Eşsiz, Şebnem

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Profile URL
https://hdl.handle.net/20.500.12469/6172
Name Variants
Eşsiz, Şebnem
Eşsiz, Sebnem
E., Sebnem
Sebnem Eşsiz
Eşsiz, Ş.
Essiz, Sebnem
Essiz,Sebnem
Şebnem Eşsiz
S. Eşsiz
Essiz,Ş.
E., Şebnem
Eşsiz, S.
DAVUTYAN N.
Eşsiz, ŞEBNEM
Ş. Eşsiz
Şebnem EŞSIZ
Eşsiz,Ş.
EŞSIZ, Şebnem
E.,Sebnem
Essiz,S.
ŞEBNEM EŞSIZ
Sebnem, Essiz
Davutyan N.
EŞSIZ, ŞEBNEM
Gökhan, Şebnem Eşsiz
Eşsiz, Şebnem
Eşsiz Gökhan, Şebnem
Gökhan Eşsiz, Şebnem
Gökhan, Şebnem Eşsiz
Essız, Sebnem
Eşsiz, Şebnem
Essız, Sebnem
Eşsiz Gökhan, Şebnem
Job Title
Dr. Öğr. Üyesi
Email Address
[email protected]
Main Affiliation
Molecular Biology and Genetics
Status
Current Staff
Website
ORCID ID
0000-0002-5476-4722
Scopus Author ID
7801565973
Turkish CoHE Profile ID
Google Scholar ID
WoS Researcher ID
GCQ-0556-2022

Sustainable Development Goals

NO POVERTY1
NO POVERTY
0
Research Products
ZERO HUNGER2
ZERO HUNGER
0
Research Products
GOOD HEALTH AND WELL-BEING3
GOOD HEALTH AND WELL-BEING
8
Research Products
QUALITY EDUCATION4
QUALITY EDUCATION
0
Research Products
GENDER EQUALITY5
GENDER EQUALITY
0
Research Products
CLEAN WATER AND SANITATION6
CLEAN WATER AND SANITATION
0
Research Products
AFFORDABLE AND CLEAN ENERGY7
AFFORDABLE AND CLEAN ENERGY
3
Research Products
DECENT WORK AND ECONOMIC GROWTH8
DECENT WORK AND ECONOMIC GROWTH
0
Research Products
INDUSTRY, INNOVATION AND INFRASTRUCTURE9
INDUSTRY, INNOVATION AND INFRASTRUCTURE
1
Research Products
REDUCED INEQUALITIES10
REDUCED INEQUALITIES
0
Research Products
SUSTAINABLE CITIES AND COMMUNITIES11
SUSTAINABLE CITIES AND COMMUNITIES
0
Research Products
RESPONSIBLE CONSUMPTION AND PRODUCTION12
RESPONSIBLE CONSUMPTION AND PRODUCTION
1
Research Products
CLIMATE ACTION13
CLIMATE ACTION
0
Research Products
LIFE BELOW WATER14
LIFE BELOW WATER
0
Research Products
LIFE ON LAND15
LIFE ON LAND
0
Research Products
PEACE, JUSTICE AND STRONG INSTITUTIONS16
PEACE, JUSTICE AND STRONG INSTITUTIONS
0
Research Products
PARTNERSHIPS FOR THE GOALS17
PARTNERSHIPS FOR THE GOALS
0
Research Products
Documents

23

Citations

270

h-index

9

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Scholarly Output

29

Articles

16

Views / Downloads

234/2486

Supervised MSc Theses

9

Supervised PhD Theses

2

WoS Citation Count

213

Scopus Citation Count

248

Patents

0

Projects

0

WoS Citations per Publication

7.34

Scopus Citations per Publication

8.55

Open Access Source

17

Supervised Theses

11

JournalCount
Journal of Molecular Modeling2
European Journal of Medicinal Chemistry2
Turkish Journal of Biology2
Chemical Biology & Drug Design1
ChemistrySelect1
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Scholarly Output Search Results

