Köksal, Mustafa
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Koksal, Mustafa
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04.03. Department of Molecular Biology and Genetics
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Former Staff
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Sustainable Development Goals
1NO POVERTY
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2ZERO HUNGER
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3GOOD HEALTH AND WELL-BEING
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4QUALITY EDUCATION
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5GENDER EQUALITY
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6CLEAN WATER AND SANITATION
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7AFFORDABLE AND CLEAN ENERGY
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8DECENT WORK AND ECONOMIC GROWTH
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9INDUSTRY, INNOVATION AND INFRASTRUCTURE
1
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10REDUCED INEQUALITIES
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11SUSTAINABLE CITIES AND COMMUNITIES
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12RESPONSIBLE CONSUMPTION AND PRODUCTION
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13CLIMATE ACTION
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14LIFE BELOW WATER
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15LIFE ON LAND
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16PEACE, JUSTICE AND STRONG INSTITUTIONS
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17PARTNERSHIPS FOR THE GOALS
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Scholarly Output
5
Articles
2
Views / Downloads
34175/3279
Supervised MSc Theses
3
Supervised PhD Theses
0
WoS Citation Count
91
Scopus Citation Count
94
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0
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0
WoS Citations per Publication
18.20
Scopus Citations per Publication
18.80
Open Access Source
5
Supervised Theses
3
| Journal | Count |
|---|---|
| Biochemistry | 1 |
| Biochimica et Biophysica Acta - General Subjects | 1 |
Current Page: 1 / 1
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5 results
Scholarly Output Search Results
Now showing 1 - 5 of 5
Master Thesis Purification and Biochemical Characterization of Xylanase Expressed in Thermophilic Geobacillus Sp.(Izmir Institute of Technology, 2015) Algan, Müge; Köksal, Mustafa; Şanlı Mohamed, Gülşah; Şanlı Mohamed, Gülşah; Köksal, MustafaXylanase is an enzyme that catalyzes the degradation of the linear polysaccharide β-1,4-xylan into xylose and breaks down the hemicellulose structure of plant cell wall. The xylanolytic property of the enzyme makes it preferable for many biotechnological applications in industry. This enzyme is possibly produced by some bacterial and fungal microorganisms. In this study, briefly, xylanase enzyme was expressed in thermophillic Geobacillus sp. and purified by cold acetone precipitation and gel filtration chromatography. Molecular weight of our xylanase was found as 40.1 kDa by SDS-PAGE and this protein band was verified by Native-PAGE activity staining. Finally, it was characterized using biochemical methods. For characterization studies, Km and Vmax values were calculated from Lineweaver-Burk plot as 10.2 mg/ml and 31.7 U/ml, respectively. The optima temperature and pH for enzyme activity were investigated using beechwood xylan as substrate and found as 55°C and 8.0, respectively. Furthermore, effects of some metal ions, various chemical reagents and organic solvents on enzyme activity were also determined and we observed that Ca2+, Mn2+ and Co2+ affected the activity positively while Zn2+, Cd2+, Fe3+, EDTA, SDS, CHAPS and DTT shielded the activity. And only β-mercaptoethanol caused a significant change amoung organic solvents. Lastly, that the enzyme has a long shelf-life was confirmed assaying the samples taken from enzyme stocks stored at +4°C and room temperature for six weeks.Master Thesis Investigation of the Effect of 4'-alkylıklavuzon Derivatives on Nucleotide Synthesis and Nucleocytoplasmic Transport(Izmir Institute of Technology, 2016) Kutluer, Meltem; Köksal, Mustafa; Çağır, Ali; Çağır, Ali; Köksal, MustafaIn anti-cancer agent development studies one of the most significant issue is to get an agent that specifically targets cancer cells without any effects on healthy cells. Goniothalamin, that is a styryl lactone isolated from Goniothalamus plant species, is an anti-cancer agent that has selective anti-proliferative activity on cancer cell lines. Klavuzon and derivatives, which can be thought as analogs of goniothalamin, are more cytotoxic in cancer cells compared to goniothalamin. Previous structure activity relationship studies implies that α,β-unsaturated δ-lactone moiety is the source of the biological activity. Since it behaves as Michael acceptor, in this thesis possible irreversible inhibitions of two separate intracellular targets are investigated. In the first part, thymineless death caused by possible thymidylate synthase inhibition has been studied. Anti-proliferative effect of 4’-methylklavuzon in HuH-7 cancer cell line was tested by using MTT. Viability of klavuzon treated cells did not changed significantly in the absence and presence of varying concentration of additional thymidine supplement, and it is concluded that thymineless death is not a crucial mechanism for klavuzon derivatives. In the second part, 4’-methylklavuzon and its derivatives were tested on HeLa cell line to investigate inhibitory effect on the nucleocytoplasmic transport. Immunocytochemistry was used to demonstrate nucleocytoplasmic localization of Riok2 protein which is transferred from nuclei to cytoplasm by CRM1 nuclear export protein. Successfully, all tested klavuzon derivatives inhibit CRM1 nuclear export protein. Potency of the inhibition depends on the size of the alkyl substituent at 4’- position of klavuzon.Master Thesis Engineering of Geranyl Diphospate