Home About the Department Site map Contact
Faculty
     
 

Coskuner-Weber, Orkid
Assistant Professor

Office Phone: (210) 458-5444
Office: BSE 1.104N
E-Mail: Orkid.CoskunerWeber@utsa.edu

Areas of Specialization
• Identification of active sites of biocomplexes
• Structure-function relationships of biomolecules and biometallic species
• Reaction mechanism description between ligands and receptors
• Molecular mechanism definition of protein folding and mis-folding induced by ligands
• Hydration phenomena.


Lab web page: http://www.utsa.edu/chem/faculty/OrkidCoskuner/home.html

 

 



Research Interests



The Coskuner group solves problems in medicine, bio-inorganic chemistry, environmental chemistry, and nanobiotechnology via implementing and applying theoretical and computational (bio)physical chemistry techniques and methods. The projects in the group focus on the identification of active sites of biocomplexes, structure-function relationships of biomolecules and biometallic species, reaction mechanism description between ligands and receptors, molecular mechanism definition of protein folding and mis-folding induced by ligands, and hydration phenomena. Our group members use and mix the fundamentals of all levels of theory including quantum chemistry, biophysics, and statistical mechanics to enable more accurate studies of biological and biometallic complexes.

 

 

The Coskuner Lab conducts research in the following areas:

 

A. Identification of the active sites of carbohydrates, glycans, and peptides toward ligands including metal ions for designing new drugs, biomarkers, and syntheses.

 

B. Prediction of amyloid protein aggregation, amyloid protein interactions with reactive oxygen species and biological metal ions, molecular mechanism description of amyloid protein mis-folding induced by ligands important in neurodegenerative diseases (Alzheimer’s disease).

 

C. Understanding and design of reaction mechanisms and reaction rates of bio-inorganic and organic reactions.

 

D. Exploring hydration phenomena and hydrophobic interactions in organic and inorganic solutions. Prediction of hydrated metal ion structure and water dissociation mechanism induced by metal ions.

 

E. Prediction of coordination and complexation chemistry, structure, and conformation of organic molecules, biocomplexes, and biometallic species in solution.

 

F. Developing new computational strategies for enabling more accurate studies of metal-organic and biometallic species and validation of our results via comparing to experimental studies performed by our collaborators.

 

 

Computational methods and techniques, such as ab initio molecular dynamics simulations, semiempirical simulations, classical molecular dynamics and Monte Carlo simulations, transition path sampling calculations, chemical reactivity calculations, and static quantum mechanical calculations are used in our Lab. In addition, we implement and apply classical simulation methods at ab initio level using dynamics.

Our theoretical and computational studies benefit from the excellent computing facilities to which we have access. These facilities include parallel supercomputers and sophisticated computer graphics systems that enable the visualization of the atomic dynamics or biological molecules by virtually reality methods.

We are involved in collaboration with Dr. Carlos A. Gonzalez (NIST), Dr. Jeffrey W. Hudgens (NIST), Dr. Thomas C. Allison (NIST), Dr. Toshiko Ichiye (Georgetown University), Dr. Cynthia S. Lo (WashU), Dr. Emily A. Jarvis (Gordon College) and Dr. Bernard Brooks (NIH).






Selected Publications

 

Identification of Active Sites of Biomolecules II: Saccharide and Transition Metal Ion in Aqueous Solution
Orkid Coskuner, Denis E. Bergeron, Luis Rincon, Jeffrey W. Hudgens, Carlos A. Gonzalez
The Journal of Physical Chemistry A, 2009, 113(11), 2491;

 

 

 

Dynamic and Structural Properties of Aqueous Arsenic Solutions
Orkid Coskuner and Thomas C. Allison
ChemPhysChem, 2009, 10(8), 1187

 

 

 

Glycosidic Linkage Conformation of methyl-α-mannopyranoside
Orkid Coskuner, Denis E. Bergeron, Luis Rincon, Jeffrey W. Hudgens, Carlos A. Gonzalez
The Journal of Chemical Physics, 2008, 129, 045102; DOI: 10.1063/1.2958916

 

 

 

 

Identification of Active Sites of Biomolecules I: Methyl-α-mamnopyranoside and Fe(III)
Orkid Coskuner, Denis E. Bergeron, Luis Rincon, Jeffrey W. Hudgens, Carlos A. Gonzalez
T
he Journal of Physical Chemistry A, 2008, 112(13), 2940

 

 

 

 

Coordination Studies of Al-EDTA in Aqueous Solution
Orkid Coskuner and Emily A. Jarvis
The Journal of Physical Chemistry
A, 112(12), 2623

 

 

 

 

Ligand Exchange Reactions in the Formation of Diphosphine-Protected Gold Clusters
Denis E. Bergeron, Orkid Coskuner, Jeffrey W. Hudgens, Carlos A. Gonzalez
The Journal of Physical Chemistry C, 2008, 112(33), 12808

 

 

 

 

Water Dissociation in the Presence of Metal Ions
Orkid Coskuner, Emily A. Jarvis, Thomas C. Allison
Angewandte Chemie, 2007, 119(41), 7999; and Angewandte Chemie International Edition, 2007, 46(41), 7853

 

 

 

 

Preferred Conformation of the Glycosidic Linkage of Methyl-β-Mannose,
Orkid Coskuner
The Journal of Chemical Physics, 2007, 127, 015101;
Selected for reprint in Virtual Journal of Biological Physics Research.

 

 

 

 

Hydrophobic Interactions of Xenon by Monte Carlo Simulations
Orkid Coskuner and Ulrich. K. Deiters
Zeitschrift für Physikalische Chemie, 2007, 221(6), 785

 

 

 

 

Hydrophobic Interactions by Monte Carlo Simulations
Orkid Coskuner and Ulrich K. Deiters
Zeitschrift für Physikalische Chemie, 2006, 220(3), 349

 

 

 

One UTSA Circle * San Antonio, TX 78249
DOC Office (210) 458-5469 Fax (210) 458-7428