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2 Acta Biochimica Polonica

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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.

tom 44

nr 3

The effect of an empirical solvation energy term on energy minimization of ribonuclease Tl was established using different sets of Atomic Solvation Parameters. The results are compared to minimization in vacuo and in a 10 A water shell. The best solvent model as judged from the comparison to the crystal structure was an empirical solvation potential derived from free energies of transfer of amino-acid side-chain analogues from vapour to water. The use of this model causes, however, energy and gradient oscillations, which make it inapplicable with standard protocols of molecular dynamics simulations. The empirical solvation model which was found by other authors (von Freyberg et al., 1993, J. Mol. Biol. 233, 275-292) to give good results in the NMR structure refinement led to distortions of the ribonuclease native structure. The model based on statistical analysis of crystal structures did not perform better than minimization in vacuo.

Denatured proteins and early folding intermediates simulated in a reduced conformational space

100%

Kmiecik S. , Kurcinski M. , Rutkowska A. , Gront D. , Kolinski A.

tom 53

nr 1

Conformations of globular proteins in the denatured state were studied using a high-resolution lattice model of proteins and Monte Carlo dynamics. The model assumes a united-atom and high-coordination lattice representation of the polypeptide conformational space. The force field of the model mimics the short-range protein-like conformational stiffness, hydrophobic interactions of the side chains and the main-chain hydrogen bonds. Two types of approximations for the short-range interactions were compared: simple statistical potentials and knowledge-based protein-specific potentials derived from the sequence-structure compatibility of short fragments of protein chains. Model proteins in the denatured state are relatively compact, although the majority of the sampled conformations are globally different from the native fold. At the same time short protein fragments are mostly native-like. Thus, the denatured state of the model proteins has several features of the molten globule state observed experimentally. Statistical potentials induce native-like conformational propensities in the denatured state, especially for the fragments located in the core of folded proteins. Knowledge-based protein-specific potentials increase only slightly the level of similarity to the native conformations, in spite of their qualitatively higher specificity in the native structures. For a few cases, where fairly accurate experimental data exist, the simulation results are in semiquantitative agreement with the physical picture revealed by the experiments. This shows that the model studied in this work could be used efficiently in computational studies of protein dynamics in the denatured state, and consequently for studies of protein folding pathways, i.e. not only for the modeling of folded structures, as it was shown in previous studies. The results of the present studies also provide a new insight into the explanation of the Levinthal's paradox.