Does trifluoroethanol affect folding pathways and can it be used as a probe of structure in transition states?
Abstract
Nonaqueous co-solvents, particularly 2,2,2-trifluoroethanol (TFE), have been used as tools to study protein folding. By analyzing FKBP12, an alpha/beta-protein that folds with two-state kinetics, we have been able to address three key questions concerning the use of TFE. First, does TFE perturb the folding pathway? Second, can the observed changes in the rate of folding and unfolding in TFE be attributed to a change in free energy of a single state? Finally, can TFE be used to infer information on secondary structure formation in the transition state? Protein engineering experiments on FKBP12, coupled with folding and unfolding experiments in 0% and 9.6% TFE, conclusively show that TFE does not perturb the folding pathway of this protein. Our results also suggest that the changes in folding and unfolding rates observed in 9.6% TFE are due to a global effect of TFE on the protein, rather than the stabilization of any elements of secondary structure in the transition state. Thus, studies with TFE and other co-solvents can be accurately interpreted only when combined with other techniques. Study holds ProTherm entries: 15054, 15055, 15056, 15057, 15058, 15059, 15060, 15061, 15062, 15063, 15064, 15065, 15066, 15067, 15068, 15069, 15070, 15071, 15072, 15073, 15074, 15075, 15076, 15077, 15078, 15079, 15080, 15081 Extra Details: dithiothreitol (DTT)(1 mM) was added in the experiment,Calculated in 0% TFE using an average mU-F (1.59 } 0.02) trifluoroethanol, protein folding, FKBP12, transition state, secondary structure
Submission Details
ID: zDRNuTyv3
Submitter: Connie Wang
Submission Date: April 24, 2018, 8:45 p.m.
Version: 1
Publication Details
Main ER;Jackson SE,Nat. Struct. Biol. (1999) Does trifluoroethanol affect folding pathways and can it be used as a probe of structure in transition states? PMID:10467094Additional Information
Study Summary
| Number of data points | 108 |
| Proteins | Peptidyl-prolyl cis-trans isomerase FKBP1A ; Peptidyl-prolyl cis-trans isomerase FKBP1A |
| Unique complexes | 13 |
| Assays/Quantities/Protocols | Experimental Assay: Cm ; Experimental Assay: m ; Experimental Assay: dG_H2O ; Derived Quantity: ddG_H2O |
| Libraries | Mutations for sequence GVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE |
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 |
|---|---|---|---|
| 1F40 | 2000-11-08 | SOLUTION STRUCTURE OF FKBP12 COMPLEXED WITH GPI-1046, A NEUROTROPHIC LIGAND | |
| 2RSE | 2012-05-30 | NMR structure of FKBP12-mTOR FRB domain-rapamycin complex structure determined based on PCS | |
| 2ND5 | 2017-05-17 | Lysine dimethylated FKBP12 | |
| 1FKR | 1994-01-31 | SOLUTION STRUCTURE OF FKBP, A ROTAMASE ENZYME AND RECEPTOR FOR FK506 AND RAPAMYCIN | |
| 1FKT | 1994-01-31 | SOLUTION STRUCTURE OF FKBP, A ROTAMASE ENZYME AND RECEPTOR FOR FK506 AND RAPAMYCIN | |
| 1FKS | 1994-01-31 | SOLUTION STRUCTURE OF FKBP, A ROTAMASE ENZYME AND RECEPTOR FOR FK506 AND RAPAMYCIN | |
