Sandbox Reserved 426
| 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-drug complex, and as such lacks any traditional protein structures such as secondary beta sheets or alpha helices. The complex consists of two complimentary strands of DNA. A simplified model of 1xcs is shown with the nitrogenous bases removed for clarity. The deoxyribose backbones can be followed from 5' to 3' following along each strand from blue to red. Note that the strands are antiparallel where they are (hydrogen) bonded. visualizes this bonding in the middle region of the complex, again following each strand from blue to red from 5' to 3' ends.
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