Servili, Burak
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Servili, Burak
B.,Servili
B. Servili
Burak, Servili
Servili, Burak
B.,Servili
B. Servili
Burak, Servili
Servili, B.
B.,Servili
B. Servili
Burak, Servili
Servili, Burak
B.,Servili
B. Servili
Burak, Servili
Servili, B.
Job Title
Misafir Öğr. Gör. Dr.
Email Address
Burak.servılı@khas.edu.tr
Main Affiliation
Core Program
Core Program
07. Core Program
01. Kadir Has University
Core Program
07. Core Program
01. Kadir Has University
Status
Former Staff
Website
ORCID ID
Scopus Author ID
Turkish CoHE Profile ID
Google Scholar ID
WoS Researcher ID
Sustainable Development Goals
15
LIFE ON LAND
0
Research Products
16
PEACE, JUSTICE AND STRONG INSTITUTIONS
0
Research Products
14
LIFE BELOW WATER
0
Research Products
6
CLEAN WATER AND SANITATION
0
Research Products
3
GOOD HEALTH AND WELL-BEING
3
Research Products
17
PARTNERSHIPS FOR THE GOALS
0
Research Products
4
QUALITY EDUCATION
0
Research Products
2
ZERO HUNGER
1
Research Products
10
REDUCED INEQUALITIES
0
Research Products
7
AFFORDABLE AND CLEAN ENERGY
0
Research Products
13
CLIMATE ACTION
0
Research Products
1
NO POVERTY
0
Research Products
9
INDUSTRY, INNOVATION AND INFRASTRUCTURE
1
Research Products
12
RESPONSIBLE CONSUMPTION AND PRODUCTION
1
Research Products
8
DECENT WORK AND ECONOMIC GROWTH
0
Research Products
11
SUSTAINABLE CITIES AND COMMUNITIES
0
Research Products
5
GENDER EQUALITY
0
Research Products
This researcher does not have a Scopus ID.
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Scholarly Output
7
Articles
6
Views / Downloads
75/279
Supervised MSc Theses
0
Supervised PhD Theses
1
WoS Citation Count
52
Scopus Citation Count
50
WoS h-index
3
Scopus h-index
3
Patents
0
Projects
0
WoS Citations per Publication
7.43
Scopus Citations per Publication
7.14
Open Access Source
1
Supervised Theses
1
Google Analytics Visitor Traffic
| Journal | Count |
|---|---|
| ChemistrySelect | 1 |
| International Journal of Biological Macromolecules | 1 |
| Journal of Molecular Liquids | 1 |
| Journal of Molecular Modeling | 1 |
| RSC Medicinal Chemistry | 1 |
Current Page: 1 / 2
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Competency Cloud
7 results
Scholarly Output Search Results
Now showing 1 - 7 of 7
Article Integrating Computational and Experimental Insights Into Osmolyte-Driven Activation of Geobacillus Kaustophilus L-Asparaginase for Acrylamide Mitigation(Elsevier B.V., 2025) Özdemir, F.İ.; Servili, B.; Demirtaş, Ö.; Şükür, G.; Tülek, A.; Yildirim, D.Osmolytes play a critical role in enhancing the stability and activity of enzymes for industrial applications. This study systematically investigated the effects of various osmolytes on the activity, optimal pH, temperature, stability, metal ion effects, storage, and acrylamide mitigation performance of L-asparaginase from the thermophilic Geobacillus kaustophilus (GkASNase). The experimental findings were further supported by computationally integrated tools such as homology modeling, docking, and molecular dynamics (MD) simulations. Among the selected osmolytes (maltose, sorbitol, trehalose, glycine, and sucrose), GkASNase showed the highest stability during 30 days of storage in the presence of maltose and arginine. Maltose increased GkASNase activity approximately 2-fold at 37 °C and 55 °C. In the presence of osmolytes, the Km values of GkASNase decreased and the Vmax values increased compared to controls at 37 °C and 55 °C. In the presence of osmolytes, the acrylamide mitigation performance of GkASNase increased by 1.7-fold in a 15 min reaction. The computational analysis indicates that L-asparagine as substrate enhances protein compactness and stability, while arginine as osmolyte increases flexibility and optimizes water distribution around the enzyme. These findings provide novel insights into enzyme stabilization that have implications for therapeutic and biotechnological applications. © 2025 Elsevier B.V.Article