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E-Posta : weber@tau.edu.tr

Dr. Orkide Coşkuner-Weber Orta Doğu Teknik Üniversitesi Kimya bölümü mezunudur. Aynı zamanda Universität zu Köln, Almanya da Kimya ve Tıp eğitimini tamamlamıştır. 2000-2003 seneleri arasında Fiziksel Kimya alanında doktorasını Universität zu Köln de (Prof. Dr. Ulrich K. Deiters ın grubunda) tamamlamıştır. 2003-2005 seneleri arasında Johns Hopkins University (Amerika Birleşik Devletleri), Kimya ve Biomoleküler Mühendisliği Bölümünde postdoctoral scientist olarak Prof. Dr. Michael E. Paulaitis in grubunda çalışmıştır. Bu süre zarfında araştırmaları A.B.D. devletinin dikkatini çekmiştir ve 2005-2007 yılları arasında Stanford University ve National Institute of Standards and Technology de postdoctoral scientist olarak çalışmıştır. 2007-2009 yılları arasında A.B.D. de research assistant professor olarak George Mason University ve National Institute of Standards and Technology de çalıştıktan sonra 2009-2014 yılları arasında University of Texas at San Antonio da yardımcı doçent doktor olarak çalışmıştır. 2014-2017 yılları arasında National Institute of Standards and Technology de bilim insanı olarak çalışmıştır. 2017 de çalışmalarını Türkiye ye taşımak için ve Türk öğrenciler yetiştirmek için Türk-Alman Üniversitesinde çalışmaya başlamıştır.

A.B.D. de üç farklı Nobel ödüllü araştırma grubuyla çalışmış olan Orkide Coşkuner-Weber in ilgi alanı kuantum mekaniği, istatiksel mekanik, biyoenformatik ve yapay zeka nın tıp alanında geliştirilmesi ve uygulanmasıdır. Alzheimer ve Parkinson hastalıklarının patolojisini incelemektedir ve antikorlar üretmektedir. Çeşitli büyük ilaç şirketleriyle beraber çalışmaktadır.

Kuantum mekaniği, istatiksel mekanik, termodinamik, biyoenformatik ve yapay zeka. Oksidatif stres, mitokondriyal disfonksiyon, genetik ve translasyon sonrası modifikasyonlar.

Özgün Makaleler:

 

1. Hydrophobic Interactions by Monte Carlo Simulations. Orkid Coskuner and Ulrich K. Deiters. Z. Phys. Chem. 2006, 220:349-369.

2. Hydrophobic Interactions of Xenon by Monte Carlo Simulations. Orkid Coskuner and Ulrich K. Deiters. Z. Phys. Chem. 2007, 221:785-799.

3. Preferred Conformation of the Glycosidic Linkage of methyl-beta-mannose. Orkid Coskuner. J. Chem. Phys. 2007, 127:015101.

4. Water Dissociation in the Presence of Metal Ions. Orkid Coskuner, Emily A. A. Jarvis, Thomas C. Allison. Ang. Chem. Int. Ed. 2007, 46:7853-7855.

5. Coordination Studies of Al-EDTA in Aqueous Solution. Orkid Coskuner and Emily A. A. Jarvis. J. Phys. Chem. A, 2008, 112:2628-2633.

6. Ligand Exchange Reactions in the Formation of Diphosphine Protected Gold Clusters. Dennis E. Bergeron, Orkid Coskuner, Jeffrey W. Hudgens, Carlos A. Gonzalez. J. Phys. Chem. C 2008, 112:12808-12814.

7. Identification of Active Sites of Biomolecules. 1-Methyl-alpha-mannopyranoside and Fe(III). Orkid Coskuner, Dennis E. Bergeron, Luis Rincon, Jeffrey W. Hudgens, Carlos A. Gonzalez. J. Phys. Chem. A 2008, 112:2940-2947.

8. Glycosidic Linkage Conformation of methyl-alpha-mannopyranoside. Orkid Coskuner, Dennis E. Bergeron, Luis Rincon, Jeffrey W. Hudgens, Carlos A. Gonzalez. J. Chem. Phys. 2008, 129:045102.

9. Dynamic and Structural Properties Aqueous Arsenic  Solutions. Orkid Coskuner and Thomas C. Allison. ChemPhyChem. 2009, 10:1187-1189.

10. Identification of Active Sites of Biomolecules II: Saccharide and Transition Metal Ion in Aqueous Solution. Orkid Coskuner, Dennis E. Bergeron, Luis Rincon, Jeffrey W. Hudgens, Carlos A. Gonzalez. J. Phys. Chem. A 2009, 113:2491-2499.

