Detection of rare partially folded molecules in equilibrium with the native conformation of RNaseH.
Abstract
Despite the general observation that single domain proteins denature in a completely cooperative manner, amide hydrogen exchange of ribonuclease H in low levels of denaturant demonstrates the existence of two partially folded species. The structures of these marginally stable species resemble kinetic folding intermediates and the molten globule state of the protein. These data suggest that the first region to fold is the thermodynamically most stable portion of the protein and that the molten globule is a high free energy conformation present at equilibrium in the native state. Study holds ProTherm entries: 9931, 9932, 9933, 9934, 9935, 9936, 9937, 9938, 9939, 9940, 9941, 9942, 9943, 9944, 9945, 9946, 9947, 9948, 9949, 9950, 9951, 9952, 9953, 9954, 9955, 9956, 9957, 9958, 9959, 9960, 9961, 9962, 9963, 9964, 9965, 9966, 9967, 9968, 9969, 9970, 9971, 9972, 9973, 9974, 9975, 9976 Extra Details: amide proton exchange in Ile7 single domain proteins; cooperative manner; partially folded species;,molten globule; free energy conformation
Submission Details
ID: DkAw9nS94
Submitter: Connie Wang
Submission Date: April 24, 2018, 8:39 p.m.
Version: 1
Publication Details
Chamberlain AK;Handel TM;Marqusee S,Nat. Struct. Biol. (1996) Detection of rare partially folded molecules in equilibrium with the native conformation of RNaseH. PMID:8784352Additional Information
Study Summary
| Number of data points | 46 |
| Proteins | Ribonuclease HI ; Ribonuclease HI |
| Unique complexes | 1 |
| Assays/Quantities/Protocols | Experimental Assay: dG_H2O buffers:Sodium acetate: 100mM ; Experimental Assay: dG_H2O buffers:Sodium acetate: 100 mM |
| Libraries | Mutations for sequence MLKQVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHCEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERCDELARAAAMNPTLEDTGYQVEV |
Structure view and single mutant data analysis
Study data
| 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 |
|---|---|---|---|
| 4Z0U | 2015-03-26T00:00:00+0000 | 2.0 | RNase HI/SSB-Ct complex |
| 1F21 | 2000-05-22T00:00:00+0000 | 1.4 | DIVALENT METAL COFACTOR BINDING IN THE KINETIC FOLDING TRAJECTORY OF E. COLI RIBONUCLEASE HI |
| 1G15 | 2000-10-10T00:00:00+0000 | 1.9 | CO-CRYSTAL OF E. COLI RNASE HI WITH TWO MN2+ IONS BOUND IN THE THE ACTIVE SITE |
| 1GOA | 1993-05-10T00:00:00+0000 | 1.9 | COOPERATIVE STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY INSERTION OF GLY-80B AND GLY-77-> ALA SUBSTITUTION |
| 1GOB | 1993-05-10T00:00:00+0000 | 2.0 | COOPERATIVE STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY INSERTION OF GLY-80B AND GLY-77-> ALA SUBSTITUTION |
| 1GOC | 1993-05-10T00:00:00+0000 | 2.0 | COOPERATIVE STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY INSERTION OF GLY-80B AND GLY-77-> ALA SUBSTITUTION |