Citation - WoS: 3Citation - Scopus: 3Biocontrol Potential of Vibrio Maritimus Chitinase: Heterologous Expression and Insecticidal Activity Against Acanthoscelides Obtectus(Elsevier, 2025) Dikbas, Neslihan; Tulek, Ahmet; Ucar, Sevda; Alim, Seyma; Servili, Burak; Pacal, Nurettin; Ercisli, SezaiIn this study, the chitinase gene from the marine bacterium Vibrio maritimus was heterologously expressed in Escherichia coli, purified via affinity chromatography and tested for its insecticidal activity against the storage pest Acanthoscelides obtectus. The recombinant VmChiA protein exhibited a molecular mass of similar to 60 kDa, with optimum activity observed at pH 6.0 and 40 degrees C. Enzyme kinetic analysis revealed a K-m value of 0.042 mM, V-max of 17.48 mu mol min(-1), k(cat) of 1.75 min(-1) and catalytic efficiency of 41.61 mM(-1) min(-1), respectively. Furthermore, a dose of 40 U mL(-1) of recombinant VmChiA showed similar efficacy to malathion insecticide against A. obtectus, with 100 % mortality in both treatments. LC50 and LC90 values of VmChiA were 13.95 U mL(-1) and 27.66 U mL(-1), respectively. Furthermore, the three-dimensional structure of the catalytic site of VmChiA was modeled. Molecular dynamics simulation technique was used to explore and analyze the dynamics and interactions. A salt bridge (GLU274-ARG296) in the alpha + beta domain was observed as a critical feature facilitating substrate (GlcNAc)(2) binding and enzymatic activity. These findings demonstrate that recombinant VmChiA possesses potent insecticidal properties, highlighting its potential as a bio-based, eco-friendly alternative for managing significant agricultural pests.Article Citation - WoS: 2Citation - Scopus: 2Correlated 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, BurakN-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.Article Citation - WoS: 41Citation - Scopus: 40Sustainable 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, DenizFormate 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.Article Citation - WoS: 3Citation - Scopus: 4Synthesis of New Imidazo[1,2-A]pyridine Triazole Hybrid Molecules as Potential Apoptotic Antitumor Agents(Wiley-v C H verlag Gmbh, 2024) Halac, Fatma Albayrak; Essiz, Sebnem; Servili, Burak; Altundas, Ramazan; Sucu, Bilgesu Onur; Kulu, IremNovel imidazo[1,2-a]pyridines bearing 1,2,3-triazole moieties at the C3 position were synthesized. After the characterization of the synthesized compounds, their in vitro therapeutic activities were evaluated in various cancer cell lines (MCF7, A549, HePG2 and T98G). Methoxy substituted derivative was identified as the most potent compound based on the results of its anti-proliferative activity on various cancer cell lines, as well as showing no cytotoxicity on the healthy human fibroblast cell line (MRC-5). As an indicator of apoptosis, a significant decrease in the level of PARP protein was observed in the MCF7 cells treated with this derivative. Molecular docking studies were conducted on wide range of targets such as phosphoinositide 3-kinase (PI3K), cyclin-independent kinase 2 (CDK2), mitogen-activated protein kinase (MEK), insulin-like growth-factor-1 (IGF-1), tubulin, DNA topoisomerase, poly (ADP-ribose) polymerase (PARP) and B-cell lymphoma-2 (BCL2). All the compounds tested showed the lowest binding energies with target PARP1. Moreover, CDK2 and tubulin displayed relatively good binding scores. The docking poses and scores were cross-checked with two different software and multiple protein conformations were included to incorporate flexible protein docking features. Finally, drug-likeness properties of the compounds are further tested via Swiss-ADME software. Novel imidazo[1,2-a]pyridine-1,2,3-triazole derivatives have been synthesized and evaluated for antiproliferative activity against MCF7, A549, HePG2, T98G cell lines. Compound 5c was found to be more potent on PARP protein in MCF7 cell line. The synthesized