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Dengue Fever: A Viral Hemorrhagic Fever of Global Concern
Published in Jagriti Narang, Manika Khanuja, Small Bite, Big Threat, 2020
Bennet Angel, Neelam Yadav, Jagriti Narang, Annette Angel, Vinod Joshi
Genome sequencing of dengue virus: The entire genetic information of all serotypes of dengue (Angel et al., 2016; Anoop et al., 2012; Chao et al., 2005; Dayaraj et al., 2011; Ong et al., 2008; Patil et al., 2011; Schreiber et al., 2009; Sharma et al., 2011; Shin et al., 2013) and partial sequences (Angel et al., 2016; Domingo et al., 2006; Kukreti et al., 2008, 2009) have been investigated. Table 4.6 depicts the results of protein sequencing. The genetic material of DENV is RNA and, thus, mutates at a fast rate (Drake, 1993; Holmes and Burch, 2000; Bennett et al., 2003). Chin-Inmanu et al. (2012) have used pyro-sequencing strategy for sequencing the viral genome. The Broad Institute Massachusetts, USA, and many pioneer institutes have contributed to huge data of DENV genome (Ong, 2010).
Molecular Biology of the Amelogenin Gene
Published in Colin Robinson, Jennifer Kirkham, Roger Shore, Dental Enamel, 2017
James P. Simmer, Malcolm L. Snead
The cDNA sequences are available for the human X- and Y-,13,31 bovine X- and Y-,35-37 and murine38-40 amelogenin genes. An alignment of these DNA sequences* is provided in Figure 2. The complete porcine amelogenin primary structure has been determined by direct protein sequencing.41,42 An alignment of the deduced and observed amino acid sequences of these amelogenins is provided in Figure 3. The DNA and protein comparisons are consistent, a condition reflected by the dashes placed in identical positions.
Molecular Recognition and Chemical Modification of Biopolymers — Two Main Components of Affinity Modification
Published in Dmitri G. Knorre, Valentin V. Vlassov, Affinity Modification of Biopolymers, 1989
Dmitri G. Knorre, Valentin V. Vlassov
The key procedures in protein sequencing are the specific fragmentation of a protein to a mixture of peptides, separation of these peptides, and stepwise degradation of each of them followed by the identification of eliminated monomers. Splitting is usually performed by enzymes, e.g., trypsin and chymotrypsin, which cleave peptide bonds formed by carboxyl groups of aromatic amino acids: phenylalanine, tyrosine, and tryptophane. In several cases, the chemical modification of proteins permits the protection of some points against enzymatic cleavage or vice versa to form new cleavable points. Thus, proteins may be treated with either trifluoroacetic or citraconic anhydride36,37 which modify ϵ-amino groups of lysine. For example:
HDX-MS study on garadacimab binding to activated FXII reveals potential binding interfaces through differential solvent exposure
Published in mAbs, 2023
Saw Yen Ow, Eugene A. Kapp, Vesna Tomasetig, Anton Zalewski, Jason Simmonds, Con Panousis, Michael J. Wilson, Andrew D. Nash, Matthias Pelzing
Exported lists of peptides from protein sequencing mapping were used as the basis for deuterated sample processing. Processing was performed using HDExaminer™ (Sierra Analytics, CA, USA) using the FASTA database for antibody and antigen separately.43 Raw data were parsed semi-automatically using predefined settings for bottom-up LCMS and the definition of deuteration at t = 0, 30, 60, 300, and 1200 seconds at 90% D2O. Charge states were set initially by those found by peptide search and expanded to a min–max of 1–4. Retention time reference was anchored to t = 0. Filtering of fit was initially performed using an automatic cutoff of ≤0.7 as low confidence and ≥0.9 as high confidence. All fits between 0.7 and 0.9 were manually reviewed. All the processed data were mapped using preloaded (1) heat map data/image, (2) peptide plot data/image, (3) peptide pool result, (4) uptake summary table, (5) uptake plot, and (6) deuteration comparison plots from HDExaminer™.
De novo sequencing of proteins by mass spectrometry
Published in Expert Review of Proteomics, 2020
Rui Vitorino, Sofia Guedes, Fabio Trindade, Inês Correia, Gabriela Moura, Paulo Carvalho, Manuel A. S. Santos, Francisco Amado
The advent of MS for protein identification, and its combination with de novo sequencing has revolutionized modern proteomics with the development of the nascent field of proteogenomics. The ability to identify novel peptides, their sequences, mutations, and modifications using these advanced techniques has broadened the understanding of molecular biology, particularly of proteins. Unraveling the genomic features of a protein is crucial for their characterization and understanding their functional role. There are various advancements in de novo sequencing of proteins, and new software are being developed continuously for robust and accurate identification. The Human Genome Project has paved the way for in-silico studies that will save time and optimize the use of resources. The limitations of such techniques are being studied to improve the usefulness of this approach in protein sequencing.
Proteomics of Pseudomonas aeruginosa: the increasing role of post-translational modifications
Published in Expert Review of Proteomics, 2018
Charlotte Gaviard, Thierry Jouenne, Julie Hardouin
An interesting alternative to bottom–up is top–down proteomics (Figure 1), recently reviewed [62]. Intact proteins are directly analyzed, without enzymatic digestion [63]. Fractionation steps are first included in the workflow, to decrease protein mixture complexity and to improve top–down analyses of whole proteins. Protein fractionation can be performed by LC, IEF, or capillary zone electrophoresis (CZE) but one-dimensional separation may be not enough efficient. Li et al. optimized capillary electrophoresis and identify 30 intact proteins of P. aeruginosa strain PAO1 by top–down proteomics [64]. Two-dimensional [65] or even four-dimensional [66] prefractionation has been described to enhance protein separation. Then, the use of high-resolution and high mass accuracy mass spectrometers is crucial to distinguish signals of the different proteoforms that can just exhibit mass differences below 0.01 Da. The precise mass of the intact proteins is determined and protein sequencing is achieved by MS/MS using ECD or ETD on FT-ICR or orbitrap mass spectrometers, respectively.