Browsing by Author "Yildirim, A."

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Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C Ns5b Protein
(Iop Publishing Ltd, 2016) Asafi, M. S.; Yildirim, A.; Tekpinar, M.
Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated.
Comparison of Eye Movement Desensitization and Reprocessing (Emdr) and Duloxetine Treatment Outcomes in Women Patients With Somatic Symptom Disorder
(Kure Iletisim Grubu A.S., 2017) Demirci, O.O.; Saǧaltici, E.; Yildirim, A.; Boysan, M.
Somatic symptom disorder (SSD) is a debilitating disorder that significantly diminishes quality of life and causes psychological distress such as anxiety and depression. The paper explored the efficiency of the eye movement desensitization and reprocessing (EMDR) therapy in SSD. The current investigation is a clinical trial investigating the effectiveness of eye movement desensitization (EMDR) therapy in the treatment of 31 first-diagnosed SSD patients in comparison to age, education and marital status matched 31-first-diagnosed SSD patients who received duloxetine over a 6-week course of treatment. Somatization subscale of the Symptom Checklist-Revised 90 (SCL-90), Beck Anxiety Inventory (BAI), Beck Depression Inventory (BDI), and Short Form Health Survey (SF-36) were administered to the participants. EMDR group showed enhanced improvement relative to baseline after 6 weeks of treatment compared to duloxetine group. We concluded that EMDR appears to be a highly promising therapy and should be considered among the first-line interventions in the treatment of SSD.
The Effect of Oxfendazole Plus Oxyclozanide Paste and Tablet Formulations on Parasite Burden and Metabolic Status of Sheep
(Medwell online, 2008) Gunes, V.; Inci, A.; Uyanik, F.; Yildirim, A.; Altug, N.; Eren, M.; Gelfert, C. C.
The aim of the present study was to evaluate the effects of anthelmintic treatment with Oxyclozanid + Oxfendazole in different formulation (paste and tablet) on parasite load and metabolic status in sheep. Forty five sheep, infected with various gastrointestinal parasites and kept on a grazing flock, were evenly divided into 3 groups. Sheep in the control group did not receive any treatment. The sheep in the remaining groups received the same dose of Oxyclozanid (5 mg kg(-1) body weight) and Oxfendazole (13.5 mg kg(-1) body weight) in combination either as tablet or as paste. Faeces and blood samples were collected pre-treatment (day 0) and on day 14 post-treatment. Several gastrointestinal nematode parasites were detected in the faecal samples. Eggs PerGram (EPG) on days 0 and 14 were 100 +/- 18 and 78 +/- 8 in CG, 96 +/- 12 and 6 +/- 3 in TG and 76 +/- 9 and 2 +/- 2 in the PG, respectively. Serum total protein and globulin concentrations increased significantly (p<0.05) in CG and PG on day 14 compare to pre-treatment levels. In both sampling times total protein levels did not differ whereas a slight decrease in paste group and a significant decrease in tablet group were detected concerning globulin level, but no significant difference was detected between the tablet group and paste group on day 14 post-treatment. In paste group serum albumin level increased (p<0.05) on day 14 compare to baseline level. Compare to control group, albumin level slightly increased in tablet group, whereas it significantly increased in paste group on day 14 post-treatment. On day 14 in paste group Pi, Mg and Cu levels were higher (p<0.05) than the post-treatment levels of the remaining groups. A combination of Oxyclozanid+Oxfendazole is effective to eliminate parasite burden in sheep. Drug formulation does not have any influence on the metabolic status of the sheep.
Only a Subset of Normal Modes Is Sufficient To Identify Linear Correlations in Proteins
(American Chemical Society, 2018) Tekpinar, M.; Yildirim, A.
Identification of correlated residues in proteins is very important for many areas of protein research such as drug design, protein domain classification, signal transmission, allostery and mutational studies. Pairwise residue correlations in proteins can be obtained from experimental and theoretical ensembles. Since it is difficult to obtain proteins in various conformational states experimentally, theoretical methods such as all-atom molecular dynamics simulations and normal-mode analysis are commonly used methods to obtain protein ensembles and, therefore, pairwise residue correlations. The extent of agreement for the correlations obtained with all-atom molecular dynamics and elastic network model based normal-mode analysis is an important issue to investigate due to orders of magnitude computational advantage in terms of wall time for normal-mode based calculation. We performed multiple microsecond long equilibrium classical molecular dynamics simulations for six proteins. We calculated normalized dynamical cross-correlations and linear mutual information as pairwise residue correlations from the trajectories of these simulations. Then, we calculated the same pairwise residue correlations with two elastic network model based normal-mode analysis methods and compared our results with the former. The results show that elastic network model based normal-mode analysis can provide a fast and accurate estimation of linear correlations within proteins. Finally, we observed that only a subset of modes is sufficient to obtain linear correlations in proteins. This conclusion has crucial implications for understanding correlations within very large protein assemblies such as viral capsids. Copyright © 2018 American Chemical Society.
Psychometric Properties of the Turkish Version of Sleep Hygiene Index in Clinical and Non-Clinical Samples
(Cambridge Univ Press, 2015) Ozdemir, P. Guzel; Boysan, M.; Selvi, Y.; Yildirim, A.; Yilmaz, E.
A Theoretical Integration Within Obsessive-Compulsive Disorder (Ocd) and Dissociative Spectrums: Obsessional Dissociation
(Kure Iletisim Grubu A.S., 2019) Yildirim, A.; Boysan, M.