Sürmeli, Nur Başak
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Sürmeli, Nur Başek
Suermeli, Nur Basak
Surmeli, N. B.
Surmeli, NB
Sürmeli, N. B.
Sürmeli, NB
Surmeli, N. Basak
Sürmeli, N. Başak
Surmeli, Nur Basak
Surmeli, Nur Basek
Suermeli, Nur Basak
Surmeli, N. B.
Surmeli, NB
Sürmeli, N. B.
Sürmeli, NB
Surmeli, N. Basak
Sürmeli, N. Başak
Surmeli, Nur Basak
Surmeli, Nur Basek
Job Title
Email Address
nursurmeli@iyte.edu.tr
Main Affiliation
03.01. Department of Bioengineering
Status
Current Staff
ORCID ID
Scopus Author ID
Turkish CoHE Profile ID
Google Scholar ID
WoS Researcher ID
Sustainable Development Goals
1NO POVERTY
0
Research Products
2ZERO HUNGER
1
Research Products
3GOOD HEALTH AND WELL-BEING
0
Research Products
4QUALITY EDUCATION
1
Research Products
5GENDER EQUALITY
0
Research Products
6CLEAN WATER AND SANITATION
2
Research Products
7AFFORDABLE AND CLEAN ENERGY
2
Research Products
8DECENT WORK AND ECONOMIC GROWTH
1
Research Products
9INDUSTRY, INNOVATION AND INFRASTRUCTURE
6
Research Products
10REDUCED INEQUALITIES
0
Research Products
11SUSTAINABLE CITIES AND COMMUNITIES
0
Research Products
12RESPONSIBLE CONSUMPTION AND PRODUCTION
2
Research Products
13CLIMATE ACTION
2
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14LIFE BELOW WATER
1
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15LIFE ON LAND
0
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16PEACE, JUSTICE AND STRONG INSTITUTIONS
0
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17PARTNERSHIPS FOR THE GOALS
0
Research Products
Documents
13
Citations
226
h-index
6
Documents
10
Citations
160
Scholarly Output
17
Articles
10
Views / Downloads
47600/6755
Supervised MSc Theses
7
Supervised PhD Theses
0
WoS Citation Count
59
Scopus Citation Count
70
Patents
0
Projects
5
WoS Citations per Publication
3.47
Scopus Citations per Publication
4.12
Open Access Source
12
Supervised Theses
7
| Journal | Count |
|---|---|
| Biotechnology and Applied Biochemistry | 3 |
| Journal of Biological Inorganic Chemistry | 2 |
| Bioinorganic Chemistry and Applications | 1 |
| International Journal of Biological Macromolecules | 1 |
| Journal of Molecular Graphics and Modelling | 1 |
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17 results
Scholarly Output Search Results
Now showing 1 - 10 of 17
Master Thesis Chemical Characterization of Caldanaerobacter Subterraneus Subsp. Tengcongensis Heme-Nitric Oxide/Oxygen Binding Protein(01. Izmir Institute of Technology, 2020) Erdal, Merve; Sürmeli, Nur Başak; Sürmeli, Nur BaşakHemoproteins, which contain the heme prosthetic group , take part in different biological processes in many stages of life. Their ability to catalyze important biosynthesis reactions makes them good candidates for understanding and elucidating complex mechanisms for biocatalysis. In this study, the catalytic properties of thermophilic Thermoanaerobacter tencogensis nitric oxide/oxygen binding protein, a heme protein reshaped by rational design, were investigated and chemical characterization was carried out. The peroxidase activity of the enzyme was investigated by the oxidation reactions of guaiacol, amplex red and 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid (ABTS). Kinetic parameters of the reactions were determined. These obtained results demonstrated that, in the presence of H2O2, wild type and Y140H TtH-NOX proteins are able to catalyze oxidation reactions of guaiacol, Amplex red and ABTS. Comparison of the kinetic parameters showed that Y140H mutant catalyzed the guaiacol and ABTS oxidation 3-fold and 15 -fold faster than wild type enzyme, respectively. The stability of TtH-NOX proteins were investigated in the presence of organic solvents. Results were demonstrated that WT TtH-NOX was more stable than Y140H mutant in the presence of organic solvents In addition to these, for the first time, thermophilic TtH-NOX proteins were immobilized with a novel enzyme immobilization method and organic-inorganic hybrid nanostrucrures were obtained. Copper ion incorporated TtH-NOX-based hybrid nanoflowers were synthesized at