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Bioinformatic Advancements in Post Translational Modifications (Ptms): An Experimental Approach
Published in Megh R Goyal, Sustainable Biological Systems for Agriculture, 2018
Saurabhh Jain, Surbhi Panwar, Ashwani Kumar, Tejpal Dhewa
Posttranslational modification (PTM) is a biochemical mechanism in which amino acid residues in a protein are covalently modified.4 It is crucial for regulating conformational changes, activities, functions of proteins, and is part of most of the cellular processes. Therefore, the identification of protein PTMs is the foundation for understanding cellular and molecular mechanisms. Bioinformatics tools can generate rapid, accurate and valuable results for PTM prediction.
Analytical Characterization
Published in Laszlo Endrenyi, Paul Jules Declerck, Shein-Chung Chow, Biosimilar Drug Product Development, 2017
In the previous section, the discussion focused on the additional structural changes that can occur to the polypeptide chain(s) of a biopharmaceutical during its production. Most of these changes are due to covalent (chemical or primary structural) modifications that occur in vivo (inside the cell) after the polypeptide chain is synthesized and released from the ribosome, and they are referred to as posttranslational modifications (PTMs). It should be noted, however, that some of these covalent modifications can actually occur while the polypeptide chain is still attached to the ribosome and is being synthesized (or translated). In this latter case, the chemical modifications are referred to as cotranslational modifications (Fedorov and Baldwin, 1997). However, for the purpose of this chapter, we will simply consider all types of chemical changes to a biopharmaceutical’s polypeptide chain(s) inside the cell (whether they occur during the synthesis or after the complete synthesis of that polypeptide) and even outside the cell as PTMs.
Phytoaccumulation of zinc from contaminated soil using ornamental plants species Helianthus annuus L. and Tagetes erecta L.
Published in International Journal of Phytoremediation, 2023
Protein content was shown to decrease as Zn concentration increase in H. annuus and T. erecta. The maximum protein content in H. annuus was 22.75 and 12.7 mg g−1 in T. erecta leaves at 100 mg kg−1 Zn, while the lowest protein content was 14.42 and 7.56 mg g−1 at 500 mg kg−1 Zn substantially (p < 0.05) treated plants after 60 days (Figure 6a). A decrease in protein content had been recorded in mungbeans plants with greater zinc concentrations (Samreen et al. 2017). Reduced protein content in leaves was produced by reducing K and Mg ion absorption, increased post-translational modification, denaturation and fragmentation of protein, decreased protein synthesis, increased protein degradation, and inhibited rubisco activity, according to the findings of this study (Romero-Puertas et al. 2007; Monteiro et al. 2009).
Syntrophy of bacteria and archaea in the anaerobic catabolism of hydrocarbon contaminants
Published in Critical Reviews in Environmental Science and Technology, 2023
Jean Damascene Harindintwali, Leilei Xiang, Fang Wang, Scott X. Chang, Zhiliang Zhao, Zhi Mei, Zhongjun Jia, Xin Jiang, Yong-guan Zhu, James M. Tiedje
Metagenomics alone cannot predict which specific function contributes to, and to what extent, the molecular activity of syntrophic communities in situ, given the fact that genes can be expressed differently or not expressed at all. In this regard, metatranscriptomics, which involves the sequencing of messenger RNA (mRNA) extracted from microbial communities, is used to quantify gene expression levels and identify key metabolic pathways in environments (Su et al., 2012). Because high-throughput sequencing (HTS) can directly count DNA/RNA fragments, RNA must first be converted to DNA before HTS can be performed. In this respect, the conversion of mRNA to complementary DNA (cDNA) by reverse transcription allows sequence analysis with HTS (Strobel et al., 2018). Since additional levels of cellular regulation and localization arise at the protein level, and post-translational modification can change the function and location of proteins, metaproteomics and metabolomics can therefore better reflect the functional expression and activity of proteins (Vanwonterghem et al., 2014). Common metaproteomics workflows involve extracting proteins from a sample of a mixed microbial community, followed by purification, and then tryptic fractionation of proteins to peptides. Further, the fractionated proteins can be separated by liquid chromatography (LC) and detected by tandem mass spectrometry (MS/MS) (Schultz et al., 2020).
Effects of various pine needle extracts on Chinese hamster ovary cell growth and monoclonal antibody quality
Published in Preparative Biochemistry & Biotechnology, 2023
Dingyue Zhang, Jinshu Qiu, Qing-Tian Niu, Tingting Liu, Rulin Gu, Xiaoying Zhang, Shun Luo
Protein glycosylation is an important post-translational modification event, and has a non-negligible impact on protein structure and function,[24,25] represents one of the most important critical quality attributes (CQAs). During the upstream production, glycosylation is altered by cell line, process conditions, and media and supplement formulations.[26] A total of ten glycoforms were found in the proteins produced in the experiments, of which G0F accounted for the highest percentage, reaching about 70% (Table 4). PNWE and PNEE did not show any effect on glycoforms except G0, where G0 levels increased with the increased concentrations of both extracts. PNPE showed different effects on glycoforms. PNPE decreased the G0F level by 8.7% at the 100 mg/L concentration compared to the control. Decreases in G0 minus GlcNAc and G0F minus GlcNAc were also observed. However, the two glycoforms G1Fa and G1Fb increased with the increased PNPE concentrations, where G1Fa increased by 0.56, 4.41, and 6.7% at the three increased concentrations, respectively, and G1Fb increased by 0.96, 2.07, and 2.91%, respectively. G0 and G1F GlcNAc reached the highest level at the 50 mg/L concentration, and G0 glycoform decreased at the 100 mg/L concentration. While Man5 and Man6 reached the highest level at the 5 mg/L PNPE concentration. PNPE had more effect on glycosylation than the other two extracts. Therefore, PNPE could be an effective component used to control product quality associated with glycosylation.