Download Nonribosomal Peptide and Polyketide Biosynthesis: Methods by Bradley Evans PDF

By Bradley Evans

This quantity offers an outline of nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) constitution and serve as. It then keeps with tools for the research of those pathways together with traditional enzymological assays, modern mass spectrometric research suggestions, really good molecular organic ways acceptable to NRPSs and PKSs, and small molecule research instruments adapted to this very detailed type of average items, and concludes via reading bioinformatics instruments for the research of those enzymes, pathways, and molecules. Written for the hugely profitable Methods in Molecular Biology sequence, chapters comprise introductions to their respective themes, lists of the mandatory fabrics and reagents, step by step, quite simply reproducible laboratory protocols, and tips about troubleshooting and averting identified pitfalls.

Authoritative and functional, Nonribosomal Peptide and Polyketide Biosynthesis: tools and Protocols serves as a beneficial reference for these skilled in learning NRPS and PKS enzymes, pathways, and common items in addition to a gateway for these simply getting into the field.

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Extra resources for Nonribosomal Peptide and Polyketide Biosynthesis: Methods and Protocols

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The SrfA-C protein is shown in (a). A model conformation that adopts the thioester-forming conformation where the PCP is bound to the adenylation domain and (b) the crystallographic structure where the PCP interacts with the condensation domain. The N-terminal subdomain of the adenylation domain, as well as the condensation and thioesterase domains, are all shown in surface representation, while the PCP and the C-terminal subdomain of the adenylation domain are shown as ribbons. The structure in panel (a) is derived by modeling the SrfA-C (PDB 2VSQ) adenylation and PCP domains onto the thioester-forming conformation observed with EntE-B (PDB 4IZ6) or PA1221 (PDB 4DG9).

53. 54. 55. 56. 57. 58. formational changes during the synthetic cycle of nonribosomal peptide synthetases. J Mol Biol 425:3137–3150 Lai JR, Fischbach MA, Liu DR et al (2006) Localized protein interaction surfaces on the EntB carrier protein revealed by combinatorial mutagenesis and selection. J Am Chem Soc 128:11002–11003 Bruner SD, Weber T, Kohli RM et al (2002) Structural basis for the cyclization of the lipopeptide antibiotic surfactin by the thioesterase domain SrfTE. Structure 10:301–310 Samel SA, Wagner B, Marahiel MA et al (2006) The thioesterase domain of the fengycin biosynthesis cluster: a structural base for the macrocyclization of a non-ribosomal lipopeptide.

ATs are proposed to employ a ping-pong bi-bi mechanism that proceeds via an acyl-enzyme intermediate. The intermediate is stabilized during catalysis by an oxyanion hole formed by backbone amides from neighboring amino acids within the enzyme active site. Resolution of the acyl-enzyme intermediate occurs only in the presence of thiol nucleophiles rendering this intermediate sufficiently stable to permit its isolation and characterization in vitro [56]. The topology of the AT active site is in part dictated by amino acids that form defined substrate-selectivity motifs.

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