Search results

1

Molecular docking-based test for affinities of two ligands toward vasopressin and oxytocin receptors.

100%

Ślusarz R., Kaźmierkiewicz R., Giełdoń A., Lammek B., Ciarkowski J.

Acta Biochimica Polonica

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2001

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vol. 48

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issue 1

131-135

EN

Molecular docking simulations are now fast developing area of research. In this work we describe an effective procedure of preparation of the receptor-ligand complexes. The amino-acid residues involved in ligand binding were identified and described.

2

Molecular dynamics simulation of zirconia melting

100%

Davis S., Belonoshko A., Rosengren A., Duin A., Johansson B.

Open Physics

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2010

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vol. 8

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issue 5

789-797

EN

The melting point for the tetragonal and cubic phases of zirconia (ZrO2) was computed using Z-method microcanonical molecular dynamics simulations for two different interaction models: the empirical Lewis-Catlow potential versus the relatively new reactive force field (ReaxFF) model. While both models reproduce the stability of the cubic phase over the tetragonal phase at high temperatures, ReaxFF also gives approximately the correct melting point, around 2900 K, whereas the Lewis-Catlow estimate is above 6000 K.

3

Computational determination of radiation damage effects on DNA structure

100%

Pinak M.

Open Physics

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2003

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vol. 1

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issue 1

179-190

EN

Molecular dynamics (MD) studies of several radiation originated lesions on the DNA molecules are presented. The pyrimidine lesions (cytosinyl radical, thymine dimer, thymine glycol) and purine lesion (8-oxoguanine) were subjected to the MD simulations for several hundred picoseconds using MD simulation code AMBER 5.0 (4.0). The simulations were performed for fully dissolved solute molecules in water. Significant structural changes in the DNA double helical structure were observed in all cases which may be categorized as: a) the breaking of hydrogen bonds network between complementary bases and resulted opening of the double helix (cytosinyl, radical, 8-oxoguanine); b) the sharp bending of the DNA helix centered at the lesion site (thymine dimer, thymine glycol); and c) the flippingout of adenine on the strand complementary to the lesion (8-oxoguanine). These changes related to the overall collapsing of the double helical structure around the lesion, are expected to facilitate the docking of the repair enzyme into the DNA in the formation of DNA-enzyme complex. The stable DNA-enzyme complex is a necessary condition for the onset of the enzymatic repair process. In addition to structural changes, specific values of electrostatic interaction energy were determined at several lesion sites (thymine dimer, thymine glycol and 8-oxoguanine). This lesion-specific electrostatic energy is a factor that enables repair enzyme to discriminate lesion from the native site during the scanning of the DNA surface.

4

Molecular dynamics simulations of EXAFS in germanium

100%

Timoshenko J., Kuzmin A., Purans J.

Open Physics

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2011

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vol. 9

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issue 3

710-715

EN

Classical molecular dynamics simulations have been performed for crystalline germanium with the aim to estimate the thermal effects within the first three coordination shells and their influence on the single-scattering and multiple-scattering contributions to the Ge K-edge extended x-ray absorption fine structure (EXAFS).

5

Effect of antisense peptide binding on the dimerization of human cystatin C - gel electrophoresis and molecular modeling studies.

100%

Stachowiak K., Rodziewicz-Motowidło S., Sosnowska R., Kasprzykowski F., Łankiewicz L., Grubb A., Grzonka Z.

Acta Biochimica Polonica

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2004

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vol. 51

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issue 1

153-160

EN

Human cystatin C (HCC) shows a tendency to dimerize. This process is particularly easy in the case of the L68Q HCC mutant and might lead to formation of amyloid deposits in brain arteries of young adults. Our purpose was to find ligands of monomeric HCC that can prevent its dimerization. Eleven antisense peptide ligands of monomeric HCC were designed and synthesized. The influence of these ligands on HCC dimerization was studied using gel electrophoresis and molecular modeling methods. The results suggest that all the designed peptides interact with monomeric HCC facilitating its dimerization rather than preventing it.

