1D5E

The role of phenylalanine 8 in the stabilization of the S protein-S peptide interaction: Packing and cavities

1D5E の概要

• エントリーDOI: 10.2210/pdb1d5e/pdb
• 関連するPDBエントリー: 1D5D 1D5H 1RBH
• 分子名称: S PEPTIDE, RNASE S, SULFATE ION, ... (4 entities in total)
• 機能のキーワード: rnase s mutant f8(norleucine), cavity s protein, s peptide, hydrolase
• 由来する生物種: Bos taurus (cattle); 詳細
• 細胞内の位置: Secreted: P61823
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 13090.72

構造登録者

Ratnaparkhi, G.S.,Varadarajan, R. (登録日: 1999-10-07, 公開日: 1999-10-20, 最終更新日: 2023-11-15)

主引用文献

Ratnaparkhi, G.S.,Varadarajan, R.
Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics.
Biochemistry, 39:12365-12374, 2000

PubMed Abstract: The hydrophobic effect is widely believed to be an important determinant of protein stability. However, it is difficult to obtain unambiguous experimental estimates of the contribution of the hydrophobic driving force to the overall free energy of folding. Thermodynamic and structural studies of large to small substitutions in proteins are the most direct method of measuring this contribution. We have substituted the buried residue Phe8 in RNase S with alanine, methionine, and norleucine. Binding thermodynamics and structures were characterized by titration calorimetry and crystallography, respectively. The crystal structures of the RNase S F8A, F8M, and F8Nle mutants indicate that the protein tolerates the changes without any main chain adjustments. The correlation of structural and thermodynamic parameters associated with large to small substitutions was analyzed for nine mutants of RNase S as well as 32 additional cavity-containing mutants of T4 lysozyme, human lysozyme, and barnase. Such substitutions were typically found to result in negligible changes in DeltaC(p)() and positive values of both DeltaDeltaH degrees and DeltaDeltaS of folding. Enthalpic effects were dominant, and the sign of DeltaDeltaS is the opposite of that expected from the hydrophobic effect. Values of DeltaDeltaG degrees and DeltaDeltaH degrees correlated better with changes in packing parameters such as residue depth or occluded surface than with the change in accessible surface area upon folding. These results suggest that the loss of packing interactions rather than the hydrophobic effect is a dominant contributor to the observed energetics for large to small substitutions. Hence, estimates of the magnitude of the hydrophobic driving force derived from earlier mutational studies are likely to be significantly in excess of the actual value.

PubMed: 11015216
DOI: 10.1021/bi000775k

実験手法

X-RAY DIFFRACTION (2.25 Å)