11. Single Ion and Dimerization Studies of the Al(III) Ion in Aqueous Solution. Orkid Coskuner. J. Phys. Chem. A 2010, 114:10981-10987.

12. Amyloid-beta Peptide Structure in Aqueous Solution Varies with Fragment Size. Olivia Wise-Scira, Liang Xu, Taizo Kitahara, George Perry, Orkid Coskuner. J. Chem. Phys. 2011, 135:205101.

13. Carbohydrate and Trivalent Iron Ion Interactions in the Gas Phase and in Aqueous Solution. Orkid Coskuner, Carlos A. Gonzalez. In Book: Metallic Systems, Taylor and Francis: CRC Press, 2011, 83.

14. Aqueous Solutions of Metal Ions. Orkid Coskuner, Thomas C. Allison. In Book: Metallic Systems, Taylor and Francis: CRC Press, 2011, 107.

15. Structural and Thermodynamic Studies of alpha-Synuclein Proteins Related to Parkinson’s Disease. Olivia Wise, Liang Xu, Orkid Coskuner. In Book: Metallic Systems, Taylor and Francis: CRC Press, 2011, 29.

16. Structures and Free Energy Landscapes of Aqueous Zinc(II)-Bound Amyloid-β (1–40) and Zinc(II)-Bound Amyloid-β (1–42) with Dynamics. Olivia Wise-Scira, Liang Xu, George Perry, Orkid Coskuner. J. Biol.  Inorg. Chem. 2012, 17:927-938.

17. The Structures of the E22Δ Mutant-Type Amyloid-β Alloforms and the Impact of E22Δ Mutation on the Structures of the Wild-Type Amyloid-β Alloforms. Orkid Coskuner, Olivia Wise-Scira, George Perry, Taizo Kitahara. ACS Chem. Neurosci. 2012, 4:310-320.

18. Probing and Trapping a Sensitive Conformation: Amyloid-β Fibrils, Oligomers, and Dimers. Janelle N. Fawver, Karen T. Duong, Olivia Wise, Rachel Petrofes Chapa, Hayley E. Schall, Orkid Coskuner,   Xiongwei Zhu, Luis V. Colom, Ian V. J. Murray. J. Alz. Dis. 2012, 32:197-215.

19. Structures of the E46K Mutant-type α-Synuclein Protein and Impact of E46K Mutation on the Structures of the Wild-Type α-Synuclein Protein. Olivia Wise-Scira, Aquila Dunn, Ahmet K. Aloglu, Isin T. Sakallioglu, Orkid Coskuner. ACS Chem. Neurosci. 2013, 4:498-508.

20. Structures and Free Energy Landscapes of the A53T Mutant-Type α-Synuclein Protein and Impact of A53T Mutation on the Structures of the Wild-Type α-Synuclein Protein with Dynamics. Orkid Coskuner, Olivia Wise-Scira. ACS Chem. Neurosci. 2013, 4:1101-1113.

21. Structures and Free Energy Landscapes of the Wild-Type and A30P Mutant-Type α-Synuclein Proteins with Dynamics. Olivia Wise-Scira, Ahmet K. Aloglu, Aquila Dunn, Isin T. Sakallioglu, Orkid Coskuner. ACS Chem. Neurosci. 2013, 4:486-497.

22. Arginine and Disordered Amyloid-β Peptide Structures: Molecular Level Insights into the Toxicity in Alzheimer’s Disease. Orkid Coskuner, Olivia Wise-Scira. ACS Chem. Neurosci. 2013, 4:1549-1558.

23. New Force Field Parameters for Metalloproteins I: Divalent Copper Ion Centers Including Three Histidine Residues and an Oxygen‐Ligated Amino Acid Residue. Olivia Wise, Orkid Coskuner. J. Comput. Chem. 2014, 35:1278-1289.

24. Adenosine Triphosphate (ATP) Reduces Amyloid-β Protein Misfolding in Vitro. Orkid Coskuner, Ian V. J. Murray. J. Alz. Dis. 2014, 41:561-574.

25. Divalent Copper Ion Bound Amyloid-β(40) and Amyloid-β(42) Alloforms are Less Preferred Than Divalent Zinc Ion Bound Amyloid-β(40) and Amyloid-β(42) Alloform. Orkid Coskuner. J. Biol. Inorg. Chem. 2016, 21:957-973.