Now showing 1 - 10 of 29
  • Thumbnail Image
    Article
    Citation - WoS: 3
    Citation - Scopus: 3
    Correlated conformational dynamics of the human GluN1-GluN2A type N-methyl-D-aspartate (NMDA) receptor
    (SPRINGER, 2021) Esşiz, Şebnem; Gencel, Melis; Aktolun, Muhammed; Demir, Ayhan; Carpenter, Timothy S.; Servili, Burak
    N-Methyl-D-aspartate receptors (NMDARs) are glutamate-gated ion channels found in the nerve cell membranes. As a result of overexcitation of NMDARs, neuronal death occurs and may lead to diseases such as epilepsy, stroke, Alzheimer's disease, and Parkinson's disease. In this study, human GluN1- GluN2A type NMDAR structure is modeled based on the X-ray structure of the Xenopus laevis template and missing loops are added by ab-initio loop modeling. The final structure is chosen according to two different model assessment scores. To be able to observe the structural changes upon ligand binding, glycine and glutamate molecules are docked into the corresponding binding sites of the receptor. Subsequently, molecular dynamics simulations of 1.3 mu s are performed for both apo and ligand-bound structures. Structural parameters, which have been considered to show functionally important changes in previous NMDAR studies, are monitored as conformational rulers to understand the dynamics of the conformational changes. Moreover, principal component analysis (PCA) is performed for the equilibrated part of the simulations. From these analyses, the differences in between apo and ligand-bound simulations can be summarized as the following: The girdle right at the beginning of the pore loop, which connects M2 and M3 helices of the ion channel, partially opens. Ligands act like an adhesive for the ligand-binding domain (LBD) by keeping the bi-lobed structure together and consequently this is reflected to the overall dynamics of the protein as an increased correlation of the LBD with especially the amino-terminal domain (ATD) of the protein.
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    Article
    Citation - WoS: 50
    Citation - Scopus: 54
    New Azole Derivatives Showing Antimicrobial Effects and Their Mechanism of Antifungal Activity by Molecular Modeling Studies
    (Elsevier France-Editions Scientifiques Medicales Elsevier, 2017) Doğan, İnci Selin; Saraç, Selma; Sarı, Suat; Kart, Didem; Eşsiz, Şebnem; Vural, İmran; Dalkara, Sevim
    Azole antifungals are potent inhibitors of fungal lanosterol 14 alpha demethylase (CYP51) and have been used for eradication of systemic candidiasis clinically. Herein we report the design synthesis and biological evaluation of a series of 1-phenyl/1-(4-chlorophenyl)-2-(1H-imidazol-1-yl) ethanol esters. Many of these derivatives showed fungal growth inhibition at very low concentrations. Minimal inhibition concentration (MIC) value of 15 was 0.125 mu g/mL against Candida albicans. Additionally some of our compounds such as 19 (MIC: 0.25 mu g/mL) were potent against resistant C. glabrata a fungal strain less susceptible to some first-line antifungal drugs. We confirmed their antifungal efficacy by antibiofilm test and their safety against human monocytes by cytotoxicity assay. To rationalize their mechanism of action we performed computational analysis utilizing molecular docking and dynamics simulations on the C. albicans and C. glabrata CYP51 (CACYP51 and CGCYP51) homology models we built. Leu130 and T131 emerged as possible key residues for inhibition of CGCYP51 by 19. (C) 2017 Elsevier Masson SAS. All rights reserved.
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    Article
    Citation - WoS: 1
    Citation - Scopus: 1
    Engineering of Geobacillus Kaustophilus Lipase for Enhanced Catalytic Efficiency and Methanol Tolerance in Biodiesel Production from Sunflower Oil
    (Elsevier, 2025) Tulek, Ahmet; Poyraz, Yagmur; Sukur, Gozde; Pacal, Nurettin; Ozdemir, F. Inci; Yildirim, Deniz; Essiz, Sebnem
