bi6b00576_si_001.pdf (2.98 MB)
Synthesis and Kinetic Analysis of Two Conformationally Restricted Peptide Substrates of Escherichia coli Penicillin-Binding Protein 5
journal contribution
posted on 2016-07-15, 19:18 authored by Venkatesh
V. Nemmara, Robert A. Nicholas, R. F. PrattEscherichia coli PBP5 (penicillin-binding protein
5) is a dd-carboxypeptidase involved in bacterial cell wall
maturation. Beyond the C-terminal d-alanyl-d-alanine
moiety, PBP5, like the essential high-molecular mass PBPs, has little
specificity for other elements of peptidoglycan structure, at least
as elicited in vitro by small peptidoglycan fragments. On the basis
of the crystal structure of a stem pentapeptide derivative noncovalently
bound to E. coli PBP6 (Protein Data Bank entry 3ITB), closely similar
in structure to PBP5, we have modeled a pentapeptide structure at
the active site of PBP5. Because the two termini of the pentapeptide
are directed into solution in the PBP6 crystal structure, we then
modeled a 19-membered cyclic peptide analogue by cross-linking the
terminal amines by succinylation. An analogous smaller, 17-membered
cyclic peptide, in which the l-lysine of the original was
replaced by l-diaminobutyric acid, could also be modeled
into the active site. We anticipated that, just as the reactivity
of stem peptide fragments of peptidoglycan with PBPs in vivo may be
entropically enhanced by immobilization in the polymer, so too would
that of our cyclic peptides with respect to their acyclic analogues
in vitro. This paper describes the synthesis of the peptides described
above that were required to examine this hypothesis and presents an
analysis of their structures and reaction kinetics with PBP5.