Proteopedia - User contributions [en]

Sandbox423

2012-05-03T00:13:51Z

Louis Pires: /* '''Presentation Dates, Teams, Topics, and Links''' */

'''This sandbox is in use for UMass Chemistry 423. Others please do not edit this page. Thanks!'''

==''' Spring 2012 Chem423 Team Projects'''==
'''Understanding the chemical basis of disease and life processes'''

Follow instructions posted at [[Student Projects for UMass Chemistry 423 Spring 2012]].

==='''Presentation Dates, Teams, Topics, and Links'''===
Following any team's entry, add your nominations of the best scenes for display at the ISB Molecular playground, using the following format:

"Your Name" nominates the scene "name of green scene" with the caption "your caption".

Choose a visually attractive scene and come up with a new caption of ≤ 12 words that is interesting/understandable to a general audience. See my example under the first project. Be creative!

3. Ryan Deeney, Jeffrey Boerth, Kate Liedell, Rebecca Bishop - [[Sandbox Reserved 427|Diabetes 3loh (insulin receptor) ]] '''Presentation 3/28/12''' '''Draft due 3/21'''

Prof Thompson nominates the scene "biological dimer" with the caption "Insulin receptor signaling goes awry in diabetes".

Rebecca Bishop nominates the scene "biological dimer" with the caption "Understanding insulin receptor signaling may be the key to treating Type II Diabetes."

6. Greg Keohane, Nicole Hofstetter, Gina Lein, Louis Pires, - [[Sandbox Reserved 430|cisplatin, 1a84 ]] '''Presentation 4/9/12''' '''Draft due 4/2'''

Jeffrey Boerth nominates the scene "binding interactions" with the caption "Cisplatin binding to adjacent guanine bases halts tumor cell growth in cancer therapy."

Louis Pires nominates the scene "DNA" with the caption "Cisplatin binding bends DNA creating a new direction in cancer research."

4. Julia Tomaszewski, Sam Kmail, Nicole Bundy, Jesse Guillet - [[Sandbox Reserved 428|restriction enzyme/DNA complex, 1rva ]] '''Presentation 4/11/12''' '''Draft due 4/4'''

Felix Alfonso nominates the scene "specific" with the caption "Target site recognition along the DNA Minor Groove by EcoRV endonuclease restriction enzyme"

5. Alec Gramann, William Frantz, Felix Alfonso, Paula Preap - [[Sandbox Reserved 429| Bone Formation & Apoptosis & 1m4u ]] '''Presentation 4/23/12''' '''Draft due 4/16'''

9. Di Lin, Jill Moore, Austin Virtue, Alexander Way - [[Sandbox Reserved 433|Caspase 3, 1RHK ]] '''Presentation 4/23/12''' '''Draft due 4/16'''

1. Jessica Royal, Anh Huynh, Stephanie Bristol, Emily Brackett - [[Sandbox Reserved 425|Catechol-O-methyltransferase, 2ZVJ, Parkinson's disease]] '''Presentation 4/25/12''' '''Draft due 4/18'''

Di Lin nominates the scene "aromatic ring" with the caption "shown to be inhibitors in vitro and in vivo of catechol-O-methyltnansfenase"

Greg Keohane nominates scene "aromatic ring" with the caption "shown to be inhibitors in vitro and in vivo of catechol-O-methyltnansfenase"

8. Max Nowak, Kyle Reed, Kevin Dillon, Chris Carr - [[Sandbox Reserved 432|dementia 1JVQ ]] '''Presentation 4/25/12''' '''Draft due 4/18'''

2. William Yarr, Ryan Colombo, Joey Nguyen, Jacqueline Pasek-Allen - [[Sandbox Reserved 426|Hemoglobin 1qxd ]] '''Presentation 4/27/12''' '''Draft due 4/20'''

7. Polina Berdnikova, James Hamblin, Jill Carlson, Brett Clinton - [[Sandbox Reserved 431|phosphatase inhibitor complexes-1nny]] '''Presentation 4/27/12''' '''Draft due 4/20'''

James Hamblin nominates the scene "three different stages" with the caption "Drug design: creating a ligand for increased insulin response"

10. Adam Ramey, Jeffrey Salemi, Nicholas Vecchiarello, Tom Foley - [[Sandbox Reserved 434|leadzyme, 1nuv]] '''Presentation 4/30/12''' '''Draft due 4/23'''

===Questions & Answers===

Here is a place to post questions and answers for each other about how to do things in Proteopedia. Here are some from me and previous students.

