Stabilization of the ribosomal protein S6 by trehalose is counterbalanced by the formation of a putative off-pathway species.


Abstract

The effect of trehalose on folding and stability of the small ribosomal protein S6 was studied. Non-disruptive point mutations distributed along the protein structure were analyzed to characterize the stabilizing effect of trehalose and map the folding pathway of S6. On average, the stability of the wild-type and S6 mutants increases by 3 kcal/mol M trehalose. Despite the non-specific thermodynamic stabilization mechanism, trehalose particularly stabilizes the less destabilized mutants. Folding/unfolding kinetics shows clearly that trehalose induces the collapse of the unfolded state to an off-pathway intermediate with non-native diffuse contacts. This state is similar to the collapsed state induced by high concentrations of stabilizing salts, as previously reported. Although it leads to the accumulation of this off-pathway intermediate, trehalose does not change the compactness of the transition state ensemble. Furthermore, the productive folding pathway of S6 is not affected by trehalose as shown by a Phi-value analysis. The unfolded state ensemble of S6 should be more compact in the presence of trehalose and therefore destabilized due to decreased conformational entropy. Increased compaction of the unfolded state ensemble might also occur for more stable mutants of S6, thus explaining the synergistic effect of trehalose and point mutations on protein stabilization. Study holds ProTherm entries: 19619, 19620, 19621, 19622, 19623, 19624, 19625, 19626, 19627, 19629, 19630, 19631, 19632, 19633, 19634, 19635, 19636, 19637, 19638, 19639, 19640, 19641, 19642, 19643, 19644, 19645, 19646, 19647, 19648, 19649, 19650, 19651, 19652, 19653, 19654, 19655, 19656, 19657, 19658, 19659, 19660, 19661, 19662, 19663, 19664, 19665, 19666, 19667, 19668, 19669, 19670, 19671, 19672, 19673, 19674, 19675, 19676, 19677, 19678, 19679, 19680, 19681, 19682, 19683, 19684, 19685, 19686 Extra Details: ribosomal protein S6; trehalose; protein folding and stability; off-pathway intermediate

Submission Details

ID: AZTuVvTv

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:51 p.m.

Version: 1

Publication Details
Chen L;Cabrita GJ;Otzen DE;Melo EP,J. Mol. Biol. (2005) Stabilization of the ribosomal protein S6 by trehalose is counterbalanced by the formation of a putative off-pathway species. PMID:16002092
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
1CQN 1999-08-08T00:00:00+0000 2.1 PROTEIN AGGREGATION AND ALZHEIMER'S DISEASE: CRYSTALLOGRAPHIC ANALYSIS OF THE PHENOMENON. ENGINEERED VERSION OF THE RIBOSOMAL PROTEIN S6 USED AS A STABLE SCAFFOLD TO STUDY OLIGOMERIZATION.
1LOU 1998-11-25T00:00:00+0000 1.95 RIBOSOMAL PROTEIN S6
1QJH 1999-06-24T00:00:00+0000 2.2 Protein Aggregation and Alzheimer's Disease: Crystallographic Analysis of the Phenomenon. Engineered version of the ribosomal protein S6 used as a stable scaffold to study oligomerization.
1RIS 1994-05-31T00:00:00+0000 2.0 CRYSTAL STRUCTURE OF THE RIBOSOMAL PROTEIN S6 FROM THERMUS THERMOPHILUS
2BVZ 2005-07-05T00:00:00+0000 2.2 Mutant of the Ribosomal Protein S6
2BXJ 2005-07-26T00:00:00+0000 2.4 Double Mutant of the Ribosomal Protein S6
6C5L 2018-01-16T00:00:00+0000 3.2 Conformation of methylated GGQ in the Peptidyl Transferase Center during translation termination (T. thermophilus)
4KVB 2013-05-22T00:00:00+0000 4.2 Thermus thermophilus HB27 30S ribosomal subunit lacking ribosomal protein S17
4V4I 2007-02-15T00:00:00+0000 3.71 Crystal Structure of a 70S Ribosome-tRNA Complex Reveals Functional Interactions and Rearrangements.
4V4J 2007-07-18T00:00:00+0000 3.83 Interactions and Dynamics of the Shine-Dalgarno Helix in the 70S Ribosome.

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 30S ribosomal protein S6 P23370 RS6_THETH
100.0 30S ribosomal protein S6 Q5SLP8 RS6_THET8
100.0 30S ribosomal protein S6 P62666 RS6_THET2