Thermodynamics and kinetics of non-native interactions in protein folding: a single point mutant significantly stabilizes the N-terminal domain of L9 by modulating non-native interactions in the denatured state.


Abstract

Comparatively little is known about the role of non-native interactions in protein folding and their role in both folding and stability is controversial. We demonstrate that non-native electrostatic interactions involving specific residues in the denatured state can have a significant effect upon protein stability and can persist in the transition state for folding. Mutation of a single surface exposed residue, Lys12 to Met, in the N-terminal domain of the ribosomal protein L9 (NTL9), significantly increased the stability of the protein and led to faster folding. Structural and energetic studies of the wild-type and K12M mutant show that the 1.9 kcal mol(-1) increase in stability is not due to native state effects, but rather is caused by modulation of specific non-native electrostatic interactions in the denatured state. pH dependent stability measurements confirm that the increased stability of the K12M is due to the elimination of favorable non-native interactions in the denatured state. Kinetic studies show that the non-native electrostatic interactions involving K12 persist in the transition state. The analysis demonstrates that canonical Phi-values can arise from the disruption of non-native interactions as well as from the development of native interactions. Study holds ProTherm entries: 17059, 17060, 17061, 17062 Extra Details: N-terminal domain (the first 56 residues of the ribosomal protein L9). protein folding; denatured state; protein stability; non-native interactions; pH-dependent folding

Submission Details

ID: piDUzPRW4

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:49 p.m.

Version: 1

Publication Details
Cho JH;Sato S;Raleigh DP,J. Mol. Biol. (2004) Thermodynamics and kinetics of non-native interactions in protein folding: a single point mutant significantly stabilizes the N-terminal domain of L9 by modulating non-native interactions in the denatured state. PMID:15099748
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 PDB Entries

Structure ID Release Date Resolution Structure Title
1CQU 1999-08-11T00:00:00+0000 0 SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L9
1DIV 1996-07-02T00:00:00+0000 2.6 RIBOSOMAL PROTEIN L9
2HBA 2006-06-14T00:00:00+0000 1.25 Crystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9) K12M
2HBB 2006-06-14T00:00:00+0000 1.9 Crystal Structure of the N-terminal Domain of Ribosomal Protein L9 (NTL9)
2HVF 2006-07-28T00:00:00+0000 1.57 Crystal Structure of N-terminal Domain of Ribosomal Protein L9 (NTL9), G34dA
487D 2000-02-23T00:00:00+0000 7.5 SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION
4V42 2001-03-30T00:00:00+0000 5.5 Crystal structure of the ribosome at 5.5 A resolution.
4V4R 2005-09-30T00:00:00+0000 5.9 Crystal structure of the whole ribosomal complex.
4V4S 2005-10-12T00:00:00+0000 6.76 Crystal structure of the whole ribosomal complex.
4V4T 2005-10-12T00:00:00+0000 6.46 Crystal structure of the whole ribosomal complex with a stop codon in the A-site.

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
95.3 50S ribosomal protein L9 Q5KU74 RL9_GEOKA
96.6 50S ribosomal protein L9 A4ITV1 RL9_GEOTN
100.0 50S ribosomal protein L9 P02417 RL9_GEOSE