26. Tyrosine Regulates β-Sheet Structure Formation in Amyloid-β42: A New Clustering Algorithm for Disordered Proteins. Orkid Coskuner and Vladimir N. Uversky. J. Chem. Inf. Mod. 2017, 57:1342-1358.

27. BMP-2 and BMP-9 Binding Specificities with ALK3 in Aqueous Solution with Dynamics. Orkid Coskuner and Vladimir N. Uversky. J. Mol. Graph. Mod. 2017, 77:181-188.

28. How accurate are your simulations? Effects of confined aqueous volume and AMBER FF99SB and CHARMM22/CMAP force field parameters on structural ensembles of intrinsically disordered proteins: Amyloid-β42 in water. Orkid Coskuner-Weber and Vladimir N. Uversky. Intr. Disordered Prot. 2017. 5:e1377813.

29. Insights into the Molecular Mechanisms of Alzheimer’s and Parkinson’s Diseases with Molecular Simulations: Understanding the Roles of Artificial and Pathological Missense Mutations in Intrinsically Disordered Proteins Related to Pathology. Orkid Coskuner-Weber and Vladimir N. Uversky. Int. J. Mol. Sci. 2018, 19:336.

30. Revisiting Divalent Copper Ion Bound Amyloid-β40 and Amyloid-β42 Alloforms at The Atomic Level with Dynamics: Varying Coordination Chemistries. Orkid Coskuner-Weber. J. Turk. Chem. Soc. 2018, 5(3):981-1008.

31. Quantum Chemistry Meets Deep Learning for Complex Carbohydrate and Glycopeptide Species I. M. Gokhan Habiboglu and Orkid Coskuner-Weber. Z. Phys. Chem. 2018, DOI: 10.1515/zpch-2018-1251.

32. Alanine Scanning Effects on the Biochemical and Biophysical Properties of Intrinsically Disordered Proteins: A Case Study of the Histidine to Alanine Mutations in Amyloid-β42, Orkid Coskuner-Weber and Vladimir N. Uversky, J. Chem. Inf. Mod. 2019, DOI: 10.1021/acs.jcim.8b00926.

 

 

Kitaplar:

 

Metallic Systems: A Quantum Chemist’s Perspective. Carlos A. Gonzalez, Orkid Coskuner, Thomas C. Allison. CRC Press. Taylor & Francis, 2011, ISBN: 978-1-4200-6077-5

 

Davetli Konferans Proceedingleri

 

1. Transition Metal Ion Interactions with Intrinsically Disordered Proteins. Journal of Clinical Toxicology 2:9, 86th OMICS Group Conference, Toxicology Summit & Expo, San Antonio, Texas, USA, 2012.

2. Structural properties of Al(III) in acidic solution. Stanford-Environmental Molecular Sciences Institute, Annual Conference, pp 17, Palo Alto, California, USA, 2006. Best Collaborative Research Activities Award based on my research direction design, which included NIST (Department of Commerce), Princeton and Stanford Universities.

3. Quantum and statistical mechanical and bioinformatics studies in Alzheimers and Parkinsons diseases, 24th World Chemistry & Systems Biology Conference, Los Angeles, California, USA, 2018.

4. Mitochondrial dysfunction, oxidative stress and genetic factors in Alzheimers disease, 4th International Conference on Biochemistry & Metabolomics, Los Angeles, California, USA, 2018.

 

Davetli Bilimsel Konuşmalar:

 

3. Unfolded Natural and Non-Natural Polymers with Biological Functions (Unfold (x)), Orkid Coskuner, Medipol University, Istanbul, Turkey, 2016.

4. Unfold(x) and ProMet, Orkid Coskuner, TUBITAK, Gebze, Turkey, 2016.

5. Disordered Polymers, Orkid Coskuner, Turkish-German University, Istanbul, Turkey, 2016.

6. Disordered Thermodynamics, Orkid Coskuner, Department of Chemistry, Middle East Technical University, Ankara, Turkey, 2016.

7. New Engineering Thermodynamics with Transition Path Sampling and Heterogeneous Thermodynamics for Disordered Species, Orkid Coskuner, Department of Physics, Trinity University, San Antonio, Texas, USA, 2014.

8. Nutrition and Environmental Effects in Neurosciences, Orkid Coskuner, Department of Biology, The University of Texas, Austin, Texas, USA, 2014.

9. Molecular Dynamics Simulations of Intrinsically Disordered Proteins and What We Can       Learn From Simulations, Orkid Coskuner, Institute of Physical Chemistry. Universität zu Köln, Germany, 2013.

