Research Project: DİNAMİK YAPISAL ANALİZ YÖNTEMİYLE TRAF6 PROTEİNİNİN ÇİNKO PARMAK KISMINA BAĞLANAN İNHİBİTÖRLERİN GELİŞTİRİLMESİ
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Contributors
Funders
ID
TB.00542
Authors
Demirci, Hasan
Faculty Member
Publications
Intersubunit coupling enables fast CO2-fixation by reductive carboxylases
(American Chemical Society (ACS), 2022) Demirci, Hasan; Rao, Y.; Stoffel, G.M.; Vögeli, B.; Schell, K.; Gomez, A.; Batyuk, A.; Gati, C.; Sierra, R.G.; Hunter, M.S.; Dao, E.H.; Ciftci, H.I.; Hayes, B.; Poitevin, F.; Li, P.-N.; Kaur, M.; Tono, K.; Saez, D.A.; Deutsch, S.; Yoshikuni, Y.; Grubmüller, H.; Erb, T.J.; Vöhringer-Martinez, E.; Wakatsuki, S.; Department of Molecular Biology and Genetics; Yes; College of Sciences
Enoyl-CoA carboxylases/reductases (ECRs) are some of the most efficient CO2-fixing enzymes described to date. However, the molecular mechanisms underlying the extraordinary catalytic activity of ECRs on the level of the protein assembly remain elusive. Here we used a combination of ambient-temperature X-ray free electron laser (XFEL) and cryogenic synchrotron experiments to study the structural organization of the ECR from Kitasatospora setae. The K. setae ECR is a homotetramer that differentiates into a pair of dimers of open- and dosed-form subunits in the catalytically active state. Using molecular dynamics simulations and structure-based mutagenesis, we show that catalysis is synchronized in the K. setae ECR across the pair of dimers. This conformational coupling of catalytic domains is conferred by individual amino acids to achieve high CO2-fixation rates. Our results provide unprecedented insights into the dynamic organization and synchronized inter- and intrasubunit communications of this remarkably efficient CO2-fixing enzyme during catalysis.
Structural characterization of TRAF6 N-terminal for therapeutic uses and computational studies on new derivatives
(Multidisciplinary Digital Publishing Institute (MDPI), 2023) Demirci, Hasan; Çiftçi, Halil İbrahim; Güven, Ömür; Sever, Belgin; Basoglu-Unal, Faika; Ece, Abdulilah; Tateishi, Hiroshi; Koga, Ryoko; Radwan, Mohamed O.; Demir, Nefise; Can, Mustafa; Aytemir, Mutlu Dilsiz; Inoue, Jun-ichiro; Otsuka, Masami; Fujita, Mikako; Department of Molecular Biology and Genetics; KUISCID (Koç University İşbank Center for Infectious Diseases); Graduate School of Sciences and Engineering; Yes; College of Sciences; GRADUATE SCHOOL OF SCIENCES AND ENGINEERING; Research Center
Tumor necrosis factor receptor-associated factors (TRAFs) are a protein family with a wide variety of roles and binding partners. Among them, TRAF6, a ubiquitin ligase, possesses unique receptor binding specificity and shows diverse functions in immune system regulation, cellular signaling, central nervous system, and tumor formation. TRAF6 consists of an N-terminal Really Interesting New Gene (RING) domain, multiple zinc fingers, and a C-terminal TRAF domain. TRAF6 is an important therapeutic target for various disorders and structural studies of this protein are crucial for the development of next-generation therapeutics. Here, we presented a TRAF6 N-terminal structure determined at the Turkish light source "Turkish DeLight" to be 3.2 angstrom resolution at cryogenic temperature (PDB ID: 8HZ2). This structure offers insight into the domain organization and zinc-binding, which are critical for protein function. Since the RING domain and the zinc fingers are key targets for TRAF6 therapeutics, structural insights are crucial for future research. Separately, we rationally designed numerous new compounds and performed molecular docking studies using this template (PDB ID:8HZ2). According to the results, 10 new compounds formed key interactions with essential residues and zinc ion in the N-terminal region of TRAF6. Molecular dynamic (MD) simulations were performed for 300 ns to evaluate the stability of three docked complexes (compounds 256, 322, and 489). Compounds 256 and 489 was found to possess favorable bindings with TRAF6. These new compounds also showed moderate to good pharmacokinetic profiles, making them potential future drug candidates as TRAF6 inhibitors.
Comparative study of high-resolution LysB29(Nε-myristoyl) des(B30) insulin structures display novel dynamic causal interrelations in monomeric-dimeric motions
(Multidisciplinary Digital Publishing Institute (MDPI), 2023) Demirci, Hasan; Destan, Ebru; Çiftçi, Halil İbrahim; Ayan, Esra; Kepçeoğlu, Abdullah; Kati, Ahmet; KUISCID (Koç University İşbank Center for Infectious Diseases); Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; Yes; College of Sciences; GRADUATE SCHOOL OF SCIENCES AND ENGINEERING; Research Center
The treatment of insulin-dependent diabetes mellitus is characterized by artificial supplementation of pancreatic beta-cell ability to regulate sugar levels in the blood. Even though various insulin analogs are crucial for reasonable glycemic control, understanding the dynamic mechanism of the insulin analogs may help to improve the best-protracted insulin analog to assist people with type 1 diabetes (T1D) to live comfortably while maintaining tight glycemic control. Here, we present the high-resolution crystal structure of NN304, known as insulin detemir, to 1.7 angstrom resolution at cryogenic temperature. We computationally further investigated our crystal structure's monomeric-dimeric conformation and dynamic profile by comparing it with a previously available detemir structure (PDB ID: 1XDA). Our structure (PDB ID: 8HGZ), obtained at elevated pH, provides electrostatically triggered minor movements in the equilibrium between alternate conformational substates compared to the previous structure, suggesting it might induce an intermediate state in the dissociation pathway of the insulin detemir's hexamer:dihexamer equilibrium. Supplemented with orientational cross-correlation analysis by a Gaussian network model (GNM), this alternate oligomeric conformation offers the distinct cooperative motions originated by loose coupling of distant conformational substates of a protracted insulin analog that has not been previously observed.
