Timucin Lab

Research

We are seeking graduate students (PhD and MSc) who are enthusiastic about proteins and computational biology. Please contact. Below is a list of ongoing studies.

Contact

Aurora A/N-Myc Complex

Prompted by the resolved complex structure of AurA/N-Myc, we investigated the complex structure by molecular dynamics simulations, to see some interesting results. See the publication in Scientific reports: https://www.nature.com/articles/s41598-023-45272-3

Functional Impact of Missense Mutations

A novel AF2 structure-based pathnogeicity predictor is now available at https://affipred.timucinlab.com/

Structural Mechanisms of IL18 and IL37

In connection with Belkaya Lab at Bilkent University, we aimed to understand how the IL1 family members initiate inflammatory of anti-inflammatory signals.

Lipase in Deep Eutectic Solvents

We are studying how enzymes behave in deep eutectic solvents.

Design of Dimer Interfaces

Aiming to understand and tune the aggregation process, we focus on identification of the dimerization interface(s) of thermoalkalophilic lipases.

Senolytic Compound Design and Screening

In connection with Eternans Co UK, Emel and Selim designed and screened senolytic compounds of peptides and small molecules targeting the Foxo4-p53 complex.

“An expert is a man who has made all the mistakes which can be made, in a narrow field.” – Niels Bohr

Selected Publications

* corresponding author

1. Le, H. H.; Cinaroglu, S. S.; Manalo, E. C.; Ors, A.; Gomes, M. M.; Duan Sahbaz, B.; Bonic, K.; Origel Marmolejo, C. A.; Quentel, A.; Plaut, J. S.; Kawashima, T. E.; Ozdemir, E. S.; Malhotra, S. V.; Ahiska, Y.; Sezerman, U.; Bayram Akcapinar, G.; Saldivar, J. C.; Timucin, E.*; Fischer, J. M.*, Molecular Modelling of the Foxo4-Tp53 Interaction to Design Senolytic Peptides for the Elimination of Senescent Cancer Cells. EBioMedicine 2021, 73, 103646.

2. Shehata, M.; Unlu, A.; Sezerman, U.; Timucin, E.*, Lipase and Water in a Deep Eutectic Solvent: Molecular Dynamics and Experimental Studies of the Effects of Water-in-Deep Eutectic Solvents on Lipase Stability. J Phys Chem B 2020, 124, 8801-8810.

3. Timucin, A. C.; Cinaroglu, S. S.; Sezerman, O. U.; Timucin, E.*, Bridging the Bridging Imidazolate in the Bimetallic Center of the Cu/Zn Sod1 and Als. Front Chem 2021, 9, 716438.

4. Cinaroglu, S. S.*; Timucin, E.*, Comparative Assessment of Seven Docking Programs on a Nonredundant Metalloprotein Subset of the PDBbind Refined. Journal of chemical information and modeling 2019, 59, 3846-3859.

5. Cinaroglu, S. S.; Timucin, E.*, Comprehensive evaluation of the MM-GBSA method on bromodomain-inhibitor sets. Briefings in bioinformatics 2019.

6. Timucin, E.*; Sezerman, O. U., Thermostability of the PYL-PP2C Heterodimer Is Dependent on Magnesium: In Silico Insights into the Link between Heat Stress Response and Magnesium Deficiency in Plants. Journal of chemical information and modeling 2018, 58, 661-672.

7. Timucin, E.*; Cousido-Siah, A.; Mitschler, A.; Podjarny, A.; Sezerman, O. U., Probing the roles of two tryptophans surrounding the unique zinc coordination site in lipase family I.5. Proteins: Structure, Function and Bioinformatics 2016, 84, 129-42.

8. Erbil, S.; Oral, O.; Mitou, G.; Kig, C.; Durmaz-Timucin, E.; Guven-Maiorov, E.; Gulacti, F.; Gokce, G.; Dengjel, J.; Sezerman, O. U.; Gozuacik, D., RACK1 Is an Interaction Partner of ATG5 and a Novel Regulator of Autophagy. The Journal of biological chemistry 2016, 291, 16753-65.

9. Timucin, E.*; Sezerman, O. U., Zinc Modulates Self-Assembly of Bacillus thermocatenulatus Lipase. Biochemistry 2015, 54, 3901-10.

10. Tada, S.; Timucin, E.; Kitajima, T.; Sezerman, O. U.; Ito, Y., Direct in vitro selection of titanium-binding epidermal growth factor. Biomaterials 2014, 35, 3497-503.

11. Timucin, E.*; Sezerman, O. U., The conserved lid tryptophan, W211, potentiates thermostability and thermoactivity in bacterial thermoalkalophilic lipases. PloS one 2013, 8, e85186.

12. Durmaz, E.*; Kuyucak, S.; Sezerman, U. O., Modifying the catalytic preference of tributyrin in Bacillus thermocatenulatus lipase through in-silico modeling of enzyme-substrate complex. Protein engineering, design & selection : PEDS 2013, 26, 325-33.

