On the relationship between protein stability and folding kinetics: a comparative study of the N-terminal domains of RNase HI, E. coli and Bacillus stearothermophilus L9.


Abstract

There is currently a great deal of interest in proteins that fold in a single highly cooperative step. Particular attention has been focused on elucidating the factors that govern folding rates of simple proteins. Recently, the topology of the native state has been proposed to be the most important determinant of their folding rates. Here we report a comparative study of the folding of three topologically equivalent proteins that adapt a particularly simple alpha/beta fold. The folding kinetics of the N-terminal domain of RNase HI and the N-terminal domain of the ribosomal protein L9 from Escherichia coli (eNTL9) were compared to the previously characterized N-terminal domain of L9 from Bacillus stearothermophilus (bNTL9). This 6.2 kDa protein, which is one of simplest examples of the ABCalphaD motif, folds via a two-state mechanism on the millisecond to submillisecond time scale. The RNase HI domain and bNTL9 have very similar tertiary structures but there is little similarity in primary sequence. bNTL9 and eNTL9 share the same biological function and a similar primary sequence but differ significantly in stability. Fluorescence-detected stopped-flow experiments showed that the three proteins fold in a two-state fashion. The folding rates in the absence of denaturant were found to be very different, ranging form 21 s(-1) to 790 s(-1) at 10 degrees C. The diverse folding rates appear to reflect large differences in the stability of the proteins. When compared at an isostability point, the folding rates converged to a similar value and there is a strong linear correlation between the log of the folding rate and stability for this set of proteins. These observations are consistent with the idea that stability can play an important role in dictating relative folding rates among topologically equivalent proteins. Study holds ProTherm entries: 12224, 12225, 12226 Extra Details: protein folding; contact order; protein stability; ribosomal protein L9

Submission Details

ID: JcJAFcop

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:43 p.m.

Version: 1

Publication Details
Sato S;Xiang S;Raleigh DP,J. Mol. Biol. (2001) On the relationship between protein stability and folding kinetics: a comparative study of the N-terminal domains of RNase HI, E. coli and Bacillus stearothermophilus L9. PMID:11563917
Additional Information

