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1

Theoretical model explaining the relationship between the molecular mass and the activation energy of the enzyme revealed by a large-scale analysis of bioinformatics data

100%
Pawlowski P. H., Zielenkiewicz P.
Acta Biochimica Polonica
|
2013
|
tom 60
|
nr 2
 A general dependence of the enzyme catalytic rate on its mass was revealed when a statistical analysis of 17065 records from the EMP database was performed. The estimated activation energy of the catalytic process decreases asymptotically with the enzyme molecular mass increase. The proposed theoretical model postulates the existence of an intermediate complex of the enzyme and the departing product. It allows for the explanation of the discovered mass-energy relationship, as an effect of the global enzyme-product interactions during complex dissociation. Fitted parameters of the model seem to be in agreement with those widely accepted for the van der Waals energy of molecular interactions. Their values also agree with the picture of the hydrogen bonding in the catalytic process and suggest that surface walk can be the favorable way of the product departure.
2

Mechanizmy krystalizacji bialek

100%
Kierzek A. M., Zielenkiewicz P.
Działalność Naukowa PAN. Wybrane Zagadnienia
|
1998
|
tom 06
45-47
3

Prediction of the BetaBp crystallin dimer structure by the complementary surfaces (CS) method

100%
Zielenkiewicz P., Rabczenko A.
Acta Biochimica Polonica
|
1987
|
tom 34
|
nr 2
4

Evolutionary analysis of eukaryotic interactome

100%
Kaczanowski S., Zielenkiewicz P.
Biological Letters
|
2005
|
tom 42
|
nr 2 Spec.Vol.
5

Mammalian DNA methyltransferases

100%
Siedlecki P., Zielenkiewicz P.
Acta Biochimica Polonica
|
2006
|
tom 53
|
nr 2
DNA methylation is an epigenetic process affecting gene expression and chromatin organization. It can heritably silence or activate transcription of genes without any change in their nucleotide sequences, and for a long time was not recognized as an important regulatory mechanism. However, during the recent years it has been shown that improper methylation, especially hypermethylation of promoter regions, is observed in nearly all steps of tumorigenesis. Aberrant methylation is also the cause of several major pathologies including developmental disorders involving chromosome instabilities and mental retardation. A great progress has been made in our understanding of the enzymatic machinery involved in establishing and maintaining methylation patterns. This allowed for the development of new diagnostic tools and epigenetic treatment therapies. The new approaches hold a great potential; several inhibitors of DNA methyltransferases have already shown very promising therapeutic effects.
6

Energy minimization of globular proteins with solvent effects included. Comparison of empirical solvation energy terms and explicit water treatment

100%
Kierzek A., Zielenkiewicz P.
Acta Biochimica Polonica
|
1997
|
tom 44
|
nr 3
The effect of an empirical solvation energy term on energy minimization of ribonuclease Tl was established using different sets of Atomic Solvation Pa­rameters. The results are compared to minimization in vacuo and in a 10 A water shell. The best solvent model as judged from the comparison to the crystal structure was an empirical solvation potential derived from free energies of transfer of amino-acid side-chain analogues from vapour to water. The use of this model causes, however, energy and gradient oscillations, which make it inapplicable with standard protocols of molecular dynamics simulations. The empirical solvation model which was found by other authors (von Freyberg et al., 1993, J. Mol. Biol. 233, 275-292) to give good results in the NMR structure refinement led to distortions of the ribonuclease native structure. The model based on statistical analysis of crystal structures did not perform better than minimization in vacuo.
7

FEDMA - a simple algorithm for theoretical modelling of linear metabolic pathways: from fuzzy data sets to prediction and experiment

100%
Pawlowski P. H., Zielenkiewicz P.
Acta Biochimica Polonica
|
2005
|
tom 52
|
nr 1
A theoretical model of a chain of irreversible Michaelis-Menten reactions proceeding inside a living cell, taking cell growth, division and subcellular compartmentation into account, was proposed. It became a basis for the construction of a “fuzzy” enzymatic data-modeling algorithm (FEDMA) - a procedure allowing the estimation of missing parameter values for the modeled system, in accordance both with the derived theoretical rules and the available experimental data. The obtained tool was tested to model the heme biosynthesis pathway in Saccharomyces cerevisiae, where about 40% of parameters remain unknown. The missing parameters estimated by means of FEDMA fall in the range of expected values.
8

Biochemical kinetics in changing volumes

100%
Pawlowski P. H., Zielenkiewicz P.
Acta Biochimica Polonica
|
2004
|
tom 51
|
nr 1
The need of taking into account the change of compartment volume when develop­ing chemical kinetics analysis inside the living cell is discussed. Literature models of a single enzymatic Michaelis-Menten process, glycolytic oscillations, and mitotic cyclin oscillations were tested with appropriate theoretical extension in the direction of volume modification allowance. Linear and exponential type of volume increase regimes were compared. Due to the above, in a growing cell damping of the ampli­tude, phase shift, and time pattern deformation of the metabolic rhythms considered were detected, depending on the volume change character. The perfomed computer simulations allow us to conclude that evolution of the cell volume can be an essential factor of the chemical kinetics in a growing cell. The phe­nomenon of additional metabolite oscillations caused by the periodic cell growth and division was theoretically predicted and mathematically described. Also, the hypoth­esis of the periodized state in the growing cell as the generalization of the steady-state was formulated.
9

MOFOID - not only the protein modelling server

80%
Szczesny P., Wieczorek G., Zielenkiewicz P.
Acta Biochimica Polonica
|
2005
|
tom 52
|
nr 1
MOFOID is a new server developed mainly for automated modeling of protein structures by their homology to the structures deposited in the PDB database. Selection of a template and calculation of the alignment is performed with the Smith-Waterman or Needleman-Wunsch algorithms implemented in the EMBOSS package. The final model is built and optimised with programs from the JACKAL package. The wide spectrum of options in the web-based interface and the possibility of uploading user’s own alignment make MOFOID a suitable platform for testing new approaches in the alignment building. The server is available at https://valis.ibb.waw.pl/mofoid/.
10

Czy i jak sie zwijac?

70%
Zielenkiewicz P.
Wiedza i Życie
|
1998
|
nr 03
20-21
11

Studies on mechanism of activation of tobacco Osmotic Stress-Activated Kinase

61%
Krlner A., Pekala I., Sikora J., Dadlez M., Siedlecki P., Zielenkiewicz P., Dobrowolska G.
Acta Biochimica Polonica
|
2003
|
tom 50
|
nr Supplement 1
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