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Integrated Omics Technology for Basic and Clinical Research
Published in Jyoti Ranjan Rout, Rout George Kerry, Abinash Dutta, Biotechnological Advances for Microbiology, Molecular Biology, and Nanotechnology, 2022
Kuldeep Giri, Vinod Singh Bisht, Sudipa Maity, Kiran Ambatipudi
The proteome—a pool of proteins—expressed within a biological entity like cell, organ, and organism by a genome at a given time (Wilkins et al., 1996). The protein primary structure (linear chain of amino acids) determines the secondary and tertiary structures (functional unit) including different protein functions. The complexity of proteins in comparison to static gene sequence of a DNA is deeper, as proteome is neither dynamic nor static as genome (Mirza and Olivier, 2008). The proteomics experimental analysis in a large scale (proteomic analysis) is important from a functional aspect (alteration in the level of gene expression) as few studies claimed that genome or their transcripts (with or without modifications) analysis is substantially unchanged but affect the phenotype (Godovac-Zimmermann and Brown, 2001). The proteome of a cell performs diverse roles including signal transduction and metabolism of the cell, which are essential for the survival of an organism. Similarly, protein–protein interactions (physical contact and their interacting partners) to form dimers (reverse transcriptase) and multiprotein complexes (proteasome degradation complexes) or with nucleic acid affect several molecular pathways and may act as regulatory element (prokaryotic/eukaryotic transcription factors) for gene or transcript expression (Gonzalez and Kann, 2012).
Trends in Biotechnology
Published in Firdos Alam Khan, Biotechnology Fundamentals, 2020
Protein biosynthesis is most commonly performed by ribosomes in human cells and protein primary structures can be directly sequenced or inferred from DNA sequences. Protein primary structure is the linear sequence of amino acids in a peptide or protein. The primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end.
Engineered enzymes and enzyme systems
Published in Ruben Michael Ceballos, Bioethanol and Natural Resources, 2017
With the development of polymerase chain reaction (PCR) for amplifying genomic DNA and with the development of methods in generating recombinant DNA, site-directed/specific mutagenesis became possible. Concurrently, methods in biomolecular imaging and modeling were rapidly under development. Using biochemical data, protein structures’ (e.g., from X-ray crystallography and protein NMR) biomolecular modeling, and molecular dynamics simulations, it became possible to make reasonable predictions about how changes in protein primary structure would result in changes in three-dimensional conformation (i.e., tertiary structure) and, ultimately, in function. Modifications to genes forcing substitutions, insertions, or deletions in the amino acid sequence at specific positions within protein primary structure ushered in the era of rational design. It is clear that success in rational design is dependent on reliable information about the enzyme structure, function, and mechanism of action. The process of rational design involves (1) choosing a suitable enzyme about which adequate information regarding structure, function, and mechanism is available; (2) identifying amino acid sites that when changed will likely result in structural alteration that produce the desired changes in function; and (3) characterizing the expressed mutants via purification, sequencing, and enzyme activity assays after each round of mutagenesis (Johnsson et al., 1993; Pleiss, 2012). With adequate information regarding structure, function, and mechanism about a target enzyme, rational design is probably the easiest and quickest approach to engineering enzymes. Computational modeling and in silico experiments are becoming more sophisticated each year making it even easier to make valid predictions on how function will change when an amino acid or group of amino acids is altered in the primary structure of the protein (Tiwari et al., 2012). Validated predictions are more probable when rational design of an enzyme is based on the knowledge of enzyme structure, function, and mechanism from several related species.
On the impact of ethanol on the rejection and transfer mechanism during ultrafiltration of a charged macromolecule in water/ethanol
Published in Environmental Technology, 2020
H. Al Jawad, M. Rabiller-Baudry, P. Loulergue, C. Bejjani, A. Lejeune, H. Mawlawi, G. Nasser, S. Taha
Equation (12) was used to calculate µLys at 25°C in water and water/ethanol mixtures with and without NaCl addition. R = RLys was used for the protein size. Z = ZLys was calculated from the protein primary structure at the appropriate pH, as already validated in water by [57] leading to ZLys = 12.6 at pH = 4.0, ZLys =7.1 at pH = 7.1 and ZLys = 6.6 at pH = 9.0. However, Z is different than ZLys in KH2PO4 because of the specific adsorption of phosphate. At pH = 9 and I = 10 × 10−3 mol.L−1 adjusted by KH2PO4 lysozyme behaves as an uncharged molecule in water [16], that is equivalent to Z = 0. As the isoelectric pH in water/ethanol 70/30 v/v is not changed when compared to water (checked on zirconia powder thanks to streaming potential measurements, not shown here [61]), µLys will be null in this mixture.
EightyDVec: a method for protein sequence similarity analysis using physicochemical properties of amino acids
Published in Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization, 2022
Ranjeet Kumar Rout, Saiyed Umer, Sabha Sheikh, Sanchit Sindhwani, Smitarani Pati
Amino acids play an important role in the determination of three dimensional structure of proteins and hence the biological processes depend upon their physiochemical properties (Chou and Shen 2007; Wu et al. 2010; Dai et al. 2013; Berlin et al. 2015). According to the side chain effect of amino acids listed in Table 1, these 20 amino acids can be classified into 8 different groups as discussed by El Maaty et al. (2010). The distribution of eight types of amino acids describes protein primary structures. For better understanding, the feature vector of protein primary structure, the classification of amino acids is defined in Equation (1).