6

Theoretical studies of binding modes of two covalent inhibitors of cysteine proteases.

88%

Drabik P., Politowska E., Czaplewski C., Kasprzykowski F., Łankiewicz L., Ciarkowski J.

Acta Biochimica Polonica

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2000

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vol. 47

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issue 4

1061-1066

EN

Physiological and pathological roles of cysteine proteases make them important targets for inhibitor development. Although highly potent inhibitors of this group of enzymes are known, their major drawback is a lack of sufficient specificity. Two cysteine protease covalent inhibitors, viz. (i) Z-RL-deoxo-V-peptide-epoxysuccinyl hybrid, and (ii) Z-RLVG-methyl-, have been developed and modeled in the catalytic pocket of papain, an archetypal thiol protease. A number of configurations have been generated and relaxed for each system using the AMBER force field. The catalytic pockets S3 and S4 appear rather elusive in view of the observed inhibitors' flexibility. This suggest rather limited chances for the development of selective structure-based inhibitors of thiol proteases, designed to exploit differences in the structure of catalytic pockets of various members of this family.

7

Theoretical Predictions of Lattice Parameters and Mechanical Properties of Pentaerythritol Tetranitrate under the Temperature and Pressure by Molecular Dynamics Simulations

88%

Tan J. J., Hu C., Li Y., Ge N., Chen T., Ji G.

Acta Physica Polonica A

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2017

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vol. 131

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issue 2

318-323

EN

Molecular dynamics simulations with condensed-phase optimized molecular potentials for atomistic simulation studies force field are performed to investigate the structure, equation of state, and mechanical properties of high energetic material pentaerythritol tetranitrate. The equilibrium structural parameters, pressure-volume relationship and elastic constants at ambient conditions agree excellently with experiments. In addition, fitting the pressure-volume data to the Birch-Murnaghan or Murnaghan equation of state, the bulk modulus B₀ and its first pressure derivative B'₀ are obtained. Moreover, the elastic constants are calculated in the pressure range of 0-10 GPa at room temperature and in the temperature range of 200-400 K at the standard pressure, respectively. By the Voigt-Reuss-Hill approximation, the mechanical properties such as bulk modulus B, shear modulus G, and the Young modulus E are also obtained successfully. The predicted physical properties under temperature and pressure can provide powerful guidelines for the engineering application and further experimental investigations.

8

Theoretical models of catalytic domains of protein phosphatases 1 and 2A with Zn2+ and Mn2+ metal dications and putative bioligands in their catalytic centers.

88%

Woźniak-Celmer E., Ołdziej S., Ciarkowski J.

Acta Biochimica Polonica

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2001

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vol. 48

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issue 1

35-52

EN

The oligomeric metalloenzymes protein phosphatases dephosphorylate OH groups of Ser/Thr or Tyr residues of proteins whose actions depend on the phosphorus signal. The catalytic units of Ser/Thr protein phosphatases 1, 2A and 2B (PP1c, PP2Ac and PP2Bc, respectively), which exhibit about 45% sequence similarity, have their active centers practically identical. This feature strongly suggests that the unknown structure of PP2Ac could be successfully homology-modeled from the known structures of PP1c and/or PP2Bc. Initially, a theoretical model of PP1c was built, including a phosphate and a metal dication in its catalytic site. The latter was modeled, together with a structural hydroxyl anion, as a triangular pseudo-molecule (Zno or Mno), composed of two metal cations (double Zn2+ or Mn2+, respectively) and the OH- group. To the free PP1c two inhibitor sequences R29RRRPpTPAMLFR40 of DARPP-32 and R30RRRPpTPATLVLT42 of Inhibitor-1, and two putative substrate sequences LRRApSVA and QRRQRKpRRTI were subsequently docked. In the next step, a free PP2Ac model was built via homology re-modeling of the PP1c template and the same four sequences were docked to it. Thus, together, 20 starting model complexes were built, allowing for combination of the Zno and Mno pseudo-molecules, free enzymes and the peptide ligands docked in the catalytic sites of PP1c and PP2Ac. All models were subsequently subjected to 250-300 ps molecular dynamics using the AMBER 5.0 program. The equilibrated trajectories of the final 50 ps were taken for further analyses. The theoretical models of PP1c complexes, irrespective of the dication type, exhibited increased mobilities in the following residue ranges: 195-200, 273-278, 287-209 for the inhibitor sequences and 21-25, 194-200, 222-227, 261, 299-302 for the substrate sequences. Paradoxically, the analogous PP2Ac models appeared much more stable in similar simulations, since only their "prosegment" residues 6-10 and 14-18 exhibited an increased mobility in the inhibitor complexes while no areas of increased mobility were found in the substrate complexes. Another general observation was that the complexes with Mn dications were more stable than those with Zn dications for both PP1c and PP2Ac units.

