Lac repressor: Difference between revisions

<StructureSection load='' size='375' side='right' scene='Morphs/1osl_19_1l1m_9_morph/2' caption=''>

[[Morphs|Morph]] of the '''lac repressor''' complexed with DNA

For a general introduction to the lac repressor, please see David Goodsell's [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb39_1.html Introduction to the lac repressor] in his series [[Molecule of the Month]], and the article in Wikipedia on the [http://en.wikipedia.org/wiki/Lac_repressor lac repressor]. Mitchell Lewis published a detailed review in 2005<ref name='lewis'>The lac repressor. Lewis, M. C R Biol. 328:521-48, 2005. [http://www.ncbi.nlm.nih.gov/pubmed/15950160 PubMed 15950160]</ref>.  See also [[Transcription and RNA Processing]].

Lac repressor binds to DNA non-specifically (<scene name='Lac_repressor/1osl_ca_dot_pdb/2'>initial scene</scene> derived <ref name='alphac'>For these scenes, the 20-model [[PDB file|PDB files]] for [[1osl]] and [[1l1m]] were reduced in size, to avoid exceeding the java memory available to the Jmol applet. All atoms except amino acid alpha carbons and DNA phosphorus atoms were removed using the free program ''alphac.exe'' from [http://www.umass.edu/microbio/rasmol/pdbtools.htm PDBTools]. Secondary structure HELIX records from the original PDB file header were retained. The results are [[Image:1osl_ca.pdb|1osl_ca.pdb]] and [[Image:1l1m_ca.pdb]].</ref> from [[1osl]], 20 [[NMR Ensembles of Models|NMR models]]), enabling it to slide rapidly along the DNA double helix until it encounters the lac operator sequence ("facilitated diffusion"<ref>PMID: 22723426</ref>). The DNA-binding domain employs a [[Helix-turn-helix motif|helix-turn-helix motif]] ({{Template:ColorKey_Helix}}, {{Template:ColorKey_Turn}}). During non-specific binding, the <font color='orange'><b>hinge region</b></font> is disordered (indicated by the range of positions of the 20 models). The <font color='#ae00ff'><b>DNA double helix</b></font> is depicted as straight in the model shown here (see [[Lac repressor morph methods|methods]]), but in actuality, straightness likely varies with sequence (see [[#DNA Kinks|below]]). The protein model shown at right ([[1osl]]) has two copies of the DNA-binding domain and <font color='orange'><b>hinge region</b></font> (<scene name='Lac_repressor/1osl_ca_dot_pdb/3'>Apply green color</scene> to distinguish the <font color='#00a060'><b>chain B hinge</b></font>). <scene name='Lac_repressor/1osl_ca_dot_pdb/8'>Animating</scene> these 20 [[NMR Ensembles of Models|NMR models]] simulates thermal motion of the disordered hinge regions. {{Template:Button Toggle Animation}}

Upon recognizing the specific operator sequence, the non-specific binding converts to <scene name='Lac_repressor/1l1m_ca_specific_bindiing/3'>specific binding</scene> (derived<ref name='alphac' /> from [[1l1m]], 20 [[NMR Ensembles of Models|NMR models]]). During this conversion, the hinge region changes from disordered loops to {{Template:ColorKey_Helix}} (<scene name='Lac_repressor/1l1m_ca_specific_bindiing/4'>highlight new helices</scene>: <u>toggle spinning off to see highlighting</u><scene name='32/324680/4/2'>!</scene>), which bind to the minor groove of the DNA. As explained below, this binding stabilizes a '''kinked ("bent")''' <font color='#ae00ff'><b>DNA double helix</b></font> conformation. What percentage of time this DNA sequence spends in  a kinked state, in the absence of bound lac repressor protein, is not known, but it may be a significant percentage (see next section below). <scene name='Lac_repressor/1l1m_ca_specific_bindiing/6'>Animating</scene> these 20 NMR models can be compared with the animation of the non-specific binding.  See [[Lac repressor morph methods]]. {{Template:Button Toggle Animation}}

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>

</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.