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Edyta Dyguda-Kazimierowicz, Ph.D.
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Research profile
Development and validation of theoretical models of catalytic and inhibitory activity of enzymes. Quantum chemical modeling of reaction pathways, especially with respect to the influence of enzyme environment. In silico simulation of the mutations within the active site of enzymes.
Publications
- A. Lodola, L. Capoferri, S. Rivara, E. Chudyk, J. Sirirak, E. Dyguda-Kazimierowicz, W. A. Sokalski, M. Mileni, G. Tarzia, D. Piomelli, M. Mor, A. J. Mulholland, Understanding the role of carbamate reactivity in fatty acid amide hydrolase inhibition by QM/MM mechanistic modelling, Chem.Comm. 47 2517-2519 (2011) DOI
- P. Szarek, E. Dyguda-Kazimierowicz, A. Tachibana, W. A. Sokalski, The physical nature of intermolecular interactions within cAMP-dependent protein kinase active site: differential transition state stabilization in phosphoryl transfer reaction, J.Phys.Chem.B 112 (37), 11819-11826 (2008) DOI [pdf available upon request]
- E. Dyguda-Kazimierowicz, W. A. Sokalski, J. Leszczynski, Gas phase mechanisms of degradation of hazardous organophosphorus compounds: do they follow a common pattern of alkaline hydrolysis reaction as in phosphotriesterase? , J.Phys.Chem.B 112 (32), 9982-9991 (2008) DOI
- R. Grzywa, E. Dyguda-Kazimierowicz, M. Sienczyk, M. Feliks, W. A. Sokalski, J. Oleksyszyn, The Molecular Basis of Urokinase Inhibition: From the Nonempirical Analysis of Intermolecular Interactions to the Prediction of Binding Affinity, J.Mol.Model. 13 (6-7), 677-683 (2007) DOI [available on request]
- E. Dyguda-Kazimierowicz, W. A. Sokalski, Non-empirical study of phosphorylation reaction catalyzed by 4-methyl-5-beta-hydroxyethylthiazole kinase. Relevance of the theory of intermolecular interactions., J.Mol.Model. 13 (6-7), 839-849 (2007) DOI
- L. Berlicki, J. Grembecka, E. Dyguda-Kazimierowicz, P. Kafarski, W. A. Sokalski, From inhibitors of LAP to inhibitors of PAL: Lessons from molecular modeling and experimental interface, In: Molecular Materials with Specific Interactions: Modeling and Design, Vol. 4, Chapter 8, p. 365-398 Editor: W.A. Sokalski, Series: Challenges and Advances in Computational Chemistry and Physics, Springer 2007 [more]
- S. Grabowski, W. A. Sokalski, E. Dyguda-Kazimierowicz, J. Leszczynski, Quantitative Classification of Covalent and Noncovalent H-bonds, J.Phys.Chem.B 110 (13), 6444-6446 (2006) DOI [copy available on request]
- E. Dyguda-Kazimierowicz, J. Grembecka, W. A. Sokalski, J. Leszczynski, Origins of the activity of pal and lap enzyme inhibitors: toward ab initio binding affinity prediction, J. Am. Chem. Soc. 127 (6), 1658-1659 (2005) DOI [copy available on request]
- E. Dyguda-Kazimierowicz, B. Szefczyk, W. A. Sokalski, The mechanism of phosphoryl transfer reaction and the role of active site residues on the basis of ribokinase-like kinases, Int. J. Mol. Sci. 5 (4), 141-153 (2004)
Conference presentations
E. Dyguda-Kazimierowicz, W. A. Sokalski, J. Leszczyński; oral presentation: "Hazardous organophosphates: computational insight into gas phase alkaline hydrolysis of phosphorus-ester bond" 6th Southern School on Computational Chemistry, Jackson, Mississippi, USA, 07-08.IV.2006 E. Dyguda, P. Szarek, W. A. Sokalski, Y. Cheng, Y. Zhang J. A. McCammon, J. Leszczyński; poster: "Determinants of kinases catalytic efficiency: from analysis of interactions in the protein kinase A and thiazole kinase active sites to catalysts design" Modeling Interactions in Biomolecules II, Prague, Czech Republic, 5-9.IX.2005 E. Dyguda, W. A. Sokalski, J. Leszczyński; oral presentation: "Gas phase alkaline hydrolysis of phosphotriesterase substrates" Summer Institute in Computational Chemistry, Computational Center for Molecular Structure and Interactions (CCMSI) at Jackson State University, Chattanooga, Tennessee, USA, 25-28.VII.2005 E. Dyguda, W. A. Sokalski, J. Leszczyński; poster: "Toxic phosphotriesters hydrolysis: do they posses common gas phase mechanisms related to the phosphotriesterase catalytic properties?" Fifth Congress of the International Society for Theoretical Chemical Physics, New Orleans, Louisiana, USA, 20-26.VII.2005 P. Szarek, E. Dyguda, W. A. Sokalski, Y. Cheng, Y. Zhang J. A. McCammon; poster: "The physical nature of cAMP-dependent protein kinase catalytic activity: ab initio differential transition state stabilization analysis of the key active site residues" 4th International Conference Inhibitors of Protein Kinases, Warsaw, 25-29.VI.2005 E. Dyguda, J. Grembecka, W. A. Sokalski, J. Leszczynski; poster: "Ab initio prediction of binding affinity: determinants of phenylalanine ammonia-lyase inhibition" Modelling and Design of Molecular Materials, Wrocław, 16-20.IX.2004
Tematy prac dyplomowych i badawczych (Research topics for students)
- Badanie sposobu wiązania inhibitorów amoniakoliazy fenyloalaninowej z wykorzystaniem technik modelowania molekularnego (dokowanie).
- Analiza natury oddziaływań w centrum aktywnym enzymu jako narzędzie do przewidywania powinowactwa wiązania inhibitorów.
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