151d: Difference between revisions
No edit summary |
No edit summary |
||
| Line 3: | Line 3: | ||
== Structural highlights == | == Structural highlights == | ||
<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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=151D FirstGlance]. <br> | <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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=151D FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DM2:DOXORUBICIN'>DM2</scene>< | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DM2:DOXORUBICIN'>DM2</scene></td></tr> | ||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=151d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=151d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=151d RCSB], [http://www.ebi.ac.uk/pdbsum/151d PDBsum]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=151d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=151d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=151d RCSB], [http://www.ebi.ac.uk/pdbsum/151d PDBsum]</span></td></tr> | ||
<table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 18: | Line 18: | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bertrand, J A | [[Category: Bertrand, J A]] | ||
[[Category: Lipscomb, L A | [[Category: Lipscomb, L A]] | ||
[[Category: Peek, M E | [[Category: Peek, M E]] | ||
[[Category: VanDerveer, D | [[Category: VanDerveer, D]] | ||
[[Category: Williams, L D | [[Category: Williams, L D]] | ||
[[Category: Zhou, F X | [[Category: Zhou, F X]] | ||
[[Category: Complexed with drug]] | [[Category: Complexed with drug]] | ||
[[Category: Dna]] | [[Category: Dna]] | ||
[[Category: Double helix]] | [[Category: Double helix]] | ||
[[Category: Right handed dna]] | [[Category: Right handed dna]] | ||
Revision as of 14:28, 22 December 2014
DIVERSITY OF WATER RING SIZE AT DNA INTERFACES: HYDRATION AND DYNAMICS OF DNA-ANTHRACYCLINE COMPLEXESDIVERSITY OF WATER RING SIZE AT DNA INTERFACES: HYDRATION AND DYNAMICS OF DNA-ANTHRACYCLINE COMPLEXES
Structural highlights
Publication Abstract from PubMedIn 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. 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:8142363[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
| ||||||||||||||||
