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A groundwater flow model for the Wolin Island area, including glaciotectonic deformation

Hoc R., Sadurski A., Wiśniowski Z.

Geologos

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2018

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Vol. 24, No. 3

207--216

EN

During the construction of mathematical models for mapping hydrogeological conditions it is necessary to apply simplifications, both in the geological structure and in hydrogeological parameters used. The present note discusses problems surrounding the mapping of glaciotectonic disturbances that occur in the northern part of Wolin Island (northwest Poland). For this part of the island, a direct outflow of groundwater towards the Baltic Sea basin has been determined on the basis of geophysical survey results. An important feature in the hydrogeological conditions here is the isolation of groundwater from both the Baltic Sea and Szczecin Lagoon by clay with a Cretaceous xenolith. Such a geological structure explains the presence of perched water at considerable heights in zones close to the cliffs, without any significant hydraulic connection with surrounding reservoirs. Hydrogeological conditions of Wolin Island have been modelled using the Visual MODFLOW package v.4.2. In the vertical section, these conditions can be simplified to one aquifer (Pleistocene-Holocene), in which two aquifers can be distinguished. In a large part of the island, these remain in mutual hydraulic contact: layer I – upper, with an unconfined aquifer, and layer II – lower, with a confined aquifer, locally an unconfined one. The schematisation of hydrogeological conditions adopted here has allowed to reproduce present groundwater dynamics in the study area.

2

Fragment Aβ(18-41) presented within the CDR3 loop region of a shark immunoglobulin new antigen receptor single-variable domain antibody analyzed based on the fuzzy oil drop model

Banach M., Konieczny L., Wiśniowski Z., Roterman I.

Bio-Algorithms and Med-Systems

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2018

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Vol. 14, no. 3

art. no. 20180028

EN

The structure of amyloid Aβ(1-41) is the object of many papers due to the neurodegenerative processes induced by this amyloid. One of the ways to investigate the possible structural forms other than the amyloid is to incorporate the fragment of this peptide into the chain of immunoglobulin. Fragment Aβ(18-41) presented within the CDR3 loop region of a shark immunoglobulin new antigen receptor single-variable domain antibody is the object of this analysis. The structure of this hybrid is available in the PDB and analyzed based on the fuzzy oil drop model. The aim is to define the status of this fragment, revealing the possible fitting to the ordered form of the hydrophobic core. Simultaneously, the verification of the predisposition to complexation is possible.

3

Comparison of the structure of Aβ(1-40) amyloid with the one in complex with polyphenol ε-viniferin glucoside (EVG)

Dułak D., Banach M., Wiśniowski Z., Konieczny L., Roterman I.

Bio-Algorithms and Med-Systems

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2018

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Vol. 14, no. 2

art. no. 20180008

EN

The analysis of amyloid structures is much easier recently due to the availability of the solid-state nuclear magnetic resonance technique, which allows the determination of the 3D structure of amyloid forms. The amyloidogenic polypeptide Aβ(1-40) (PDB ID 2M9R, 2M9S) in its soluble form is the object of analysis in this paper. The solubility of this polypeptide is reached due to the presence of a complexed ligand: polyphenol ε-viniferin glucoside. Two forms of complexes available in the PDB were taken for analysis with respect to the presence of a hydrophobic core in the 3D structure of these complexes. The idealized hydrophobic core structure assumed to be accordant with the 3D Gauss function distribution was taken as the pattern. The aim of this analysis is the possible further comparison to the structures of the hydrophobic core present in amyloids. It is shown that the discordant (versus the 3D Gauss function) fragments present in amyloids appear accordant in the discussed complexes.

4

Chromatin 3D - will it make understanding of cancer transformation finally possible?

Drabik G., Kaszuba-Zwoińska J., Wiśniowski Z., Konieczny L., Roterman I.

