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| [[Image:151d.gif|left|200px]]<br /><applet load="151d" size="450" color="white" frame="true" align="right" spinBox="true"
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| caption="151d, resolution 1.400Å" />
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| '''DIVERSITY OF WATER RING SIZE AT DNA INTERFACES: HYDRATION AND DYNAMICS OF DNA-ANTHRACYCLINE COMPLEXES'''<br />
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| ==Overview== | | ==DIVERSITY OF WATER RING SIZE AT DNA INTERFACES: HYDRATION AND DYNAMICS OF DNA-ANTHRACYCLINE COMPLEXES== |
| 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.
| | <StructureSection load='151d' size='340' side='right'caption='[[151d]], [[Resolution|resolution]] 1.40Å' scene=''> |
| | | == Structural highlights == |
| ==About this Structure== | | <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> |
| 151D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with DM2 as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=151D OCA].
| | </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> |
| | | <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> |
| ==Reference== | | <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> |
| 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://ispc.weizmann.ac.il//pmbin/getpm?pmid=8142363 8142363]
| | </table> |
| [[Category: Protein complex]]
| | __TOC__ |
| [[Category: Bertrand, J.A.]]
| | </StructureSection> |
| [[Category: Lipscomb, L.A.]] | | [[Category: Large Structures]] |
| [[Category: Peek, M.E.]]
| | [[Category: Bertrand JA]] |
| [[Category: VanDerveer, D.]] | | [[Category: Lipscomb LA]] |
| [[Category: Williams, L.D.]] | | [[Category: Peek ME]] |
| [[Category: Zhou, F.X.]] | | [[Category: VanDerveer D]] |
| [[Category: DM2]] | | [[Category: Williams LD]] |
| [[Category: complexed with drug]] | | [[Category: Zhou FX]] |
| [[Category: double helix]] | |
| [[Category: right handed dna]] | |
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| ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 21:58:00 2007''
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