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Characterization of binding‐induced changes in dynamics suggests a model for sequence‐nonspecific binding of ssDNA by replication protein A
Author(s) -
Bhattacharya Shibani,
Botuyan MariaVictoria,
Hsu Fred,
Shan Xi,
Arunkumar A.I.,
Arrowsmith Cheryl H.,
Edwards Aled M.,
Chazin Walter J.
Publication year - 2002
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.0209202
Subject(s) - dna , binding site , biophysics , binding domain , dna replication , chemistry , plasma protein binding , replication protein a , hmg box , dna binding site , dna binding protein , sequence (biology) , protein secondary structure , crystallography , stereochemistry , biology , biochemistry , gene , transcription factor , promoter , gene expression
Single‐stranded‐DNA‐binding proteins (SSBs) are required for numerous genetic processes ranging from DNA synthesis to the repair of DNA damage, each of which requires binding with high affinity to ssDNA of variable base composition. To gain insight into the mechanism of sequence‐nonspecific binding of ssDNA, NMR chemical shift and 15 N relaxation experiments were performed on an isolated ssDNA‐binding domain (RPA70A) from the human SSB replication protein A. The backbone 13 C, 15 N, and 1 H resonances of RPA70A were assigned for the free protein and the d‐CTTCA complex. The binding‐induced changes in backbone chemical shifts were used to map out the ssDNA‐binding site. Comparison to results obtained for the complex with d‐C 5 showed that the basic mode of binding is independent of the ssDNA sequence, but that there are differences in the binding surfaces. Amide nitrogen relaxation rates ( R 1 and R 2 ) and 1 H– 15 N NOE values were measured for RPA70A in the absence and presence of d‐CTTCA. Analysis of the data using the Model‐Free formalism and spectral density mapping approaches showed that the structural changes in the binding site are accompanied by some significant changes in flexibility of the primary DNA‐binding loops on multiple timescales. On the basis of these results and comparisons to related proteins, we propose that the mechanism of sequence‐nonspecific binding of ssDNA involves dynamic remodeling of the binding surface.