1D5D

The role of phenylalanine 8 in the stabilization of the s protein-s peptide interaction: packing and cavities

Summary for 1D5D

• Entry DOI: 10.2210/pdb1d5d/pdb
• Related: 1D5E 1D5H 1RBH
• Descriptor: S PEPTIDE, RNASE S, SULFATE ION, ... (4 entities in total)
• Functional Keywords: rnase s mutant(f8m), cavity s protein, s peptide, hydrolase
• Biological source: Bos taurus (cattle); More
• Cellular location: Secreted: P61823
• Total number of polymer chains: 2
• Total formula weight: 13108.75

Authors

Ratnaparkhi, G.S.,Varadarajan, R. (deposition date: 1999-10-07, release date: 1999-10-20, Last modification date: 2018-03-14)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.25 Å)