng. This study sought to explore the structural characteristics of the MPD gene and the effect of adaptive evolution on the gene by comparing and analyzing MPD gene sequences of different campanulids species. For that, phylogenetic and adaptive evolution analyses were carried out using sequences for 11 Campanulids species. MPD sequence characteristics of each species were then analyzed, and the collinearity analysis of the genes was performed. As a result, a total of 21 MPD proteins were identified in 11 Campanulids species through BLAST analysis. Phylogenetic analysis, physical and chemical properties prediction, gene family analysis, and gene structure prediction showed that the MPD gene has undergone purifying selection and exhibited highly conserved structure. Analysis of physicochemical properties further showed that the MPD protein was a hydrophilic protein without a transmembrane region. Moreover, collinearity analysis in Apiales showed that MPD gene on chromosome 2 of D. carota and chromosome 1 of C. sativum were collinear. The findings showed that MPD gene is highly conserved. This may be a common characteristic of all essential enzymes in the biosynthesis pathways of medicinal plants. Notably, MPD gene is significantly affected by environmental factors which subsequently modulate its expression. The current study’s findings provide a basis for follow-up studies on MPD gene and key enzymes in other medicinal plants.

Effects on Gene Transcription Profile and Fatty Acid Composition by Genetic Modification of Mevalonate Diphosphate Decarboxylase MVD/Erg19 in Aspergillus Oryzae

Mevalonate diphosphate decarboxylase MVD/Erg19 is required for ergosterol biosynthesis, growth, sporulation, and stress tolerance in Aspergillus oryzae. In this study, RNA-seq was used to analyze the gene transcription profile in AoErg19 overexpression (OE) and RNAi strains. There were 256 and 74 differentially expressed genes (DEGs) in AoErg19 OE and RNAi strains, respectively, compared with the control strain (CK). The most common DEGs were transport- and metabolism-related genes. Only 22 DEGs were obtained that were regulated in both OE and RNAi strains. The transcriptomic comparison between CK and AoErg19 overexpression strain (CK vs. OE), and between CK and AoErg19 RNAi strain (CK vs. RNAi) revealed that the greatest difference existed in the number of genes belonging to the cytochrome P450 family; 12 were found in CK vs. OE, whereas 1 was found in CK vs. RNAi. The expression patterns of lipid biosynthesis and metabolism related genes were altered in OE and RNAi strains, either by gene induction or suppression. Moreover, the total fatty acid content in the RNAi strain was 12.1% greater than the control strain, but no difference in total acid content was found between the overexpression strain and the control strain. Therefore, this study highlights the gene expression regulation within mevalonate (MVA), ergosterol biosynthesis, and fatty acid biosynthesis pathways.

Mevalonate Diphosphate Decarboxylase MVD/Erg19 Is Required for Ergosterol Biosynthesis, Growth, Sporulation and Stress Tolerance in Aspergillus oryzae

Mevalonate diphosphate decarboxylase (MVD; EC 4.1.1.33) is a key enzyme of the mevalonic acid (MVA) pathway. In fungi, the MVA pathway functions as upstream of ergosterol biosynthesis, and MVD is also known as Erg19. Previously, we have identified Aoerg19 in Aspergillus oryzae using bioinformatic analysis. In this study, we showed that AoErg19 function is conserved using phylogenetic analysis and yeast complementation assay. Quantitative reverse transcription-PCR (qRT-PCR) indicated that Aoerg19 expression changed in different growth stages and under different forms of abiotic stress. Subcellular localization analysis showed that AoErg19 was located in the vacuole. Overexpression of Aoerg19 decreased the ergosterol content in A. oryzae, which may due to the feedback-mediated downregulation of Aoerg8. Consistent with the decrease in ergosterol content, both Aoerg19 overexpression and RNAi strains of A. oryzae are sensitive to abiotic stressors, including ergosterol biosynthesis inhibitor, temperature, salt and ethanol. Thus, we have identified the function of AoErg19 in A. oryzae, which may assist in genetic modification of MVA and the ergosterol biosynthesis pathway.