A computational study on the structures and proton affinities of B3+ ions; peptide mass fragment product için kapak resmi
A computational study on the structures and proton affinities of B3+ ions; peptide mass fragment product
Başlık:
A computational study on the structures and proton affinities of B3+ ions; peptide mass fragment product
Yazar:
Boz, Seçkin, author.
Yazar Ek Girişi:
Fiziksel Tanımlama:
viii, 49 leaves:+ 1 computer laser optical disc.
Özet:
Mass spectrometry is the tool of choice during most of the proteomics studies to get amino acid sequence. However, unambiguously identifying amino acid sequence from mass spectra is not easy and straight forward task. Deeper understanding is needed to support both existing knowledge and develop newer models on dissociation patterns of protonated peptides and it will help to improve efficiency of current algorithms used in peptide identification. In this study, the structures of b3+ ions and their neutral forms were investigated by using computational methods. First, potential energy surface of b ions are scanned using molecular dynamics simulations and conformer samples are collected. Then, in order to reduce number of conformers, principal coordinate analysis was applied to find and select different structures within the sample. Selected conformers were optimized using density functional theory calculations. Proton affinities of b ions are determined by the energy difference between most stable conformers of the positively charged and neutral peptide fragments. Different amino acids were used to understand the role of side chain of amino acids on both structures and proton affinities of b3+ ions; XA2+ where X=N, H, C, Y, D, L and F. The results showed that, b3+ ions prefer to have linear oxazolone structure. However, in their neutral states, cyclic structures are relatively far more stable than linear isomers. Histidine display different behavior than other amino acids. Side chain of histidine holds protons and forms stable structures. The energies of cyclic and linear isomers of Histidine containing b ions are close to each other. Histidine containing peptide fragments have larger proton affinity comparing to others. Difference of proton affinities between linear and cyclic conformers varies based on amino acid used. This difference is lower than 10kcal/mol in histidine, asparagine and aspartic acid containing peptide fragments. There is no dramatic position preference of the X-amino acid for the N- or C- terminals or middle position with the exception of Asn and Asp (unlike the center) and Histidine which likes to be at C-terminal .
Konu Başlığı:
Yazar Ek Girişi:
Tek Biçim Eser Adı:
Thesis (Master)--İzmir Institute of Technology: Molecular Biology and Genetics.

İzmir Institute of Technology: Molecular Biology and Genetics.--Thesis (Master).
Elektronik Erişim:
Access to Electronic Versiyon.
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