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
1FKK 1995-08-18T00:00:00+0000 2.2 ATOMIC STRUCTURE OF FKBP12, AN IMMUNOPHILIN BINDING PROTEIN
1FKL 1995-08-18T00:00:00+0000 1.7 ATOMIC STRUCTURE OF FKBP12-RAPAYMYCIN, AN IMMUNOPHILIN-IMMUNOSUPPRESSANT COMPLEX
1TCO 1996-08-21T00:00:00+0000 2.5 TERNARY COMPLEX OF A CALCINEURIN A FRAGMENT, CALCINEURIN B, FKBP12 AND THE IMMUNOSUPPRESSANT DRUG FK506 (TACROLIMUS)
3J8H 2014-10-26T00:00:00+0000 3.8 Structure of the rabbit ryanodine receptor RyR1 in complex with FKBP12 at 3.8 Angstrom resolution
5GKY 2016-07-07T00:00:00+0000 3.8 Structure of RyR1 in a closed state (C1 conformer)
5GKZ 2016-07-07T00:00:00+0000 4.0 Structure of RyR1 in a closed state (C3 conformer)
5GL0 2016-07-07T00:00:00+0000 4.2 Structure of RyR1 in a closed state (C4 conformer)
5GL1 2016-07-07T00:00:00+0000 5.7 Structure of RyR1 in an open state
1A7X 1998-03-18T00:00:00+0000 2.0 FKBP12-FK1012 COMPLEX
1B6C 1999-01-13T00:00:00+0000 2.6 CRYSTAL STRUCTURE OF THE CYTOPLASMIC DOMAIN OF THE TYPE I TGF-BETA RECEPTOR IN COMPLEX WITH FKBP12

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