| 2PPN | 2008-05-27 | 0.92 | Crystal structure of FKBP12 |
| 2PPP | 2008-09-02 | 0.94 | Crystal structure of E60Q mutant of FKBP12 |
| 4N19 | 2014-02-12 | 1.2 | Structural basis of conformational transitions in the active site and 80 s loop in the FK506 binding protein FKBP12 |
| 2PPO | 2008-05-27 | 1.29 | Crystal structure of E60A mutant of FKBP12 |
| 1BKF | 1996-08-01 | 1.6 | FK506 BINDING PROTEIN FKBP MUTANT R42K/H87V COMPLEX WITH IMMUNOSUPPRESSANT FK506 |
| 2DG4 | 2006-04-25 | 1.7 | FK506-binding protein mutant WF59 complexed with Rapamycin |
| 1FKF | 1991-07-15 | 1.7 | ATOMIC STRUCTURE OF FKBP-FK506, AN IMMUNOPHILIN-IMMUNOSUPPRESSANT COMPLEX |
| 1FKL | 1995-12-07 | 1.7 | ATOMIC STRUCTURE OF FKBP12-RAPAYMYCIN, AN IMMUNOPHILIN-IMMUNOSUPPRESSANT COMPLEX |
| 4IPX | 2013-06-05 | 1.7 | Analyzing the visible conformational substates of the FK506 binding protein FKBP12 |
| 2DG9 | 2006-04-25 | 1.7 | FK506-binding protein mutant WL59 complexed with Rapamycin |
| 1FKB | 1993-10-31 | 1.7 | ATOMIC STRUCTURE OF THE RAPAMYCIN HUMAN IMMUNOPHILIN FKBP-12 COMPLEX |
| 2DG3 | 2006-04-25 | 1.7 | Wildtype FK506-binding protein complexed with Rapamycin |
| 1FKJ | 1995-12-07 | 1.7 | ATOMIC STRUCTURE OF FKBP12-FK506, AN IMMUNOPHILIN IMMUNOSUPPRESSANT COMPLEX |
| 2FKE | 1994-01-31 | 1.72 | FK-506-BINDING PROTEIN: THREE-DIMENSIONAL STRUCTURE OF THE COMPLEX WITH THE ANTAGONIST L-685,818 |
| 1FKD | 1994-01-31 | 1.72 | FK-506 BINDING PROTEIN: THREE-DIMENSIONAL STRUCTURE OF THE COMPLEX WITH THE ANTAGONIST L-685,818 |
| 4ODP | 2015-01-14 | 1.75 | Structure of SlyD delta-IF from Thermus thermophilus in complex with S2-W23A peptide |
| 1J4R | 2001-12-19 | 1.8 | FK506 BINDING PROTEIN COMPLEXED WITH FKB-001 |
| 1J4H | 2003-06-03 | 1.8 | crystal structure analysis of the FKBP12 complexed with 000107 small molecule |
| 1J4I | 2003-06-03 | 1.8 | crystal structure analysis of the FKBP12 complexed with 000308 small molecule |
| 1D7J | 1999-10-21 | 1.85 | FKBP COMPLEXED WITH 4-HYDROXY-2-BUTANONE |
| 3FAP | 2000-09-13 | 1.85 | ATOMIC STRUCTURES OF THE RAPAMYCIN ANALOGS IN COMPLEX WITH BOTH HUMAN FKBP12 AND FRB DOMAIN OF FRAP |
| 1D6O | 1999-10-21 | 1.85 | NATIVE FKBP |
| 1D7H | 1999-10-21 | 1.9 | FKBP COMPLEXED WITH DMSO |
| 1BL4 | 1998-09-02 | 1.9 | FKBP MUTANT F36V COMPLEXED WITH REMODELED SYNTHETIC LIGAND |
| 1D7I | 1999-10-21 | 1.9 | FKBP COMPLEXED WITH METHYL METHYLSULFINYLMETHYL SULFIDE (DSS) |
| 5I7Q | 2017-03-08 | 1.9 | Crystal structure of Fkbp12-IF(SlpA), a chimeric protein of human Fkbp12 and the insert in flap domain of Ecoli SlpA |
| 4ODR | 2015-01-14 | 1.93 | Structure of SlyD delta-IF from Thermus thermophilus in complex with FK506 |
| 1FKH | 1994-01-31 | 1.95 | DESIGN, SYNTHESIS, AND KINETIC EVALUATION OF HIGH-AFFINITY FKBP LIGANDS, AND THE X-RAY CRYSTAL STRUCTURES OF THEIR COMPLEXES WITH FKBP12 |
| 1A7X | 1998-06-17 | 2.0 | FKBP12-FK1012 COMPLEX |
| 4ODQ | 2015-01-14 | 2.0 | Structure of SlyD delta-IF from Thermus thermophilus in complex with S3 peptide |
