Browsing by KHAS Author "Akdoğan, Ebru Demet"
Exploring distinct binding site regions of beta(2)-adrenergic receptor via coarse-grained molecular dynamics simulations Authors:Cakan, Sibel; Akdoğan, Ebru Demet
Publisher and Date:(Scientific Technical Research Council Turkey-Tubitak, 2013)beta(2)-Adrenergic receptor (beta(2)AR) is a G protein-coupled receptor that is highly flexible and able to recognize a wide range of ligands through its conformational variations. Active and inactive conformations revealed by recent crystallographic experiments do not provide a complete dynamic picture of the receptor especially in the binding site. In this study molecular dynamics (MD) simulation through a residue-based coarse-grained model is used as an alternative and efficient method to explore ...
Authors:Kürkçüoğlu, Zeynep; Fındık, Doğa; Akdoğan, Ebru Demet; Doruker, Pemra
Publisher and Date:(Cell Press, 2015)The tunnel region at triosephosphate isomerase (TIM)'s dimer interface distant from its catalytic site is a target site for certain benzothiazole derivatives that inhibit TIM's catalytic activity in Trypanosoma cruzi the parasite that causes Chagas disease. We performed multiple 100-ns molecular-dynamics (MD) simulations and elastic network modeling (ENM) on both apo and complex structures to shed light on the still unclear inhibitory mechanism of one such inhibitor named bt10. Within the time ...
Authors:Akdoğan, Ebru Demet; Erman, Burak; Yelekçi, Kemal
Publisher and Date:(Scientific Technical Research Council Turkey-Tubitak, 2011)Histone lysine-specific demethylase (LSD1) is involved in a wide range of epigenetic processes and plays important roles in gene silencing DNA transcription DNA replication DNA repair and heterochromatin formation. Its active site shows a resemblance to those of 2 homologous enzymes monamine oxidase A and B (MAO-A and MAO-B.) In the present work starting from suitable scaffolds and generating thousands of structures from them 10 potential inhibitors were obtained with structural and physicochemical ...