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Biochemical kinetics in changing volumes.

100%
Pawłowski P. H., Zielenkiewicz P.
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vol. 51
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issue 1
231-243
EN
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.
2
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Mammalian DNA methyltransferases

100%
Siedlecki P., Zielenkiewicz P.
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2006
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vol. 53
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issue 2
245-256
EN
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.
3
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FEDMA - a simple algorithm for theoretical modeling of linear metabolic pathways: from fuzzy data sets to prediction and experiment.

100%
Pawlowski P. H., Zielenkiewicz P.
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2005
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vol. 52
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issue 1
71-86
EN
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.
4
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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
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1997
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vol. 44
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issue 3
549-556
5
Content available remote

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.
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2013
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vol. 60
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issue 2
239-247
EN
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.
6
Content available remote

MOFOID - not only the protein modeling server.

81%
Szczesny P., Wieczorek G., Zielenkiewicz P.
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2005
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vol. 52
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issue 1
267-269
EN
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/.
7
Content available remote

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

80%
Zielenkiewicz P., Rabczenko A.
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issue 2
87-91
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