View source for Student Projects for UMass Chemistry 423 Spring 2012-2

=='''Cisplatin-DNA complex- 1a84'''==
by Greg Keohane,	Nicole Hofstetter,	Gina Lein,	Louis Pires, 
[[Student Projects for UMass Chemistry 423 Spring 2012]]
===Introduction===
<Structure load='1a84' size='500' frame='true' align='right' caption='Cisplatin' scene='Insert optional scene name here' />

The figure to the right shows <scene name='Sandbox_Reserved_430/Cisplatin_intro_with_caption/2'>cisplatin</scene> bound to a 12 base pair double stranded DNA.  Cisplatin, cis-PtCl2(NH3)2, is an “alkylating” chemotherapy drug, administered intravenously, used in the treatment of various types of cancer. <ref> adhttp://en.wikipedia.org/wiki/Chemotherapy</ref>   
	
There are three fundamental components in the mechanism of cisplatin – cisplatin, DNA, and HMG-protein.  Cisplatin makes contact with the cell membrane and enters the cell through active transport, but some molecules are passively diffused.  This platinum-based drug acts in vivo by <scene name='Sandbox_Reserved_430/Guanine_in_black_caption/2'>binding</scene> to two consecutive adjacent '''guanine''' bases in DNA leading to the loss of its chlorine atoms for the nitrogen on the guanine; this occurs to better balance the platinum charge.<ref> David, G.S. The Molecular Perspective: Cisplatin. doi: 10.1634/theoncologist.11-3-316 The Oncologist March 2006 vol. 11 no. 3 316-317.</ref> The binding of cisplatin creates a 49<scene name='Sandbox_Reserved_430/49_bend_caption/1'>49°</scene> bend with an overall helix bend of 78<scene name='Sandbox_Reserved_430/78_bend/2'>78°</scene>, which is crucial to cisplatin’s role as an anticancer drug.[5]  The bend in the <scene name='Sandbox_Reserved_430/Hmg-proetin_bound/1'>DNA</scene>, as seen in pdb 1ckt, allows for  <font color='magenta'>HMG-protein</font> to bind to the DNA, and when bound it inserts a wedge like phenol group of '''phenylalanine''' <scene name='Sandbox_Reserved_430/37_phenylalanine/2'>37</scene> into the widened minor grove.  HMG-proteins, high mobility group-proteins, are found everywhere and regulate transcription, replication, recombination and repair, and once bound to the DNA it de-stacks the <font color='cyan'>nucleotide base pairs </font>, which in turn kinks the already mutated DNA.  With the HMG-protein bound to the DNA, the cell cannot properly repair the DNA, leading to apoptosis.<ref> Gelasco, Andrew. "NMR solution and structure of DNA Dodecamer Duplex Containing cis-Diammaineplatium" Department of Chemistry, MIT:1998</ref>  

This link shows a video on the mechanism of cisplatin.[http://www.youtube.com/watch?v=Wq_up2uQRDo]

Unfortunately, there is not yet a definitive way to regulate which cells are affected by cisplatin, so the cytotoxic effects damage normal cells as well, in particular rapidly dividing cells such as those found in the gastrointestinal tract, bone marrow, testicles, ovaries, and hair growth.  It is the foundation to many combination treatments for cancers, but not all cancers are effected by cisplatin, the majority of patients using cisplatin will relapse with platinum resistant diseases.  Another way cisplatin can be in effective, is when the cancers gets too old; when a tumor starts out it divides more frequently and this is when it is effected.  This same logic goes for solid tumors, other treatments are needed for these types of issues.



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===Overall Structure===
<Structure load='1a84' size='500' frame='true' align='right' caption='This conformation shown above has the widening and flattening of the minor groove of the DNA molecule which resembles A-DNA not found in B DNA. This change is due to the guanine bases that cisplatin interacts with. They compact the major groove and unwind the DNA.' scene='Sandbox_Reserved_430/Intra-strand_phosphate/1' />
The original view shows a double stranded DNA helix and the cisplatin ligand. It is a "duplex dodecamer" d(CCTCTG*G*TCTCCGGAGACCAGAGG), and the asterisks are denoting which base pairs the Ciplatin binds to. This molecule is in its <scene name='Sandbox_Reserved_430/Z-dna_form_due_to_cisplatin/1'>A-DNA conformation due to Cisplatin</scene> which means it stll has the right handed helix, but the widened minor groove distorts its structure. To prove this, the animation shows the distance between intrastrand phosphate groups has been changed due to the insertion of the Cisplatin. Based on the chart found in <font color='purple'>([[Forms of DNA]])</font>, the distance should changed from 7 [Å] to 5.9 [Å]. It is much more rare than the common B-DNA[2]<scene name='Sandbox_Reserved_430/Intra-strand_phosphate/1'>Intra-strand Phosphate</scene> <ref>Takahara, P. M., Rosenzweig, A. C., Frederick, C. A., and Lippard, S. J. (1995) Nature 377, 649-652. Takahara, P. M., Frederick, C. A., and Lippard, S. J. (1996) J. Am. Chem. Soc 118, 12309-12321</ref>. 