*For step-by-step instructions on creating example scenes, try [[Proteopedia:DIY:Scenes]].
*Safari currently not working for making a scene... LKT 2/27 But it just worked for Xuni! Test saving a simple scene first.

*A very useful color scheme is "chain" which colors separate proteins or DNA strands in different colors (first select all protein or DNA).

*To show the biological unit, follow directions at [[Biological Unit: Showing]]. The pdb file will display the "asymmetric unit" = the smallest unit that can be replicated to generate the full crystal. Example: the protein may function as a dimer (you need biochemical experiments to tell you this -- crystallography and NMR won't tell you), but the pdb file may display a monomer (if the dimer is symmetric) or two dimers (if they have slightly different conformations in the crystals -- perhaps due to crystal contacts or perhaps representing 2 functional states of the protein!).

*Anyone know what format we should be putting our references in?

Complete instructions for references are at [[Help:Editing#Citing_Literature_References]].You can follow the format used in the example on the Asp receptor and they will be put in automatically.
You just find out the PMID code (listed in pubmed for example) and insert it into the following, at the place where you want the reference cited (click edit to see what is actually inserted here).
<ref>PMID: 8486661</ref>
You also need to add the section:

'''References'''
<references/>

*Hey guys this is just a useful tip:
If you get an xml error after you try to save your changes it is due to the green scene coding. Our group experienced this issue and it would not let us access our sandbox. In order to fix this go back (or find the page to edit in your history) and delete the green scene code that was just entered. Then save the page and you should be back to your sandbox. This may be trivial to many, but just throwing it out there.

*To highlight some interesting portion of your protein:
Under the selections tab, you can "limit to residue numbers." So for example enter in 60-65, then click "replace selection" below. Then if you go to the colors tab you can pick a color for just the residues you have selected. If it is a loop or if they are hard to see you can go to the representation tab and set selection to ball and stick or spacefill.

It is also useful to click the "selection halos:" box under the picture. That shows you what you have in your selection.

*If you suddenly can't get to your sandbox page (error message XML error: Mismatched tag at line 1), try [[Help:Errors]]

===Tips from feedback/edits of your Proteopedia Projects===
Please read the feedback on all of the sections to give you ideas for improving your own section -- leave the red text until you're all done with all sections.

Each section should start with the line that inserts the Jmol window: then each scene for that section will appear in that window, along side your text (which should only extend 1-2 lines beyond the jmol window).

Every jmol window should have a caption so we know what we are looking at (include the name of the molecule and pdb code) Replace "insert caption here' with 'your caption'.

Captions in each section: come up with a cool (short) caption that fits your best scene that you think would be good for the Molecular Playground -- something that's understandable on its own and will capture the attention of a broad audience.

Careful with repetition of the same points in multiple sections -- instead organize the topics logically and you can have multiple people contribute to a section if you want.

Feel free to work together on sections and add people to the credits if that helps to make a coherent and organized story.

Follow the correct format for references, including citations in text -- see instructions and link above.

Make green scenes to illustrate your points, and weave your scenes into the text.

Use colored text to help the reader easily see your points in the scene and to keep your text concise. For example "This view shows the 2 alpha helices packed against the 4-stranded antiparallel beta sheet." The word view would like to a scene in which the alpha helices are red and the beta sheet is blue. Go into edit mode on this page to copy the colored text section for use on your page.

Avoid a list of miscellaneous facts. Choose the most interesting points to tell us in some detail and illustrate with green scenes.

Keep the length of your text similar to the length of the jmol window.

Sandbox Reserved 430

2012-04-13T14:27:32Z

Louis Pires: /* Binding Interactions */

{{Template:Sandbox Reserved Lynmarie Thompson}}


=='''Cisplatin-DNA complex- 1a84'''==

===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 HMG-protein 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 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.<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.

