Mapping the interactions present in the transition state for unfolding/folding of FKBP12.


Abstract

The structure of the transition state for folding/unfolding of the immunophilin FKBP12 has been characterised using a combination of protein engineering techniques, unfolding kinetics, and molecular dynamics simulations. A total of 34 mutations were made at sites throughout the protein to probe the extent of secondary and tertiary structure in the transition state. The transition state for folding is compact compared with the unfolded state, with an approximately 30 % increase in the native solvent-accessible surface area. All of the interactions are substantially weaker in the transition state, as probed by both experiment and molecular dynamics simulations. In contrast to some other proteins of this size, no element of structure is fully formed in the transition state; instead, the transition state is similar to that found for smaller, single-domain proteins, such as chymotrypsin inhibitor 2 and the SH3 domain from alpha-spectrin. For FKBP12, the central three strands of the beta-sheet, beta-strand 2, beta-strand 4 and beta-strand 5, comprise the most structured region of the transition state. In particular Val101, which is one of the most highly buried residues and located in the middle of the central beta-strand, makes approximately 60 % of its native interactions. The outer beta-strands and the ends of the central beta-strands are formed to a lesser degree. The short alpha-helix is largely unstructured in the transition state, as are the loops. The data are consistent with a nucleation-condensation model of folding, the nucleus of which is formed by side-chains within beta-strands 2, 4 and 5, and the C terminus of the alpha-helix. The precise residues involved in the nucleus differ in the two simulated transition state ensembles, but the interacting regions of the protein are conserved. These residues are distant in the primary sequence, demonstrating the importance of tertiary interactions in the transition state. The two independently derived transition state ensembles are structurally similar, which is consistent with a Bronsted analysis confirming that the transition state is an ensemble of states close in structure. Study holds ProTherm entries: 6217, 6218, 6219, 6220, 6221, 6222, 6223, 6224, 6225, 6226, 6227, 6228, 6229, 6230, 6231, 6232, 6233, 6234, 6235, 6236, 6237, 6238, 6239, 6240, 6241, 6242, 6243, 6244, 6245, 6246, 6247, 6248, 6249, 6250 Extra Details: FKBP12; protein engineering; molecular dynamics;,phi-value analysis; nucleation-condensation

Submission Details

ID: SYq52Ueo3

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:31 p.m.

Version: 1

Publication Details
Fulton KF;Main ER;Daggett V;Jackson SE,J. Mol. Biol. (1999) Mapping the interactions present in the transition state for unfolding/folding of FKBP12. PMID:10438631
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
1FKT 1994-01-31 SOLUTION STRUCTURE OF FKBP, A ROTAMASE ENZYME AND RECEPTOR FOR FK506 AND RAPAMYCIN
1FKR 1994-01-31 SOLUTION STRUCTURE OF FKBP, A ROTAMASE ENZYME AND RECEPTOR FOR FK506 AND RAPAMYCIN
2ND5 2017-05-17 Lysine dimethylated FKBP12
2RSE 2012-05-30 NMR structure of FKBP12-mTOR FRB domain-rapamycin complex structure determined based on PCS
1FKS 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
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
2DG3 2006-04-25 1.7 Wildtype FK506-binding protein complexed with Rapamycin
2DG4 2006-04-25 1.7 FK506-binding protein mutant WF59 complexed with Rapamycin
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
1FKF 1991-07-15 1.7 ATOMIC STRUCTURE OF FKBP-FK506, AN IMMUNOPHILIN-IMMUNOSUPPRESSANT COMPLEX
4IPX 2013-06-05 1.7 Analyzing the visible conformational substates of the FK506 binding protein FKBP12
1FKB 1993-10-31 1.7 ATOMIC STRUCTURE OF THE RAPAMYCIN HUMAN IMMUNOPHILIN FKBP-12 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
1D7I 1999-10-21 1.9 FKBP COMPLEXED WITH METHYL METHYLSULFINYLMETHYL SULFIDE (DSS)
1BL4 1998-09-02 1.9 FKBP MUTANT F36V COMPLEXED WITH REMODELED SYNTHETIC LIGAND
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
1A7X 1998-06-17 2.0 FKBP12-FK1012 COMPLEX
1EYM 2000-08-09 2.0 FK506 BINDING PROTEIN MUTANT, HOMODIMERIC 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
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?
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
1FKK 1995-12-07 2.2 ATOMIC STRUCTURE OF FKBP12, AN IMMUNOPHILIN BINDING PROTEIN
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
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