<scene name='Sandbox_Reserved_430/Cisplatin_ligand/1'>Platination bond d(GpG)</scene>. The cisplatin ligand is a cis-diammineplatinum molecule, which is a platinum atom attached to two N7 nitrogen atoms, each apart of a <font color='blue'>guanine bases</font>, and two NH3 molecules attached to the other side. They attach to the 6 and 7 <font color='blue'>guanine bases</font> which links the two bases together and alters the bend in the helix by 49 degrees.The guanine still pair with the 18 and 19 <font color='red'>cytosine bases.</font><ref>Fichtinger-Schepman, A. M. J., van der Veer, J. L., den Hartog, J. H. J., Lohman, P. H. M., and Reedijk, J. (1985) Biochemistry
24, 707-713.</ref> 

Normally, the Cisplatin molecule has two Cl atoms attached to Pt's last two electrons <font color='purple'>[PtCl2(NH3)2]</font>. The Cl atoms can be displaced by "aquation" to form <font color='purple'>[PtCl(H2O)(NH3)2]+</font>. The resulting ligand can be linked to bases now and guanine is the preferred choice. It can then cross-link as in the Cisplatin molecules shown above to form <font color='purple'>[Pt(guanine-DNA)2(NH3)2]+</font>.<ref>http://en.wikipedia.org/wiki/Cisplatin,last accessed 4/8/12.</ref> The N-Pt-N angles, two N7 nitrogens from the guanine base and two NH3 attached directly as part of the Cisplatin ligand, are planar and at 90 degrees, as well as each being a distance of 2.05 [Å] from the PT atom. Another interesting feature about the platinated lesion is in a 5 base section between C4-G21 and T8-A17. The minor groove of the molecule is roughly 9-12 [Å] with a depth range of roughly .4-2.5 [Å] which is much shorter than the B form with a depth of 6.5 [Å]<ref>Andrew Gelasco and Stephen J. Lippard* Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
ReceiVed December 30, 1997; ReVised Manuscript ReceiVed March 27, 1998</ref>.











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===Binding Interactions===
<Structure load='1a84' size='500' frame='true' align='right' caption='Cisplatin' scene='Insert optional scene name here' />
As described above, the cisplatin ligand binds to the N7 atoms of the adjacent G6 and G7 guanine bases in a strand of DNA.  The green screen
<scene name='Sandbox_Reserved_430/Binding/1'>binding interactions</scene> shows the platinum atom in pink, which is bound to the two N7 atoms of gaunine labeled in green.  The N7 atoms are bound to the platinum atom in the ligand, creating a bend in the helix towards the guanine bases of 49 degrees and a total bend in the DNA of 79 degrees<ref>Gelasco, Andrew. "NMR solution and structure of DNA Dodecamer Duplex Containing cis-Diammaineplatium" Department of Chemistry, MIT:1998</ref>.  The guanine bases are favored over the adenine because of hydrogen bonding between the amine-hydrogens of the cisplatin and the O=C6 moiety of guanine<ref>Baik MH, Friesner RA, Lippard SJ. "Theoretical Study of Cisplatin binding to purine bases: why doe cisplatin prefer guanine over adenine?" J Am Chem Soc, 2003 Nov 19;125(46):14082-92. 1.↑ 2.0 2.1 2.2 2.3 2.4 2.5 Wang G, Vasquez KM. Z-DNA, an active element in the genome. Front Biosci. 2007 May 1;12:4424-38. PMID:17485386 </ref>.  The <scene name='Sandbox_Reserved_430/Hbonding/1'>hydrogen bonding</scene> is shown in this green screen, between the green labeled ammine hydrogens and the oxygen atom labeled in pink. The resulting platination also causes the duplex to unwind by approximately 25 degrees at the site of platination from the base pair T8-A17 to T5-A20.  The <scene name='Sandbox_Reserved_430/Minor_groove/6'>minor groove</scene> screen shows the thymine molecules in pink and the adenine ones in green, showing the opening of the helix.  These distortions in the duplex allow the minor groove opposite the platinum to be opened to 9.0-12 angstroms, making it shallow and wide.  

