Energetics of folding and DNA binding of the MAT alpha 2 homeodomain.


Abstract

Homeodomains are a class of DNA-binding protein domains which play an important role in genetic regulation in eukaryotes. We have characterized the thermodynamics of folding and sequence-specific association with DNA of the MAT alpha 2 homeodomain of yeast. Using differential scanning and isothermal titration calorimetry, we measured the enthalpy, heat capacity, and Gibbs free energy changes of these processes. The protein-DNA interaction is enthalpically driven at physiological temperatures. DSC data on the process of melting the protein-DNA complex at different salt concentrations were dissected into its endothermic components, yielding the enthalpy change and dissociation constant of binding. A comparison of the circular dichroism spectra of the free and DNA-bound protein species revealed the formation of additional alpha-helical structure upon binding to DNA. We propose that the latter half of helix 3, the recognition helix, is substantially unfolded in the free protein under the conditions used, as has been observed with other homeodomains [Tsao, D. H. H., et al. (1994) Biochemistry 33, 15053-15060: Cox, M., et al. (1995) J. Biomol. NMR 5, 23-32]. Formation of protein structure is induced by DNA binding, and the energies measured for association therefore include a component due to folding. Study holds ProTherm entries: 4903, 4904, 4905, 4906, 4907, 4908, 4909 Extra Details: additive : EDTA(1 mM), DNA-binding protein domains; protein-DNA interaction;,alpha-helical structure; association

Submission Details

ID: Ws4PULMN

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:27 p.m.

Version: 1

Publication Details
Carra JH;Privalov PL,Biochemistry (1997) Energetics of folding and DNA binding of the MAT alpha 2 homeodomain. PMID:9012668
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
1K61 2002-12-11 2.1 MATALPHA2 HOMEODOMAIN BOUND TO DNA
1MNM 1998-03-18 2.25 YEAST MATALPHA2/MCM1/DNA TERNARY TRANSCRIPTION COMPLEX CRYSTAL STRUCTURE
1LE8 2002-05-03 2.3 Crystal Structure of the MATa1/MATalpha2-3A Heterodimer Bound to DNA Complex
1AKH 1998-05-20 2.5 MAT A1/ALPHA2/DNA TERNARY COMPLEX
1YRN 1996-01-29 2.5 CRYSTAL STRUCTURE OF THE MATA1/MATALPHA2 HOMEODOMAIN HETERODIMER BOUND TO DNA
1APL 1993-10-21 2.7 CRYSTAL STRUCTURE OF A MAT-ALPHA2 HOMEODOMAIN-OPERATOR COMPLEX SUGGESTS A GENERAL MODEL FOR HOMEODOMAIN-DNA INTERACTIONS

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
200.0 C,D (MAT-ALPHA2 HOMEODOMAIN) P0CY08 MTAL2_YEAST
200.0 C,D (MAT-ALPHA2 HOMEODOMAIN) P0CY12 MATA2_YEASX
200.0 C,D (MAT-ALPHA2 HOMEODOMAIN) P0CY13 HMRA2_YEAST
200.0 C,D (MAT-ALPHA2 HOMEODOMAIN) P0CY09 HMAL2_YEAST