Lac repressor: Difference between revisions
No edit summary |
No edit summary |
||
| (3 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
__NOTOC__ | __NOTOC__ | ||
<StructureSection load=' | <StructureSection load='' size='375' side='right' scene='Morphs/1osl_19_1l1m_9_morph/2' caption=''> | ||
[[Morphs|Morph]] of the '''lac repressor''' complexed with DNA | [[Morphs|Morph]] of the '''lac repressor''' complexed with DNA | ||
<scene name="Morphs/1osl_19_1l1m_9_morph/2">restore initial scene</scene> {{Template:Button Toggle Animation2}} | (<scene name="Morphs/1osl_19_1l1m_9_morph/2">restore initial scene</scene>) After displaying interactive model: {{Template:Button Toggle Animation2}} | ||
showing the differences between non-specific binding (straight DNA) vs. specific recognition of the operator sequence (kinked DNA). Whether the binding kinks the DNA, or simply stabilizes a pre-existing kink, is unknown. [[#Specific Binding| Details Below]]. | showing the differences between non-specific binding (straight DNA) vs. specific recognition of the operator sequence (kinked DNA). Whether the binding kinks the DNA, or simply stabilizes a pre-existing kink, is unknown. [[#Specific Binding| Details Below]]. | ||
__TOC__ | __TOC__ | ||
| Line 50: | Line 50: | ||
====DNA Kinks==== | ====DNA Kinks==== | ||
Strictly speaking, ''bends'' in DNA are distinguished from ''kinks''. DNA is said to be '''kinked''' when the stacking contact between two adjacent base pairs is disrupted<ref name="rohsrev2010" />. The DNA on either side of a kink may be straight or bent. A <scene name='Lac_repressor/Kink/2'>kink occurs in the complex between the lac repressor and specific DNA</scene>: a single CpG base pair is partially separated from the adjacent CpG base pair. <scene name='Lac_repressor/Kink/3'>Zoom in</scene>. Pyrimidine-purine base pairs have the weakest stacking interactions, and are most susceptible to kinking<ref name="rohsrev2010" />. In the complex of lac repressor with specific DNA, <scene name='Lac_repressor/Kink_leu56/1'>two leucines (Leu56)</scene> (<jmol> | Strictly speaking, ''bends'' in DNA are distinguished from ''kinks''. DNA is said to be '''kinked''' when the stacking contact between two adjacent base pairs is disrupted<ref name="rohsrev2010" />. The DNA on either side of a kink may be straight or bent. A <scene name='Lac_repressor/Kink/2'>kink occurs in the complex between the lac repressor and specific DNA</scene>: a single CpG base pair is partially separated from the adjacent CpG base pair. <scene name='Lac_repressor/Kink/3'>Zoom in</scene>. Pyrimidine-purine base pairs have the weakest stacking interactions, and are most susceptible to kinking<ref name="rohsrev2010" />. In the complex of lac repressor with specific DNA, <scene name='Lac_repressor/Kink_leu56/1'>two leucines (Leu56)</scene> (if scene is blank,<jmol> | ||
<jmolLink> | <jmolLink> | ||
<script> model 0;</script> | <script> model 0;</script> | ||
<text>click | <text>please click</text> | ||
</jmolLink> | </jmolLink> | ||
</jmol>)<!--(<font color="red">Sorry, this scene is temporarily broken.</font>)--> are partially intercalated between the separated CpG base pairs, which helps to stabilize the kink. It may often be the case that sequence-dependent kinks and bends are present in DNA prior to the binding of protein<ref name="rohsrev2010" />. DNA structure is dynamic. For example, recently Hoogsteen base pairing was observed to occur transiently in equilibrium with Watson-Crick base pairing<ref>PMID: 21270796</ref> (See ''News & Views''<ref>PMID: 21350476</ref>). Also, the binding of p53 to some but not all DNA sequences stabilizes Hoogsteen (rather than Watson-Crick) base pairing<ref>PMID: 20364130</ref>. Thus, the "bending" (actually kinking) depicted in '''the morph on this page may give the wrong impression''': lac repressor binding may simply stabilize a kink (or transient kink) that pre-existed in the cognate DNA sequence. | </jmol>)<!--(<font color="red">Sorry, this scene is temporarily broken.</font>)--> are partially intercalated between the separated CpG base pairs, which helps to stabilize the kink. It may often be the case that sequence-dependent kinks and bends are present in DNA prior to the binding of protein<ref name="rohsrev2010" />. DNA structure is dynamic. For example, recently Hoogsteen base pairing was observed to occur transiently in equilibrium with Watson-Crick base pairing<ref>PMID: 21270796</ref> (See ''News & Views''<ref>PMID: 21350476</ref>). Also, the binding of p53 to some but not all DNA sequences stabilizes Hoogsteen (rather than Watson-Crick) base pairing<ref>PMID: 20364130</ref>. Thus, the "bending" (actually kinking) depicted in '''the morph on this page may give the wrong impression''': lac repressor binding may simply stabilize a kink (or transient kink) that pre-existed in the cognate DNA sequence. | ||