Energetics of repacking a protein interior.


Abstract

To test whether interactions in the hydrophobic core of a protein can be adequately modeled based on the properties of a liquid hydrocarbon, we measured the unfolding free energies of the wild-type bacteriophage f1 gene V protein and 29 mutants with apolar substitutions at positions 35 and 47. Stability changes arising from identical mutations at these two buried sites are quite different, suggesting that one site is more rigid than the other. Reversals of residues at positions 35 and 47 confirm that their environments are distinct. Mutants containing weakly polar residues at these two sites suggest that the protein interior is more polar than a liquid hydrocarbon. Interactions between residues at the two sites appear to be minimal. These observations are compatible with a view of protein interiors that incorporates properties of liquid hydrocarbons but also includes polar interactions and a site-dependent "packing energy" associated with changes in internal structure. Study holds ProTherm entries: 850, 851, 852, 853, 854, 855, 856, 857, 858, 859, 860, 861, 862, 863, 864, 865, 866, 867, 868, 869, 870, 871, 872, 873, 874, 875, 876, 877, 878, 879 Extra Details: additive : EDTA(1 mM),dG and ddG values were measured in the presence of 2M GdnHCl gene V protein, protein stability, hydrophobic effect;,protein engineering

Submission Details

ID: efjyBbW63

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:16 p.m.

Version: 1

Publication Details
Sandberg WS;Terwilliger TC,Proc. Natl. Acad. Sci. U.S.A. (1991) Energetics of repacking a protein interior. PMID:2000379
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
2GVB 1995-10-15 REFINED SOLUTION STRUCTURE OF THE TYR 41--> HIS MUTANT OF THE M13 GENE V PROTEIN. A COMPARISON WITH THE CRYSTAL STRUCTURE
2GVA 1995-10-15 REFINED SOLUTION STRUCTURE OF THE TYR 41--> HIS MUTANT OF THE M13 GENE V PROTEIN. A COMPARISON WITH THE CRYSTAL STRUCTURE
1GVP 1997-09-04 1.6 GENE V PROTEIN (SINGLE-STRANDED DNA BINDING PROTEIN)
1GKH 1997-09-04 1.7 MUTANT K69H OF GENE V PROTEIN (SINGLE-STRANDED DNA BINDING PROTEIN)
1VQI 1997-02-12 1.8 GENE V PROTEIN MUTANT WITH ILE 47 REPLACED BY VAL 47 (I47V)
1VQB 1997-02-12 1.8 GENE V PROTEIN (SINGLE-STRANDED DNA BINDING PROTEIN)
1VQH 1997-02-12 1.8 GENE V PROTEIN MUTANT WITH ILE 47 REPLACED BY MET 47 (I47M)
1VQJ 1997-02-12 1.8 GENE V PROTEIN MUTANT WITH VAL 35 REPLACED BY ILE 35 (V35I)
1VQF 1997-02-12 1.8 GENE V PROTEIN MUTANT WITH VAL 35 REPLACED BY ILE 35 AND ILE 47 REPLACED BY VAL 47 (V35I, I47V)
1VQE 1997-02-12 1.8 GENE V PROTEIN MUTANT WITH VAL 35 REPLACED BY ILE 35 AND ILE 47 REPLACED BY MET 47 (V35I, I47M)
1VQC 1997-02-12 1.8 GENE V PROTEIN MUTANT WITH VAL 35 REPLACED BY ILE 35 AND ILE 47 REPLACED BY PHE 47 (V35I, I47F)
1VQA 1997-02-12 1.8 GENE V PROTEIN MUTANT WITH VAL 35 REPLACED BY ALA 35 AND ILE 47 REPLACED BY LEU 47 (V35A, I47L)
1VQD 1997-02-12 1.82 GENE V PROTEIN MUTANT WITH VAL 35 REPLACED BY ILE 35 AND ILE 47 REPLACED BY LEU 47 (V35I, I47L)
1VQG 1997-02-12 1.82 GENE V PROTEIN MUTANT WITH ILE 47 REPLACED BY LEU 47 (I47L)
1AE2 1997-09-04 2.0 MUTANT L32R OF GENE V PROTEIN (SINGLE-STRANDED DNA BINDING PROTEIN)
1AE3 1997-09-04 2.0 MUTANT R82C OF GENE V PROTEIN (SINGLE-STRANDED DNA BINDING PROTEIN)
1YHB 1994-06-22 2.2 CRYSTAL STRUCTURES OF Y41H AND Y41F MUTANTS OF GENE V PROTEIN FROM FF PHAGE SUGGEST POSSIBLE PROTEIN-PROTEIN INTERACTIONS IN GVP-SSDNA COMPLEX
2GN5 1986-01-21 2.3 REFINED STRUCTURE OF THE GENE 5 DNA BINDING PROTEIN FROM BACTERIOPHAGE FD
1YHA 1994-06-22 2.5 CRYSTAL STRUCTURES OF Y41H AND Y41F MUTANTS OF GENE V PROTEIN FROM FF PHAGE SUGGEST POSSIBLE PROTEIN-PROTEIN INTERACTIONS IN GVP-SSDNA COMPLEX

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 DNA-Binding protein G5P P69544 G5P_BPM13
100.0 DNA-Binding protein G5P P69542 G5P_BPFD
100.0 DNA-Binding protein G5P P69543 G5P_BPF1