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Biochemistry
Published in W. M. Haynes, David R. Lide, Thomas J. Bruno, CRC Handbook of Chemistry and Physics, 2016
W. M. Haynes, David R. Lide, Thomas J. Bruno
Symbol Name 6-Aminohexanoic acid 2-Amino-2-methylpropanoic acid -3-Amino-2-methylpropanoic acid 9-Aminononanoic acid 8-Aminooctanoic acid 5-Amino-4-oxopentanoic acid 5-Aminopentanoic acid Aniline-2-carboxylic acid Azaserine Canavanine --Carboxyglutamic acid Carnosine Citrulline Creatine -Cysteic acid -Cystine 2,4-Diaminobutanoic acid 3,5-Dibromo- -tyrosine 3,5-Dichloro- -tyrosine 3,5-Diiodo- -tyrosine Dopamine -Ethionine N-Glycylglycine Guanidinoacetic acid Histamine -Homocysteine Homocystine -Homoserine 3-Hydroxy- -glutamic acid 5-Hydroxylysine trans-4-Hydroxy- -proline -3-Iodotyrosine -Kynurenine -Lanthionine Levodopa -1-Methylhistidine -Norleucine -Norvaline -Ornithine O-Phosphoserine -Pyroglutamic acid Sarcosine Taurine - yroxine Mol. form. C6H13NO2 C4H9NO2 C4H9NO2 C9H19NO2 C8H17NO2 C5H9NO3 C5H11NO2 C7H7NO2 C5H7N3O4 C5H12N4O3 C6H9NO6 C9H14N4O3 C6H13N3O3 C4H9N3O2 C3H7NO5S C6H12N2O4S2 C4H10N2O2 C9H9Br2NO3 C9H9Cl2NO3 C9H9I2NO3 C8H11NO2 C6H13NO2S C4H8N2O3 C3H7N3O2 C5H9N3 C4H9NO2S C8H16N2O4S2 C4H9NO3 C5H9NO5 C6H14N2O3 C5H9NO3 C9H10INO3 C10H12N2O3 C6H12N2O4S C9H11NO4 C7H11N3O2 C6H13NO2 C5H11NO2 C5H12N2O2 C3H8NO6P C5H7NO3 C3H7NO2 C2H7NO3S C15H11I4NO4 Mol. wt. 131.173 103.12 103.12 173.253 159.227 131.13 117.147 137.137 173.128 176.174 191.138 226.232 175.185 131.133 169.157 240.3 118.134 338.98 250.078 432.981 153.179 163.238 132.118 117.107 111.145 135.185 268.354 119.119 163.129 162.186 131.13 307.084 208.213 208.235 197.188 169.181 131.173 117.147 132.161 185.073 129.115 89.094 125.147 776.871 tm/ºC 205 335 185 pKa 2.36 pKb 10.21 pKc
Biophysical and Biochemical Characterization of Peptide, Protein, and Bioconjugate Products
Published in Sandeep Nema, John D. Ludwig, Parenteral Medications, 2019
Tapan K. Das, James A. Carroll
Pyroglutamic acid formation is a common modification for proteins and occurs spontaneously when the N-terminal residue is a glutamine, or less commonly, a glutamic acid. The formation of pyroglutamic acid from an N-terminal glutamine residue generates a net acidic shift and a loss of 17 Da. This is due to cyclization with the N-terminus with the loss of NH3 from the side chain, which blocks the N-terminal amine. For monoclonal antibodies, N-terminal glutamine and glutamic acid residues are common for both heavy and light chains, and pyroglutamic acid formation is a very common posttranslational modification for IgG molecules [106].
Advanced Molecular Tools and Techniques for Assessment of Microbial Diversity in Fermented Food Products
Published in Deepak Kumar Verma, Ami R. Patel, Sudhanshu Billoria, Geetanjali Kaushik, Maninder Kaur, Microbial Biotechnology in Food Processing and Health, 2023
Damanpreet Kaur, Sushma Gurumayum, Prasad Rasane, Sawinder Kaur, Jyoti Singh, Navneet Kaur, Kajal Dhawan, Ashwani Kumar
Metabolomics analysis is classified as targeted and untargeted analysis. The detection and separation techniques involved in the analysis of metabolite is illustrated in Figure 9.3. Lee et al. (2012) applied mass-spectrometry (MS) based metabolite profiling to characterize the bacterial population of Meju. The study demonstrated the changes in metabolites taking place during fermentation and provided the knowledge about the relationship between metabolites and bacterial population. LAB and Bacillus predominated Meju microflora and microbial analysis of Meju fermentation revealed a higher proportion of LAB than Bacillus during fermentation. However, the LAB species were present in less proportion than Bacillus as lactic acid decreased sharply after 36 days of fermentation. These MS-based metabolite profiling showed that the amino acids (alanine, pyroglutamic acid, leucine, glutamic acid, and tyrosine) responsible for the taste of the product are increased during fermentation. The status of low molecular weight oligosaccharides (sucrose, raffinose, and stachyose) was also studied during metabolite profiling. Metabolomic studies on cheonggukanj provided complete information on the metabolic changes that has taken place during the whole process of fermentation (Kim et al., 2012). Microbial profile of Italian mozzarella cheese produced from cow and buffalo milk using metabolomics was studied by Pisano et al. (2016). GC-MS was employed to analyze the metabolite changes occurring during fermentation in doenjang. The study concluded that metabolites like leucine, aminoadipic acid, isoleucine, malic acid, lysine, glucosamine, and oxalic acid were the major contributors to distinguish the samples during the entire fermentation process (Namgung et al., 2010). H-NMR spectroscopy detection technique has been used to study the metabolite profile of fermented soymilk. Study Yang et al. (2009) revealed that the inoculated microbial strains during fermentation process resulted in decrease sugars content along with simultaneous increase in lactic acid and succinic acid concentration.
Computational studies on nonenzymatic pyroglutamylation mechanism of N-terminal glutamic acid residues in aqueous conditions*
Published in Molecular Physics, 2020
Tomoki Nakayoshi, Koichi Kato, Eiji Kurimoto, Akifumi Oda
Glutamic acid (Glu) residues located at N-termini in peptides and proteins are prone tointramolecular cyclisation, resulting in the formation of pyroglutamic acid (pGlu) residues [1–5]. The pGlu residues are formed by the nucleophilic attack of the N-terminal amino nitrogen on the side-chain carboxyl carbon with the release of a water molecule (Scheme 1). This post-translational modification is called ‘pyroglutamylation.’ Until now, although conversion from N-terminal Glu residues to pGlu residues has been observed in several peptides and proteins, for example, in neurons of Aplysia californica [1], monoclonal antibodies [2–5], and amyloid β (Aβ) [6–10], there are no reports describing the formation of pGlu residues from Glu residues not located at N-termini. Twardzik et al. proposed that the N-terminal Glu-residue cyclisation is enzymatic rather than spontaneous, based on studies using mouse plasmacytoma protein [11]. In fact, the inhibition of glutaminyl cyclase, an enzyme that catalyses pyroglutamylation, has been reported to significantly reduce the pGlu-residue formation in Aβ [12,13]. However, Chelius et al. showed for the first time that N-terminal Glu residues can cyclize in aqueous buffer without any enzymes and suggested that pGlu residues can be formed from N-terminal Glu residues during fermentation and purification processes of immunoglobulin γ (IgG) antibodies [2]. Liu et al. also showed that the rate of pGlu-residue formation from N-terminal Glu residue in phosphate buffer under physiological pH and temperature is very close to that in vivo and assumed that pGlu residues can be nonenzymatically formed from N-terminal Glu residues in vivo [5].