HMG-domain proteins (High-mobility group) bind to recognition sequences found in the minor groove.  The bend in DNA caused by cisplatin leaves the minor groove more vulnerable and open for recognition by HMG-domain proteins.  Since the expression of these proteins are correlated to tumor cells, the recognition of them by cisplatin-bound DNA could lead to a therapy of cancerous tumors<ref>Gelasco, Andrew. "NMR solution and structure of DNA Dodecamer Duplex Containing cis-Diammaineplatium" Department of Chemistry, MIT:1998</ref>.















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===Additional Features===
<Structure load='1a84' size='500' frame='true' align='right' caption='The width of the minor groove of the cisplatin-DNA complex can be compared to the minor groove width of HMG protein-DNA complexes. The similar widths are evidence that Cisplatin is affiliated with HMG proteins.' scene='Insert optional scene name here' />
Structural studies of Cisplatin-modified DNA are underway in hope to find a significant correlation
between Cisplatin distorted DNA and its ability to bind to high mobility group proteins (HMG proteins). 
HMG proteins are responsible for many actions within the cell such as transcription, replication and DNA repair. 
Studies show that over/under expression of these proteins may be the cause of tumors. 
On the other hand, if HMG proteins attach to a Cisplatin modified double helix, then this may prevent 
the excision of the helix to be repaired. Resulting in DNA destruction.

HMG proteins bind to the minor groove of the DNA duplex where their recognition sequences are located. 
Cisplatin is known to cause the bending of DNA helix as well as the extension of the minor groove width. 
This opening of the minor groove allows HMG domain proteins to attached to their recognition sequences within
the minor groove DNA base pairs
<scene name='Sandbox_Reserved_430/Cisplatin_minor_groove_distanc/1'>Cisplatin minor groove</scene>

This deformation of the DNA duplex with cisplatin forms important complexes with HMG proteins, such as <font color='orange'>LEF-1</font> and hSRY. Binding of these proteins to the already damaged DNA causes further bending. The <font color='orange'>LEF-1</font> HMG protein structure was determined by experiment and superimposed over the known cisplatin-DNA structure.<ref> Gelasco, Andrew. "NMR solution and structure of DNA Dodecamer Duplex Containing cis-Diammaineplatium" Department of Chemistry, MIT:1998</ref> The best fit was shown be over the portion of the cisplatin-DNA structure containing the platinated guanonsines of the 1,2 intrastrand cross link, the similarity holds a good overlap of RMSD of 3.2A.

<scene name='Sandbox_Reserved_430/2lef/1'>Lef-1 Minor groove</scene>

This experiment showed that the distortion caused by the <font color='orange'>LEF-1</font>  protein is very similar to that caused buy the
binding of cisplatin. This comparison of <font color='orange'>LEF-1</font>  to cisplatin-modified DNA brings structural evidence that 
cisplatin –modified DNA may signal the recognition of HMG proteins. 

Another important example is the <font color='red'>HMG1</font> protein binding to the Cisplatin complex. This <font color='red'>HMG1</font>protein is known to bind to the Cisplatin DNA minor groove about the hydrophobic kink created by the distortion. Evidence shows that the phenylalanine residue  <font color='red'>HMG1</font> protein is essential for <font color='red'>HMG1</font> interaction with DNA. <ref>Love, JJ. "Structural basis for DNA bending by the architectural transcription factor LEF-1." PubMed:1995 http://www.rcsb.org/pdb/explore/explore.do?structureId=2LEF</ref>Substitution experiments of the phenylalanine with alanine showed that <font color='red'>HMG1</font>HMG1 binding reduced, therefore <font color='red'>HMG1</font> binding is dependent on the phenylalanine and the hydrophobic notch
<scene name='Sandbox_Reserved_430/Hmg1_to_cisplatin/6'>HMG1 and the hydrophobic notch</scene>

<scene name='Sandbox_Reserved_430/Hmg1_to_cisplatin/8'>HMG1-DNA minor groove distance</scene>

===Credits===

Introduction - Gina Lein

Overall Structure - Greg Keohane

Drug Binding Site - Louis Pires

Additional Features - Nicole Hofstetter

===References===
<references/>