9

Statistical Properties of a Polymer Chain in the Environment with Low Concentration of Nanoparticles

88%

A. Tsehay D., Luo M.-B.

Acta Physica Polonica A

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2018

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vol. 133

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issue 5

1274-1280

EN

We have investigated the statistical properties of polymer in the environment with low concentration of nanoparticles by using large-scale molecular dynamics simulations. The scaling law for the mean square radius of gyration was examined and simulation results for the polymer lengths 64≤N≤144 yielding a reasonably accurate value of the Flory exponent ν=0.58 at weak polymer-nanoparticle interaction ε_{PN}. Within the same range of N, the mean asphericity of the chain is independent of N. We found that the polymer behaves like a self-avoiding walk chain at small ε_{PN} and a compact sphere at large ε_{PN}. The results are attributed to the increase in the contact between polymer and nanoparticles with increasing ε_{PN}. Normal diffusions of polymer are always observed at whatever ε_{PN} and size and concentration of nanoparticles. Our result shows that the normal diffusion behavior of polymer is independent of polymer's state even though there is a phase transition from a desorbed polymer phase at small ε_{PN} to an adsorbed polymer phase at large ε_{PN}.

10

Estimation of phonon relaxation time for silicon by means of using the velocity autocorrelation function of atoms in molecular dynamics

88%

Andriyevsky B., Maliński M., Buryło Ł., Stadnyk V. Y., Romanyuk M. O., Piekarski J., Andriyevska L.

Bulletin of the Polish Academy of Sciences: Technical Sciences

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2019

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issue 3

11

Free energy of helix propagation in short polyalanine chains determined from peptide growth simulations of La3+-binding model peptides. Comparison with experimental data

88%

Maciejczyk M., Hermans J., Bierzyński A.

Acta Biochimica Polonica

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2006

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vol. 53

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issue 1

121-130

EN

Molecular dynamics (MD) is, at present, a unique tool making it possible to study, at the atomic level, conformational transitions in peptides and proteins. Nevertheless, because MD calculations are always based on a more or less approximate physical model, using a set of approximate parameters, their reliability must be tested by comparison with experimental data. Unfortunately, it is very difficult to find a peptide system in which conformational transitions can be studied both experimentally and using MD simulations so that a direct comparison of the results obtained in both ways could be made. Such a system, containing a rigid α-helix nucleus stabilized by La3+ coordination to a 12-residue sequence taken from an EF-hand protein has recently been used to determine experimentally the helix propagation parameters in very short polyalanine segments (Goch et al. (2003) Biochemistry 42: 6840-6847). The same parameters were calculated here for the same peptide system using the peptide growth simulation method with, alternatively, charmm 22 and cedar potential energy functions. The calculated free energies of the helix-coil transition are about two times too large for cedar and even three times too large for charmm 22, as compared with the experimental values. We suggest that these discrepancies have their origin in the incorrect representation of unfolded peptide backbone in solution by the molecular mechanics force fields.

12

MOLECULAR DYNAMICS SIMULATIONS OF THE AFFINITY OF CHITIN AND CHITOSAN FOR COLLAGEN: THE EFFECT OF pH AND THE PRESENCE OF SODIUM AND CALCIUM CATIONS

88%

Przybyłek M., Bełdowski P.

