Chemical derivatization of peptide carboxyl groups for highly efficient electron transfer dissociation.

The carboxyl groups of tryptic peptides were derivatized with a tertiary or quaternary amine labeling reagent to generate more highly charged peptide ions that fragment efficiently by electron transfer dissociation (ETD). All peptide carboxyl groups-aspartic and glutamic acid side-chains as well as C-termini-were derivatized with an average reaction efficiency of 99 %. This nearly complete labeling avoids making complex peptide mixtures even more complex because of partially-labeled products, and it allows the use of static modifications during database searching. Alkyl tertiary amines were found to be the optimal labeling reagent among the four types tested. Charge states are substantially higher for derivatized peptides: a modified tryptic digest of bovine serum albumin (BSA) generates ~90% of its precursor ions with z > 2, compared with less than 40 % for the unmodified sample. The increased charge density of modified peptide ions yields highly efficient ETD fragmentation, leading to many additional peptide identifications and higher sequence coverage (e.g., 70 % for modified versus only 43 % for unmodified BSA). The utility of this labeling strategy was demonstrated on a tryptic digest of ribosomal proteins isolated from yeast cells. Peptide derivatization of this sample produced an increase in the number of identified proteins, a >50 % increase in the sequence coverage of these proteins, and a doubling of the number of peptide spectral matches. This carboxyl derivatization strategy greatly improves proteome coverage obtained from ETD-MS/MS of tryptic digests, and we anticipate that it will also enhance identification and localization of post-translational modifications.

Valence parity renders z(*)-type ions chemically distinct.

Here we report that the odd electron z (*) -type ions formed by the electron-based peptide dissociation methods (electron capture or transfer, ECD or ETD) have distinctive chemical compositions from other common product ion types. Specifically, b-, c-, and y-type ions have an odd number of atoms with an odd valence (e.g., N and H), while z (*)-type ions contain an even number of atoms with an odd valence. This tenet, referred to as the valence parity rule, mandates that no c-type ion shall have the same chemical composition, and by extension mass, as a z (*) -type ion. By experiment we demonstrate that nearly half of all observed c- and z (*) -type product ions resulting from 226 ETD product ion spectra can be assigned to a single, correct, chemical composition and ion type by simple inspection of the m/ z peaks. The assignments provide (1) a platform to directly determine amino acid composition, (2) an input for database search algorithms, or (3) a basis for de novo sequence analysis.

IpaA targets beta1 integrins and rho to promote actin cytoskeleton rearrangements necessary for Shigella entry.

Shigella invasion into the colonic epithelium involves many steps including the formation of large membrane protrusions by the epithelial cells that facilitate bacterial engulfment. IpaA, a Shigella protein secreted into target cells upon cell contact induces a loss of actin stress fibers in cells and promotes the reorganization of actin at the site of entry. The mechanism for this is not known but is thought to involve recruitment of the focal adhesion protein vinculin to IpaA. Here we have examined the mechanism for the effects of IpaA on the actin cytoskeleton. We show that IpaA-induced loss of actin stress fibers and cell rounding do not require vinculin expression or an intact vinculin binding site on IpaA. Rather, we find that cells expressing IpaA exhibited elevated Rho activity and increased myosin light chain phosphorylation. In addition, IpaA decreases integrin affinity for extracellular matrix ligands by interfering with talin recruitment to the integrin cytoplasmic tail. The combination of these two effects, namely weakened adhesion and increased contractility, account for the loss of actin stress fibers and cell rounding observed in cells exposed to IpaA.