TY - JOUR
T1 - Quantitative modeling of DNA-protein interactions
T2 - Effects of amino acid substitutions on binding specificity of the Mnt repressor
AU - Man, Tsz Kwong
AU - Yang, Joshua Sung Woo
AU - Stormo, Gary D.
N1 - Funding Information:
We would like to thank Frauzi Silbaq for the purified His-tagged Mnt proteins used in this study and to Xing Xu for help with the figures. This work is supported by the National Institutes of Health through grant GM28755.
PY - 2004
Y1 - 2004
N2 - Understanding DNA-protein recognition quantitatively is essential to developing computational algorithms for accurate transcriptional binding site prediction. Using a quantitative, multiple fluorescence, relative affinity (QuMFRA) assay, we determine the binding specificity of 11 different position 6 variants of the Mnt repressor for operators containing all 16 possible dinucleotides at operator positions 16 and 17. We show that the wild-type and all variant proteins interact with the two positions in a non-independent manner, but that a simple independent model provides a close approximation to the true binding affinities. The wild-type His at amino acid 6 is the only protein to prefer the AC sequence of the wild-type operator, whereas most of the variant proteins prefer TA. H6R is unique in having a strong preference for C at position 16. A comparison of the quantitative binding data for all of the protein variants with a model for recognition of the early growth response (EGR) zinc finger family suggests that interactions of Mnt with positions 16 and 17 are similar to interactions of EGR with positions 1 and 2, respectively. This information leads to an augmented model for the interaction of Mnt with its operator.
AB - Understanding DNA-protein recognition quantitatively is essential to developing computational algorithms for accurate transcriptional binding site prediction. Using a quantitative, multiple fluorescence, relative affinity (QuMFRA) assay, we determine the binding specificity of 11 different position 6 variants of the Mnt repressor for operators containing all 16 possible dinucleotides at operator positions 16 and 17. We show that the wild-type and all variant proteins interact with the two positions in a non-independent manner, but that a simple independent model provides a close approximation to the true binding affinities. The wild-type His at amino acid 6 is the only protein to prefer the AC sequence of the wild-type operator, whereas most of the variant proteins prefer TA. H6R is unique in having a strong preference for C at position 16. A comparison of the quantitative binding data for all of the protein variants with a model for recognition of the early growth response (EGR) zinc finger family suggests that interactions of Mnt with positions 16 and 17 are similar to interactions of EGR with positions 1 and 2, respectively. This information leads to an augmented model for the interaction of Mnt with its operator.
UR - http://www.scopus.com/inward/record.url?scp=3242885203&partnerID=8YFLogxK
U2 - 10.1093/nar/gkh729
DO - 10.1093/nar/gkh729
M3 - Article
C2 - 15289576
AN - SCOPUS:3242885203
SN - 0305-1048
VL - 32
SP - 4026
EP - 4032
JO - Nucleic acids research
JF - Nucleic acids research
IS - 13
ER -