--

===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 ([[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]<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 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.<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 [PtCl2(NH3)2]. The Cl atoms can be displaced by "aquation" to form [PtCl(H2O)(NH3)2]+. 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 [Pt(guanine-DNA)2(NH3)2]+.<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>.

--
===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>.

--

===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 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.<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 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. <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 HMG1HMG1 binding reduced, therefore HMG1 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/>

Sandbox Reserved 430

2012-04-13T14:12:29Z

Louis Pires: /* Binding Interactions */

{{Template:Sandbox Reserved Lynmarie Thompson}}


=='''Cisplatin-DNA complex- 1a84'''==

===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 HMG-protein 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 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.<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.

--

===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 ([[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]<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 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.<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 [PtCl2(NH3)2]. The Cl atoms can be displaced by "aquation" to form [PtCl(H2O)(NH3)2]+. 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 [Pt(guanine-DNA)2(NH3)2]+.<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>.

--
===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/H-bonding/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>.

--

===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 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.<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 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. <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 HMG1HMG1 binding reduced, therefore HMG1 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/>

Sandbox Reserved 430

2012-04-13T14:02:31Z

Louis Pires: /* References */

{{Template:Sandbox Reserved Lynmarie Thompson}}


=='''Cisplatin-DNA complex- 1a84'''==

===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 HMG-protein 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 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.<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.

--

===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 ([[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]<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 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.<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 [PtCl2(NH3)2]. The Cl atoms can be displaced by "aquation" to form [PtCl(H2O)(NH3)2]+. 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 [Pt(guanine-DNA)2(NH3)2]+.<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>.

--
===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_site/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/H-bonding/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>.

--

===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 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.<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 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. <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 HMG1HMG1 binding reduced, therefore HMG1 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/>

Sandbox Reserved 430

2012-04-13T14:02:14Z

Louis Pires: /* Binding Interactions */

{{Template:Sandbox Reserved Lynmarie Thompson}}


=='''Cisplatin-DNA complex- 1a84'''==

===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 HMG-protein 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 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.<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.

--

===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 ([[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]<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 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.<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 [PtCl2(NH3)2]. The Cl atoms can be displaced by "aquation" to form [PtCl(H2O)(NH3)2]+. 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 [Pt(guanine-DNA)2(NH3)2]+.<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>.

--
===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_site/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/H-bonding/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>.

--

===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 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.<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 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. <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 HMG1HMG1 binding reduced, therefore HMG1 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/>
9. 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

Sandbox Reserved 430

2012-04-13T14:01:22Z

Louis Pires: /* Binding Interactions */

{{Template:Sandbox Reserved Lynmarie Thompson}}


=='''Cisplatin-DNA complex- 1a84'''==

===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 HMG-protein 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 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.<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.

--

===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 ([[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]<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 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.<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 [PtCl2(NH3)2]. The Cl atoms can be displaced by "aquation" to form [PtCl(H2O)(NH3)2]+. 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 [Pt(guanine-DNA)2(NH3)2]+.<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>.

--
===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_site/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[9]. The <scene name='Sandbox_Reserved_430/H-bonding/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>.

--

===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 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.<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 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. <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 HMG1HMG1 binding reduced, therefore HMG1 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/>
9. 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

Sandbox Reserved 430

2012-04-09T14:09:50Z

Louis Pires: /* Binding Interactions */

{{Template:Sandbox Reserved Lynmarie Thompson}}


=='''Cisplatin-DNA complex- 1a84'''==

===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-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 <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/1'>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 HMG-protein 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 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.<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.

===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/Z-dna_form_due_to_cisplatin/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 and loses its major groove. 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]<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>. "In Z-DNA only a minor groove is present".<ref>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.</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 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.<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 [PtCl2(NH3)2]. The Cl atoms can be displaced by "aquation" to form [PtCl(H2O)(NH3)2]+. 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 [Pt(guanine-DNA)2(NH3)2]+.<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.

===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_site/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[7]. 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[9]. The <scene name='Sandbox_Reserved_430/H-bonding/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[7].

