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Cisplatin-DNA complex- 1a84

Introduction

The figure to the right shows bound to a 12 base pair double stranded DNA. Cisplatin, cis-PtCl2(NH3)2, is an “alkylating-like” chemotherapy drug, administered intravenously, used in the treatment of various types of cancer.

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 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. The binding of cisplatin creates a 49 bend with an overall helix bend of 78, which is crucial to cisplatin’s role as an anticancer drug. The bend in the , as seen in pdb 1ckt, allows for HMG-protien to bind to the DNA, and when bound it inserts a wedge like phenol group of phenylalanine into the wind 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 nucleotide base pairs , 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.

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.

references:

• http://www.ncbi.nlm.nih.gov/pubmed/9888812
• http://www.pdb.org/pdb/explore/explore.do?structureId=1a84
• http://theoncologist.alphamedpress.org/content/11/3/316.full
• http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2739446/
• http://www.ncbi.nlm.nih.gov/pmc/articles/PMC321124/pdf/nar00384-0251.pdf
• http://pubs.acs.org.silk.library.umass.edu/doi/pdf/10.1021/bi973176v
• http://home.ccr.cancer.gov/metabolism/bustin/hmg_proteins.htm

Overall Structure

The original view shows a double stranded DNA helix and the cisplatin ligand. This molecule is in its which means it stll has the right handed helix, but the widened minor groove distorts its structure and loses its major curve. To prove this, the jmol to the right shows the distance between intrastrand phosphate groups has been changed sue to the insertion of the Cisplatin. Based on the chart found in (Forms of DNA), the distance should changed from 7 [Å] to 5.9 [Å]. It is much more rare than the common B-DNA[2] [3]. "In Z-DNA only a minor groove is present".[2] . The cisplatin ligand is a cis-diammineplatinum molecule, which is a platinum atom attached to two N7 nitrogen atoms, each apart of a guanine bases, and two NH3 molecules attached to the other side. They attach to the 6 and 7 guanine bases 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 cytosine bases.

Good start. Suggestions:

1. Parts of your description of Z DNA are almost identical to the description on the Z DNA Proteopedia page: that's plagiarism! Delete that text and you could link to the Z DNA page to show the nice side-by side comparisons of A,B, Z DNA (bottom of page), highlighting some feature that convincingly shows us that your structure with cisplatin is in the Z form. Make a green scene of the DNA in your structure that helps to illustrate whichever feature best illustrates that it is in the Z form.

2. Color your text so that it's easier to follow what's in your green scene (e.g. G's same color as text: "guanine bases" (not base pair), C's same color as "cytosine bases".

3. Omit sentence about alpha helices.

4. You need references and make your section about the length of the jmol window.

Binding Interactions

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 N7 atoms are bound to the platinum atom in the ligand, creating a bend in the helix towards the guanine bases of 49 degrees. 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. 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.

1. Why did you choose the color scheme you used in your green scene? Make it logical and clear. For instance, color your text so that it's easier to follow what's in your green scene (e.g. G's same color as text: "guanine bases"). Perhaps better to use CPK colors so we can see which is N7 etc, and you could use distance markers so we can see the Pt to N bonds.

2. Make more green scenes that illustrate your other points: the unwinding, the base pairs T8-A17 in another color. Point us to the major vs minor groove. Show us the 9-12 Å opening (use distance markers)? Perhaps use space fill to see wide/shallow -- compare to another part that's not distorted.

3. Why does it bind to G bases?

4. You need references and make your section about the length of the jmol window.

Additional Features

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

This deformation of the DNA duplex with cisplatin forms important complexes with HMG proteins, such as LEF-1 and hSRY. Binding of these proteins to the already damaged DNA causes further bending. The LEF-1 HMG protein structure was determined by experiment and superimposed over the known cisplatin-DNA structure.^[1] 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.

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

Another important example is the HMG1 protein binding to the Cisplatin complex. This HMG1protein is known to bind to the Cisplatin DNA minor groove about the hydrophobic kink created by the distortion. Evidence shows that the phenylalanine residue HMG1 protein is essential for HMG1 interaction with DNA. ^[2]Substitution experiments of the phenylalanine with alanine showed that HMG1HMG1 binding reduced, therefore HMG1 binding is dependent on the phenylalanine and the hydrophobic notch

1. Delete or explain these green scenes (18 19 20 21).

2. Your major groove green scene is clearer, with the backbone trace, than the minor groove green scene. But both are on different DNA (B DNA?) -- not so relevant to your cisplatin complex. Instead show major/minor grooves on the cisplatin structure DNA.

3. Which pdb file are you showing with LEF-1? Ideally you would show green scenes of the cisplatin and LEF-1 structures that are both in the same orientation (turn off rotation) and highlight a similar DNA bend angle (with a marker) to convince us of the similarity.

4. You need references.

Credits

Introduction - Gina Lein

Overall Structure - Greg Keohane

Drug Binding Site - Louis Pires

Additional Features - Nicole Hofstetter

References

1. ↑ Gelasco, Andrew. "NMR solution and structure of DNA Dodecamer Duplex Containing cis-Diammaineplatium" Department of Chemistry, MIT:1998
2. ↑ 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

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

2.↑ 2.0 Rich A, Zhang S. Timeline: Z-DNA: the long road to biological function. Nat Rev Genet. 2003 Jul;4(7):566-72. PMID:12838348 doi:10.1038/nrg1115

3. 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.