Evidence for strained interactions between side-chains and the polypeptide backbone.


In most proteins, a small but significant fraction of residues adopt phi,psi angles that generate unfavorable steric interactions between side-chain atoms and the peptide backbone. For the small protein staphylococcal nuclease, the X-ray structure reveals that 18 of 133 residues occupy unusual and, presumably, energetically unfavorable backbone conformations. To quantify the amount of strain energy generated by these local interactions, we have analyzed the changes in stability that accompany replacement of the wild-type side-chain with glycine, a residue that can access a much larger set of phi,psi angles without energy penalty. To correct for the many other sources of stability loss that might accompany this mutation, the glycine mutant was compared to an alanine mutant at the same position and the resulting free energy difference delta delta GG-->A was then compared to the average delta delta GG-->A at all other, unstrained positions in the nuclease occupied by similar amino acid types. In addition, potential steric clashes were introduced by substituting alanine at each of six positions occupied in the wild-type by glycine with phi,psi angles that are unfavorable for all other residue types. The data suggest that residues with phi,psi angles outside the preferred alpha-helical and beta-sheet regions represent sites of local strain energy that lower the stability of the native state by 1 to 2 kcal/mol and, in some cases, as much as 3 to 4 kcal/mol. Given that 10 to 20% of residues in globular proteins adopt phi,psi angles outside the preferred alpha-helical and beta-sheet regions, this implies that there is on the order of 20 kcal/mol of strain energy in a protein of 100 residues that may be relieved by appropriate mutations. Study holds ProTherm entries: 8660, 8661, 8662, 8663, 8664, 8665, 8666, 8667, 8668, 8669, 8670, 8671, 8672, 8673, 8674, 8675, 8676, 8677, 8678, 8679, 8680, 8681, 8682, 8683, 8684, 8685, 8686, 8687, 8688, 8689, 8690, 8691, 8692, 8693, 8694, 8695, 8696, 8697, 8698, 8699, 8700, 8701, 8702 Extra Details: staphylococcal nuclease; protein folding; ramachandran plot;,steric interactions; mutagenesis

Submission Details

ID: 9RicnyFS4

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:36 p.m.

Version: 1

Publication Details
Stites WE;Meeker AK;Shortle D,J. Mol. Biol. (1994) Evidence for strained interactions between side-chains and the polypeptide backbone. PMID:8289248
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Thermonuclease P00644 NUC_STAAU
99.3 Thermonuclease Q5HHM4 NUC_STAAC
99.1 Thermonuclease Q99VJ0 NUC_STAAM
99.1 Thermonuclease Q7A6P2 NUC_STAAN
99.3 Thermonuclease Q6GB41 NUC_STAAS
99.3 Thermonuclease Q8NXI6 NUC_STAAW
99.3 Thermonuclease Q6GIK1 NUC_STAAR