different pH values. SEM and EDX analysis of TtH-NOX-based hybrid nanoflowers proved that free TtH-NOXs were immobilized successfully.Article Optimization of Hnox Protein Production in Escherichia Coli(Sivas Cumhuriyet Üniversitesi, 2017) Sürmeli, Nur BaşakHemoproteinler canlılarda steroid biyosentezinden solunuma, sinyalizasyondan ilaç metabolizmasına kadar pek çok farklı biyolojik süreçlerde önemli görevler üstlenirler. Endüstride, hemoproteinler kolesterol düşürücü pravastatin, rahim ve rahim ağzı kanserlerinin hormonal tedavisinde kullanılan progesteron, alerji ve yangı'ya karşı kullanılan kortizon gibi ilaçların üretiminde kullanılmaktadır. Bunların yanı sıra hemoproteinlerin ilaç geliştirilmesi, biyolojik iyileştirme gibi alanlarda kullanılması da planlanmaktadır. Moleküler biyoloji ve protein tasarımı tekniklerinin gelişmesi ile bu proteinlerin endüstriyel uygulama alanları da genişleyecektir. Hemoproteinlerin bu alanlarda yaygın kullanımı karşısındaki en önemli engellerden biri Hem kofaktörüne bağlı bir şekilde yüksek miktarda hemoprotein üretilememesidir. Bu çalışmada Hem kofaktörüne bağlı bir şekilde üretilen hemoprotein miktarını en yüksek seviyeye getirebilecek koşullar araştırılmıştır. Bu çalışma kapsamında bakteride hemoprotein üretimini etkileyen en önemli üç etken olan indükleyici izopropil ?-D-l-tiyogalaktopiranosid (IPTG), ve Hem öncül molekülü ?-aminolevülinik asit (ALA), ve ekspresyon sıcaklığı incelenmiştir. Bu etkenlerin termofilik hemoprotein TtHNOK üretimine etkisi araştırılmıştır. Özellikle, ALA pahalı bir molekül olduğu için hemoproteinlerin üretiminde kullanılan ALA miktarının optimizasyonu önemlidir. Bu çalışma sonucunda Escherichia coli bakterisinde Hem kofaktörüne bağlı TtHNOK proteinin üretimi için en uygun koşulların düşük sıcaklık, 0,5 mM IPTG ve 1 mM ALA olduğu gösterilmiştir. Bu çalışmada çıkan sonuçlar Hem kofaktörüne bağlı hemoprotein üretiminde ALA konsantrasyonun ve ekspresyon sıcaklığının önemli olduğunu göstermiştirMaster Thesis Developing Mobile, Electronic and Positioning Applications for Emergency Situations Inside the Hospital(Izmir Institute of Technology, 2018) Keskin, Özge Sevin; Sürmeli, Nur Başak; Karabudak, Engin; Karabudak, Engin; Sürmeli, Nur BaşakThe aim of this project is to prevent mortality by providing emergency response on time. The communication inside the hospital is provided via developing application for Android and Ios operating system. The content of application is suitable for everyone’s use. The emergency call button makes it easy to call, and if the button is disabled, the heart rate rhythm starts for emergency intervention. This application is associated with bluetooth low energy systems in terms of help to locate the patient. Beacon systems provide data transfer through bluetooth by this means location is detected without internet. The project will be tested primarily at the laboratory following these steps. If it succeeds statistically, the project will be tried at the Tepecik Education and Research Hospital. The success of the project will be reviewed depends on the scenarios in the hospital.Article Citation - WoS: 6Citation - Scopus: 6Functional Characterization of a Novel Cyp119 Variant To Explore Its Biocatalytic Potential(Wiley, 2021) Sakallı, Tuğçe; Sürmeli, Nur BaşakBiocatalysts are increasingly applied in the pharmaceutical and chemical industry. Cytochrome P450 enzymes (P450s) are valuable biocatalysts due to their ability to hydroxylate unactivated carbon atoms using molecular oxygen. P450s catalyze reactions using nicotinamide adenine dinucleotide phosphate (NAD(P)H) cofactor and electron transfer proteins. Alternatively, P450s can utilize hydrogen peroxide (H2O2) as an oxidant, but this pathway is inefficient. P450s that show higher efficiency with peroxides are sought after in industrial applications. P450s from thermophilic organisms have more potential applications as they are stable toward high temperature, high and low pH, and organic solvents. CYP119 is an acidothermophilic P450 from Sulfolobus acidocaldarius. In our previous study, a