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NuranElmac�?±, S�?±laKaraca and SeckinBoz
Department of Chemistry, Izmir Institute of Technology, Turkey
Department of Molecular Biology, Izmir Institute of Technology, Turkey
Posters & Accepted Abstracts: J Chromatogr Sep Tech
Tandem mass spectrometry (MS/MS) coupled with collision-induced dissociation (CID) is commonly used method for proteomic studies. Upon low-energy CID, protonated or multiply-protonated peptides undergo fragmentation via cleavage of amide bonds to generate N-terminal b and a and/or C-terminal y ions. Understanding the gas-phase structures of these ions and their fragmentation reactions has played a vital role for correct and reliable peptide/protein identification. It has been shown that, bn (n=2-4) ions commonly have oxazolone structure. However, for some cases b2 ions also adopt a sixmembered ring; diketopiperazine structure. The formation of these two different structures entirely depends on the amino acid composition of the peptide sequence as well as peptide chain length.Themacrocyclic structure of b5 + and larger b ions has been predicted for aliphatic peptides in experimental and theoretical studies. The macrocyclic structure is a problem for determining the amino acid sequence of a peptide. The memory of original primary structure is lost if reopening of the macrocycle takes place at different sites on the cycle. In such cases, the databases of computer programs which are used with the MS/MS results will be insufficient to identify peptide/protein. These databases must be improved by the detailed and comprehensive studies of the gas phase fragmentations of protonated peptides. This will lead to get reliable results for the proteomic researches.In this work, the structures of b5 ions; XA4 composed of alanine and X= X; Asn, Asp, Leu, Phe, Tyr, Cys, amino acid residues have been investigated by using molecular dynamics simulation method and quantum chemical methods. The X-residues have different type of substituent groups; aliphatic (-CH2-), aromatic (C rings), alcohol (-OH), thiol (-SH), amides (-CONH2) and carboxyl (-COOH). To examine the position influence of X residue, three types of linear peptide sequences have been used in the computational calculations for b5 + fragment; XAAAA, AAXAA, AAAAX. It has been observed that the b5 ions prefer to have a macrocyclic structure rather than linear oxazolone isomer. The macrocycle has some common features (backbone structure, proton location, H-bond etc.) for all b-ionsstudied in this research. The results of this work will be useful to understand the gas phase dissociation chemistry of peptides and will support and insight to the experimental studies.