Agnieszka Szarecka, Ph.D.

Assistant Professor of CMB
Phone: 616-331-3376
Email: szarecka@gvsu.edu

Office hours:

HRY 320: MF 12-12:45pm, MW 2-3pm

DeVOS 204A: T 5-6pm

Advising - HRY 320: F 11-12


Education

Ph.D. Chemistry, 1999
          Adam Mickiewicz University, Poznan, Poland

M.Sc. Chemistry 1995
          Adam Mickiewicz University, Poznan, Poland

British Council Fellow 1998
          UMIST and King's College, UK

Soros and Foreign&Commonwealth Office Scholar 1995 - 96
          Oxford University, UK

Postdoctoral research
          Carnegie Mellon University
          University of Pittsburgh School of Medicine
          Florida State University


Courses

CMB 452 / 552 - Computational Biology  / offered in Winter

CMB 351 / 551 - Bioinformatics for Life Sciences / offered in Fall

CMB 150 - Biotechnology and Society / offered in Fall

CMB 495 - Perspectives in CMB / offered in Winter

CMB 697 - Colloquium in Biotechnology / offered in Winter

CMB 501 - Scientific Communication / offered in Fall


Research Interests

My research projects involve computational modeling of biomolecules using a variety of techniques such as Molecular Dynamics and QM/MM simulations, protein-ligand docking, and electronic structure calculations.  

 Current projects:

* mechanisms of enzymatic reactions: ligand selectivity of OXA type beta-lactamases, mechanism of enzyme inhibition and evolution of function

* modes of inhibition of telomerase by non-nucleosidic drug candidates

* structure and function of neurotransmitter receptors and ion channels: dynamics of proteins and the mechanism of allosteric response of the channel to the neurotransmitter binding.

Publications                                                                                   

*      Z. Liu, A. Szarecka, M. Yonkunas, K. Sperranskiy, M. Kurnikova, M. Cascio. Crosslinking Constraints and Computational Models as Complementary Tools in Modeling the Extracellular Domain of the Glycine Receptor. PLOS One, 9, e102571 (2014)

*      A. Szarecka, K. R. Lesnock, C. A. Ramirez-Mondragon, H. B. Nicholas Jr., T. Wymore. The Class D β-lactamase family: residues governing the maintenance and diversity of function. Protein Engineeing Design and Selection 24(10):801-809 (2011) (on the cover)

*     A. Szarecka, P. Tang, Y. Xu. Dynamics of Firefly Luciferase Inhibition by General Anesthetics: Gaussian and Anisotropic Network Analyses.  Biophys. J. 93, 1895-1905 (2007)
•    A. Szarecka, Y. Xu and P. Tang. Dynamics of Heteropentameric Nicotinic Acetylcholine Receptor: Implications of the Gating Mechanism.  Proteins: Structure, Function, and Bioinformatics, 68, 948-960 (2007)


•    A. Szarecka, H. Meirovitch.  Optimization of GB/SA Solvation Model for Predicting the Structure of Surface Loops in Proteins.  J. Phys. Chem. B, 110, 2869-2880 (2006)
•    A. Szarecka, R.P. White, and H. Meirovitch.  Absolute Entropy and Free Energy of Fluids Using the Hypothetical Scanning Method. I. Calculation of Transition Probabilities from Local Grand Canonical Partition Functions.  J. Chem. Phys.  119, 12084-12095 (2003)


•    J. Cioslowski, A. Szarecka, and D. Moncrieff.  Energetics, Electronic Structures and Geometries of Naphthalene, Quinoline, and Isoquinoline Analogs of 1,2-didehydrobenzene.  Mol. Phys. 101, 1221-1225 (2003)
•    J. Cioslowski, A. Szarecka, and D. Moncrieff.  Energetics, Electronic Structures and Geometries of Didehydroazines.  Mol. Phys. 101, 839-858 (2003)
•    J. Cioslowski, A. Szarecka, and D. Moncrieff.  Conformations of the S5+ and S6+ Homocyclic Radical Cations.  Int. J. Quant. Chem. 90, 1049-1054 (2002)
•    J. Cioslowski, A. Szarecka, and D. Moncrieff.  Conformations and Thermodynamic Properties of Sulfur Homocycles. II. The Fluxional S8+ Radical Cation. Mol. Phys. 100, 1559-1566 (2002)
•    J. Cioslowski, N. Rao, A. Szarecka, and K. Pernal.  Theoretical Thermochemistry of the C60F18, C60F36, and C60F48 Fluorofullerenes.  Mol. Phys. 99, 1229-1232 (2001)
•    J. Cioslowski and A. Szarecka.  First Principles Conformational Analysis of the C36H36 Spheriphane, a Prototype Hydrocarbon Host Cage.  J. Comp. Chem. 22, 1279-1286 (2001)
•    J. Cioslowski, A. Szarecka, and D. Moncrieff.  Conformations and Thermodynamic Properties of Sulfur Homocycles. I. The S5, S6, S7, and S8 Molecules. J. Phys Chem. A  105, 501-505 (2001)


•    U. Rychlewska, A. Szarecka, J. Rychlewski, R. Mota?a.  Mediated Hydrogen Bond in the Alpha-Hydroxycarboxyl Group : X-ray Structure of (R,R)- Mono(N-methyl)Tartramide Monohydrate and Ab Initio Study of Model Systems.  Acta Crystallographica B 55, 617-625 (1999)
•    A. Szarecka, J. Rychlewski, U. Rychlewska.   Modes of Dimerization of Alpha-Hydroxyamide Group.  J. Mol. Struct.  474, 25-42 (1999)
•    A. Szarecka, J. Rychlewski, U. Rychlewska.  Hydrogen Bond Between Alpha-Hydroxycarboxyl, Alpha-Hydroxyester, and Alpha-Hydroxyamide Groups: Ab Initio Gas-Phase and Solution Study of a Double Linkage via Hydroxyl Group in Prog. Theoret. Chem. Phys., Vol. 2, A. Hernandez-Laguna (Ed.), p.355 (2000)
•    A. Szarecka, G. Day, P.J. Grout, S. Wilson.  An Investigation of the Effects of Basis Set Truncation and Electron Correlation in the Gas-Phase Conformers of the 2-Hydroxyacetamide.  Adv. Quant. Chem. 32, 93-107 (1998)
•    M. Hoffmann, A. Szarecka, J. Rychlewski.  Gas-Phase Conformational Analysis of (R,R)-Tartaric Acid, Its Diamide, N,N,N',N'-Tetramethyldiamide and Model Compounds.  Adv. Quant. Chem. 32, 109-125 (1998)
•    A. Szarecka, J. Rychlewski, U. Rychlewska.  Theoretical Solvation Models : Ab Initio Study of Molecular Aggregation.  Comput. Meth. Sci. Tech. 4, 25-33 (1998)
•    J. Gawronski, K. Gawronska, P. Skowronek, U. Rychlewska, B. Warzajtis, J. Rychlewski, M. Hoffmann, A. Szarecka.  Factors Affecting Conformation of (R,R)-Tartaric Acid Ester, Amide and Nitrile Derivatives: X-Ray Diffraction, Circular Dichroism, Nuclear Magnetic Resonance and Ab Initio Studies.  Tetrahedron 53, 6113-6144 (1997)
•    A. Szarecka, M. Hoffmann, U. Rychlewska, J. Rychlewski.  X-ray Diffraction and Theoretical Studies of the Methyl Ester of (R,R)-Tartaric Acid Monoamide : Semiempirical and Ab Initio Study of Some Model Compounds.  J. Mol. Structure 374, 363-372 (1996)

 

Page last modified September 18, 2014