Bio-Algorithms and Med-Systems

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2018

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Vol. 14, no. 1

art. no. 20180002

EN

Despite enormous progress in molecular analysis of cancer cell genomes, the mechanism of tumorigenesis remains unclear. The information present in the genome is not limited to the DNA sequence itself. Indeed, a significant portion of this information is concealed in the spatial structure of chromatin. Ongoing scientific studies that focus on the three-dimensional structure of chromatin raise hopes of arriving at a general explanation of the cancer transformation phenomenon.

5

The variability of protein structure with respect to the hydrophobic core

Banach M., Wiśniowski Z., Kalinowska B., Konieczny L., Roterman I.

Bio-Algorithms and Med-Systems

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2017

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Vol. 13, no. 2

63--67

EN

The application of the fuzzy oil drop model to the analysis of protein structure is shown using two proteins. The selection of these two examples is due to their opposite character. Two proteins were selected representing very high order and very high disorder with respect to the organized uni-central hydrophobic core in proteins (one centrally localized concentration of high hydrophobicity). These two cases are to show examples of the large spectrum of variability of local organization of the hydrophobic core in proteins. The importance of the observation presented in this paper is significant with respect to large sets of proteins discussed in separate publications.

6

Structure of hydrophobic core in plant carboxylesterase

Banach M., Konieczny L., Wiśniowski Z., Roterman I.

Bio-Algorithms and Med-Systems

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2017

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Vol. 13, no. 1

13--16

EN

The fuzzy oil drop model was applied to characterize the hydrophobic core structure in plant carboxylesterase. The characteristics revealed the status of β-sheets in the central part of the molecule as discordant as opposed to the expected hydrophobicity distribution. Particularly, the β-strands and helices in close proximity to the enzymatic residues recognized as discordant with respect to the ideal hydrophobicity distribution of hydrophobic core are of high importance. It is assumed that this local irregularity is the form of coding the specificity of enzymes. The protein under consideration appears to be the next example proving this assumption.

7

Role of the hydrophobic core in cytoskeleton protein: cardiac myosin binding protein C

Gołda M., Banach M., Wiśniowski Z., Ziajka W., Roterman I.

Bio-Algorithms and Med-Systems

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2017

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Vol. 13, no. 3

161--165

EN

Cardiac myosin binding protein C is the object of analysis presented in this paper. The fuzzy oil drop model was applied to analyze the status of the hydrophobic core in two forms of this protein: WT and R502W mutant. The status of the mutant is revealed to be of lower stability than the WT form. The high order of the hydrophobic core is interpreted as the factor of stability of the tertiary structure. The muscle proteins, which undergo significant structural changes as the consequence of external stretching forces, are expected to return to initial structures after the release of an external force. The mutant R502W appears to represent lower stability; thus, the return to the initial structure may be of lower probability. The comparable analysis to other muscle domains (titin) and immunoglobulin domains suggests the very subtle relation to the biological activity of these proteins.

8

Mechanism of ligand binding – PDZ domain taken as example

Dułak D., Banach M., Wiśniowski Z., Konieczny L., Roterman I.

Bio-Algorithms and Med-Systems

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2017

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Vol. 13, no. 4

175--178

EN

Abstract: The mechanism of specific ligand binding by proteins is discussed using the PDZ domain complexing the pentapeptide. This process is critical for clustering the membrane ion channel. The traditional model based on the Beta-sheet extension by complexed pentapeptide is interpreted as a hydrophobic core extension supported by additional Beta-strand generated by complexed pentapeptide. The explanation is based on the fuzzy oil drop model applied to the crystal structure of PDZ-pentapeptide.

9

Chain-chain complexation and heme binding in haemoglobin with respect to the hydrophobic core structure

Ptak M., Banach M., Wiśniowski Z., Konieczny L., Roterman I.

Bio-Algorithms and Med-Systems

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2017

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Vol. 13, no. 4

179--185

EN

Heme binding by proteins and protein-protein complexation are the processes strongly related to the biological activity of proteins. The mechanism of these processes has not been still recognised. These phenomena are presented using haemoglobin as the example. Half of the mature haemoglobin (one α-chain and one β-chain) treated as a dissociation step in haemoglobin degradation reveals a specific change in heme binding after dissociation. This phenomenon is the object of analysis that interprets the structure of both complexes (tetramer and dimer) with respect to their hydrophobic core structure. The results suggest the higher stability of the complex in the form of one α-chain and one β-chain with respect to the hydrophobic core.