    Lipase-mediated biodiesel production offers a sustainable and environmentally friendly alternative to conventional chemical methods. However, enzyme limitations such as low activity, poor thermal stability, and limited solvent tolerance remain challenges. In this study, a lipase from Geobacillus kaustophilus (Gklip) was engineered for improved biodiesel production using molecular docking, molecular dynamics (MD) simulations, and molecular mechanics/generalized born surface area (MM/GBSA) free energy calculations. Five mutants (Y29S, Q114T, F289D, Q184M, and Q114F) were generated via site-directed mutagenesis and expressed in Escherichia coli. Biochemical characterization revealed that all mutants retained the wild-type's optimal temperature (50 degrees C) and pH (8.0), while showing varying pH ranges, with the broadest observed in Q184M. Thermal stability increased significantly in Q184M (32.86-fold) and Q114F (5.93-fold). Catalytic efficiencies improved by 2.07-, 2.05-, and 2.63-fold in Q184M, F289D, and Y29S, respectively, compared to the wild-type (0.57). In the presence of 60 % methanol, the wild-type retained only 30.4 % activity, while Q184M maintained 67.5 %, highlighting superior solvent tolerance. Biodiesel conversion assays using sunflower oil showed no product formation by the wild-type, whereas Q184M, Q114F, and F289D achieved yields of 58.7 %, 56.3 %, and 49.2 %, respectively. These findings identify Q184M and Q114F as promising enzyme candidates for enzymatic biodiesel production.
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    Master Thesis
    G. Kaustophilius Lipazinin Mutasyon Çalışmaları Kullanılarak Substrat Seçiciliğinin ve Aktivitesinin Geliştirilmesi
    (2025) Poyraz, Yağmur; Eşsiz, Şebnem
    Lipazlar, yağların hidrolizini katalize eden hidrolaz sınıfı enzimlerdir. Biyoteknolojide özellikle biyodizel üretimi alanında önemli bir yeri bulunmaktadır. Bu enzimler, yağların transesterifikasyon reaksiyonunu katalize ederek bitkisel veya hayvansal yağlardan biyodizel elde etmeye yardımcı olmaktadır. Fakat, biyodizel üretiminde lipaz kullanımının bir takım sorunları bulunmaktadır. Reaksiyon verimliliğinin yetersizliği, özellikle yüksek serbest yağ asidi içeriğine sahip ham yağların transesterifikasyonunda önemli bir sorundur. Ayrıca, lipazların reaksiyon hızı açısından yeterince hızlı olmama duumu söz konusudur. Bunlara ek olarak, bu enzimler çevre koşullarına duyarlıdır; uygun sıcaklık veya pH koşulları olmaması durumu enzim aktivitesini olumsuz etkileyebilirken, kararlılık sorunlarını da beraberinde getirebilmektedir. Araştırmacılar, lipazların performansını artırmak ve süreç verimliliğini iyileştirmek için sürekli olarak yenilikçi yöntemler ve teknolojiler araştırmaktadır. Enzim mutasyonu ve lipaz immobilizasyonu, bu çabada odaklanılan önemli alanlardır. Bu çalışma, Geobacillus kaustophilus termofilik lipazının yapısal ve dinamik özellikleri hakkındaki anlayışımızı geliştirmeyi ve aktivitesini, substrat seçiciliğini ve termal kararlılığını iyileştirmek için mutasyonları kullanmayı amaçlamaktadır. İdeal mutasyonları bulmak için Gklip lipazı modellenmiş ve hem yabani tip hem de mutasyonlu yapıların ligand seçiciliğini değerlendirmek için farklı uzunlukta karbon zincirli yağ asitleri ile dok çalışmaları yürütülmüştür. Daha sonra, tüm protein-ligand kompleksleri için 50 ns moleküler dinamik simülasyonları gerçekleştirilmiştir. Simülasyonların son 30 ns'si MM/GBS analizi için kullanılmıştır. 36 mutasyondan, en iyi 5 tanesi daha ileri deneysel çalışmalar için seçilmiştir.
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    Article
    Citation - WoS: 42
    Citation - Scopus: 41
    Sustainable production of formic acid from CO2 by a novel immobilized mutant formate dehydrogenase
    (Elsevier, 2023) Tulek, Ahmet; Gunay, Elif; Servili, Burak; Essiz, Sebnem; Binay, Baris; Yildirim, Deniz
