Sandbox Reserved 426

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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.

Contents 1 Structure of Oligonucleotide/Drug complex (1xcs)[1] 2 Introduction 3 Overall Structure 4 Binding Interactions 5 Additional Features 6 Quiz Question 1 7 See Also 8 Credits 9 References

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

Introduction

spinqualitylabelsall models 1xcs, Hello Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Notice the similarity in shape and side chains.

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 Structure

spinqualitylabelsall models Three dimensional representation of the 1xcs structure. Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

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 Interactions

spinqualitylabelsall models pdbcode, :) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Additional Features

spinqualitylabelsall models pdbcode, akjnfja Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

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 1

spinqualitylabelsall models 1xcs, chemchemchem Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

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 Also

• 1bp8
• 1d3x
• 1p3x

Credits

Introduction - Daniel Marco

Overall Structure - Nathaneal Park

Drug Binding Site - Annie Burton

Additional Features - Michael Beauregard

Quiz Question 1 - Jianlong Li

References

1. ↑ 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