Yılmaz, İrem

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Yilmaz,Irem
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Y., İrem
Yilmaz, İRem
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Y., İRem
I., Yilmaz
İrem Yılmaz
Irem, Yilmaz
İrem, Yilmaz
Yılmaz İ.
Yılmaz, İRem
Yilmaz,İ.
İrem, Yılmaz
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Yılmaz,I.
Y.,Irem
Yilmaz, Irem
I., Yılmaz
İrem, Yılmaz
Yılmaz I.
Y., Irem
Yılmaz,İ.
Yilmaz,I.
Y.,İRem
Job Title
Öğretim Üyesi
Email Address
irem.yilmaz@atilim.edu.tr
ORCID ID
0009-0002-9551-329X
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Scholarly Output

2

Articles

2

Citation Count

7

Supervised Theses

0

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2020 - 20222
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Now showing 1 - 2 of 2
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    Article
    Citation Count: 2
    Investigations of pH-dependent dynamic properties of OmpG-16SL, an outer membrane protein G mutant by ATR-FTIR spectroscopy
    (Elsevier, 2022) Yilmaz, Irem; Korkmaz, Filiz; Avionics; Physics Group
    In this paper, the dynamic properties of outer membrane protein G mutant (OmpG-16SL) are investigated with ATR-FTIR spectroscopy. While OmpG-WT has 14 beta-strands in its structure, the mutant is designed to have 16 beta-strands with the intention of creating an enlarged pore. Loop L6 is elongated by introducing six residues, two of which are negatively charged. The solvent accessibility of the OmpG-16SL mutant is compared with WT and a previously reported mutant OmpG-16S by tracking the H-1/H-2 exchange kinetics in acidic and neutral buffer conditions. The exchange kinetics and dynamics in the fast and slow exchange phases are separately investigated using the 2DCOS technique, which enables the tracking of the structural changes at each phase of the exchange process. The results suggest that the mutant OmpG-16SL is equally exposed to buffer in both acidic and neutral pH conditions. Additionally, the time range in the fast phase is very short - one-tenth of that for WT - and most of the exchange is completed in this phase. This fast exchange within minutes is also indicative of the presence of highly flexible and/or unstructured regions. In all, the fast exchange rates independent of the buffer pH justify the assumption that there is an altered interaction among the charged residues, which leads to a steadily-open pore. The role of the side-chain interactions within the pore and between the loops involving the loop L6 is also discussed.
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    Article
    Citation Count: 5
    Structural properties of an engineered outer membrane protein G mutant, OmpG-16SL, investigated with infrared spectroscopy
    (Taylor & Francis inc, 2020) Yilmaz, Irem; Yildiz, Ozkan; Korkmaz, Filiz; Avionics; Physics Group
    The structural and functional differences between wild type (WT) outer membrane protein G and its two mutants are investigated with Fourier transform infrared spectroscopy. Both mutants have a long extension to the primary sequence to increase the number of beta-strands from 14 (wild type) to 16 in an attempt to enlarge the pore diameter. The comparison among proteins is made in terms of pH-dependent conformational changes and thermal stability. Results show that all proteins respond to pH change but at different degrees. At acidic environment, all proteins contain the same number of residues participated in beta-sheet structure. However, at neutral pH, the mutants have less ordered structure compared to WT porin. Thermal stability tests show that mutants differ significantly from WT porin at neutral pH. Although the transition temperature is directly proportional with the amount of beta-sheet content, the changes in the pre-transition phase that pave the way to structural breakdown are shown to involve interactions among charged residues by two-dimensional correlation spectroscopy analysis. Results of the analysis show that side chain interactions play an active role under increasing temperature. Both mutants have more unordered secondary structure but they respond to pH change in tertiary structure level. Findings of this study provided deeper insight on the active players in structural stability of the WT porin. Communicated by Ramaswamy H. Sarma