The effects of conformation and N-alkylation on gas phase peptide fragmentation

Persistent Link:
http://hdl.handle.net/10150/289755
Title:
The effects of conformation and N-alkylation on gas phase peptide fragmentation
Author:
Breci, Linda Anne
Issue Date:
2001
Publisher:
The University of Arizona.
Rights:
Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.
Abstract:
Investigations described in this dissertation found that cleavage at Xxx-Pro bonds depends upon the identity of the Xxx residue, and this finding is immediately applicable to improved peptide sequencing algorithms because enhanced cleavage was evident for Pro-containing peptides when Xxx is His, Asp, Val, Ile, or Leu, and reduced cleavage was evident when Xxx is Gly or Pro. A greater understanding of the mechanism of cleavage at Pro residues was gained in these studies. A non-Pro N-alkylated residue in a peptide directs cleavage C-terminal to the N-alkylated residue; this is dependent upon the conformation of the peptide as cleavage is directed N-terminal to the residue when the D-stereoisomer of the N-alkylated residue is substituted into the peptide. Cleavage rarely occurs C-terminal to Pro residues in peptides, presumably due to steric limitations that are imposed by the 5-membered ring and that hinder formation of necessary intermediates. Dramatically different gas-phase H/D exchange results observed for L-Pro-containing peptides after substitution with the D-stereoisomer of Pro in addition to evidence of Pro-cleavage dependence upon the residue preceding Pro and conformational dependence of cleavage of other N-alkylated residues leads us to conclude that the conformational turn in a peptide backbone and the steric limitations imposed by the Pro ring are the primary factors affecting cleavage at Pro. Fragmentation patterns of peptides containing Pro and other N-alkylated residues support a mechanism of bond cleavage that begins with protonation at a carbonyl oxygen rather than an amide nitrogen. Transfer of the ionizing proton (or its equivalent) to the C-terminal fragment forms "b" ions which may be followed by the transfer of the hydrogen bound to the amide nitrogen N-terminal to the cleavage site for "y" ion formation. The types of experiments designed to investigate Pro-containing peptides also provided new results that answered questions about gas-phase structure of other peptides. Gas-phase H/D exchange of Arg-containing oligoalanines and their derivatives suggests that salt bridge structures may form for these 5-residue peptides. MS3 and gas-phase H/D exchange results of fragment ions from Asp-containing peptides suggest different "b" ion structures formed at Asp-Xxx and non-Asp cleavage positions.
Type:
text; Dissertation-Reproduction (electronic)
Keywords:
Chemistry, Analytical.
Degree Name:
Ph.D.
Degree Level:
doctoral
Degree Program:
Graduate College; Chemistry
Degree Grantor:
University of Arizona
Advisor:
Wysocki, Vicki H.

Full metadata record

DC FieldValue Language
dc.language.isoen_USen_US
dc.titleThe effects of conformation and N-alkylation on gas phase peptide fragmentationen_US
dc.creatorBreci, Linda Anneen_US
dc.contributor.authorBreci, Linda Anneen_US
dc.date.issued2001en_US
dc.publisherThe University of Arizona.en_US
dc.rightsCopyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.en_US
dc.description.abstractInvestigations described in this dissertation found that cleavage at Xxx-Pro bonds depends upon the identity of the Xxx residue, and this finding is immediately applicable to improved peptide sequencing algorithms because enhanced cleavage was evident for Pro-containing peptides when Xxx is His, Asp, Val, Ile, or Leu, and reduced cleavage was evident when Xxx is Gly or Pro. A greater understanding of the mechanism of cleavage at Pro residues was gained in these studies. A non-Pro N-alkylated residue in a peptide directs cleavage C-terminal to the N-alkylated residue; this is dependent upon the conformation of the peptide as cleavage is directed N-terminal to the residue when the D-stereoisomer of the N-alkylated residue is substituted into the peptide. Cleavage rarely occurs C-terminal to Pro residues in peptides, presumably due to steric limitations that are imposed by the 5-membered ring and that hinder formation of necessary intermediates. Dramatically different gas-phase H/D exchange results observed for L-Pro-containing peptides after substitution with the D-stereoisomer of Pro in addition to evidence of Pro-cleavage dependence upon the residue preceding Pro and conformational dependence of cleavage of other N-alkylated residues leads us to conclude that the conformational turn in a peptide backbone and the steric limitations imposed by the Pro ring are the primary factors affecting cleavage at Pro. Fragmentation patterns of peptides containing Pro and other N-alkylated residues support a mechanism of bond cleavage that begins with protonation at a carbonyl oxygen rather than an amide nitrogen. Transfer of the ionizing proton (or its equivalent) to the C-terminal fragment forms "b" ions which may be followed by the transfer of the hydrogen bound to the amide nitrogen N-terminal to the cleavage site for "y" ion formation. The types of experiments designed to investigate Pro-containing peptides also provided new results that answered questions about gas-phase structure of other peptides. Gas-phase H/D exchange of Arg-containing oligoalanines and their derivatives suggests that salt bridge structures may form for these 5-residue peptides. MS3 and gas-phase H/D exchange results of fragment ions from Asp-containing peptides suggest different "b" ion structures formed at Asp-Xxx and non-Asp cleavage positions.en_US
dc.typetexten_US
dc.typeDissertation-Reproduction (electronic)en_US
dc.subjectChemistry, Analytical.en_US
thesis.degree.namePh.D.en_US
thesis.degree.leveldoctoralen_US
thesis.degree.disciplineGraduate Collegeen_US
thesis.degree.disciplineChemistryen_US
thesis.degree.grantorUniversity of Arizonaen_US
dc.contributor.advisorWysocki, Vicki H.en_US
dc.identifier.proquest3040138en_US
dc.identifier.bibrecord.b42488540en_US
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