Hox protein: Difference between revisions
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===Minor Groove Shape Readout=== | ===Minor Groove Shape Readout=== | ||
Minor groove contacts, in addition to base readout in the major groove, provide the level of specificity that contributes to distinguishing factors within the Hox family. It has been shown that minor groove contacts are essential for achieving specificity. Three side chains, <scene name='Sandbox_Reserved_169/Scr_mg/8'>His-12, | Minor groove contacts, in addition to base readout in the major groove, provide the level of specificity that contributes to distinguishing factors within the Hox family. It has been shown that minor groove contacts are essential for achieving specificity. Three side chains, <scene name='Sandbox_Reserved_169/Scr_mg/8'>His-12, Arg-3, and Arg-5 are observed to contact the minor groove</scene> of the Scr in vivo site ''fkh250''. However, this additional level of binding specificity is not achieved through hydrogen bonds between protein side chains and functional groups of the bases. Such direct interactions are unable to distinguish A/T and T/A, or C/G and G/C base pairs due to the overlapping location of hydrogen bond donors and acceptors.<br/> | ||
The mechanism through which these three residues recognize the DNA minor groove is called '''shape readout''' as they do not form base-specific hydrogen bonds but rather recognize the sequence-specific narrowing of the minor groove. AT-rich regions can be characterized through an intrinsically narrow minor groove, leading to enhanced negative electrostatic potential, which in turn attracts basic side chains. This shape readout mechanism was found to be broadly employed by arginine residues <ref name="nature">Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B. The role of DNA shape in protein-DNA recognition. Nature. 2009;461(7268):1248-53. [http://www.ncbi.nlm.nih.gov/pubmed/19865164 PMID:19865164]</ref>.<br/> | The mechanism through which these three residues recognize the DNA minor groove is called '''shape readout''' as they do not form base-specific hydrogen bonds but rather recognize the sequence-specific narrowing of the minor groove. AT-rich regions can be characterized through an intrinsically narrow minor groove, leading to enhanced negative electrostatic potential, which in turn attracts basic side chains. This shape readout mechanism was found to be broadly employed by arginine residues <ref name="nature">Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B. The role of DNA shape in protein-DNA recognition. Nature. 2009;461(7268):1248-53. [http://www.ncbi.nlm.nih.gov/pubmed/19865164 PMID:19865164]</ref>.<br/> | ||