novel T213R/T214I (double mutant [DM]) variant of CYP119 was obtained by screening a mutant library for higher peroxidation activity utilizing H2O2. Here, we characterized the substrate scope; stability toward peroxides; and temperature and organic solvent tolerance of DM CYP119 to identify its potential as an industrial biocatalyst. DM CYP119 displayed higher stability than wild-type (WT) CYP119 toward organic peroxides. It shows higher peroxidation activity for non-natural substrates and higher affinity for progesterone and other bioactive potential substrates compared to WT CYP119. DM CYP119 emerges as a new biocatalyst with a wide range of potential applications in the pharmaceutical and chemical industry.Article Citation - WoS: 33Citation - Scopus: 34Effects of N-Terminal and C-Terminal Polyhistidine Tag on the Stability and Function of the Thermophilic P450 Cyp119(Hindawi Publishing Corporation, 2019) Aslantaş, Yaprak; Sürmeli, Nur BaşakBiocatalysts are sought-after in synthesis of pharmaceuticals and agrochemicals due to their high regioselectivity and enantioselectivity. Among biocatalysts, heme-containing cytochrome P450 (P450) oxygenases are an attractive target since they catalyze oxidation of "unactivated" carbon-hydrogen bonds with high efficiency. CYP119 is an acidothermophilic P450 from Sulfolobus acidocaldarius, which has the potential to be widely used as a biocatalyst since it shows activity at high temperatures and low pH. Polyhistidine tags (His-tags) are widely used to simplify purification of proteins. However, His-tags can cause changes to protein structure and function. Here, we demonstrate the effects of His-tags on CYP119. To this end, the His-tags were cloned at the N-terminus or C-terminus of the CYP119, and His-tagged proteins were expressed and isolated. The thermostability and peroxidase activity of His-tagged CYP119s were tested and compared to wild type CYP119. Results indicated that while addition of His-tags increased the yield and simplified isolation of CYP119, they also influenced the electronic structure of active site and the activity of the protein. We show that N-terminal His-tagged CYP119 has desirable properties and potential to be used in industrial applications, but mechanistic studies using this protein need careful interpretation since the His-tag affects electronic properties of the active site heme iron.Master Thesis Mimicking the Tumor Microenvironment in Lab-On Devices(Izmir Institute of Technology, 2019) Bilgen, Müge; Pesen Okvur, Devrim; Sürmeli, Nur BaşakBreast cancer is one of the cancers with the highest incidence and mortality rates in women in the world. The leading cause of death for cancer patients is tumor metastasis. Cancer cells can extravasate the blood vessel, go through the distant organs and form the metastasis. Tumor microenvironment comprises of cancer and normal cells, extracellular matrix, soluble biological and chemical factors. Biochemical aspects of the interactions of cancer cells with the constituents of the microenvironment are widely studied whereas biophysical studies are at limited numbers. There is increasing evidence that extracellular matrix can change the mechanics and function of cancer and stroma cells. It has been observed that cancer cells show different responses to soft and stiff tissues they are in direct contact with than normal cells. New cell culture setups should be developed to better understand the interactions of cancer cells with their microenvironment. To develop a three dimensional (3D) in vitro model will allow the study of stiffness which is one of the mechanical features of extracellular matrix features first, 3D (dimensional) Controlled in vitro Microenvironments (CivMs) that mimic a blood vessel and its neighboring tissue in vivo will be fabricated using UV lithography. Monolayer which was formed by endothelial cells play a role in pathophysiological processes, so it shows a barrier role between both blood and tissues. To form a blood vessel bEnd.3 cell line was used. Collagen which is the most abundant protein