C-Methyltransferase for the Development of New Diterpenoid Precursors(Izmir Institute of Technology, 2014) Akıl, Caner; Köksal, Mustafa; Köksal, MustafaTerpenoids constitute the most diverse family of natural products. They are involved in several biological functions and are used in medical and industrial applications. The key to their diverse biological activities is their structural diversity. Terpenoids are synthesized in three stages, all of which contribute to generation of structural diversity. In the terpenoid biosynthetic pathways, terpene synthases generate larger linear terpenoid precursors from smaller units via condensation reactions, terpene cyclases transform precursors via cyclization reactions, and then tailoring enzymes modify terpenoid products via addition of functional groups. Recently discovered geranyl diphosphate C-methyltransferase (GPPMT) from Streptomyces coelicolor A3(2) is able to modify a linear monoterpenoid precursor, geranyl diphoshate (GPP), to produce a non-canonical terpenoid precursor, 2-methylgeranyl diphosphate. Modification of GPP by GPPMT is the first example of modification of a canonical linear isoprenoid precursor in nature. This study aims to achieve enzymatic synthesis of novel methylated non-canonical diterpenoid precursors, such as 2-methylgeranylgeranyl diphosphate (2MGGPP) by engineering GPPMT. The novel non-canonical precursors may later be utilized by cyclases to enhance the diversity of the terpenome. For example, taxadiene synthase could utilize 2MGGPP to generate variants of taxadiene, the precursor of the leading anti-cancer drug paclitaxel (Taxol®). Candidate mutants predicted to use GGPP as substrate were selected via in silico analysis of GPPMT structure. These mutations were introduced using the Quick-change site-directed mutagenesis. Mutant genes were expressed in E.coli strains. Mutant proteins were purified by Fast Protein Liquid Chromatography. Catalytic activities of mutants against canonical terpenoid precursors were determined by SAM methyltransferase assay.Article Citation - WoS: 53Citation - Scopus: 581.55 Å-Resolution Structure of Ent-Copalyl Diphosphate Synthase and Exploration of General Acid Function by Site-Directed Mutagenesis(Elsevier, 2014) Köksal, Mustafa; Christianson, David W.; Peters, Reuben John; Potter, KevinBackground The diterpene cyclase ent-copalyl diphosphate synthase (CPS) catalyzes the first committed step in the biosynthesis of gibberellins. The previously reported 2.25 Å resolution crystal structure of CPS complexed with (S)-15-aza-14,15-dihydrogeranylgeranyl thiolodiphosphate (1) established the αβγ domain architecture, but ambiguities regarding substrate analog binding remained. Method Use of crystallization additives yielded CPS crystals diffracting to 1.55 Å resolution. Additionally, active site residues that hydrogen bond with D379, either directly or through hydrogen bonded water molecules, were probed by mutagenesis. Results This work clarifies structure-function relationships that were ambiguous in the lower resolution structure. Well-defined positions for the diphosphate group and tertiary ammonium cation of 1, as well as extensive solvent structure, are observed. Conclusions Two channels involving hydrogen bonded solvent and protein residues lead to the active site, forming hydrogen bonded "proton wires" that link general acid D379 with bulk solvent. These proton wires may facilitate proton transfer with the general acid during catalysis. Activity measurements made with mutant enzymes indicate that N425, which donates a hydrogen bond directly to D379, and T421, which hydrogen bonds with D379 through an intervening solvent molecule, help orient D379 for catalysis. Residues involved in hydrogen bonds with the proton wire, R340 and D503, are also important. Finally, conserved residue E211, which is located near the diphosphate group of 1, is proposed to be a ligand to Mg2 + required for optimal catalytic activity. General significance This work establishes structure-function relationships for class II terpenoid cyclases.Article Citation - WoS: 38Citation - Scopus: 36Structural Studies of Geosmin Synthase, a Bifunctional Sesquiterpene Synthase With ?? Domain Architecture That Catalyzes a Unique Cyclization-Fragmentation Reaction Sequence(American Chemical Society, 2015) Harris, Golda G.; Lombardi, Patrick M.; Pemberton, Travis A.; Matsui, Tsutomu; Weiss, Thomas M.; Cole, Kathryn E.; Köksal, Mustafa; Murphy, Frank V.; Vedula, L. Sangeetha; Chou, Wayne K. W.; Cane, David E.; Christianson, David W.Geosmin synthase from Streptomyces coelicolor (ScGS) catalyzes an unusual, metal-dependent terpenoid cyclization and fragmentation reaction sequence. Two distinct active sites are required for catalysis: the N-terminal domain catalyzes the ionization and cyclization of farnesyl diphosphate to form germacradienol and inorganic pyrophosphate (PPi), and the C-terminal domain catalyzes the protonation, cyclization, and fragmentation of germacradienol to form geosmin and acetone through a retro-Prins reaction. A unique αα domain architecture is predicted for ScGS based on amino acid sequence: each domain contains the metal-binding motifs typical of a class I terpenoid cyclase, and each domain requires Mg2+ for catalysis. Here, we report the X-ray crystal structure of the unliganded N-terminal domain of ScGS and the structure of its complex with three Mg2+ ions and alendronate. These structures highlight conformational changes required for active site closure and catalysis. Although neither full-length ScGS nor constructs of the C-terminal domain could be crystallized, homology models of the C-terminal domain were constructed on the basis of 36% sequence identity with the N-terminal domain. Small-angle X-ray scattering experiments yield low-resolution molecular envelopes into which the N-terminal domain crystal structure and the C-terminal domain homology model were fit, suggesting possible αα domain architectures as frameworks for bifunctional catalysis. © 2015 American Chemical Society.