===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 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.<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 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. <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 HMG1HMG1 binding reduced, therefore HMG1 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>



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===
<references/>
9. 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

Sandbox Reserved 430

2012-04-09T14:08:47Z

Louis Pires: /* References */

{{Template:Sandbox Reserved Lynmarie Thompson}}


=='''Cisplatin-DNA complex- 1a84'''==

===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-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 <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/1'>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 HMG-protein 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 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.<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.

===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/Z-dna_form_due_to_cisplatin/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 and loses its major groove. 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]<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>. "In Z-DNA only a minor groove is present".<ref>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.</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 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.<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 [PtCl2(NH3)2]. The Cl atoms can be displaced by "aquation" to form [PtCl(H2O)(NH3)2]+. 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 [Pt(guanine-DNA)2(NH3)2]+.<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.

===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_site/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. 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. The <scene name='Sandbox_Reserved_430/H-bonding/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.

===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 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.<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 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. <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 HMG1HMG1 binding reduced, therefore HMG1 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>



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===
<references/>
9. 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

Sandbox Reserved 430

2012-04-09T14:02:07Z

Louis Pires: /* Binding Interactions */

{{Template:Sandbox Reserved Lynmarie Thompson}}


=='''Cisplatin-DNA complex- 1a84'''==

===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-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 <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/1'>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 HMG-protein 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 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.<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.

===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/Z-dna_form_due_to_cisplatin/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 and loses its major groove. 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]<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>. "In Z-DNA only a minor groove is present".<ref>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.</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 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.<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 [PtCl2(NH3)2]. The Cl atoms can be displaced by "aquation" to form [PtCl(H2O)(NH3)2]+. 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 [Pt(guanine-DNA)2(NH3)2]+.<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.

===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_site/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. 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. The <scene name='Sandbox_Reserved_430/H-bonding/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.

===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 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.<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 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. <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 HMG1HMG1 binding reduced, therefore HMG1 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>



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===
<references/>
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

Sandbox Reserved 430

2012-04-09T14:00:37Z

Louis Pires: /* Binding Interactions */

{{Template:Sandbox Reserved Lynmarie Thompson}}


=='''Cisplatin-DNA complex- 1a84'''==

===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-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 <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/1'>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 HMG-protein 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 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.<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.

===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/Z-dna_form_due_to_cisplatin/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 and loses its major groove. 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]<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>. "In Z-DNA only a minor groove is present".<ref>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.</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 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.<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 [PtCl2(NH3)2]. The Cl atoms can be displaced by "aquation" to form [PtCl(H2O)(NH3)2]+. 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 [Pt(guanine-DNA)2(NH3)2]+.<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.

===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_site/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. 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. The <scene name='Sandbox_Reserved_430/H-bonding/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.


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===
<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 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.<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 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. <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 HMG1HMG1 binding reduced, therefore HMG1 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>



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===
<references/>
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

Sandbox Reserved 430

2012-04-09T13:31:12Z

Louis Pires: /* Binding Interactions */

{{Template:Sandbox Reserved Lynmarie Thompson}}


=='''Cisplatin-DNA complex- 1a84'''==

===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-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 <scene name='Sandbox_Reserved_430/Guanine_in_black_caption/1'>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. 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/1'>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 HMG-protein 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 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.[2] 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.

===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/Z-dna_form_due_to_cisplatin/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 and loses its major groove. 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]<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>. "In Z-DNA only a minor groove is present".<ref>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.</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 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.<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 [PtCl2(NH3)2]. The Cl atoms can be displaced by "aquation" to form [PtCl(H2O)(NH3)2]+. 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 [Pt(guanine-DNA)2(NH3)2]+.<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.

===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_site/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. 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. The <scene name='Sandbox_Reserved_430/H-bonding/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. 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===
<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 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.<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 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. <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 HMG1HMG1 binding reduced, therefore HMG1 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>



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===
<references/>
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.David, G.S. The Molecular Perspective: Cisplatin. doi: 10.1634/theoncologist.11-3-316 The Oncologist March 2006 vol. 11 no. 3 316-317.

