Agnieszka Szarecka, Ph.D.
Professor of CMB
Graduate Program Director, Certificate in Bioinformatics and Genomics
KHS 3359 / Email: [email protected]
Office and advising hours in Fall 24
Monday 11:30-12:30 (KHS 3359)
Tuesday 2:30-3:30 (KHS 3359) and 5-6 (DEV 204A)
Wednesday 2-5 (KHS 3359)
Zoom meeting times available on MTWR / please email me to schedule.
Please email me if you are interested in the Certificate in Bioinformatics and Genomics Program for undergraduate or graduate students. Information on the Certificate Programs can also be found at https://www.gvsu.edu/cmb/certificates-93.htm. Email me also if you are interested in any of my research projects and would like to join my lab.
Education
Ph.D. Chemistry, 1999, Adam Mickiewicz University, Poznan, Poland
M.S. 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 - Computer Modeling and Drug Design / offered in Winter
CMB 451 / 551 - Bioinformatics for Life Sciences / offered in Fall and Winter
* CMB 452 and 451 are core courses for Certificate in Bioinformatics and Genomics. Please email me for more information.
CMB 150 - Biotechnology and Society / offered in Fall
CMB 495 - Perspectives in CMB / offered in Fall and Winter
CMB 501 - Scientific Communication / offered in Fall
My research projects involve computational modeling of biomolecules using a variety of techniques such as Molecular Dynamics and QM/MM simulations , elastic network models, protein-ligand docking, and electronic structure calculations.
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
* evolution of PEPC and RBCL proteins
* inhibition of 1,3-beta-glucan synthase by antifungal agents
* 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
* Klamer Z.L., June, C.M., Wawrzak Z., Taracila M.A., Grey J.A., Benn, A.M., Russell, C.P., Bonomo R.A., Powers R.A., Leonard D.A., Szarecka A. Structural and Dynamic Features of Acinetobacter baumannii OXA-66 β-Lactamase Explain Its Stability and Evolution of Novel Variants. Journal of Molecular Biology, 436(12):168603 (2024)
* Szarecka, A. and C. Dobson. A Tool to Teach Evolution of Protein Sequences and Structures: Prediction of Protein Structure by Building Homology Models. The American Biology Teacher, 86(2):108-115 (2024)
* Szarecka, A. and C. Dobson. Protein structure analysis: Introducing students to rational drug design. The American Biology Teacher, 81(6):1-7 (2019)
* N. Simakov, D. A. Leonard, J. C. Smith, T. Wymore, A. Szarecka. A Distal Disulfide Bridge in OXA-1 β-Lactamase Stabilizes the Catalytic Center and Alters the Dynamics of Specificity Determining Ω Loop. J. Phys. Chem. B, 121(15):3285-3296 (2017)
* C. M. June, T. J. Muckenthaler, E. C. Schroder, Z. L. Klamer, Z. Wawrzak, R. A. Powers, A. Szarecka, D. A. Leonard. The Structure of a Doripenem-Bound OXA-51 Class D β-Lactamase Variant with Enhanced Carbapenemase Activity. Protein Science, 25, 2152-2163 (2016)
* E.C. Schroder, Z.L. Klamer, A. Saral, K.A. Sugg, C.M. June, T. Wymore, A. Szarecka, D.A. Leonard. Clinical Variants of the Native Class D β-Lactamase of Acinetobacter baumannii Pose an Emerging Threat through Increased Hydrolytic Activity against Carbapenems. Antimicrobial Agents and Chemotherapy, 60, 6155-6164 (2016)
* J.M. Mitchell, J.R. Clasman, C.M. June, K.J. Kaitany, J.R. LaFleur, M.A. Taracila, N.V. Klinger, R.A. Bonomo, T. Wymore, A. Szarecka, R.A. Powers, D.A. Leonard. Structural Basis of Activity against Aztreonam and Extended Spectrum Cephalosporins for Two Carbapenem-Hydrolyzing Class D Beta-Lactamases from Acinetobacter baumannii. Biochemistry, 54, 1976-1987 (2015)
* 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 -lactamase family: residues governing the maintenance and diversity of function. Protein Engineering 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-Hydroxyam ide 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'-Tetr amethyldiamide 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)