Zeynep Aslıhan Durer

• Doctor of Philosophy
• Professor (Associate) at Acıbadem University

Background/aim Ischemic heart diseases continue to be a significant global cardiovascular problem in today’s world. Myocardial reperfusion (R) is provided with an effective and rapid treatment; however, it can lead to fatal results, as well as ischemia (I). This study aims to use proteomic analysis to assess proteins and pathways in H9C2 cardiomyob...

G protein‐coupled receptors (GPCRs) constitute the largest and most diverse superfamily of mammalian transmembrane proteins. These receptors are involved in a wide range of physiological functions and are targets for more than a third of available drugs in the market. Autophagy is a cellular process involved in degrading damaged proteins and organe...

Detailed molecular information on G-actin assembly into filaments (F-actin), and their structure, dynamics, and interactions, is essential for understanding their cellular functions. Previous studies indicate that a flexible DNase I binding loop (D-loop, residues 40–50) plays a major role in actin's conformational dynamics. Phalloidin, a “gold stan...

Formins are a conserved group of proteins that nucleate and processively elongate actin filaments. Among them, the formin homology domain-containing protein (FHOD) family of formins contributes to contractility of striated muscle and cell motility in several contexts. However, the mechanisms by which they carry out these functions remain poorly und...

Formins are a conserved group of proteins that nucleate and processively elongate actin filaments. Among them, the formin homology domain-containing protein (FHOD) family of formins contributes to contractility of striated muscle and cell motility in several contexts. However, the mechanisms by which they carry out these functions remain poorly und...

25 (OH) vitamin D3 (25(OH)D) and parathyroid hormone (PTH) are important regulators of calcium homeostasis. The aim of this study was to retrospectively determine the cut–off for sufficient 25(OH)D in a four-season region and the influence of age, seasons, and gender on serum 25(OH)D and PTH levels. Laboratory results of 9890 female and 2723 male i...

Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) imaging mass spectrometry (IMS) enables localization of analytes of interest along with histology. More specifically, MALDI-IMS identifies the distributions of proteins, peptides, small molecules, lipids, and drugs and their metabolites in tissues, with high spatial resolution...

Essential cellular processes involving the actin cytoskeleton are regulated by auxiliary proteins that can sense the nucleotide state of actin. Here we report cryo-EM structures for ADP-bound and ADP-beryllium fluoride (ADP-BeFx, an ADP-Pi mimic)-bound actin filaments in complex with the β-propeller domain of yeast coronin 1 (crn1), at 8.6-Å resolu...

Vinculin is a ubiquitously expressed adhesion protein of cell-matrix and cell-cell junctions. A larger splice-isoform of vinculin, metavinculin, is specifically expressed in cardiac and smooth muscles where it co-localizes with vinculin. Metavinculin has a 68 amino acid insert at its C-terminal actin binding tail (metavinculin tail: MVT). Mutations...

Conformational changes induced by ATP hydrolysis on actin are involved in the regulation of complex actin networks. Previous structural and biochemical data implicate the DNase I binding loop (D-loop) of actin in such nucleotide-dependent changes. Here, we investigated the structural and conformational states of the D-loop (in solution) using cyste...

Actin and myosin are the two main proteins required for cell motility and muscle contraction. The structure of their strongly bound complex-rigor state-is a key for delineating the functional mechanism of actomyosin motor. Current knowledge of that complex is based on models obtained from the docking of known atomic structures of actin and myosin s...

The conformational dynamics of filamentous actin (F-actin) is essential for the regulation and functions of cellular actin networks. The main contribution to F-actin dynamics and its multiple conformational states arises from the mobility and flexibility of the DNase I binding loop (D-loop; residues 40-50) on subdomain 2. Therefore, we explored the...

Atomic force microscopy of SOD1 amyloid. Amyloid was formed by incubating SOD1 in 1 M guanidine, pH 3, at 37°C. The right-hand image is the phase image. The field of each image is a 10 µM×10 µM square. (1.98 MB TIF)

Kinetic Parameters for Amyloid Formation from Apo-SOD1 proteins (0.02 MB DOC)

Mal-PEG reactivity of as-isolated and remetalated preparations. For remetalation, apo-proteins in 0.1 M sodium acetate, pH 5.5, were incubated overnight on ice with 2 equivalents of ZnSO4 per dimer; then 0.5 equivalents of CuSO4 were added at 2-hr intervals. Protein samples were reacted with Mal-PEG as desribed in Materials and Methods. Lane 1, WT;...

Electron microscopy of amyloid formed from apo- and reduced SOD1. Apo-SOD1 was incubated in 50 mM citrate, 0.1 M NaCl, 1 M guanidine, pH 3 (A) or in 50 mM MOPS, 0.1 M NaCl, 1 mM EDTA, pH 7, with (B–D) or without (E–G) 1 M guanidine. Metalated SOD1 was incubated in 50 mM MOPS, 0.1 M NaCl, pH 7, with 1 M guanidine and 10 mM TCEP (H–I) or 0.1 M TCEP (...

Spectroscopic Characterization of Amyloid (0.02 MB DOC)

Remetalation of SOD1 (0.03 MB DOC)

Dye-binding and spectroscopic properties of SOD1 amyloid. A. SOD1 amyloid binds Congo Red. SOD1 amyloid was prepared by incubation for 3 days at 37°C at pH 3 and 1 M guanidine as in Figure 1 and collected by pelleting. Spectra are 5 µM Congo Red (solid line), 5 µM Congo Red plus 10 µM SOD (dash line), and the difference spectrum (dot-dash line). SO...

Mutations in the gene encoding Cu-Zn superoxide dismutase (SOD1) are one of the causes of familial amyotrophic lateral sclerosis (FALS). Fibrillar inclusions containing SOD1 and SOD1 inclusions that bind the amyloid-specific dye thioflavin S have been found in neurons of transgenic mice expressing mutant SOD1. Therefore, the formation of amyloid fi...

The Gram-negative bacterium Vibrio cholerae is the causative agent of a severe diarrheal disease that afflicts three to five million persons annually, causing up to 200,000 deaths. Nearly all V. cholerae strains produce a large multifunctional-autoprocessing RTX toxin (MARTXVc), which contributes significantly to the pathogenesis of cholera in mode...