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Article Citation - WoS: 15Citation - Scopus: 13K+-induced Conformational Changes in the Trimeric Betaine Transporter Betp Monitored by Atr-Ftir Spectroscopy(Elsevier Science Bv, 2013) Korkmaz, Filiz; Ressl, Susanne; Ziegler, Christine; Maentele, Werner; Mäntele, WernerThe trimeric Na+-coupled betaine symporter BetP from Corynebactrium glutamicum adjusts transport activity according to the external osmolality. BetP senses the increasing internal K+ concentration, which is an immediate consequence of osmotic upshift in C. glutamicum. It is assumed that BetP specifically binds potassium to yet unidentified binding sites, thereby inducing conformational changes resulting in activation. Atomic structures of BetP were obtained in the absence of potassium allowing only a speculative glimpse on a putative mechanism of K+-induced transport activation. The structural data suggest that activation in BetP is crucially linked to its trimeric state involving an interaction network between several arginines and glutamates and aspartates. Here, we describe the effect of K+-induced activation on the specific ionic interaction sites in terminal domains and loops and on the protomer-protomer interactions within the trimer studied by ATR-FTIR spectroscopy. We suggest that arginine and aspartate and/or glutamate residues at the trimeric interface rearrange upon K+-induced activation, although they remain assembled in an interaction network. Our data propose a two-step mechanism comprising first a change in solvent exposure of charged residues and second a modification of their interaction sites in a partner-switching manner. FTIR reveals a higher alpha-helical content than expected from the X-ray structures that we attribute to the structurally unresolved N-terminal domain modulating regulation. In situ H-1/H-2 exchange studies point toward an altered exposure of backbone regions to buffer solution upon activation, most likely due to conformational changes in both terminal domains, which further affects ionic interactions within the trimer. (C) 2013 Elsevier B.V. All rights reserved.Article Citation - WoS: 32Citation - Scopus: 32Urine Analysis Using Ftir Spectroscopy: a Study on Healthy Adults and Children(Wiley-v C H verlag Gmbh, 2021) Sarigul, Neslihan; Kurultak, Ilhan; Gokceoglu, Arife Uslu; Korkmaz, Filiz; Uslu Gökceoğlu, ArifeUrine spectra from 108 healthy volunteers are studied by attenuated total refraction-Fourier transform infrared (ATR-FTIR) spectroscopy. The spectral features are correlated with observable urine components. The variation of spectra within a healthy population is quantified and a library of reference spectra is constructed. Using the band assignments, these spectra are compared with both age-wise and gender-wise. Children show the least intensity variations compared to both adult groups. Young adults show the highest variation, particularly in the 1650 to 1400 cm(-1) and 1200 to 900 cm(-1) regions. These results indicate the importance of the size of the control group in comparative studies utilizing FTIR. Age-wise comparisons reveal that phosphate and sulfate excretion decreases with age, and that the variance of phosphate among individuals is higher with adults. As for gender-wise comparisons, females show a slightly higher citrate content at 1390 cm(-1) regardless of the age and they show a higher variance in the 1200 to 1000 cm(-1) region when compared to men.Article Citation - WoS: 2Citation - Scopus: 2Investigations of Ph-Dependent Dynamic Properties of Ompg-16sl, an Outer Membrane Protein G Mutant by Atr-Ftir Spectroscopy(Elsevier, 2022) Yilmaz, Irem; Korkmaz, FilizIn 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.Article Citation - WoS: 5Citation - Scopus: 5Structural Properties of an Engineered Outer Membrane Protein G Mutant, Ompg-16sl, Investigated With Infrared Spectroscopy(Taylor & Francis inc, 2020) Yilmaz, Irem; Yildiz, Ozkan; Korkmaz, FilizThe 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. SarmaArticle Citation - WoS: 31Citation - Scopus: 30Interaction of a Novel Platinum Drug With Bovine Serum Albumin: Ftir and Uv-Vis Spectroscopy Analysis(Royal Soc Chemistry, 2015) Korkmaz, Filiz; Erdogan, Deniz Altunoz; Ozalp-Yaman, SenizPlatinum complexes have proven to be very effective in cancer treatment. However, severe side effects of these drugs have lead scientists to pursue new platinum complex derivatives. A novel blue platinum compound, called Platinum-Blue (Pt-Blue), is one of the promising candidate platinum compounds to be used for tumor treatment. In this study, the interaction of Pt-Blue with bovine serum albumin (BSA) has been investigated using UV-Vis and FTIR spectroscopy. One of the findings is that the drug-protein interaction type depends on the drug concentration. Though Pt-Blue is attached to the surface of BSA at high concentrations, it interacts with a hydrophobic region of the protein at low concentrations with a binding constant of 1.93 x 10(5) M-1. Spectroscopic results indicate the hydrophobic docking position to be around Trp 213 in domain II, which is surrounded by a number of Asp and Glu. During this interaction, helices such as helix-10, helix-18, helix-19 and helix-24 change orientation and/or partially unfold to make room for the compound. Binding constants at high and low concentrations of Pt-Blue are determined using UV-Vis spectroscopy, which are found to be comparable to cisplatin. FTIR spectroscopy also reveals that the interaction between Pt-Blue and BSA is noncovalent, which makes the candidate drug favorable because it is available for DNA binding while being carried by albumin.