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People

Emel Timuçin

Zeynep Şevval Düvenci, PhD student

Holding a BSc degree in Mol. Bio. & Gen in 2007 and a PhD degree in in Biological Sciences and Bioengineering in 2012. Currently working as a professor at the department of Biostatistics and Medical Informatics, School of Medicine, Acibadem University.

Enthusiastic about proteins and their structures.

Zeynep Şevval Düvenci, PhD student

Bio and thesis

Rumeysa Fayetorbay, PhD student

Zeynep Şevval Düvenci, PhD student

Rumeysa Fayetorbay, PhD student

Bio and thesis

İnci Şardağ, BSc student

Lara Naserikhojasteh, MSc (alumnus)

Rumeysa Fayetorbay, PhD student

Bio and thesis

İlayda Amanoğlu, MSc (alumnus)

Lara Naserikhojasteh, MSc (alumnus)

Thesis: Molecular insights into the surface of thermoalkalophilic lipases toward unraveling the interplay between thermostability and oligomerization

Lara Naserikhojasteh, MSc (alumnus)

Thesis: Computational and experimental characterization of peptide inhibitors targeting the aurora kinase A and n-Myc complex

Zeynep Kavalcı, MSc (alumnus)

Mohamed Shehata, PhD (alumnus)

Dila Nur Kamalı, MSc (alumnus)

Thesis: Dissecting the effect of viscosity of deep eutectic solvents on the structure and dynamics of thermostable lipases

Dila Nur Kamalı, MSc (alumnus)

Mohamed Shehata, PhD (alumnus)

Dila Nur Kamalı, MSc (alumnus)

Thesis: Assessing the performance of molecular dynamics simulations for predicting the conformations of flexible protein-protein complexes

Mohamed Shehata, PhD (alumnus)

Mohamed is an Egyptian biochemist who received his PhD degree in 2022 and started his postdoctoral studies in UCSD.

Pınar Altıner, MSc (alumnus)

Süleyman Selim Çınaroğlu, MSc (alumnus)

Mohamed Shehata, PhD (alumnus)

Pinar received her MSc degree in 2021 and is currently a PhD student at the CNRS-IPBS.

Narod Kebabcı, MSc (alumnus)

Süleyman Selim Çınaroğlu, MSc (alumnus)

Narod received her MSc degree in 2021 on understanding dataset biases for ddG predictors. She is currently a PhD student at the National University of Ireland.

Süleyman Selim Çınaroğlu, MSc (alumnus)

Selim received his MSc degree in 2018 and is currently a PhD student at the University of Oxford.

Join our research team of lifelong learners!

Research

Aurora A/N-Myc Complex

Functional Impact of Missense Mutations

Structural Mechanisms of IL18 and IL37

Lipase in Deep Eutectic Solvents

Design of Dimer Interfaces

Senolytic Compound Design and Screening

Selected Publications

People

Emel Timuçin

Zeynep Şevval Düvenci, PhD student

Zeynep Şevval Düvenci, PhD student

Zeynep Şevval Düvenci, PhD student

Zeynep Şevval Düvenci, PhD student

Zeynep Şevval Düvenci, PhD student

Rumeysa Fayetorbay, PhD student

Zeynep Şevval Düvenci, PhD student

Rumeysa Fayetorbay, PhD student

İnci Şardağ, BSc student

Lara Naserikhojasteh, MSc (alumnus)

Rumeysa Fayetorbay, PhD student

İlayda Amanoğlu, MSc (alumnus)

Lara Naserikhojasteh, MSc (alumnus)

Lara Naserikhojasteh, MSc (alumnus)

Lara Naserikhojasteh, MSc (alumnus)

Lara Naserikhojasteh, MSc (alumnus)

Lara Naserikhojasteh, MSc (alumnus)

Zeynep Kavalcı, MSc (alumnus)

Mohamed Shehata, PhD (alumnus)

Dila Nur Kamalı, MSc (alumnus)

Dila Nur Kamalı, MSc (alumnus)

Mohamed Shehata, PhD (alumnus)

Dila Nur Kamalı, MSc (alumnus)

Mohamed Shehata, PhD (alumnus)

Mohamed Shehata, PhD (alumnus)

Mohamed Shehata, PhD (alumnus)

Pınar Altıner, MSc (alumnus)

Süleyman Selim Çınaroğlu, MSc (alumnus)

Mohamed Shehata, PhD (alumnus)

Narod Kebabcı, MSc (alumnus)

Süleyman Selim Çınaroğlu, MSc (alumnus)

Süleyman Selim Çınaroğlu, MSc (alumnus)

Süleyman Selim Çınaroğlu, MSc (alumnus)

Süleyman Selim Çınaroğlu, MSc (alumnus)

Süleyman Selim Çınaroğlu, MSc (alumnus)

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