compounds were docked to PI3K, CDK2, MEK1, IGF-1, TUB1, DNA topoisomerase, PARP1, and BCL2. The best docking poses for PARP1 and CDK2 were obtained from 5c, 5d and 5 f. imageArticle Citation - WoS: 3Citation - Scopus: 1Newly Synthesized 6-Substituted Piperazine/Phenyl-9-cyclopentyl Containing Purine Nucleobase Analogs Act as Potent Anticancer Agents and Induce Apoptosis via Inhibiting Src in Hepatocellular Carcinoma Cells(Royal Soc Chemistry, 2023) Bilget Guven, Ebru; Durmaz Sahin, Irem; Altiparmak, Duygu; Servili, Burak; Essiz, Sebnem; Cetin-Atalay, Rengul; Tuncbilek, MeralNewly synthesized 6-substituted piperazine/phenyl-9-cyclopentyl-containing purine nucleobase analogs were tested for their in vitro anticancer activity against human cancer cells. Compounds 15, 17-24, 49, and 56 with IC50 values less than 10 mu M were selected for further examination on an enlarged panel of liver cancer cell lines. Experiments revealed that compound 19 utilizes its high cytotoxic potential (IC50 < 5 mu M) to induce apoptosis in vitro. Compound 19 displayed a KINOMEscan selectivity score S35 of 0.02 and S10 of 0.01 and demonstrated a significant selectivity against anaplastic lymphoma kinase (ALK) and Bruton's tyrosine kinase (BTK) over other kinases. Compounds 19, 21, 22, 23, and 56 complexed with ALK, BTK, and (discoidin domain-containing receptor 2) DDR2 were analyzed structurally for binding site interactions and binding affinities via molecular docking and molecular dynamics simulations. Compounds 19 and 56 displayed similar interactions with the activation loop of the kinases, while only compound 19 reached toward the multiple subsites of the active site. Cell cycle and signaling pathway analyses exhibited that compound 19 decreases phosho-Src, phospho-Rb, cyclin E, and cdk2 levels in liver cancer cells, eventually inducing apoptosis.Doctoral Thesis Yapısal ve Mutasyonel Çalışmalar: Nmda Tipi Glutamat Reseptörü ve Format Dehidrogenaz Enziminin Moleküler Dinamik Simülasyonları(2023) Servili, Burak; Eşsiz, ŞebnemYapısal biyoloji ve moleküler dinamik (MD) simülasyon çalışmaları, moleküler düzeyde moleküller arası/içi etkileşimleri anlamanın temellerinden, ilaç ve protein tasarımının önde gelen yöntemlerinden biridir. Bu tez, iki farklı alandaki protein simülasyonlarından oluşmaktadır: Sinir hücrelerinde elektrik sinyali yayılımında bir iyon kanalı reseptör kompleksi olan N-metil-D-aspartat reseptörü (NMDAR) ve formatın bikarbonata biyokatalizinde format dehidrojenaz enzimi (FDH). Tezin ilk amacı NMDAR iyon kanalının açık yapısını mutasyonlarla elde etmektir. İkinci amaç ise allosterik bölgede Asp188Arg mutasyonu yaparak FDH enziminin hem format hem de bikarbonat substratları ile etkileşimlerini anlamaktır. Bu mutasyon deneysel olarak FDH'nin bikarbonat/CO2 yakalama için kullanımı yönünde olan ters reaksiyon için daha aktif bir enzim yaratmıştır. Bu amaçla, nano ölçekli moleküler dinamik (NAMD) uygulaması, kök-ortalama-kare sapması, kök-ortalama-kare dalgalanması ve protein-ligand etkileşim analizi yöntemleriyle birlikte simülasyonları çalıştırmak için kullanılmıştır. İlk durumda, NMDAR iyon kanalının üst kapısındaki Lurcher motifindeki alanin (A7), deneysel çalışmalara dayanarak arginin/tirozin ile değiştirildi. Analiz sonucunda NMDAR iyon kanalının açık yapısı elde edildi. FDH'nin MD simülasyonlarında, bikarbonat bağlı yapı, enzimin subtrat ve koenzim bağlanma bölgelerini ayıran önemli bir tuz köprüsünü korumuştur. Ek olarak, bağlanma bölgesinden substrat taşınımı, vahşi tip ve mutasyona uğramış yapılar için farklı yollar sergilemiştir. Her iki protein sistemi için de MD, harici pertürbasyonların proteinlerin yapısı ve işlevi, yani işlevsel mutasyonlar üzerindeki etkisini incelemek için ana araç olarak kullanılmıştır. Her iki protein de hareketlerin zaman ölçeği, sistem boyutu ve istenen ters reaksiyon yönünde düşük enzim aktivitesi nedeniyle yapısal bir çalışma için karmaşık sistemler oluşturmuştur.
