Molecular Modelling Of Peptide-metal Interactions In A Model Yeast Saccharomyces Cerevisiae

Thesis (M.Sc.) -- İstanbul Technical University, Institute of Science and Technology, 2009Bu çalışmada, bakır tutan proteinlerde, bakırı bağlayan MXCXXC ortak motifinin, X yerine 4 farklı amino asit (A, G, T ve V) kullanılması durumunda bakır bağlama verimliliği, hesapsal yöntemler yardımıyla incelenmiştir. Enerji hesaplamaları için HyperChem yazılımı ve CHARMM22 kuvvet alanı (force field) kullanılmıştır. Hesaplamalar önce nötr hale getirilmiş peptitler için yapılmış, daha sonra her bir olası peptitin terminallerine metil grupları bağlanarak tüm hesaplamalar tekrarlanmıştır. Elde edilen enerjiler, en kararlı peptit-bakır kompleksine ve stabilizasyon enerji değerlerine göre değerlendirilmiştir. En iyi motif olarak MTCGTC öne çıkarken, birinci ve üçüncü pozisyondaki X için Treonin’in kullanılması verimliliği arttırmaktadır. İkinci pozisyondaki X yerine herhangi bir amino asit kullanılması verimliliği dikkate değer ölçüde etkilememiştir. Birinci pozisyondaki X için Treonin amino asidinin iyi sonuç vermesi, literatürdeki bazı yayınlarda bu pozisyonda Treoninin zaten sabit kabul edilmesiyle uyumluluk göstermiştir.In this study conserved MXCXXC motif in copper chaperone proteins was investigated through computational analysis to determine the copper-binding efficiency by using four different amino acids (A, G, T, and V) instead of X residues. HyperChem software, and CHARMM22 force field were used for energy calculations. Calculations were done first for neutralized peptides and then repeated for all combinations of MXCXXC peptides with methyl at the terminals. Energies obtained by calculations were analized according to two criteria, most stable peptide-copper complex and stabilization energy. While MTCGTC was concluded as the best peptide, using Threonine for the first and the third X position increased the effectiveness on copper binding. There existed no meaningful effect of using any of the four amino acids for the second X position. Good results of Threonine in the first X position is compatible with some studies accepting Treonine as conserved on the first X residue between Methionine and Cysteine.Yüksek LisansM.Sc

Genomic, transcriptomic and physiological analyses of silver‐resistant Saccharomyces cerevisiae obtained by evolutionary engineering

International audienceSilver is a non-essential metal used in medical applications as an antimicrobial agent, but it is also toxic for biological systems. To investigate the molecular basis of silver resistance in yeast, we employed evolutionary engineering using successive batch cultures at gradually increased silver stress levels up to 0.25-mM AgNO(3)in 29 populations and obtained highly silver-resistant and genetically stableSaccharomyces cerevisiaestrains. Cross-resistance analysis results indicated that the silver-resistant mutants also gained resistance against copper and oxidative stress. Growth physiological analysis results revealed that the highly silver-resistant evolved strain 2E was not significantly inhibited by silver stress, unlike the reference strain. Genomic and transcriptomic analysis results revealed that there were mutations and/or significant changes in the expression levels of the genes involved in cell wall integrity, cellular respiration, oxidative metabolism, copper homeostasis, endocytosis and vesicular transport activities. Particularly the missense mutation in theRLM1gene encoding a transcription factor involved in the maintenance of cell wall integrity and with 707 potential gene targets might have a key role in the high silver resistance of 2E, along with its improved cell wall integrity, as confirmed by the lyticase sensitivity assay results. In conclusion, the comparative physiological, transcriptomic and genomic analysis results of the silver-resistantS. cerevisiaestrain revealed potential key factors that will help understand the complex molecular mechanisms of silver resistance in yeast