in connective tissues were used to mimic extracellular matrix. pH value of collagen was changed and represented two different stiffness value. Here, the in vitro model we define as controlled in vitro microenvironments (CivM) is a lab-on-a-chip (LOC) application. In this microenvironment; MDA-MB-231 cells which are known to be invasive and MCF10A which is normal mammary epithelial cells were used as control. LOC devices were used to investigate cancer cell extravasation which is the prominent step of metastasis and extracellular matrix relation.Article Citation - WoS: 2Citation - Scopus: 2Small Angle X-Ray Scattering Analysis of Thermophilic Cytochrome P450 Cyp119 and the Effects of the N-Terminal Histidine Tag(Elsevier B.V., 2024) Doğru,E.K.; Sakallı,T.; Liu,G.; Sayers,Z.; Surmeli,N.B.Combining size exclusion chromatography-small angle X-ray scattering (SEC-SAXS) and molecular dynamics (MD) analysis is a promising approach to investigate protein behavior in solution, particularly for understanding conformational changes due to substrate binding in cytochrome P450s (CYPs). This study investigates conformational changes in CYP119, a thermophilic CYP from Sulfolobus acidocaldarius that exhibits structural flexibility similar to mammalian CYPs. Although the crystal structure of ligand-free (open state) and ligand-bound (closed state) forms of CYP119 is known, the overall structure of the enzyme in solution has not been explored until now. It was found that theoretical scattering profiles from the crystal structures of CYP119 did not align with the SAXS data, but conformers from MD simulations, particularly starting from the open state (46 % of all frames), agreed well. Interestingly, a small percentage of closed-state conformers also fit the data (9 %), suggesting ligand-free CYP119 samples ligand-bound conformations. Ab initio SAXS models for N-His tagged CYP119 revealed a tail-like unfolded structure impacting protein flexibility, which was confirmed by in silico modeling. SEC-SAXS analysis of N-His CYP119 indicated pentameric structures in addition to monomers in solution, affecting the stability and activity of the enzyme. This study adds insights into the conformational dynamics of CYP119 in solution. © 2024 Elsevier B.V.Article Citation - WoS: 4Citation - Scopus: 6Rational Design of Thermophilic Cyp119 for Progesterone Hydroxylation by in Silico Mutagenesis and Docking Screening(Elsevier, 2023) Kestevur Doğru, Ekin; Güralp, Gülce; Uyar, Arzu; Sürmeli, Nur BaşakSteroid-based chemicals can affect the metabolism, immune functions, and development of sexual characteristics. Because of these effects, steroid derivatives are widely used in the pharmaceutical industry. Progesterone is a steroid-based hormone that mainly controls the ovulation period of women but is also a precursor molecule for the synthesis of important hormones like testosterone and cortisone. Cytochrome P450 (CYP) enzymes are important for the production of hydroxyprogesterones in the industry since they can catalyze regio- and enantioselective hydroxylation reactions. Although human CYP enzymes can catalyze hydroxyprogesterone synthesis with high selectivity, these enzymes are membrane bound, which limits their application for industrial production. CYP119 is a soluble and thermophilic enzyme from the archaea Sulfolobus acidocaldarius. Even though the native substrate of the enzyme is not known, CYP119 can catalyze styrene epoxidation, lauric acid hydroxylation, and Amplex®Red peroxidation. In this work, an in silico mutagenesis approach was used to design CYP119 mutants with high progesterone affinity. Energy scores of progesterone docking simulations were used for the design and elimination of single, double, and triple mutants of CYP119. Among designed 674 mutants, five of them match the criteria for progesterone hydroxylation. The most common mutation of these five mutants, L69G mutant was analyzed using independent molecular dynamics (MD) simulations in comparison with the wild-type (WT) enzyme. L69G CYP119, was expressed and isolated from Escherichia