10. A New Force Field Parameter Development Method for Metalloproteins, Orkid  Coskuner,  National Institute of Standards and Technology, Gaithersburg, Maryland, USA, 2012.

11. Theoretical Studies of Intrinsically Disordered Metalloproteins: Combined Quantum Mechanical and Classical Mechanical Approaches, Orkid Coskuner, Department of Chemistry Seminar, George Washington University, Washington D. C., USA, 2012.

12. Imaging and Visualization in Neurosciences. Orkid Coskuner, SNRP, The University of Texas at San Antonio, San Antonio, Texas, USA, 2011.

13. The Structures of Amyloid-β(1-16), Amyloid-β(1-28) and Amyloid-β(1-42), Orkid Coskuner, SNRP, The University of Texas at San Antonio, San Antonio, Texas, USA, 2011.

14. Early Aggregation Studies Important in Neurodegenerative Diseases, Orkid Coskuner, Chemistry Department Seminars, The University of Texas at San Antonio, San Antonio,    Texas, USA, 2011.

15. Computational and Biophysical Chemistry at UTSA, American Chemical Society, Student Chapter, Orkid Coskuner, The University of Texas at San Antonio, San Antonio, Texas, USA, 2010.

16. Protein and Metal Ion Interactions Important in Alzheimer’s and Parkinson’s Diseases, Orkid Coskuner, Ege University, Izmir, Turkey, 2010. See, http://www.hurriyet.com.tr/alzheimer-yasi-3e-indi-14931880.

17. Metal Ions and Organic Complexes in Aqueous Solution, Orkid Coskuner, Universitaet Saarland, Saarbrücken, Germany, 2010.

18. Identification of Active Sites of Carbohydrate Complexes Toward Ligands in Aqueous Solution, Orkid Coskuner, South Texas Center for Emerging Infectious Diseases, San Antonio, Texas, 2010.

19. Proteins and Metals Important in Alzheimer’s Disease, Orkid Coskuner, Georgetown University, Washington D. C., USA, 2009.

20. Metal Ions, Metal-Organic Complexes, and Biometallic Species, Orkid Coskuner, National Institute of Standards and Technology, Gaithersburg, Maryland, USA, 2008.

21. Metallic Systems: Metal Ions, Metal-Organic Complexes, and Metalloproteins, Orkid Coskuner, Brooks/Pastor Meetings, National Institutes of Health, Rockville, Maryland, USA, 2008.

22. Transition Path Sampling Calculations in Condensed Systems, Orkid Coskuner, National Institute of Standards and Technology, Gaithersburg, Maryland, USA, 2008.

23. Metal Ions and Metal-Organic Complexes in Solution, Orkid Coskuner, Materials Sciences  Colloquium, George Mason University, Fairfax, Virginia, USA, 2007.

24. Coordination Chemistry Studies of Metal-Organic Species in Aqueous Solution, Orkid  Coskuner, Bioinformatics Colloquium, George Mason University, Manassas, Virginia, USA, 2007.

25. Hydrophobic Interactions and Carbohydrate Solutions, Orkid Coskuner, National Institute of Standards and Technology, Gaithersburg, Maryland, USA, 2005.

26. Secondary Cell Wall Polymers and Carbohydrate Simulations, Orkid Coskuner, Johns Hopkins University, Biophysics Seminar, Baltimore, Maryland, USA, 2004.

27. Hydrophobic Interactions, Orkid Coskuner, Bosphorus University, Istanbul, Turkey, 2002.

28. Quantum Corrections and Phase Diagrams, Orkid Coskuner, Sabanci University, Istanbul, Turkey, 2002.

29. Molecular Dynamics Simulations, Orkid Coskuner, BIG Meeting, Koeln, Germany, 2001.

 

Uluslararasi Konferans Sunumları:

 

Pathological Modifications and Disordered Proteins in Alzheimer ´s Disease, 6th International BAU Drug Design Conference, Istanbul, Turkey, 2018.

Intrinsically Disordered Proteins and Metalloproteins. Orkid Coskuner. Seminar Talk. American Chemical Society Regional Meeting, Waco, Texas, USA, 2013.

Studying the Structures of Genetic Missense Mutant-Type Proteins in Neurodegenerative Diseases. Orkid Coskuner, Olivia Wise. Poster. 2nd Annual Austin Translational Neuroscience Symposium, Austin, Texas, USA, 2012.

The Structures of the E46K Mutant-Type and Wild-Type α-Synuclein Proteins. Aquila Dunn, Orkid Coskuner. Poster.  Collaborative Basic & Translational Research in the Sciences, San Antonio, Texas, USA, 2012.