Sandbox Reserved 430

2012-04-09T13:18:16Z

Louis Pires: /* Binding Interactions */

{{Template:Sandbox Reserved Lynmarie Thompson}}


=='''Cisplatin-DNA complex- 1a84'''==

===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-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 <scene name='Sandbox_Reserved_430/Guanine_in_black_caption/1'>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. The binding of cisplatin creates a 49<scene name='Sandbox_Reserved_430/49_bend/1'>49°</scene> bend with an overall helix bend of 78<scene name='Sandbox_Reserved_430/78_bend/1'>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 HMG-protein 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 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.[2] 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.

===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/Z-dna_form_due_to_cisplatin/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 and loses its major groove. 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]<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>. "In Z-DNA only a minor groove is present".<ref>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.</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 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.<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 [PtCl2(NH3)2]. The Cl atoms can be displaced by "aquation" to form [PtCl(H2O)(NH3)2]+. 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 [Pt(guanine-DNA)2(NH3)2]+.<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.

===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_site/1'>binding interactions</scene> shows the platinum atom in pink, which is bound to the two N7 atoms of gaunine labeled in pink. 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. 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. <scene name='Sandbox_Reserved_430/1a84_binding/1'>Binding</scene> 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===
<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 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.<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 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. <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 HMG1HMG1 binding reduced, therefore HMG1 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>



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===
<references/>
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.David, G.S. The Molecular Perspective: Cisplatin. doi: 10.1634/theoncologist.11-3-316 The Oncologist March 2006 vol. 11 no. 3 316-317.

Sandbox Reserved 430

2012-04-09T13:17:25Z

Louis Pires: /* Binding Interactions */

{{Template:Sandbox Reserved Lynmarie Thompson}}


=='''Cisplatin-DNA complex- 1a84'''==

===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-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 <scene name='Sandbox_Reserved_430/Guanine_in_black_caption/1'>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. The binding of cisplatin creates a 49<scene name='Sandbox_Reserved_430/49_bend/1'>49°</scene> bend with an overall helix bend of 78<scene name='Sandbox_Reserved_430/78_bend/1'>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 HMG-protein 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 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.[2] 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.

===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/Z-dna_form_due_to_cisplatin/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 and loses its major groove. 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]<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>. "In Z-DNA only a minor groove is present".<ref>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.</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 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.<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 [PtCl2(NH3)2]. The Cl atoms can be displaced by "aquation" to form [PtCl(H2O)(NH3)2]+. 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 [Pt(guanine-DNA)2(NH3)2]+.<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.

===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_site/1'>TextToBeDisplayed</scene> shows the platinum atom in pink, which is bound to the two N7 atoms of gaunine labeled in pink. 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. 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. <scene name='Sandbox_Reserved_430/1a84_binding/1'>Binding</scene> 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===
<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 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.<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 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. <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 HMG1HMG1 binding reduced, therefore HMG1 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>



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===
<references/>
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.David, G.S. The Molecular Perspective: Cisplatin. doi: 10.1634/theoncologist.11-3-316 The Oncologist March 2006 vol. 11 no. 3 316-317.

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Louis Pires: /* Binding Interactions */

{{Template:Sandbox Reserved Lynmarie Thompson}}


=='''Cisplatin-DNA complex- 1a84'''==

===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/4'>cisplatin</scene> 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 <scene name='Sandbox_Reserved_430/Guanine_in_black/1'>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. The binding of cisplatin creates a 49<scene name='Sandbox_Reserved_430/49_bend/1'>49°</scene> bend with an overall helix bend of 78<scene name='Sandbox_Reserved_430/78_bend/1'>78°</scene>, which is crucial to cisplatin’s role as an anticancer drug. The bend in the <scene name='Sandbox_Reserved_430/Hmg-proetin_bound/1'>DNA</scene>, 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''' <scene name='Sandbox_Reserved_430/37_phenylalanine/2'>37</scene> 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===
<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/Z-dna_form_due_to_cisplatin/1' />
The original view shows a double stranded DNA helix and the cisplatin ligand. 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 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]<scene name='Sandbox_Reserved_430/Intra-strand_phosphate/1'>Intra-strand Phosphate</scene> [3]. "In Z-DNA only a minor groove is present".[2] <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 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===
<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 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. 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. <scene name='Sandbox_Reserved_430/1a84_binding/1'>Binding</scene> 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===
<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 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.<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 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. <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 HMG1HMG1 binding reduced, therefore HMG1 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>



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===
<references/>
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.

