4gre: Difference between revisions
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==DNA holliday junction stabilized by iodine halogen bond. I2J Construct of related reference== | ==DNA holliday junction stabilized by iodine halogen bond. I2J Construct of related reference== | ||
<StructureSection load='4gre' size='340' side='right' caption='[[4gre]], [[Resolution|resolution]] 1.70Å' scene=''> | <StructureSection load='4gre' size='340' side='right' caption='[[4gre]], [[Resolution|resolution]] 1.70Å' scene=''> | ||
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</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene></td></tr> | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2org|2org]], [[2orf|2orf]], [[2orh|2orh]], [[3tok|3tok]], [[4gqd|4gqd]], [[4gs2|4gs2]], [[4gsg|4gsg]], [[4gsi|4gsi]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2org|2org]], [[2orf|2orf]], [[2orh|2orh]], [[3tok|3tok]], [[4gqd|4gqd]], [[4gs2|4gs2]], [[4gsg|4gsg]], [[4gsi|4gsi]]</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=4gre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gre OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gre RCSB], [http://www.ebi.ac.uk/pdbsum/4gre 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=4gre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gre OCA], [http://pdbe.org/4gre PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4gre RCSB], [http://www.ebi.ac.uk/pdbsum/4gre PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4gre ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 4gre" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
Revision as of 16:53, 11 August 2016
Structural highlights
Publication Abstract from PubMedInterest in noncovalent interactions involving halogens, particularly halogen bonds (X-bonds), has grown dramatically in the past decade, propelled by the use of X-bonding in molecular engineering and drug design. However, it is clear that a complete analysis of the structure-energy relationship must be established in biological systems to fully exploit X-bonds for biomolecular engineering. We present here the first comprehensive experimental study to correlate geometries with their stabilizing potentials for fluorine (F), chlorine (Cl), bromine (Br), or iodine (I) X-bonds in a biological context. For these studies, we determine the single-crystal structures of DNA Holliday junctions containing halogenated uracil bases that compete X-bonds against classic hydrogen bonds (H-bonds), estimate the enthalpic energies of the competing interactions in the crystal system through crystallographic titrations, and compare the enthalpic and entropic energies of bromine and iodine X-bonds in solution by differential scanning calorimetry. The culmination of these studies demonstrates that enthalpic stabilization of X-bonds increases with increasing polarizability from F to Cl to Br to I, which is consistent with the sigma-hole theory of X-bonding. Furthermore, an increase in the X-bonding potential is seen to direct the interaction toward a more ideal geometry. However, the entropic contributions to the total free energies must also be considered to determine how each halogen potentially contributes to the overall stability of the interaction. We find that bromine has the optimal balance between enthalpic and entropic energy components, resulting in the lowest free energy for X-bonding in this DNA system. The X-bond formed by iodine is more enthalpically stable, but this comes with an entropic cost, which we attribute to crowding effects. Thus, the overall free energy of an X-bonding interaction balances the stabilizing electrostatic effects of the sigma-hole against the competing effects on the local structural dynamics of the system. Enthalpy-Entropy Compensation in Biomolecular Halogen Bonds Measured in DNA Junctions.,Carter M, Voth AR, Scholfield MR, Rummel B, Sowers LC, Ho PS Biochemistry. 2013 Jul 9. PMID:23789744[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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