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Characterization of Microorganisms by Pyrolysis-GC, Pyrolysis-GC/MS, and Pyrolysis-MS
Published in Karen D. Sam, Thomas P. Wampler, Analytical Pyrolysis Handbook, 2021
Stephen L. Morgan, Bruce E. Watt, Randolph C. Galipo
The cell envelope usually consists of a cell membrane, a cell wall, and an outer membrane [21,22]. Figure 9.1 shows schematic representations of the structure of Gram-positive and Gram-negative cell envelopes. The cell wall consists of the peptidoglycan (PG) layer and associated structures. PG is the only substance common to almost all bacteria (except Mycoplasma and Chlamydia) and absent in non-bacterial matter [23]. PG and its associated chemical components may account for up to 10–40% of the dry weight of the cell [5]. As seen in Figure 9.2, PG consists of a polysaccharide backbone that is a repeating polymer of N-acetylglucosamine and N-acetylmuramic acid. Attached covalently to the lactyl group of muramic acid are tetra- and pentapeptides (composed of repeating l- and d-amino acids) cross-linked by peptide bridges. The amino sugar muramic acid (3-O--carboxethyl-D-glucosamine) is a fairly definitive marker for bacteria. Other chemical markers in PG include d-alanine, d-glutamic acid, and diaminopimelic acid [24,25]. The d-amino acids are sometimes found in other bacterial components but are not synthesized by mammals. Different bacteria may vary in the sequence of the amino acids in the peptide sidechains and crossbridge.
Arsenals of Pharmacotherapeutically Active Proteins and Peptides: Old Wine in a New Bottle
Published in Debarshi Kar Mahapatra, Swati Gokul Talele, Tatiana G. Volova, A. K. Haghi, Biologically Active Natural Products, 2020
The L-form of amino acids is a naturally occurring form of amino acids. The L-amino acids found in the natural proteins are laevorotatory as well as dextrorotatory. The values of specific rotation for L-amino acids are indicated in Table 2.4. The D-forms of amino acids were reported in bacteria Bacillus brevis, Lactobacillus arabinosus, etc. [17]. The peptidoglycan of bacteria contains D-Ala and D-Glu. The bacterial peptides like Gramicidine S (D-Phe is present), Gramicidine D (D-Leu, D-Val, and D-Phe), etc., contain D-amino acids. D-Amino acid oxidase (DAO) is an enzyme found in humans for catabolizing D-amino acids. It brings about oxidative deamination of D-amino acids in the body, i.e., D-Ala from bacteria of the small intestine, D-Ser, endogenous co-agonist of N-methyl D-aspartate glutamate receptors [19, 20].
Biocatalysts: The Different Classes and Applications for Synthesis of APIs
Published in Peter Grunwald, Pharmaceutical Biocatalysis, 2019
A strategy used by bacteria and fungi to produce peptides as secondary metabolites among them antibiotics (vancomycin, bacitracin), immunosuppressives (cyclosporine) or biosurfactants (surfactin) which are in part of high pharmacological/medical relevance is the nonribosomal synthesis catalyzed by large multi-enzyme complexes the so-called nonribosomal peptide synthases (NRPS) as well as the polyketide synthases (PKS, Type I–III) that, e.g., generate erythromycin, an alternative to β-lactam antibiotics (Streptomyces erythreus) or the blood cholesterol lowering lovastatin (Aspergillus terreus; Hajjaj et al., 2001). In this kind of peptide or polyketide syntheses, the role of mRNA as matrix is taken over by single modules of the enzyme complex enabling a stepwise elongation of the respective metabolite. The accepted building blocks are not restricted to the canonical amino acids but D-amino acids and modified amino acids may be also incorporated (Sieber and Marahiel, 2005).
Theoretical study on spectral differences of polypeptides constituted by L- and D-amino acids
Published in Molecular Physics, 2021
Ren-Hui Zheng, Wen-Mei Wei, Yan-Ying Liu
In general, if the polypeptide formed from L-amino acids is a right-handed helix, the polypeptide formed from D-amino acids is a left-handed helix, which is the mirror image of the right-handed L-polypeptide helix. Scientists have experimentally performed many studies not only on polypeptides and proteins composed of L-amino acids but also on those of D-amino acids, which can be potential drugs such as oral anti-HIV drugs, D-protein drugs and the mirror-image biomolecules for therapy [15–22]. Investigations on D-polypeptide and D-protein are useful and meaningful. The theoretical and experimental studies showed that the IR and Raman spectra of polypeptides and proteins composed of L- and D-amino acids are the same and their chiral spectra such as ROA, VCD and ECD [15,21,22] are mirror symmetric.
Computational studies on non-succinimide-mediated stereoinversion mechanism of aspartic acid residues assisted by phosphate
Published in Molecular Physics, 2018
Tomoki Nakayoshi, Shuichi Fukuyoshi, Ohgi Takahashi, Akifumi Oda
It has been believed that nearly all of the amino acid residues in higher organisms are l-form, but various d-amino acids, mostly aspartate (Asp) residues, have been recently found in higher organisms [1–5]. Proteins have unique three-dimensional (3D) structures and their conformations highly depend on the amino acid sequences. When amino acid residues are isomerised, the activity of proteins can decrease dramatically with protein conformational change. d-amino acid residues have been detected in crystallin in lens [3], elastin in sun-damaged skin [4], and β-amyloid protein in the brain [5]. The d-amino acid residues are more commonly detected in ageing tissues, so it is presumed that an increase of d-amino acid residues causes age-related diseases. Fujii et al. experimentally derived an Arrhenius plot for stereoinversion of the Asp residue in a human αA-crystallin peptide, from which the activation energy was estimated to be 21.4–28.3 kcal mol−1 [6]. l-Asp residues in proteins are thought to undergo non-enzymatic reactions to form l-β-Asp, d-α-Asp, and d-β-Asp residues via a five-membered ring succinimide intermediate (Scheme 1).