    Formate dehydrogenase (NAD+-dependent FDH) is an enzyme that catalyzes the reversible oxidation of formate to CO2 while reducing NAD+ to NADH. The enzyme has been used in industrial and chemical applications for NADH regeneration for a long time. However, discovering the unique ability of FDHs, which is to reduce CO2 and produce formic acid, leads studies focusing on discovering or redesigning FDHs. Despite using various protein engineering techniques, these studies mostly target the same catalytic site amino acids of FDHs. Here, for the first time, the effect of an Asp188 mutation on a potential allosteric site in NAD+-dependent CtFDH around its subunit-subunit interface was studied by molecular modelling and simulation in the presence of bicarbonate and formate. Biochemical and kinetic characterization of this Asp188Arg mutant and wild type CtFDH enzymes were performed in detail. Both enzymes were also immobilized on newly synthesized MWCNT-Ni-O-Si/Ald and MWCNT-Ni-O-Si/Glu supports designed to overcome well-known CtFDH stability problems including thermostability and reuse resistance. Integrating mutation and immobilization provided about a 25-fold increase in catalytic efficiency for carbonate activity. The one-way ANOVA analysis also ensured significant effect of the mutation and immobilization on kinetic constants. After characterizing the immobilization of highly purified wild type and mutant enzyme with instrumental analysis techniques, the thermal stability of MWCNT-Ni-Si@wtCtFDH and MWCNT-Ni-Si@mt-CtFDH was found to increase about 11-and 18-fold, respectively, compared to their free counterparts at 50 degrees C. The mutant CtFDH and its immobilized counterpart produced around 2-fold more formic acid than those of wild type CtFDH and its immobilized counterpart under the same conditions. MWCNT-Ni-Si@wt-CtFDH and MWCNT-Ni-Si@mt-CtFDH remained around 82 % and 86 % of their initial activities respectively after lots of recycling. Integration of subunit interface amino acid position of NAD+ dependent FDHs engineering and immobilization provides a new insight can be scientifically and rationally employed for this current application FDHs as a solution to produce formic acids from renewable sources.
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    Conference Object
    Soman as a Wrench in the Works of Human Acetylcholinesterase: Soman Induced Conformational Changes Revealed by Molecular Dynamics Simulations
    (Amer Chemical Soc, 2014) Bennion, Brian J.; Eşsiz, Şebnem; Lau, Edmond Y.; Fattebert, Jean-Luc; Emigh, Aiyana; Lightstone, Felice C.
    [Abstract Not Available]
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    Master Thesis
    Structural Study of Gaba Type a Receptor : the Effect of Intrasubunit Disulphide Bridges on Dynamics
    (Kadir Has Üniversitesi, 2014) Ayan, Meral; Gökhan Eşsiz, Şebnem
    In the mammalian brain the gamma-aminobutyric acid type A receptor is the most commonly expressed subtype of receptor family. Although there is a rich pharmacological activity of R, specific molecular features are still not well known. In this study, we developed a new homology model based on a recently available X-Ray structure of the glutamate-gated chloride channel. When it is compared with previous homology models of the based on lower sequence identity templates, there are three additional disulphide bridges occurring in between membrane spanning alpha helices namely two in the alpha and one in the gamma subunits. These new disulphide bridges are occurring due to the differences in the sequence alignments of template and target structures. Additionally, we performed molecular dynamics simulations with two models, one with the disulphide bridges in the transmembrane domanin, and the other without disulphide bridges. To analyze simulation results, minimum pore radius along the pore, root-mean-square deviation of proteins and root mean square fluctuation of alpha are analyzed. Finally principal component analysis of the 100 nanosecond long trajectory is calculated to compare the differences in the correlated motions of two models
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    Article
    Citation - WoS: 8
    Citation - Scopus: 9
    Antifungal Screening and in Silico Mechanistic Studies of an In-House Azole Library
