期刊
JOURNAL OF PHYSICAL CHEMISTRY B
卷 113, 期 16, 页码 5657-5660出版社
AMER CHEMICAL SOC
DOI: 10.1021/jp9004746
关键词
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资金
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Czech Republic [Z40550506]
- Ministry of Education, Youth and Sports of the Czech Republic [LC512, MSM6198959216]
- Czech Science Foundation [203/06/1727]
- Academy of Sciences of the Czech Republic [AVOZ505200701]
- Praemium Academiae
The structure of proteins as well as their folding/unfolding equilibrium are commonly attributed to H-bonding and hydrophobic interactions. We have used the molecular dynamic simulations in an explicit water environment based on the standard empirical potential as well as more accurately (and thus also more reliably) on the QM/MM potential. The simulations where the dispersion term was suppressed have led to a substantial change of the tryptophan-cage protein structure (unfolded structure). This structure cannot fold without the dispersion energy term, whereas, if it is covered fully, the system finds its native structure relatively quickly. This implies that after such physical factors as temperature and pH, the dispersion energy is an important factor in protein structure determination as well as in the protein folding/unfolding equilibrium. The loss of dispersion also affected the a.-helical structure. On the other hand, weakening the electrostatic interactions (and thus H-bonding) affected the a.-helical structure only to a minor extent.
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