Thermodynamics of core hydrophobicity and packing in the hyperthermophile proteins Sac7d and Sso7d.


Abstract

The influence of core hydrophobicity and packing on the structure and stability of the hyperthermophile proteins Sac7d and Sso7d have been studied by calorimetry, circular dichroism, and NMR. Valine 30 is positioned in Sac7d to allow a cavity-filling Val --> Ile substitution which occurs naturally in the homologous more thermostable Sso7d. The cavity-filling mutation in Sac7d has been characterized and compared to the reciprocal Ile --> Val mutation in Sso7d. A detailed analysis of the stability of the proteins was obtained by globally fitting the variation of DSC parameters and circular dichroism intensities as a function of temperature (0-100 degrees C), salt (0-0.3 M), and pH (0-8). A global analysis over such a range of conditions permitted an unusually precise measure of the thermodynamic parameters, as well as the separation of the thermodynamics of the intrinsic unfolding reaction from the linked effects of protonation and chloride binding associated with acid-induced folding. The results indicate differences in the energetics of unfolding Sac7d and Sso7d that would not be apparent from an analysis of DSC data alone using conventional methods. The sign and magnitude of the changes in DeltaG, DeltaH, TDeltaS, and DeltaC(P) of unfolding resulting from core Ile/Val substitutions in the two proteins were consistent with differences in hydrophobicity of Val and Ile and negligible changes in packing (van der Waals) interactions. The benefit of increased hydrophobicity of the core increased with temperature, with maximal effect around 116 degrees C. Increased hydrophobicity of the core achieved not only an increase in the free energy of unfolding, but also a lateral shift of the temperature of maximal stability to higher temperature. Study holds ProTherm entries: 16987, 16988, 16989, 16990, 16991, 16992 Extra Details: hydrophobicity; packing; hyperthermophile; cavity-filling

Submission Details

ID: tgi4tcAo

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:48 p.m.