    (2019) Sarı, Suat; Kart, Didem; Sabuncuoğlu, Suna; Doğan, İnci Selin; Özdemir, Zeynep; Bozbey, İrem; Gencel, Melis; Eşsiz, Şebnem; Reynisson, Jóhannes; Karakurt, Arzu; Saraç, Selma; Dalkara, Sevim
    Systemic Candida infections pose a serious public health problem with high morbidity and mortality. C. albicans is the major pathogen identified in candidiasis; however, non-albicans Candida spp. with antifungal resistance are now more prevalent. Azoles are first-choice antifungal drugs for candidiasis; however, they are ineffective for certain infections caused by the resistant strains. Azoles block ergosterol synthesis by inhibiting fungal CYP51, which leads to disruption of fungal membrane permeability. In this study, we screened for antifungal activity of an in-house azole library of 65 compounds to identify hit matter followed by a molecular modeling study for their CYP51 inhibition mechanism. Antifungal susceptibility tests against standard Candida spp. including C. albicans revealed derivatives 12 and 13 as highly active. Furthermore, they showed potent antibiofilm activity as well as neglectable cytotoxicity in a mouse fibroblast assay. According to molecular docking studies, 12 and 13 have the necessary binding characteristics for effective inhibition of CYP51. Finally, molecular dynamics simulations of the C. albicans CYP51 (CACYP51) homology model's catalytic site complexed with 13 were stable demonstrating excellent binding.
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    Article
    Citation - WoS: 3
    Citation - Scopus: 2
    Modelling of C-Terminal Tail of Human Sting and Its Interaction With Tank-Binding Kinase 1
    (Tubitak Scientific & Technical Research Council Turkey, 2022) Ata Ouda Al-Masri, Rahaf; Audu-Bida, Hajara; Essiz, Sebnem
    Stimulator of interferon genes (STING) plays a significant role in a cell's intracellular defense against pathogens or self DNA by inducing inflammation or apoptosis through a pathway known as cGAS-cGAMP-STING. STING uses one of its domains, the C-terminal tail (CTT) to recruit the members of the pathway. However, the structure of this domain has not been solved experimentally. STING conformation is open and more flexible when inactive. When STING gets activated by cGAMP, its conformation changes to a closed state covered by 4 beta-sheets over the binding site. This conformational change leads to its binding to Tank-binding kinase 1 (TBK1). TBK1 then phosphorylates STING aiding its entry to the cell's nucleus. In this study, we focused on the loop modeling of the CTT domain in both the active and inactive STING conformations. After the modeling step, the active and inactive STING structures were docked to one of the cGAS-cGAMP-STING pathway members, TBK1, to observe the differences of binding modes. CTT loop stayed higher in the active structure, while all the best-scored models, active or inactive, ended up around the same position with respect to TBK1. However, when the STING poses are compared with the cryo-EM image of the complex structure, the models in the active structure chain B displayed closer results to the complex structure.
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    Doctoral Thesis
    Structural, Optical and Antibacterial Properties of Ws2 Doped Zno Nanoparticles
    (2023) Beytür, Sercan; Uysal, Bengü Özuğur; Eşsiz, Şebnem
    Yapısal ve optik özelliklerinin yanı sıra antibakteriyel özellikleri ile tanınan ZnO nanoparçacıkları, çeşitli alanlarda yaygın olarak uygulanmaktadır. Metaller veya metal oksitler gibi farklı malzemelerin ZnO'ya katkılanmasının özelliklerini iyileştirdiği bilinmektedir. Burada %5, %15 ve %25 oranlarında WS2 katkılı ZnO'dan oluşan nanofilmler sentezlenmekte ve özellikleri araştırılmaktadır. Moleküler yerleştirme analizleri ile desteklenen, farklı oranlarda WS2 ilave edildikten sonra bakterisidal özelliklerin arttırılması vurgulanmaktadır ve ilgili proteinlerin hedeflenmesi yoluyla bakteriyel hayatta kalmada çok önemli bir rol oynayan kalıntıların inhibe edici etkileşimi tarafından desteklenmektedir.