PDBsum entry 1d5e

Hydrolase

PDB id: 1d5e

Contents

Protein chains

15 a.a.

101 a.a. *

Ligands

SO4

Waters ×138

* Residue conservation analysis

PDB id:

1d5e

Name:

Hydrolase

Title:

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

Structure:

S peptide. Chain: a. Fragment: residues 1-15. Engineered: yes. Mutation: yes. Other_details: synthetic. Rnase s. Chain: b. Fragment: residues 24-124

Source:

Synthetic: yes. Other_details: s15 peptide synthesized by solid phase peptide synthesis. Bos taurus. Cattle. Organism_taxid: 9913. Other_details: derieved from a limit digest of bovine pancreatic rnase a

Biol. unit:

Dimer (from PQS)

Resolution:

2.25Å R-factor: 0.209 R-free: 0.231

Authors:

G.S.Ratnaparkhi,R.Varadarajan

Key ref:

G.S.Ratnaparkhi and R.Varadarajan (2000). 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. PubMed id: 11015216 DOI: 10.1021/bi000775k

Date:

07-Oct-99 Release date: 20-Oct-99

Protein chain

P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic from Bos taurus

Seq: 150 a.a.

Struc: 15 a.a.*

Protein chain

P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic from Bos taurus

Seq: 150 a.a.

Struc: 101 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.4.6.1.18 - pancreatic ribonuclease.
• Reaction:
  1. an [RNA] containing cytidine + H2O = an [RNA]-3'-cytidine- 3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]
  2. an [RNA] containing uridine + H2O = an [RNA]-3'-uridine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]

DOI no: 10.1021/bi000775k

Biochemistry 39:12365-12374 (2000)

PubMed id: 11015216

Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics.

G.S.Ratnaparkhi, R.Varadarajan.

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.