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2 TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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Influence of antifreeze proteins on local waters structure dynamics in presence of osmolytes

Krishnamoorthy A. N.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

2013

Vol.17, No 1-2

5--42

Antifreeze proteins are synthesized by various organisms to enable their cells to survive subzero environment in the arctic and polar regions. These proteins produce a difference between the melting and freezing points termed as thermal hysteresis. The main objective of this study is to examine the dynamics of water molecules and hydrogen bonds at the protein-water interface of antifreeze protein using atomistic molecular dynamics simulations using GROMACS. For this work a prototype of AFP (antifreeze protein) from antarctic notothenioids (ala-ala-thr repeats) and a mutant which is not antifreeze active were generated using PRODRG server. The hydration dynamics results revealed that the retarded water dynamics in the AFP compared to its mutant was responsible for the antifreeze activity. Furthermore a considerable increase in antifreeze activity were observed for the AFP in presence of osmolytes. The mechanism of action were tested using preferential binding parameter derived from Kirkwood-Buff integerals.

Preferential solvation of amides by methanol - a comparison of molecular dynamics calculations with the experimental data

Zielkiewicz J.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

2001

Vol. 5, No 3

317-329

Using the Kirkwood-Buff theory of solutions, the preferential solvation of the N-methylacet-amide (NMA), N-methylformamide, (NMF), and N,N-dimethylformamide, (DMF), molecule has been investigated in the binary {amide+methanol} mixtures at 313.15 K. Moreover, for the {amide+methanol} mixtures, where amide = NMF, DMF, and NMA, the molecular dynamics calculations at xamide=0.518 were performed. From the obtained molecule-molecule radial distribution functions, (rdf), and atom-atom rdf, it was possible to estimate the local mole fractions around the amide molecule, the orientation effects of molecules within the solvation shell, and a possibility of the formation of complexes. The general picture obtained from analysis of the molecular dynamics results is consistent with the deductions derived from thermodynamic data.