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Probing of Cu2+ ions binding to A β (5−16) peptide using ITC measurements and MD simulations

Makowska J., Żmudzińska W., Wyrzykowski D., Brzozowski K., Zblewska H., Chmurzyński L.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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2016

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Vol. 20, No 4

409--416

EN

It is shown that probably three residues: His6, His14 and His16 in the original sequence A β (1−42) serve as metal-binding sites for Cu2+ions. On the other hand, there is a possibility that only one of them plays a crucial role in the formation of the{A β (1-42)-Cu2+} complex. The isothermal titration calorimetry (ITC) measurements supported by molecular dynamic simulation (MD) with the NMR-derived restrains were used to investigate the interactions of Cu2+ with A β(5-16), a fragment of the A β(1-42) protein, with the following sequence: Ac-Arg-His-Asp-Ser-Gly-Tyr-Glu-Val-His-His-Gln-Lys-NH2, termed HZ1. The conditional thermodynamic parameters suggest that the formation of the Cu2+-HZ1 complex is both an enthalpy and entropy driven process under the experimental conditions. The studies presented here (after comparison with our previous results) show that the affinity of peptides to copper metal ions depends on two factors: the primary structure (amino acid composition) and the shape of the peptide conformation adopted.

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Conformational analysis of fragment of human Pin1 ww domain: influence of charged amino-acid residues on β-hairpin structure

Makowska J., Uber D., Żmudzińska W., Chmurzyński L.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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2014

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Vol. 18, No 4

343--349

EN

We examined the effect of like-charged residues on the conformation of an original nine amino-acid-residue fragment of the human Pin1 WW domain (hPin1) with the f ollowing sequence: Ac-Arg-Met-Ser-Arg-Ser-Ser-Gly-Arg-Val-NH 2 (U9). This was facilitated by CD and NMR spectroscopic measurements, and molecular dynamics calculations. Our ear lier studies suggested that the presence of like-charged residues at the end of a shor t polypeptide chain composed of nonpolar residues could induce a chain reversal. For the U9 pep tide, canonical MD simulations with NMR -derived restraints demonstrated the presence of ensembles of stru ctures with a tendency to form a β -chain reversal. Additionally, thermal stabilities of the peptide und er study were measured using differential scanning calorimetry ( DSC ). The estimated well defined phase transition point showed that conformational equilibria in the U9 pe ptide were strongly dependent on temperature.

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Ab initio Study of the Energetics of Protonation and Cationic Homoconjugation of Trimethylamine

Makowski M., Makowska J., Chmurzyński L.

Polish Journal of Chemistry

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2003

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Vol. 77 / nr 11

1447-1459

EN

Ab initio methods at the RHF (Restricted Hartree Fock) and MP2 (Moller-Plesset) levels were used to study the energetics of protonation of trimethylamine and its derivative trimethylamine N-oxide, as well as the energetics of formation of hydrogen bonded (NźźźHźźźN)+ and (OźźźHźźźO)+ type, respectively, homocomplexed cations. The Gaussian functional basis sets 3-21G, 6-31G, 6-311G, 6-31G* and 6-31+G*were employed to calculate energy and Gibbs free energy of protonation and cationic homoconjugation in the gas phase and with the inclusion of solvation effects (usingPCMmethod). The calculated energetic parameters in the gas phase and in solution, as well as experimental values of equilibrium constants of the acid dissociation and cationic homoconjugation reaction for trimethylamine and trimethylamine N-oxide systems provided a basis for a comparison of the basicity and tendency towards cationic homoconjugation of both compounds under study. Consequently, the acid-base properties of aliphatic bases have been compared with those of heterocyclic bases containing both oxygen and nitrogen.