| 1FKG | 1994-01-31 | 2.0 | DESIGN, SYNTHESIS, AND KINETIC EVALUATION OF HIGH-AFFINITY FKBP LIGANDS, AND THE X-RAY CRYSTAL STRUCTURES OF THEIR COMPLEXES WITH FKBP12 |
| 5I7P | 2017-03-08 | 2.0 | Crystal structure of Fkbp12-IF(SlyD), a chimeric protein of human Fkbp12 and the insert in flap domain of Ecoli SlyD |
| 1EYM | 2000-08-09 | 2.0 | FK506 BINDING PROTEIN MUTANT, HOMODIMERIC COMPLEX |
| 3MDY | 2010-05-19 | 2.05 | Crystal structure of the cytoplasmic domain of the bone morphogenetic protein receptor type-1B (BMPR1B) in complex with FKBP12 and LDN-193189 |
| 4DH0 | 2012-02-15 | 2.1 | X-ray Crystal Structure of 28-O-Methylrapamycin complexed with FKBP12: Is the Cyclohexyl Moiety Part of the Effector Domain of Rapamycin? |
| 1FKK | 1995-12-07 | 2.2 | ATOMIC STRUCTURE OF FKBP12, AN IMMUNOPHILIN BINDING PROTEIN |
| 1FKI | 1994-01-31 | 2.2 | DESIGN, SYNTHESIS, AND KINETIC EVALUATION OF HIGH-AFFINITY FKBP LIGANDS, AND THE X-RAY CRYSTAL STRUCTURES OF THEIR COMPLEXES WITH FKBP12 |
| 1NSG | 1998-03-18 | 2.2 | THE STRUCTURE OF THE IMMUNOPHILIN-IMMUNOSUPPRESSANT FKBP12-RAPAMYCIN COMPLEX INTERACTING WITH HUMAN FRAP |
| 2FAP | 1999-05-18 | 2.2 | THE STRUCTURE OF THE IMMUNOPHILIN-IMMUNOSUPPRESSANT FKBP12-(C16)-ETHOXY RAPAMYCIN COMPLEX INTERACTING WITH HUMA |
| 3H9R | 2009-06-02 | 2.35 | Crystal structure of the kinase domain of type I activin receptor (ACVR1) in complex with FKBP12 and dorsomorphin |
| 1TCO | 1997-02-12 | 2.5 | TERNARY COMPLEX OF A CALCINEURIN A FRAGMENT, CALCINEURIN B, FKBP12 AND THE IMMUNOSUPPRESSANT DRUG FK506 (TACROLIMUS) |
| 1QPF | 1999-08-16 | 2.5 | FK506 BINDING PROTEIN (12 KDA, HUMAN) COMPLEX WITH L-709,858 |
| 1B6C | 1999-06-15 | 2.6 | CRYSTAL STRUCTURE OF THE CYTOPLASMIC DOMAIN OF THE TYPE I TGF-BETA RECEPTOR IN COMPLEX WITH FKBP12 |
| 1FAP | 1997-07-23 | 2.7 | THE STRUCTURE OF THE IMMUNOPHILIN-IMMUNOSUPPRESSANT FKBP12-RAPAMYCIN COMPLEX INTERACTING WITH HUMAN FRAP |
| 4FAP | 2000-09-13 | 2.8 | ATOMIC STRUCTURES OF THE RAPAMYCIN ANALOGS IN COMPLEX WITH BOTH HUMAN FKBP12 AND FRB DOMAIN OF FRAP |
| 1QPL | 1999-08-16 | 2.9 | FK506 BINDING PROTEIN (12 KDA, HUMAN) COMPLEX WITH L-707,587 |
| 3J8H | 2014-12-10 | 3.8 | Structure of the rabbit ryanodine receptor RyR1 in complex with FKBP12 at 3.8 Angstrom resolution |
| 5GKY | 2016-08-24 | 3.8 | Structure of RyR1 in a closed state (C1 conformer) |
| 5GKZ | 2016-08-24 | 4.0 | Structure of RyR1 in a closed state (C3 conformer) |
| 5GL0 | 2016-08-24 | 4.2 | Structure of RyR1 in a closed state (C4 conformer) |
| 5GL1 | 2016-08-24 | 5.7 | Structure of RyR1 in an open state |
Relevant UniProtKB Entries
| Percent Identity | Matching Chains | Protein | Accession | Entry Name |
|---|---|---|---|---|
| 97.2 | Peptidyl-prolyl cis-trans isomerase FKBP1A | Q62658 | FKB1A_RAT | |
| 97.2 | Peptidyl-prolyl cis-trans isomerase FKBP1A | P26883 | FKB1A_MOUSE | |
| 97.2 | Peptidyl-prolyl cis-trans isomerase FKBP1A | P18203 | FKB1A_BOVIN | |
| 100.0 | Peptidyl-prolyl cis-trans isomerase FKBP1A | P62943 | FKB1A_RABIT | |
| 100.0 | Peptidyl-prolyl cis-trans isomerase FKBP1A | P62942 | FKB1A_HUMAN |