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Louis Pires:

<Structure load='1a84' size='500' frame='true' align='right' caption='Cisplatin' scene='Insert optional scene name here' />
{{Template:Sandbox Reserved Lynmarie Thompson}}


<scene name='Sandbox_Reserved_430/Test/2'>TextToBeDisplayed</scene>

=='''Cisplatin-DNA complex- 1a84'''==

===Introduction===
In this figure <scene name='Sandbox_Reserved_430/Cisplatin_intro/4'>cisplatin</scene> is <scene name='Sandbox_Reserved_430/Cisplatin_intro/7'>bound</scene> to a 12 base pair double stranded DNA, creating a 49° bend with an overall helix bend of 78°. This bend in the DNA is crucial to cisplatin’s role as an anticancer drug.
Cisplatin, cis-PtCl2(NH3)2, is a chemotherapy drug, administered intravenously, used in the treatment of various types of cancer. This platinum-based drug acts in vivo by binding to two consecutive adjacent guanine bases in DNA. The binding of cisplatin bends the DNA, allowing for HMG-protein to bind. Once the <scene name='Sandbox_Reserved_430/Hmg-proetin_bound/1'>HMG-protein</scene> is bound, de-stacking of the nucleotide base pairs occurs, which in turn kinks the DNA. With the HMG-protein bound to the DNA, the cell cannot properly repair the DNA, leading to apoptosis.

===Overall Structure===
The original view shows a double stranded DNA helix and the cisplatin ligand. This molecule is in its Z configuration <scene name='Sandbox_Reserved_430/Z-dna/2'>Z-DNA</scene> which means it has a left handed helix. It is much more rare than the common B-DNA which is right handed. The sugar-phosphate backbone has a zigzag pattern due to the alternate stacking of bases in anti-conformation and syn conformation. In Z-DNA only a minor groove is present and the major groove is absent. This DNA form is thought to play a role in the regulation of gene expression, DNA processing events and/or genetic instability.[2] <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 guanine base pair, and two NH3 molecules attached to the other side. They attach to the 6 and 7 guanine base pairs 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. There are no alpha helixs or beta strands because cisplatin works with DNA and not on proteins.

===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. <scene name='Sandbox_Reserved_430/1a84_binding/1'>Binding</scene> 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.

===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.

HMG proteins bind to the minor groove of the DNA duplex where their recognition sequences are located.
Cisplatin is known to cause a large helix bend of DNA as well as the extension of the minor groove width. This opening of the minor groove
allows the recognitions of HMG domain proteins.
<scene name='Sandbox_Reserved_430/Minor_groove/3'>Minor Groove</scene>
<scene name='Sandbox_Reserved_430/Major_groove/4'>Major Groove</scene>

The positioning of this bend is over a length of 5 base pairs from C4-G21 to T8-A17. This the results in a 49 degree roll of the G6*pG7*
guanine-guanine interaction causing a helical bend of 78 degrees. <scene name='Sandbox_Reserved_430/Minor_groove_cisplatin/2'>Minor Groove Cisplatin</scene>

This deformation of the DNA duplex can be compared to that cause by HMG proteins, LEF-1 and hSRY . The LEF-1 structure is bent by 117 degrees
and the hSRY complex is bent by 70-80 degrees. The overall global deformation of both the LEF-1 and hSRY highly resemble that if the cisplatin
bound duplex.
<scene name='Sandbox_Reserved_430/Lef_1/1'>LeF 1 Minor Groove</scene>
This comparison of LEF-1 and hSRY DNA to cisplatin-modified DNA brings structural evidence that cisplatin –modified DNA may signal the recognition
of HMG protiens.

<scene name='Sandbox_Reserved_430/18_19/1'>18 19</scene>

<scene name='Sandbox_Reserved_430/20_21/1'>20 21</scene>

===Credits===

Introduction - Gina Lein

Overall Structure - Greg Keohane

Drug Binding Site - Louis Pires

Additional Features - Nicole Hofstetter

===References===
<references/>
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

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Louis Pires:

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Louis Pires: /* Binding Interactions */

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Louis Pires: