Context-dependent nature of destabilizing mutations on the stability of FKBP12.


Abstract

The context-dependent nature in which mutations affect protein stability was investigated using the FK506-binding protein, FKBP12. Thirty-four mutations were made at sites throughout the protein, including residues located in the hydrophobic core, the beta-sheet, and the solvent-exposed face of the alpha-helix. Urea-induced denaturation experiments were used to measure the change in stability of the mutants relative to that of the wild type (Delta DeltaGU-F). The results clearly show that the extent of destabilization, or stabilization, is highly context-dependent. Correlations were sought in order to link Delta DeltaGU-F to various structural parameters. The strongest correlation found was between Delta DeltaGU-F and N, the number of methyl(ene) groups within a 6 A radius of the group(s) deleted. For mutations of buried hydrophobic residues, a correlation coefficient of 0.73 (n = 16,where n is the number of points) was obtained. This increased to 0.81 (n = 24) on inclusion of mutations of partially buried hydrophobic residues. These data could be superimposed on data obtained for other proteins for which similarly detailed studies have been performed. Thus, the contribution to stability from hydrophobic side chains, independent of the extent to which a side chain is buried, can be estimated quantitatively using N. This correlation appears to be a general feature of all globular proteins. The effect on stability of mutating polar and charged residues in the alpha-helix and beta-sheet was also found to be highly context-dependent. Previous experimental and statistical studies have shown that specific side chains can stabilize the N-caps of alpha-helices in proteins. Substitutions of Ile56 to Thr and Asp at the N-cap of the alpha-helix of FKBP12, however, were found to be highly destabilizing. Thus, the intrinsic propensities of an amino acid for a particular element of secondary structure can easily be outweighed by tertiary packing factors. This study highlights the importance of packing density in determining the contribution of a residue to protein stability. This is the most important factor that should be taken into consideration in protein design. Study holds ProTherm entries: 3180, 3181, 3182, 3183, 3184, 3185, 3186, 3187, 3188, 3189, 3190, 3191, 3192, 3193, 3194, 3195, 3196, 3197, 3198, 3199, 3200, 3201, 3202, 3203, 3204, 3205, 3206, 3207, 3208, 3209, 3210, 3211, 3212, 3213, 3214 Extra Details: context-dependent; protein stability; FK506-binding protein;,hydrophobic core; beta-sheet; alpha-helix; solvent-exposed

Submission Details

ID: aVAcP6RE4

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:21 p.m.

Version: 1

Publication Details
Main ER;Fulton KF;Jackson SE,Biochemistry (1998) Context-dependent nature of destabilizing mutations on the stability of FKBP12. PMID:9558354
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
2ND5 2017-05-17 Lysine dimethylated FKBP12
1FKT 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
1FKR 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
2RSE 2012-05-30 NMR structure of FKBP12-mTOR FRB domain-rapamycin complex structure determined based on PCS
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
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
1FKL 1995-12-07 1.7 ATOMIC STRUCTURE OF FKBP12-RAPAYMYCIN, AN IMMUNOPHILIN-IMMUNOSUPPRESSANT COMPLEX
2DG3 2006-04-25 1.7 Wildtype FK506-binding protein complexed with Rapamycin
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
1FKJ 1995-12-07 1.7 ATOMIC STRUCTURE OF FKBP12-FK506, AN IMMUNOPHILIN IMMUNOSUPPRESSANT COMPLEX
1FKD 1994-01-31 1.72 FK-506 BINDING PROTEIN: THREE-DIMENSIONAL STRUCTURE OF THE COMPLEX WITH THE ANTAGONIST L-685,818
2FKE 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
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
1D7J 1999-10-21 1.85 FKBP COMPLEXED WITH 4-HYDROXY-2-BUTANONE
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
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
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
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
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
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?
2FAP 1999-05-18 2.2 THE STRUCTURE OF THE IMMUNOPHILIN-IMMUNOSUPPRESSANT FKBP12-(C16)-ETHOXY RAPAMYCIN COMPLEX INTERACTING WITH HUMA
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
1FKK 1995-12-07 2.2 ATOMIC STRUCTURE OF FKBP12, AN IMMUNOPHILIN BINDING PROTEIN
1NSG 1998-03-18 2.2 THE STRUCTURE OF THE IMMUNOPHILIN-IMMUNOSUPPRESSANT FKBP12-RAPAMYCIN COMPLEX INTERACTING WITH HUMAN FRAP
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