10

Ab initio protein structure prediction – the hydrophobicity distribution analysis

Evangelista G., Minervini G., Polticelli F, Malawski M., Szepieniec T., Flis Ł., Prymula K., Kochańczyk M., Matczyńska E., Wiśniowski Z., Salapa K., Banach M., Roterman I.

Bio-Algorithms and Med-Systems

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2011

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Vol. 7, no. 2

5--12

EN

The three-dimensional structures generated for 20 “never born proteins” (NBP – random amino acid sequence with no significant homology to existing proteins) using two different techniques: ROSETTA (called R in the paper) and “fuzzy oil drop” model (called S in the paper) were compared to estimate the accordance with the assumed model estimating the influence of an external force field on the final structure of the protein. Selected structures are those corresponding to the highest (10 proteins) and lowest (10 proteins) RMS-D values obtained measuring the similarity between the R and S structures. The R structures generated according to an internal force field (the individual inter-molecular interaction) including solvation effects were analyzed using the “fuzzy oil drop” model as target model. The second applied model “fuzzy oil drop” generated structures characterized by an ordered hydrophobic core structure. 13 of the 20 selected S structures appeared to be accordant with the “fuzzy oil drop” model while 6 out of the 20 structures appeared to be accordant with external force field for R structures which suggests a general interpretation of the influence of an external force field on the folding simulation.

11

Warunki hydrogeologiczne Pojezierza Myśliborskiego i obszarów sąsiednich w granicach jednolitej części wód podziemnych nr 23

Wiśniowski Z.

Przegląd Geologiczny

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2010

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Vol. 58, nr 8

704-711

EN

The area of the GWB (groundwater body) No. 23 is a part of West Pomeranian and Lubusz Voivodeships and the water region of the Lower Odra and Przymorze Zachodnie. It includes districts: gryfiński, myśliborski, pyrzycki and gorzowski. The geological conditions of the study area are visibly corresponding to the deep tectonic structures of Szczecin basin and Gorzów block. Fresh groundwater is occurring here in porous sediments of the Quaternary, Neogene and Paleogene and fissured-porous rocks of the Upper Cretaceous. In the area of Szczecin basin, structures of Cretaceous aquifers are associated with Mesozoic secondary anticlines. In the Odra valley the aquifers are constituted from shallow laying Quaternary sediments (depth: 10 to 50 m). Thickness of Upper Cretaceous marbles leading fresh water does not exceed 30 m. The primal structures of the youngest sediments of Neogene- Miocene (-50 to -80 m above sea level) were disrupted during the earlier glaciations. During this geological period many of the geomorphological forms - egzaration depressions and glacitectonic extrusions formed from the Paleogene and Neogene sediments, and also elevations built from xenoliths coming from deeper rock bed, were formed by the complex of different geomorphological processes. The sediments of Neogene-Miocene have variable thickness, from a few meters within the deep erosion structures, up to 200 m within the Tertiary elevations. The Quaternary aquifers occur in multilayer system of groundwater layers constituted by fluvioglacial and fluvial sedimentation (sand and gravel) during successive glaciations and interglacials. Aquifers are often divided in multiple different layers, isolated by low-permeable layers of clays or glacial silts and proglacial clays. There are selected few regional aquifers: four Quaternary aquifers - first unconfined; upper, interior and lower intertill aquifers; two Miocene - upper and lower aquifers and one Cretaceous aquifer. The thickness of individual aquifer is variable; it's locally up to 50 m. The GWB No. 23 aquifers were aggregated to 3 levels (hydrogeological zones) belonging to different systems of groundwater flow: I level - first unconfined and upper intertill aquifer (locally Cretaceous aquifer); II level - interior intertill aquifer; III - lower intertill aquifer and upper Miocene aquifer. Because of the multilayer character, the GWB No. 23 groundwater system is very rich in water.