The Impact of EΔ22 Genetic Missense Mutation on the Structures of Amyloid-β. Olivia Wise, Orkid Coskuner. Poster. Collaborative Basic & Translational Research in the Sciences, San Antonio, Texas, USA, 2012.

ProtMet: A New Molecular Simulation Software Package for Metalloprotein Simulations. Orkid Coskuner. Seminar Talk. 68th Southwest Regional Meeting of the American Chemical Society, Austin, Texas, USA, 2011.

Impact of Parkinson’s Disease Related Single Point Mutations and Aqueous Solution on α-Synuclein Proteins. Olivia Wise-Scira, Andrew Roque, Liang Xu. Seminar Talk. 66th Southwest and 62nd Southeastern Regional Meeting of the American Chemical Society, New Orleans, USA, 2010.

Peptides and Metal Ion Coordination. Orkid Coskuner. Seminar Talk. 239th American Chemical Society National Meeting, San Francisco, California, USA, 2010.

Conformations and Active Sites of Carbohydrates, Orkid Coskuner, Poster. American Chemical Society National Meeting, San Francisco, California, USA, 2010.

Molecular Mechanism of Folding and Mis-folding of Proteins Induced by Metal Ions: Neurodegenerative Diseases. Orkid Coskuner, Poster. 239th American Chemical Society National Meeting, San Francisco, California, USA, 2010.

Polymerization Studies of Metallic Solutions. Orkid Coskuner, Jacob Cavazos. Poster. 239th American Chemical Society National Meeting, San Francisco, California, USA, 2010.

The Structural and Thermodynamic Properties of Amyloid-β in Aqueous Solution. Orkid Coskuner, Taizo Kitahara. Seminar Talk. Welch Summer Symposium, San Antonio, Texas, USA, 2010.

How Do Single Point Mutations Impact Protein Folding in Parkinson’s Disease? Olivia Wise, Andrew Roque, Liang Xu, Orkid Coskuner. Poster. Joint Fall 2010 Meeting of the Texas Sections of the APS, AAPT, Zone 13 of SPS and the National Society of Hispanic Physicists, San Antonio, Texas, USA, 2010.

Metal Ions, Metal-Organic Complexes and Transition Path Sampling. Orkid Coskuner. Poster. American Institute of Chemical Engineers Annual Meeting, Philadelphia, Pennsylvania, USA, 2008.

 Local Bonding Interactions on the Condensed Phase Structure and Reactivity. Emily Jarvis, Orkid Coskuner, Anne Chaka. Seminar Talk. American Chemical Society National Meeting, Boston, Massachusetts, USA, 2007.

The Applicability of Different Quantum Mechanical Methods to Transition Metal Oxides.  Orkid Coskuner, Emily Jarvis, Thomas C. Allison, Carlos A. Gonzalez, Anne Chaka. Seminar Talk. American Physical Society National Meeting, Baltimore, Maryland, USA, 2006.

Coordination Environment of Aqueous-Phase Aluminum, Michael Hay, Orkid Coskuner, Emily Jarvis, Anne Chaka, Satish Myneni. Seminar Talk. American Chemical Society National Meeting, Atlanta, Georgia, 2006.

The Nature of Metal-Oxygen Bonding at Corrundum (0001) Surfaces in the Presence of Oxygen. Emily Jarvis, Orkid Coskuner, Anne Chaka. Seminar Talk. American Physical Society National Meeting, Baltimore, Maryland, USA, 2006.

Classical Molecular Dynamics and Quantum Mechanical Studies of Carbohydrates. Orkid Coskuner, Dilip A. Asthagiri, Michael E.  Paulaitis. Poster. Annual Biophysical Society Meeting, Long Beach, California, USA, 2005.

A Monte Carlo Method for Calculating Energy Landscapes from Dynamical Force Spectroscopy Measurements. Orkid Coskuner, Denis Wirtz, Michael E. Paulaitis. Poster. Annual Biophysical Society Meeting, Baltimore, Maryland, USA, 2005.

Secondary Cell Wall Polymers of Bacteria. Orkid Coskuner, Michael E. Paulaitis. Seminar Talk. Annual Biophysical Society Meeting, Johns Hopkins University, Baltimore, Maryland,  USA, 2004.

Quantum Effects of Neon, Orkid Coskuner, Ulrich K. Deiters. Poster. Global Phase Diagrams Meeting, Bonn, Germany, 2000.