sebnem2

Asst. Prof. Şebnem EŞSİZ


Contact:

Phone:      +90 212 533 6532 / 1437 e-mail:      sebnem.gokhan@khas.edu.tr Office:      D-317


Education:

logo.dik.tr Undergrad: Koç University – Department of Chemistry (2002)
pittsburgh PhD: University of Pittsburgh – Biophysical Chemistry (2009) Advisor: Prof. Rob D. Coalson

Lab Members

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- Burak Servili

- Sevilay Güleşen

- Büşra Savaş

- Melis Gencel

Past Lab Members:

- İrem Kara
- Umutcan Unaldı
- Muhammed Aktolun
- Ayhan Demir
- Fatma Alnemsi
- Meral Ayan
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Academic Experience:

ucsf 2 Post doc: University of California, San Francisco – Bioengineering and Theuropatical Science (2009-2010) Danışman: Prof. Andrej Šali
llnl 2 Post doc: Lawrence Livermore National Lab - Biological Science and Biotechnology (2011-2012)
kadir has Asst. Prof.: Kadir Has University Department of Bioinformatics and Genetics (2012- )

Research

o   Ion Channel Proteins, Picture1 Nerve Cell GABA Receptors o   Protein Homology Modeling with The Genetic Algorithm o   Effective rigid-body Protein Simulation Techniques o   Langevin and Molecular Dynamics, Normal Mode Analysis


Past and Current Projects:

tubitak TÜBİTAK: 115S387 Novel azole compounds with potential antifungal and anticonvulsant effects: Molecular modeling, synthesis and biological activity research. Researcher. Budget: 126,993 TL (2016-2017)
tubitak TÜBİTAK-3501 114Z867. “The working mechanism for NMDA type receptors and the interaction with open ion channel inhibitors”. Project Director. 164,930 TL (2015-2017)
llnl 2 US Department of Energy, LLNL Grant #12-SI-004. Biological Science and Biotechnology, LLNL, CA, USA. “Agonist and antagonist binding on Gamma-Aminobutyric acid(GABA) receptors. Free energy analysis of carbonic anhydrase binding site biomimetic. Acetylcholine Estarase Docking Studies.” Researcher. (2011 – 2012)

Recent Publications:

- Sarı S., Kart D., Öztürk N., Kaynak F.B., Gencel M., Taşkor G., Karakurt A., Saraç S., Essiz Ş., Vural İ., Dalkara S. “Discovery of new azoles with potent activity against Candida spp. and Candida albicans biofilms through virtual screening”, Eur J Med Chem. 2019 Jun 29; DOI: 10.1016/j.ejmech.2019.06.083

- Burmaoglu S., Ozcan S., Balcioglu S., Gencel M., Noma S.A.A., Essiz S., Ates B., Algul O. “Synthesis, biological evaluation and molecular docking studies of bis-chalcone derivatives as xanthine oxidase inhibitors and anticancer agents”, accepted, Bioorganic Chemistry (July 2019)

- Sarı S., Kart D., Sabuncuoğlu S., Doğan İ.S., Özdemir Z., Bozbey İ., Gencel M., Essiz Ş., Reynisson J., Karakurt A., Saraç S., Dalkara S. “Antifungal screening and in silico mechanistic studies of an in-house azole library”,  Chemical Biology & Drug Design, 2019 July 01; DOI: 10.1111/cbdd.13587

- Ayan M. and Essiz S. “The neural γ2α1β2α1β2 gamma amino butyric acid ion channel receptor: structural analysis of the effects of the ivermectin molecule and disulfide bridges”, Journal of Molecular Modeling. Volume 24 (206), (2018) https://rdcu.be/2023

- Doğan İ.S., Saraç S., Sari S., Eşsiz Gökhan Ş., Vural İ., Dalkara S., “New azole derivatives showing antimicrobial effects and their mechanism of antifungal activity by molecular modeling studies“. European Journal of Medicinal Chemistry. Volume 130, 21 April 2017, Pages 124–138 (2017)

- Bennion B.J.*, Essiz S.G.*Lau E.Y, Fattebert,J.C., Emigh A. , Lightstone, F.C, A wrench in the works of human acetylcholinesterase: soman induced conformational changes revealed by molecular dynamics simulations, * equally contributed. PLoS ONE 10 (4), (2015)

- Koziol L., Essiz S.G., Wong S, Lau E.Y., Valdez C., Satcher J.H., Aines R.D., Lightstone F. “Computational analysis of a Zn-bound tris(imidazolyl) calix[6]arene aqua complex: toward incorporating the second-coordination sphere into carbonic anhydrase biomimetics”. J. Chem. Theory Comput., 9, 1320 (2013)

- Essiz S. G. and R. D. Coalson, “Dynamical Linear Response Theory for Conformational Relaxation of Proteins”. J. Phys. Chem. B, 113, 10859 (2009)

- Essiz S. G. and R. D. Coalson, “Langevin dynamics of molecules with internal rigid fragments in the harmonic regime”. J. Chem. Phys. 127, 104109 (2007)

- Essiz, S. and R.D. Coalson, “A rigid-body Newtonian propagation scheme based on instantaneous decomposition into rotation and translation blocks”. J. Chem. Phys. 124, 144116 (2006). 

- Essiz S. and E. Yurtsever, A coarse-graining approach in molecular simulations: Fuzzy   Potentials. The Bulletin of Istanbul Technical University. 53, p.41-44 (2003)


Theses Supervised

Meral Ayan. Master’s Thesis. “Structural Study of GABA Type A Receptor: The Effect on Intrasubunit Disulphide Bridges on Dynamics”. (2014)

Fatma Alnemsi. Master’s Thesis. “Docking Study of Resveratrol like Molecules on Histone Deacetylase VIII”. (2016)

Ayhan Demir. Master’s Thesis.HOMOLOGY MODELING AND NORMAL MODE ANALYSIS OF HUMAN NR1-NR2A NMDA TYPE RECEPTORS. (2017)

Muhammed Aktolun. Master’s Thesis. “LOOP MODELING AND MOLECULAR DYNAMICS SIMULATIONS OF APO AND LIGAND-BOUND HUMAN GLUN1-GLUN2A NMDA TYPE RECEPTORS”. (2017)

Melis Gencel. Master’s Thesis. “Structural Studies of NMDA Receptor and Xanthine Oxidase Enzyme”. (2019)


Awards:

- Workshop Travel Award, University Of Pittsburgh,(2006, 2008) - Univ. of Pittsburgh, PhD and Research Assistant Fellowhsip (2002-2008) - Werner von-Siemens Award, Chemistry Department, grad as 1st . Koç University (2002) - Vehbi Koç Honor List (2000-2002)


Membership:

- Biophysical Society - American Chemical Society