Lac repressor: Difference between revisions
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DNA sequence recognition in the '''minor groove''', often accompanied by kinking or bending of the DNA, is more complex. Direct readout is less important, since, unlike in the major groove, the four bases do not present unique hydrogen-bonding surfaces in the minor groove<ref name="rohsrev2010" />. Recognition of the shape of the DNA seems more important<ref>PMID: 17981120</ref><ref name="rohs2009" />. In many cases, cationic arginines are believed to be attracted to a region of the minor groove with high aninoic charge density resulting from narrowing of the groove<ref name="rohs2009" >PMID: 19865164</ref>. In these cases, the protein appears to recognize the shape of the DNA minor groove (''indirect readout'')<ref name="rohs2009" />. | DNA sequence recognition in the '''minor groove''', often accompanied by kinking or bending of the DNA, is more complex. Direct readout is less important, since, unlike in the major groove, the four bases do not present unique hydrogen-bonding surfaces in the minor groove<ref name="rohsrev2010" />. Recognition of the shape of the DNA seems more important<ref>PMID: 17981120</ref><ref name="rohs2009" />. In many cases, cationic arginines are believed to be attracted to a region of the minor groove with high aninoic charge density resulting from narrowing of the groove<ref name="rohs2009" >PMID: 19865164</ref>. In these cases, the protein appears to recognize the shape of the DNA minor groove (''indirect readout'')<ref name="rohs2009" />. | ||
<applet size='450' frame='true' align='right' scene='Lac_repressor/ | <applet size='450' frame='true' align='right' scene='Lac_repressor/Arg51/1' /> | ||
In the lac repressor complex with specific DNA, a pair of arginines (Arg51 in each chain) is close to the minor groove, but points away from the groove. <!--[Remove this in view of <ref>PMID: 20232938</ref>? Also this portion of the minor groove does not contain ApT or ApA (TpT) which are associated with minor groove narrowing and high negative charge density.]--> Hence the binding of arginines to narrow minor grooves does not appear to be involved in specific DNA recognition by the lac repressor. | In the lac repressor complex with specific DNA, a pair of arginines (Arg51 in each chain) is close to the minor groove, but points away from the groove (<scene name='Lac_repressor/Arg51/1'>restore initial scene</scene>). <!--[Remove this in view of <ref>PMID: 20232938</ref>? Also this portion of the minor groove does not contain ApT or ApA (TpT) which are associated with minor groove narrowing and high negative charge density.]--> Hence the binding of arginines to narrow minor grooves does not appear to be involved in specific DNA recognition by the lac repressor. | ||
====DNA Kinks==== | ====DNA Kinks==== | ||