Progress on Chemistry and Application of Chitin and its Derivatives

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2023

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vol. 28

136-150

EN

Chitosan and chitin are promising biopolymers used in many areas including biomedical applications, such as tissue engineering and viscosupplementation. Chitosan shares similar properties with hyaluronan, a natural component of synovial fluid, making it a good candidate for joint disease treatment. The structural and energetic consequences of intermolecular interactions are crucial for understanding the biolubrication phenomenon and other important biomedical features. However, the properties of biopolymers, including their complexation abilities, are influenced by the nature of the aqueous medium with which they interact. In this study, we employed molecular dynamics simulations to describe the effect of pH and the presence of sodium and calcium cations on the stability of molecular complexes formed by collagen type II with chitin and chitosan oligosaccharides. Based on Gibbs free energy of binding, all considered complexes are thermodynamically stable over the entire pH range. The affinity between chitosan oligosaccharide and collagen is highly influenced by pH, while oligomeric chitin shows no pH-dependent effect on the stability of molecular assemblies with collagen. On the other hand, the presence of sodium and calcium cations has a negligible effect on the affinity of chitin and chitosan for collagen.

13

Nanovortex evolution in entrance part of the 2D open type long nanocavity

75%

Kordos A., Kucaba-Piętal A.

Bulletin of the Polish Academy of Sciences: Technical Sciences

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2018

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issue 2

14

Structural analysis of base mispairing in DNA containing oxidative guanine lesion

75%

Fujimoto H., Pinak M., Nemoto T., Bunta J.

Open Physics

|

2007

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vol. 5

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issue 1

49-61

EN

Classical molecular dynamics methods were used to analyze the importance of 8-oxoguanine (8-oxoG) pairing with other DNA bases in order to determine the impact of oxidative guanine lesions on DNA structure. Six lesioned molecules, each containing 8-oxoG mispaired with one of the four normal bases on the the opposite strand at the center of 40-mer DNA, and one non-damaged DNA molecule, were simulated for 2 nanoseconds of real time. The 8-oxoG lesioned bases were found to incorporate opposite all normal bases. There are observed conformational and energetical differences among these parings. 8-oxoG in anti-form creates firm hydrogen bonds with cytosine and this bonding has a strong attractive electrostatic interaction energy similar to that of a native base pair-guanine to cytosine. Meanwhile, it does not form a stable base pair with purine bases (adenine and guanine) nor with the pyrimidine base thymine. On the other hand, the 8-oxoG in syn-form was found to pair with adenine.

Refine search results

Molecular docking-based test for affinities of two ligands toward vasopressin and oxytocin receptors.

Molecular dynamics simulation of zirconia melting

Computational determination of radiation damage effects on DNA structure

Molecular dynamics simulations of EXAFS in germanium

Effect of antisense peptide binding on the dimerization of human cystatin C - gel electrophoresis and molecular modeling studies.

Theoretical studies of binding modes of two covalent inhibitors of cysteine proteases.

Theoretical Predictions of Lattice Parameters and Mechanical Properties of Pentaerythritol Tetranitrate under the Temperature and Pressure by Molecular Dynamics Simulations

Theoretical models of catalytic domains of protein phosphatases 1 and 2A with Zn2+ and Mn2+ metal dications and putative bioligands in their catalytic centers.

Statistical Properties of a Polymer Chain in the Environment with Low Concentration of Nanoparticles

Estimation of phonon relaxation time for silicon by means of using the velocity autocorrelation function of atoms in molecular dynamics

Free energy of helix propagation in short polyalanine chains determined from peptide growth simulations of La3+-binding model peptides. Comparison with experimental data

MOLECULAR DYNAMICS SIMULATIONS OF THE AFFINITY OF CHITIN AND CHITOSAN FOR COLLAGEN: THE EFFECT OF pH AND THE PRESENCE OF SODIUM AND CALCIUM CATIONS

Nanovortex evolution in entrance part of the 2D open type long nanocavity

Structural analysis of base mispairing in DNA containing oxidative guanine lesion