| 1JL1 | 2001-07-13T00:00:00+0000 | 1.3 | D10A E. coli ribonuclease HI |
| 1JL2 | 2001-07-13T00:00:00+0000 | 1.76 | Crystal structure of TCEO RNase H-a chimera combining the folding core from T. thermophilus RNase H and the remaining region of E. coli RNase H |
| 1JXB | 2001-09-06T00:00:00+0000 | 1.6 | I53A, a point mutant of the cysteine-free variant of E. coli Rnase HI |
| 1KVA | 1996-10-04T00:00:00+0000 | 1.8 | E. COLI RIBONUCLEASE HI D134A MUTANT |
Relevant UniProtKB Entries
| Percent Identity | Matching Chains | Protein | Accession | Entry Name |
|---|---|---|---|---|
| 90.9 | Ribonuclease HI | A6T512 | RNH_KLEP7 | |
| 90.9 | Ribonuclease HI | B5Y1G2 | RNH_KLEP3 | |
| 92.9 | Ribonuclease HI | C0Q6N2 | RNH_SALPC | |
| 93.5 | Ribonuclease HI | P0A2B9 | RNH_SALTY | |
| 93.5 | Ribonuclease HI | P0A2C0 | RNH_SALTI | |
| 93.5 | Ribonuclease HI | B4TYH0 | RNH_SALSV | |
| 93.5 | Ribonuclease HI | B5BDW5 | RNH_SALPK | |
| 93.5 | Ribonuclease HI | A9MZ19 | RNH_SALPB | |
| 93.5 | Ribonuclease HI | Q5PFD8 | RNH_SALPA | |
| 93.5 | Ribonuclease HI | B4SV39 | RNH_SALNS | |
| 93.5 | Ribonuclease HI | B4TK85 | RNH_SALHS | |
| 93.5 | Ribonuclease HI | B5R5L3 | RNH_SALG2 | |
| 93.5 | Ribonuclease HI | B5R449 | RNH_SALEP | |
| 93.5 | Ribonuclease HI | B5FJ58 | RNH_SALDC | |
| 93.5 | Ribonuclease HI | Q57SZ6 | RNH_SALCH | |
| 93.5 | Ribonuclease HI | A9MPF1 | RNH_SALAR | |
| 93.5 | Ribonuclease HI | B5F8X2 | RNH_SALA4 | |
| 93.5 | Ribonuclease HI | A8AKR0 | RNH_CITK8 | |
| 99.4 | Ribonuclease HI | Q0TLC3 | RNH_ECOL5 | |
| 99.4 | Ribonuclease HI | A7ZWF6 | RNH_ECOHS | |
| 99.4 | Ribonuclease HI | B7LHC0 | RNH_ECO55 | |
| 99.4 | Ribonuclease HI | B7UJB0 | RNH_ECO27 | |
| 100.0 | Ribonuclease HI | Q3Z5E9 | RNH_SHISS | |
| 100.0 | Ribonuclease HI | P0A7Y7 | RNH_SHIFL | |
| 100.0 | Ribonuclease HI | Q32JP9 | RNH_SHIDS | |
| 100.0 | Ribonuclease HI | Q325T2 | RNH_SHIBS | |
| 100.0 | Ribonuclease HI | B2U352 | RNH_SHIB3 | |
| 100.0 | Ribonuclease HI | B7LW89 | RNH_ESCF3 | |
| 100.0 | Ribonuclease HI | B1LHM3 | RNH_ECOSM | |
| 100.0 | Ribonuclease HI | B6HZS7 | RNH_ECOSE | |
| 100.0 | Ribonuclease HI | B7N876 | RNH_ECOLU | |
| 100.0 | Ribonuclease HI | P0A7Y4 | RNH_ECOLI | |
| 100.0 | Ribonuclease HI | B1IPU4 | RNH_ECOLC | |
| 100.0 | Ribonuclease HI | P0A7Y5 | RNH_ECOL6 | |
| 100.0 | Ribonuclease HI | B1XD78 | RNH_ECODH | |
| 100.0 | Ribonuclease HI | C4ZRV1 | RNH_ECOBW | |
| 100.0 | Ribonuclease HI | B7M213 | RNH_ECO8A | |
| 100.0 | Ribonuclease HI | B7MQ23 | RNH_ECO81 | |
| 100.0 | Ribonuclease HI | B7NKW4 | RNH_ECO7I | |
| 100.0 | Ribonuclease HI | B5Z0I8 | RNH_ECO5E | |
| 100.0 | Ribonuclease HI | P0A7Y6 | RNH_ECO57 | |
| 100.0 | Ribonuclease HI | B7MBJ0 | RNH_ECO45 | |
| 100.0 | Ribonuclease HI | A7ZHV1 | RNH_ECO24 |