Study Summary

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
5WF0 2017-07-11T00:00:00+0000 3.6 70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C2)
5WFS 2017-07-12T00:00:00+0000 3.0 70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C4)
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.
5WF0 2017-07-11T00:00:00+0000 3.6 70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C2)
5WFS 2017-07-12T00:00:00+0000 3.0 70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C4)
6DNC 2018-06-06T00:00:00+0000 3.7 E.coli RF1 bound to E.coli 70S ribosome in response to UAU sense A-site codon
1C04 1999-07-14T00:00:00+0000 5.0 IDENTIFICATION OF KNOWN PROTEIN AND RNA STRUCTURES IN A 5 A MAP OF THE LARGE RIBOSOMAL SUBUNIT FROM HALOARCULA MARISMORTUI
1EG0 2000-02-11T00:00:00+0000 11.5 FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
90.6 50S ribosomal protein L9 A1JIT1 RL9_YERE8
91.9 50S ribosomal protein L9 B5Y305 RL9_KLEP3
91.9 50S ribosomal protein L9 B2VCV8 RL9_ERWT9
93.3 50S ribosomal protein L9 A6THB4 RL9_KLEP7
94.0 50S ribosomal protein L9 A7MM80 RL9_CROS8
93.3 50S ribosomal protein L9 A4W5T2 RL9_ENT38
95.3 50S ribosomal protein L9 Q8ZK80 RL9_SALTY
95.3 50S ribosomal protein L9 A9N521 RL9_SALPB
95.3 50S ribosomal protein L9 B4T3F4 RL9_SALNS
95.3 50S ribosomal protein L9 B4TFD8 RL9_SALHS
95.3 50S ribosomal protein L9 B5R9F1 RL9_SALG2
95.3 50S ribosomal protein L9 B5R0S1 RL9_SALEP
95.3 50S ribosomal protein L9 B5FSA4 RL9_SALDC
96.6 50S ribosomal protein L9 A8AMJ4 RL9_CITK8
96.0 50S ribosomal protein L9 Q8Z163 RL9_SALTI
96.0 50S ribosomal protein L9 B4TT36 RL9_SALSV
96.0 50S ribosomal protein L9 B5BKL2 RL9_SALPK
96.0 50S ribosomal protein L9 C0Q6G1 RL9_SALPC
96.0 50S ribosomal protein L9 Q5PJ55 RL9_SALPA
96.0 50S ribosomal protein L9 Q57GI8 RL9_SALCH
96.0 50S ribosomal protein L9 A9MF07 RL9_SALAR
96.0 50S ribosomal protein L9 B5F3C0 RL9_SALA4
99.3 50S ribosomal protein L9 Q328J6 RL9_SHIDS
100.0 50S ribosomal protein L9 Q3YUE4 RL9_SHISS
100.0 50S ribosomal protein L9 P0A7R4 RL9_SHIFL
100.0 50S ribosomal protein L9 Q0SX83 RL9_SHIF8
100.0 50S ribosomal protein L9 Q31TD4 RL9_SHIBS
100.0 50S ribosomal protein L9 B2TY76 RL9_SHIB3
100.0 50S ribosomal protein L9 B7LLY5 RL9_ESCF3
100.0 50S ribosomal protein L9 Q1R357 RL9_ECOUT
100.0 50S ribosomal protein L9 B1LR79 RL9_ECOSM
100.0 50S ribosomal protein L9 B6I2A9 RL9_ECOSE
100.0 50S ribosomal protein L9 B7NGD7 RL9_ECOLU
100.0 50S ribosomal protein L9 P0A7R1 RL9_ECOLI
100.0 50S ribosomal protein L9 B1IT03 RL9_ECOLC
100.0 50S ribosomal protein L9 P0A7R2 RL9_ECOL6
100.0 50S ribosomal protein L9 Q0T9J0 RL9_ECOL5
100.0 50S ribosomal protein L9 A1AJA7 RL9_ECOK1
100.0 50S ribosomal protein L9 A8A7U9 RL9_ECOHS
100.0 50S ribosomal protein L9 B1XDV3 RL9_ECODH
100.0 50S ribosomal protein L9 C4ZR80 RL9_ECOBW
100.0 50S ribosomal protein L9 B7M9G5 RL9_ECO8A
100.0 50S ribosomal protein L9 B7MT77 RL9_ECO81
100.0 50S ribosomal protein L9 B7NTQ8 RL9_ECO7I
100.0 50S ribosomal protein L9 B5Z2K8 RL9_ECO5E
100.0 50S ribosomal protein L9 P0A7R3 RL9_ECO57
100.0 50S ribosomal protein L9 B7LCR4 RL9_ECO55
100.0 50S ribosomal protein L9 B7MLK8 RL9_ECO45
100.0 50S ribosomal protein L9 B7UQL2 RL9_ECO27
100.0 50S ribosomal protein L9 A7ZV74 RL9_ECO24
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
90.4 N 50S ribosomal protein L1 B5RC63 RL25_SALG2
91.5 N 50S ribosomal protein L1 A8AE31 RL25_CITK8
90.4 N 50S ribosomal protein L1 A9MK27 RL25_SALAR
91.5 N 50S ribosomal protein L1 Q7CQ71 RL25_SALTY
91.5 N 50S ribosomal protein L1 Q8XFE7 RL25_SALTI
91.5 N 50S ribosomal protein L1 B4TPC7 RL25_SALSV
91.5 N 50S ribosomal protein L1 B5BE12 RL25_SALPK
91.5 N 50S ribosomal protein L1 C0Q0R6 RL25_SALPC
91.5 N 50S ribosomal protein L1 A9N6F6 RL25_SALPB
91.5 N 50S ribosomal protein L1 Q5PE20 RL25_SALPA
91.5 N 50S ribosomal protein L1 B4SYR0 RL25_SALNS
91.5 N 50S ribosomal protein L1 B4TAP8 RL25_SALHS
91.5 N 50S ribosomal protein L1 B5R194 RL25_SALEP
91.5 N 50S ribosomal protein L1 B5FNN0 RL25_SALDC
91.5 N 50S ribosomal protein L1 Q57MB4 RL25_SALCH
91.5 N 50S ribosomal protein L1 B5EYS6 RL25_SALA4
92.6 N 50S ribosomal protein L1 B7LJS7 RL25_ESCF3
96.8 N 50S ribosomal protein L1 B1LKT4 RL25_ECOSM
96.8 N 50S ribosomal protein L1 B7N5E9 RL25_ECOLU
96.8 N 50S ribosomal protein L1 Q8FFS1 RL25_ECOL6
96.8 N 50S ribosomal protein L1 Q0TFQ4 RL25_ECOL5
96.8 N 50S ribosomal protein L1 B7MXK1 RL25_ECO81
96.8 N 50S ribosomal protein L1 B7NN00 RL25_ECO7I
96.8 N 50S ribosomal protein L1 B7MFA0 RL25_ECO45
96.8 N 50S ribosomal protein L1 B7UFK2 RL25_ECO27
98.9 N 50S ribosomal protein L1 Q31YZ2 RL25_SHIBS
98.9 N 50S ribosomal protein L1 B2TV63 RL25_SHIB3
98.9 N 50S ribosomal protein L1 B5YWX8 RL25_ECO5E
98.9 N 50S ribosomal protein L1 Q8XE69 RL25_ECO57
100.0 N 50S ribosomal protein L1 Q3Z022 RL25_SHISS
100.0 N 50S ribosomal protein L1 P68918 RL25_SHIFL
100.0 N 50S ribosomal protein L1 Q32HY5 RL25_SHIDS
100.0 N 50S ribosomal protein L1 B6I184 RL25_ECOSE
100.0 N 50S ribosomal protein L1 P68919 RL25_ECOLI
100.0 N 50S ribosomal protein L1 B1IY84 RL25_ECOLC
100.0 N 50S ribosomal protein L1 A8A248 RL25_ECOHS
100.0 N 50S ribosomal protein L1 B1X883 RL25_ECODH
100.0 N 50S ribosomal protein L1 C4ZU30 RL25_ECOBW
100.0 N 50S ribosomal protein L1 B7M535 RL25_ECO8A
100.0 N 50S ribosomal protein L1 B7LAK9 RL25_ECO55
100.0 N 50S ribosomal protein L1 A7ZP09 RL25_ECO24
96.2 L 50S ribosomal protein L1 B9KBJ9 RL11_THENN
97.7 L 50S ribosomal protein L1 A5IJW7 RL11_THEP1
100.0 L 50S ribosomal protein L1 B1L939 RL11_THESQ
100.0 L 50S ribosomal protein L1 P29395 RL11_THEMA
95.1 M 50S ribosomal protein L1 B7GJ77 RL14_ANOFW
98.4 M 50S ribosomal protein L1 C5D3S7 RL14_GEOSW
99.2 M 50S ribosomal protein L1 A4IJJ9 RL14_GEOTN
100.0 M 50S ribosomal protein L1 P04450 RL14_GEOSE
100.0 M 50S ribosomal protein L1 Q5L413 RL14_GEOKA
99.4 J 50S ribosomal protein L1 P02391 RL6_GEOSE
99.4 J 50S ribosomal protein L1 Q5L408 RL6_GEOKA
98.7 H 50S ribosomal protein L1 Q5SLP7 RL1_THET8
99.6 H 50S ribosomal protein L1 P27150 RL1_THETH
99.6 H 50S ribosomal protein L1 Q72GV9 RL1_THET2
97.0 I 50S ribosomal protein L1 C5D3S0 RL2_GEOSW
97.0 I 50S ribosomal protein L1 A4IJJ2 RL2_GEOTN
100.0 I 50S ribosomal protein L1 P04257 RL2_GEOSE
100.0 I 50S ribosomal protein L1 Q5L3Z4 RL2_GEOKA