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| - | [[Image:151d.gif|left|200px]] | |
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| - | <!--
| + | ==DIVERSITY OF WATER RING SIZE AT DNA INTERFACES: HYDRATION AND DYNAMICS OF DNA-ANTHRACYCLINE COMPLEXES== |
| - | The line below this paragraph, containing "STRUCTURE_151d", creates the "Structure Box" on the page.
| + | <StructureSection load='151d' size='340' side='right'caption='[[151d]], [[Resolution|resolution]] 1.40Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[151d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=151D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=151D FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4Å</td></tr> |
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| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DM2:DOXORUBICIN'>DM2</scene></td></tr> |
| - | {{STRUCTURE_151d| PDB=151d | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=151d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=151d OCA], [https://pdbe.org/151d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=151d RCSB], [https://www.ebi.ac.uk/pdbsum/151d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=151d ProSAT]</span></td></tr> |
| - | | + | </table> |
| - | '''DIVERSITY OF WATER RING SIZE AT DNA INTERFACES: HYDRATION AND DYNAMICS OF DNA-ANTHRACYCLINE COMPLEXES'''
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | ==Overview== | + | [[Category: Bertrand JA]] |
| - | In crystallographic structures of biological macromolecules, one can observe many hydration rings that originate at one water molecule, pass via hydrogen bonds through several others, and return to the original water molecule. Five-membered water rings have been thought to occur with greater frequency than other ring sizes. We describe a quantitative assessment of relationships between water ring size and frequency of occurrence in the vicinity of nucleic acid interfaces. This report focuses on low-temperature X-ray crystallographic structures of two anthracyclines, adriamycin (ADRI) and daunomycin (DAUN), bound to d(CGATCG) and on several DNA structures published previously by others. We have obtained excellent low-temperature (-160 degrees C, LT) X-ray intensity data for d(CGATCG)-adriamycin and d(CGATCG)-daunomycin with a multiwire area detector. The LTX-ray data sets contain 20% (daunomycin, LT-DAUN) and 35% (adriamycin, LT-ADRI) more reflections than were used to derive the original room-temperature (15 degrees C) structures [Frederick, C.A., Williams, L.D., Ughetto, G., van der Marel, G. A., van Boom, J.H., Rich, A., & Wang, A.H.-J. (1990) Biochemistry 29, 2538-2549]. The results show that five-membered water rings are not preferred over other ring sizes. This assessment is consistent with our observation of broad dispersion W-W-W angles (sigma = 20 degrees). In addition, we report that the thermal mobility, distinct from the static disorder, of the amino sugar of daunomycin and adriamycin is significantly greater than that of the rest of the complex. This mobility implies that if the central AT base pair is switched to a CG base pair, there should be a low energy cost in avoiding the guanine amino group. The energy difference (for the sugar-binding preference) between d(CGTACG) and d(CGCGCG) could be considerably less than 20 kcal/mol, a value proposed previously from computation.
| + | [[Category: Lipscomb LA]] |
| - | | + | [[Category: Peek ME]] |
| - | ==About this Structure== | + | [[Category: VanDerveer D]] |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=151D OCA]. | + | [[Category: Williams LD]] |
| - | | + | [[Category: Zhou FX]] |
| - | ==Reference== | + | |
| - | Water ring structure at DNA interfaces: hydration and dynamics of DNA-anthracycline complexes., Lipscomb LA, Peek ME, Zhou FX, Bertrand JA, VanDerveer D, Williams LD, Biochemistry. 1994 Mar 29;33(12):3649-59. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8142363 8142363]
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| - | [[Category: Bertrand, J A.]]
| + | |
| - | [[Category: Lipscomb, L A.]] | + | |
| - | [[Category: Peek, M E.]] | + | |
| - | [[Category: VanDerveer, D.]] | + | |
| - | [[Category: Williams, L D.]] | + | |
| - | [[Category: Zhou, F X.]] | + | |
| - | [[Category: Complexed with drug]] | + | |
| - | [[Category: Double helix]] | + | |
| - | [[Category: Right handed dna]] | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 09:30:45 2008''
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