Sandbox Reserved 426: Difference between revisions
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<font color='red'>Everyone -- note that this is NOT a protein, but a complex with DNA. Edit your text accordingly, eg discussing alpha helices etc does not make sense. </font> | <font color='red'>Everyone -- note that this is NOT a protein, but a complex with DNA. Edit your text accordingly, eg discussing alpha helices etc does not make sense. </font> | ||
==Overall Structure== | ==Overall Structure== | ||
The 1xcs (model at right) complex is a small, simple globular DNA-peptide complex, and as such lacks secondary beta sheets or alpha helices. The complex consists of two non-identical dimers. A simplified model of 1xcs is shown <scene name='48/483883/Title/4'>here,</scene> with the side chains removed for clarity. The peptide backbones can be followed from N to C termini following along each strand from blue to red. Note that the strands are antiparallel where they are non-covalently bound. <scene name='48/483883/1xcs_with_side_chains/2'>1xcs with the side chains displayed (black)</scene> visualizes this bonding in the middle region of the complex, again following each strand from blue to red from N to C terminus. | The 1xcs (model at right) complex is a small, simple globular DNA-peptide complex, and as such lacks secondary beta sheets or alpha helices. The complex consists of two non-identical dimers. A simplified model of 1xcs is shown <scene name='48/483883/Title/4'>here,</scene> with the side chains removed for clarity. The peptide backbones can be followed from N to C termini following along each strand from blue to red. Note that the strands are antiparallel where they are non-covalently bound. <scene name='48/483883/1xcs_with_side_chains/2'>1xcs with the side chains displayed (black)</scene> visualizes this bonding in the middle region of the complex, again following each strand from blue to red from N to C terminus. | ||
==Binding Interactions== | ==Binding Interactions== | ||
<scene name='48/483883/1xcs_binding_site/2'>Click here to see the binding site | <scene name='48/483883/1xcs_binding_site/2'>Click here to see the binding site | ||
1xcs is a complex with DNA and it is a two chain structure. It has ligands A4L, BA and CO. There are strong cation interactions that help form a crystal structure. The complex crystallizes when there is either Co(2+), Ba(2+) and Na(+) ions. </scene> | 1xcs is a complex with DNA and it is a two chain structure. It has ligands A4L, BA and CO. There are strong cation interactions that help form a crystal structure. The complex crystallizes when there is either Co(2+), Ba(2+) and Na(+) ions. </scene> | ||
==Additional Features== | ==Additional Features== | ||
Click <scene name='48/483883/Protein_between_dna_strands/1'>here</scene> to see that the drug binds directly between strands of DNA. This interrupts the expression of this section of DNA. | Click <scene name='48/483883/Protein_between_dna_strands/1'>here</scene> to see that the drug binds directly between strands of DNA. This interrupts the expression of this section of DNA. | ||
I will then go on to explain how specifically this complex interrupts/changes gene expression. | I will then go on to explain how specifically this complex interrupts/changes gene expression. | ||
==Quiz Question 1== | ==Quiz Question 1== | ||
Why is it important for the protein to bind <scene name='48/483883/Quiz_question/1'>here</scene>? | Why is it important for the protein to bind <scene name='48/483883/Quiz_question/1'>here</scene>? | ||
A unique site is the __ ion found associated with the <scene name='48/483883/O6_atom_of_two_guanines/1'>O6_atom_of_two_guanines</scene>, which gives additional strength to the guanine–Co2+–guanine interaction. A Mg2+ B Co2+ C Ba2+ D Mg2+ | |||
==See Also== | ==See Also== | ||
Revision as of 00:45, 3 March 2016
| This Sandbox is Reserved from January 19, 2016, through August 31, 2016 for use for Proteopedia Team Projects by the class Chemistry 423 Biochemistry for Chemists taught by Lynmarie K Thompson at University of Massachusetts Amherst, USA. This reservation includes Sandbox Reserved 425 through Sandbox Reserved 439. |
Structure of Oligonucleotide/Drug complex (1xcs)[1]Structure of Oligonucleotide/Drug complex (1xcs)[1]
by Michael Beauregard, Annie Burton, Jianlong Li, Daniel Marco, and Nathaneal Park
Student Projects for UMass Chemistry 423 Spring 2016 <StructureSection load='1xcs' size='350' side='right' caption='caption for Molecular Playground (PDB entry 1xcs)' scene=>
IntroductionIntroduction
The intercalation of DNA and drug compounds has been studied thoroughly, in this case the nucleotide d(CGTACG) was complexed with an anthraquinone derivative. This derivative, 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione, provided researchers with the information needed to solve using X-Ray crystallography. Along with the structure, the important forces involved in binding were analyzed and described as heavily reliant on cations. Furthermore, the binding site seems to be specific to anthracene and similar molecules. Therefore, the potential for drug compounds to be carrying by this nucleotide complex requires further research.
Everyone -- note that this is NOT a protein, but a complex with DNA. Edit your text accordingly, eg discussing alpha helices etc does not make sense.
Overall StructureOverall Structure
The 1xcs (model at right) complex is a small, simple globular DNA-peptide complex, and as such lacks secondary beta sheets or alpha helices. The complex consists of two non-identical dimers. A simplified model of 1xcs is shown with the side chains removed for clarity. The peptide backbones can be followed from N to C termini following along each strand from blue to red. Note that the strands are antiparallel where they are non-covalently bound. visualizes this bonding in the middle region of the complex, again following each strand from blue to red from N to C terminus.
Binding InteractionsBinding Interactions
Additional FeaturesAdditional Features
Click to see that the drug binds directly between strands of DNA. This interrupts the expression of this section of DNA. I will then go on to explain how specifically this complex interrupts/changes gene expression.
Quiz Question 1Quiz Question 1
Why is it important for the protein to bind ? A unique site is the __ ion found associated with the , which gives additional strength to the guanine–Co2+–guanine interaction. A Mg2+ B Co2+ C Ba2+ D Mg2+
See AlsoSee Also
CreditsCredits
Introduction - Daniel Marco
Overall Structure - Nathaneal Park
Drug Binding Site - Annie Burton
Additional Features - Michael Beauregard
Quiz Question 1 - Jianlong Li
ReferencesReferences
- ↑ Valls N, Steiner RA, Wright G, Murshudov GN, Subirana JA. Variable role of ions in two drug intercalation complexes of DNA. J Biol Inorg Chem. 2005 Aug;10(5):476-82. Epub 2005 Sep 23. PMID:15926069 doi:10.1007/s00775-005-0655-3