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:10467094
Additional 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

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
1FKS 1994-01-31 SOLUTION STRUCTURE OF FKBP, A ROTAMASE ENZYME AND RECEPTOR FOR FK506 AND RAPAMYCIN
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
1F40 2000-11-08 SOLUTION STRUCTURE OF FKBP12 COMPLEXED WITH GPI-1046, A NEUROTROPHIC LIGAND
1FKT 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
6I1S 2019-09-11 1.52 Crystal structure of the ACVR1 (ALK2) kinase in complex with FKBP12 and the inhibitor E6201
1BKF 1996-08-01 1.6 FK506 BINDING PROTEIN FKBP MUTANT R42K/H87V COMPLEX WITH IMMUNOSUPPRESSANT FK506
1FKF 1991-07-15 1.7 ATOMIC STRUCTURE OF FKBP-FK506, AN IMMUNOPHILIN-IMMUNOSUPPRESSANT COMPLEX
1FKB 1993-10-31 1.7 ATOMIC STRUCTURE OF THE RAPAMYCIN HUMAN IMMUNOPHILIN FKBP-12 COMPLEX
4IPX 2013-06-05 1.7 Analyzing the visible conformational substates of the FK506 binding protein FKBP12
1FKJ 1995-12-07 1.7 ATOMIC STRUCTURE OF FKBP12-FK506, AN IMMUNOPHILIN IMMUNOSUPPRESSANT COMPLEX
1FKL 1995-12-07 1.7 ATOMIC STRUCTURE OF FKBP12-RAPAYMYCIN, AN IMMUNOPHILIN-IMMUNOSUPPRESSANT COMPLEX
2DG9 2006-04-25 1.7 FK506-binding protein mutant WL59 complexed with Rapamycin
2DG4 2006-04-25 1.7 FK506-binding protein mutant WF59 complexed with Rapamycin
2DG3 2006-04-25 1.7 Wildtype FK506-binding protein complexed with Rapamycin
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
1J4I 2003-06-03 1.8 crystal structure analysis of the FKBP12 complexed with 000308 small molecule
1J4H 2003-06-03 1.8 crystal structure analysis of the FKBP12 complexed with 000107 small molecule
1J4R 2001-12-19 1.8 FK506 BINDING PROTEIN COMPLEXED WITH FKB-001
1D6O 1999-10-21 1.85 NATIVE FKBP
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
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)
1D7H 1999-10-21 1.9 FKBP COMPLEXED WITH DMSO
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
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
4ODQ 2015-01-14 2.0 Structure of SlyD delta-IF from Thermus thermophilus in complex with S3 peptide
1EYM 2000-08-09 2.0 FK506 BINDING PROTEIN MUTANT, HOMODIMERIC COMPLEX
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
1A7X 1998-06-17 2.0 FKBP12-FK1012 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?
1NSG 1998-03-18 2.2 THE STRUCTURE OF THE IMMUNOPHILIN-IMMUNOSUPPRESSANT FKBP12-RAPAMYCIN COMPLEX INTERACTING WITH HUMAN FRAP
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
6OQA 2020-04-29 2.2 Crystal structure of CEP250 bound to FKBP12 in the presence of FK506-like novel natural product
2FAP 1999-05-18 2.2 THE STRUCTURE OF THE IMMUNOPHILIN-IMMUNOSUPPRESSANT FKBP12-(C16)-ETHOXY RAPAMYCIN COMPLEX INTERACTING WITH HUMA
6M4U 2020-08-26 2.2 Crystal structure of FKBP-FRB T2098L mutant in complex with rapamycin
3H9R 2009-06-02 2.35 Crystal structure of the kinase domain of type I activin receptor (ACVR1) in complex with FKBP12 and dorsomorphin
1QPF 1999-08-16 2.5 FK506 BINDING PROTEIN (12 KDA, HUMAN) COMPLEX WITH L-709,858
1TCO 1997-02-12 2.5 TERNARY COMPLEX OF A CALCINEURIN A FRAGMENT, CALCINEURIN B, FKBP12 AND THE IMMUNOSUPPRESSANT DRUG FK506 (TACROLIMUS)
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
6M4V 2020-08-26 2.92 Crystal structure of MBP fused split FKBP in complex with rapamycin
6M4W 2020-08-26 3.11 Crystal structure of MBP fused split FKBP-FRB T2098L mutant in complex with rapamycin
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
100.0 Peptidyl-prolyl cis-trans isomerase FKBP1A P62942 FKB1A_HUMAN
100.0 Peptidyl-prolyl cis-trans isomerase FKBP1A P62943 FKB1A_RABIT
97.2 Peptidyl-prolyl cis-trans isomerase FKBP1A P18203 FKB1A_BOVIN
97.2 Peptidyl-prolyl cis-trans isomerase FKBP1A P26883 FKB1A_MOUSE
97.2 Peptidyl-prolyl cis-trans isomerase FKBP1A Q62658 FKB1A_RAT