Version: 1

Publication Details
Clark AT;McCrary BS;Edmondson SP;Shriver JW,Biochemistry (2004) Thermodynamics of core hydrophobicity and packing in the hyperthermophile proteins Sac7d and Sso7d. PMID:15005619
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
1XX8 2005-02-08 NMR Structure of the W24A Mutant of the Hyperthermophile Sac7d Protein
1B4O 2000-01-05 NMR STUDY OF SSO7D MUTANT (F31A) MINIMIZED AVERAGE STRUCTURE
1SSO 1995-05-08 SOLUTION STRUCTURE AND DNA-BINDING PROPERTIES OF A THERMOSTABLE PROTEIN FROM THE ARCHAEON SULFOLOBUS SOLFATARICUS
1BBX 1998-10-14 NON-SPECIFIC PROTEIN-DNA INTERACTIONS IN THE SSO7D-DNA COMPLEX, NMR, 1 STRUCTURE
1JIC 1998-10-14 SOLUTION NMR STRUCTURE OF RECOMBINANT SSO7D WITH RNASE ACTIVITY, MINIMIZED AVERAGE STRUCTURE
2CVR 2006-08-29 NMR solution structure of sso7d mutant, K12L, 12 conformers
1SAP 1995-09-15 HYPERTHERMOPHILE PROTEIN, RELAXATION MATRIX REFINEMENT STRUCTURE
1C8C 2001-05-04 1.45 CRYSTAL STRUCTURES OF THE CHROMOSOMAL PROTEINS SSO7D/SAC7D BOUND TO DNA CONTAINING T-G MISMATCHED BASE PAIRS
1XYI 2005-02-08 1.45 Hyperthermophile chromosomal protein Sac7d double mutant Val26Ala/Met29Ala in complex with DNA GCGATCGC
4CJ2 2014-05-21 1.5 Crystal structure of HEWL in complex with affitin H4
2XIW 2011-07-13 1.5 Crystal structure of the Sac7d-derived IgG1-binder C3-C24S
1WTO 2005-02-22 1.5 Hyperthermophile chromosomal protein SAC7D double mutant V26F/M29F in complex with DNA GCGATCGC
1BF4 1999-11-10 1.6 CHROMOSOMAL DNA-BINDING PROTEIN SSO7D/D(GCGAACGC) COMPLEX
1WTV 2005-02-22 1.6 Hyperthermophile chromosomal protein SAC7D single mutant M29A in complex with DNA GTAATTAC
1AZP 1999-01-13 1.6 HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D BOUND WITH KINKED DNA DUPLEX
4CJ1 2014-05-21 1.63 Crystal structure of CelD in complex with affitin H3
1WTQ 2005-02-22 1.7 Hyperthermophile chromosomal protein SAC7D single mutant M29F in complex with DNA GTAATTAC
1WTR 2005-02-22 1.8 Hyperthermophile chromosomal protein SAC7D single mutant M29A in complex with DNA GCGATCGC
1WTP 2005-02-22 1.9 Hyperthermophile chromosomal protein SAC7D single mutant M29F in complex with DNA GCGA(UBr)CGC
1WD0 2004-08-03 1.9 Crystal structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers
1AZQ 1999-01-13 1.94 HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D BOUND WITH KINKED DNA DUPLEX
1BNZ 1998-11-11 2.0 SSO7D HYPERTHERMOPHILE PROTEIN/DNA COMPLEX
1WTX 2005-02-22 2.2 Hyperthermophile chromosomal protein SAC7D single mutant V26A in complex with DNA GTAATTAC
1CA6 2000-02-23 2.2 INTERCALATION SITE OF HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SSO7D/SAC7D BOUND TO DNA
1WD1 2004-08-03 2.2 Crystal structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers
1CA5 2000-02-23 2.2 INTERCALATION SITE OF HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SSO7D/SAC7D BOUND TO DNA
1WTW 2005-02-22 2.2 Hyperthermophile chromosomal protein SAC7D single mutant V26A in complex with DNA GCGATCGC
5B02 2016-03-23 2.21 Structure of the prenyltransferase MoeN5 with a fusion protein tag of Sso7d
6J8V 2019-04-17 2.23 Structure of MOEN5-SSO7D fusion protein in complex with ligand 2
5B0I 2016-03-23 2.26 Structure of MoeN5-Sso7d fusion protein in complex with beta-octyl glucoside
5GWW 2017-09-20 2.3 Structure of MoeN5-Sso7d fusion protein in complex with a permethylated substrate analogue
6J8W 2019-04-17 2.35 Structure of MOEN5-SSO7D fusion protein in complex with lig 1
5GWV 2017-09-20 2.4 Structure of MoeN5-Sso7d fusion protein in complex with a substrate analogue
5B0J 2016-03-23 2.5 Structure of MoeN5-Sso7d fusion protein in complex with beta-undecyl maltoside
1WVL 2005-08-02 2.6 Crystal Structure of Multimeric DNA-binding Protein Sac7d-GCN4 with DNA decamer
5B03 2016-03-23 2.6 Structure of MoeN5-Sso7d fusion protein in complex with geranyl pyrophosphate
5B0K 2016-03-23 2.75 Structure of MoeN5-Sso7d fusion protein in complex with beta-decyl maltoside
5B0L 2016-03-23 2.8 Structure of MoeN5-Sso7d fusion protein in complex with beta-nonyl glucoside
5B0M 2016-03-23 3.05 Structure of MoeN5-Sso7d fusion protein in complex with beta-dodecyl maltoside
5U1C 2017-01-11 3.9 Structure of tetrameric HIV-1 Strand Transfer Complex Intasome

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
93.2 DNA-binding protein 7a Q96X56 DN7_SULTO
98.4 DNA-binding protein 7a F0NJT3 DN7B_SULIH
96.9 DNA-binding protein 7d O59632 DN7B_SACSH
100.0 DNA-binding protein 7a D2PHL8 DN7A_SULID
100.0 DNA-binding protein 7a P61990 DN7A_SACSH
100.0 DNA-binding protein 7a P61991 DN7A_SACS2
100.0 DNA-binding protein 7d P39476 DN7D_SACS2
92.9 DNA-binding protein 7d F4B8X5 DN7C_ACIHW
91.4 DNA-binding protein 7d F4B9I5 DN7B_ACIHW
92.3 DNA-binding protein 7d P13125 DN7E_SULAC
100.0 DNA-binding protein 7d P13123 DN7D_SULAC