Wyniki wyszukiwania

1

A comparative study of the primary structures of protein and sugar kinases

100%

Leluk J., Lesyng B.

Cellular and Molecular Biology Letters

|

2003

|

tom 08

|

nr 2A

2

Modelling the 3D structure of protein kinase C gamma and its interaction with specific inhibitor, chelerythrine

81%

Brodacki P., Ginalski K., Lesyng B.

Cellular and Molecular Biology Letters

|

2001

|

tom 06

|

nr 2B

548

3

Prediction of protonation states of phosphotyrosine in short peptides and proteins

81%

Wojciechowski M., Grycuk T., Antosiewicz J., Lesyng B.

Cellular and Molecular Biology Letters

|

2001

|

tom 06

|

nr 2B

552-553

4

Quantum-mechanical calculations of the potential energy function for the phosphate transfer in model systems

81%

Ginalski K., Grochowski P., Lesyng B.

Cellular and Molecular Biology Letters

|

2001

|

tom 06

|

nr 2B

549

5

Modelling of active forms of protein kinases: p38 - a case study

81%

Ginalski K., Lesyng B., Sowadski J., Wojciechowski M.

Acta Biochimica Polonica

|

1997

|

tom 44

|

nr 3

An active form of p38 protein kinase, belonging to the mitogen-activated protein kinases subfamily, has been designed based on crystallographically known structures of two other kinases, an active form of protein kinase A (PKA) and an inactive form of extracellular signal-regulated kinase 2 (ERK2). The modelling procedure is described. Its general scheme can also be applied to other kinases. The structure of the active forms of p38 and PKA is very similar in the region which binds the substrate. The ATP-binding mode is very similar in the active forms of all the three studied kinases. Models of the active forms allow for further studies on transphosphorylation processes at the molecular level, and modelling of inhibitors competitive with ATP and/or substrates.

6

Structural basis of oncogenesis caused by point mutations in the kinase domain of the MET proto-oncogene

81%

Miller M., Zbar B., Ginalski K., Lesyng B.

Cellular and Molecular Biology Letters

|

1998

|

tom 03

|

nr 3

7

Modelling of insulin receptor tyrosine kinase in its active form: a case study for validation of theoretical methods

81%

Ginalski K., Wojciechowski M., Lesyng B.

Acta Biochimica Polonica

|

1999

|

tom 46

|

nr 3

An active form of an insulin receptor tyrosine kinase (IRK) catalytic core was modelled based on its experimentally known inactive form and the active form of a serine/threonine kinase, protein kinase A (PKA). This theoretical model was compared with the crystallographic structure of the active form of IRK reported later. The structures are very similar, which shows that all the most important features and interactions have been taken into account in the modelling procedure. The elaborated procedure can be applied to other tyrosine kinases. This would allow designing of a wide class of tyrosine kinase inhibitors, very important potential anti-cancer and/or anti-viral drugs.

8

SCC DFT-TB energy calculations of the phosphoryl transfer reaction in the PKA active site

81%

Rakowski F., Grochowski P., Lesyng B.

Cellular and Molecular Biology Letters

|

2003

|

tom 08

|

nr 2A

9

Classification and characterization of natural protein inhibitors of protein kinases

81%

Meglicz A., Leluk J., Lesyng B.

Cellular and Molecular Biology Letters

|

2005

|

tom 10

|

nr Suppl.2

10

A simple model for predicting the free energy of binding between anthracycline antibiotics and DNA

71%

Rudnicki W. R., Kurzepa M., Szczepanik T., Priebe W., Lesyng B.

Acta Biochimica Polonica

|

2000

|

tom 47

|

nr 1

A theoretical model for predicting the free energy of binding between anthracycline antibiotics and DNA was developed using the electron density functional (DFT) and molecular mechanics (MM) methods. Partial DFT-ESP charges were used in calculating the MM binding energies for complexes formed between anthracycline antibiotics and oligodeoxynucleotides. These energies were then compared with experimental binding free energies. The good correlation between the experimental and theoretical energies allowed us to propose a model for predicting the binding free energy for derivatives of anthracycline antibiotics and for quickly screening new anthracycline derivatives.

11

Protonation equilibria of residues in protein kinases and phosphatases. Poisson-Boltzmann model studies

71%

Antosiewicz J., Blachut-Okrasinska E., Lesyng B., Briggs J. M., McCammon J.

Cellular and Molecular Biology Letters

|

1998

|

tom 03

|

nr 3

12

Onkogenic activation caused by poitn mutations in the kinase domain of the met proto-oncogene: molecular modeling studies

61%

Miller M., Ginalski K., Lesyng B., Nakaigawa N., Schmidt L., Zbar B.

Cellular and Molecular Biology Letters

|

2001

|

tom 06

|

nr 2B

550

13

Binding of SPXK- and APXK-peptide motifs to At-rich DNA. Experimental and theoretical studies

61%

Brzeski J., Grycuk T., Lipkowski A. W., Rudnicki W., Lesyng B., Jerzmanowski A.

Acta Biochimica Polonica

|

1998

|

tom 45

|

nr 1

The binding properties of the SPXK- and APXK-type peptides to the AT-rich DNA fragments of different length were studied by measuring the competition of peptides with Hoechst 33258 dye for DNA binding and by the gel shift assay analysis. In parallel to the experimental studies, molecular modeling techniques were used to analyze possible binding modes of the SPXZ and APXK motifs to the AT-rich DNA. The results of the competition measurements and gel shift assays suggest that serine at the i-1 position (i is proline) can be replaced by alanine without affecting the binding properties of the motif. Thus, the presence of the conserved serine in this motif in many DNA-binding proteins is probably not dictated by structural requirements. Based on the results of molecular modeling studies we propose that the binding mode of the SPXK- type motifs to the AT-rich DNA resembles closely that between the N-terminal arm of the homeodomain and DNA. This model confirms that serine in the SPXK motifs is not essential for the DNA binding. The model also indicates that if X in the motif is glutamic acid, this residue is probably protonated in the complex with DNA.

Ograniczanie wyników

A comparative study of the primary structures of protein and sugar kinases

Modelling the 3D structure of protein kinase C gamma and its interaction with specific inhibitor, chelerythrine

Prediction of protonation states of phosphotyrosine in short peptides and proteins

Quantum-mechanical calculations of the potential energy function for the phosphate transfer in model systems

Modelling of active forms of protein kinases: p38 - a case study

Structural basis of oncogenesis caused by point mutations in the kinase domain of the MET proto-oncogene

Modelling of insulin receptor tyrosine kinase in its active form: a case study for validation of theoretical methods

SCC DFT-TB energy calculations of the phosphoryl transfer reaction in the PKA active site

Classification and characterization of natural protein inhibitors of protein kinases

A simple model for predicting the free energy of binding between anthracycline antibiotics and DNA

Protonation equilibria of residues in protein kinases and phosphatases. Poisson-Boltzmann model studies

Onkogenic activation caused by poitn mutations in the kinase domain of the met proto-oncogene: molecular modeling studies

Binding of SPXK- and APXK-peptide motifs to At-rich DNA. Experimental and theoretical studies