coli; it showed 800-fold higher affinity for progesterone compared to WT CYP119. L69G CYP119 also catalyzed progesterone hydroxylation. The novel designed enzyme L69G CYP119 is a potential versatile biocatalyst for progesterone hydroxylation that is expected to be stable under industrial production conditions.Master Thesis Generation of Mutant Libraries for Directed Evolution of a Thermophilic P450 Enzyme(Izmir Institute of Technology, 2018) Haklı, Emre; Sürmeli, Nur Başak; Bedir, ErdalDirected evolution, inspires from natural selection, is a frequently utilized approach in protein engineering for designing enzymes. It allows iterative evolution of existing proteins towards the ones with desired characteristics by the application of random mutagenesis in the laboratory. However, library construction constitutes the most fundamental part of directed evolution. Application of different construction methods affects both the number and diversity of variants created and the screening/selection techniques used. Early procedures including error-prone PCR, mutator strains, chemical mutagens and gene shuffling have been successful in whole gene mutagenesis yet have been required more screening/selection effort by leading larger libraries. On the other hand, recent approaches such as use of degenerate primers and site saturation mutagenesis have decreased the screening/selection effort by allowing random mutagenesis of amino acids located at specific positions in the polypeptide chain. Especially, active site residues of biocatalysts were chosen as targets and the catalytic efficiencies were enhanced. CYP119, a member of cytochrome P450 protein family, from Sulfolobus Acidocaldarius is a thermostable enzyme capable of catalyzing peroxidation, monooxygenation and oxidoreduction reactions. Here, a library of mutants consist of CYP119 variants was created via application of combinatorial active site saturation test (CAST) in amino acid positions 213 – 214 and an effective fluorescence-based method was developed to screen the library for increased peroxidase activity while utilizing hydrogen peroxide as oxidant. After screening of mutant library, a variant with Thr213Arg – Thr214Ile substitutions showed 1.32-fold increased peroxidase activity in the catalysis of Amplex Red compared to wild type CYP119.Article Citation - Scopus: 6Functional Characterization of a Novel Cyp119 Variant To Explore Its Biocatalytic Potential(John Wiley and Sons Inc, 2022) Sakalli, T.; Surmeli, N.B.Biocatalysts are increasingly applied in the pharmaceutical and chemical industry. Cytochrome P450 enzymes (P450s) are valuable biocatalysts due to their ability to hydroxylate unactivated carbon atoms using molecular oxygen. P450s catalyze reactions using nicotinamide adenine dinucleotide phosphate (NAD(P)H) cofactor and electron transfer proteins. Alternatively, P450s can utilize hydrogen peroxide (H2O2) as an oxidant, but this pathway is inefficient. P450s that show higher efficiency with peroxides are sought after in industrial applications. P450s from thermophilic organisms have more potential applications as they are stable toward high temperature, high and low pH, and organic solvents. CYP119 is an acidothermophilic P450 from Sulfolobus acidocaldarius. In our previous study, a novel T213R/T214I (double mutant [DM]) variant of CYP119 was obtained by screening a mutant library for higher peroxidation activity utilizing H2O2. Here, we characterized the substrate scope; stability toward peroxides; and temperature and organic solvent tolerance of DM CYP119 to identify its potential as an industrial biocatalyst. DM CYP119 displayed higher stability than wild-type (WT) CYP119 toward organic peroxides. It shows higher peroxidation activity for non-natural substrates and higher affinity for progesterone and other bioactive potential substrates compared to WT CYP119. DM CYP119 emerges as a new biocatalyst with a wide range of potential applications in the pharmaceutical and chemical industry. © 2021 International Union of Biochemistry and Molecular Biology, Inc.