Dynamics of the Mrf-2 DNA-binding domain free and in complex with DNA.
Mrf-2 is a member of a new class of DNA-binding proteins known as the AT-rich interaction domain family or ARID. Chemical shift indices and characteristic NOE values indicate that the three-dimensional structure of the Mrf-2 ARID in complex with DNA is nearly identical to that of the free protein. The backbone dynamics of the Mrf-2 domain free and in complex with DNA have been characterized by (15)N NMR relaxation measurements and model-free analysis. Chemical shift perturbations and dynamic studies suggest that two flexible interhelical loops, the flexible C-terminal tail, and one alpha-helix are involved in DNA recognition, indicating the importance of protein dynamics in DNA binding. Some well-structured regions, in particular the putative DNA-contacting helix, in Mrf-2 show a decrease in the order parameters (S(2)) upon complex formation. The less well-structured loops and the unstructured C-terminus show reduced flexibility upon DNA binding. In addition, the model-free analysis indicates motions on the picosecond to nanosecond and micro- to millisecond time scales at the DNA-binding surface of the bound Mrf-2 ARID, suggesting a model where interactions between the protein and DNA are highly dynamic.
Zhu
L
L
Division of Immunology, Beckman Institute of the City of Hope, Duarte, California 91010, USA.
Hu
J
J
Lin
D
D
Whitson
R
R
Itakura
K
K
Chen
Y
Y
D016880:Anisotropy; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D046911:Macromolecular Substances; D008958:Models, Molecular; D018006:Myogenic Regulatory Factors / Q000737:chemistry* / Q000378:metabolism*; D009587:Nitrogen Isotopes; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013816:Thermodynamics; D014157:Transcription Factors
C503805:ARID5B protein, human; D004268:DNA-Binding Proteins; D046911:Macromolecular Substances; D018006:Myogenic Regulatory Factors; D009587:Nitrogen Isotopes; D010446:Peptide Fragments; D014157:Transcription Factors; D004247:DNA