2ru7

From Proteopedia

(Difference between revisions)

Revision as of 01:09, 5 August 2016

Refined structure of RNA aptamer in complex with the partial binding peptide of prion protein

Structural highlights

2ru7 is a 4 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	2rsk
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

[PRIO_BOVIN] Note=Variations in PRNP are responsible of transmissible bovine spongiform encephalopathies (BSE), a class of neurodegenerative diseases that affect various mammals. These diseases are caused by abnormally folded prion proteins. BSE can be subdivided into at least three groups: classical, H-type and L-type, with the latter 2 collectively referred to as atypical BSE. Susceptibility or resistance to a BSE disease can be influenced by at least 3 factors related to the host prion protein: protein expression levels, number of octapeptide repeats, and specific polymorphisms. In cattle, as in humans, BSEs can occur as infectious, spontaneous and genetic diseases.

Function

[PRIO_BOVIN] May play a role in neuronal development and synaptic plasticity. May be required for neuronal myelin sheath maintenance. May play a role in iron uptake and iron homeostasis. Soluble oligomers are toxic to cultured neuroblastoma cells and induce apoptosis (in vitro). Association with GPC1 (via its heparan sulfate chains) targets PRNP to lipid rafts. Also provides Cu(2+) or ZN(2+) for the ascorbate-mediated GPC1 deaminase degradation of its heparan sulfate side chains (By similarity).

Publication Abstract from PubMed

It is a central issue to elucidate the new type of molecular recognition accompanied by a global structural change of a molecule upon binding to its targets. Here we investigate the driving force for the binding of R12 (a ribonucleic acid aptamer) and P16 (a partial peptide of a prion protein) during which P16 exhibits the global structural change. We calculate changes in thermodynamic quantities upon the R12-P16 binding using a statistical-mechanical approach combined with molecular models for water which is currently best suited to studies on hydration of biomolecules. The binding is driven by a water-entropy gain originating primarily from an increase in the total volume available to the translational displacement of water molecules in the system. The energy decrease due to the gain of R12-P16 attractive (van der Waals and electrostatic) interactions is almost canceled out by the energy increase related to the loss of R12-water and P16-water attractive interactions. We can explain the general experimental result that stacking of flat moieties, hydrogen bonding and molecular-shape and electrostatic complementarities are frequently observed in the complexes. It is argued that the water-entropy gain is largely influenced by the geometric characteristics (overall shapes, sizes and detailed polyatomic structures) of the biomolecules.

Binding of an RNA aptamer and a partial peptide of a prion protein: crucial importance of water entropy in molecular recognition.,Hayashi T, Oshima H, Mashima T, Nagata T, Katahira M, Kinoshita M Nucleic Acids Res. 2014 May 6. PMID:24803670^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Hayashi T, Oshima H, Mashima T, Nagata T, Katahira M, Kinoshita M. Binding of an RNA aptamer and a partial peptide of a prion protein: crucial importance of water entropy in molecular recognition. Nucleic Acids Res. 2014 May 6. PMID:24803670 doi:http://dx.doi.org/10.1093/nar/gku382

1 Structural highlights
2 Disease
3 Function
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2ru7"

@@ Line 1: / Line 1: @@
 ==Refined structure of RNA aptamer in complex with the partial binding peptide of prion protein==
 <StructureSection load='2ru7' size='340' side='right' caption='[[2ru7]], [[NMR_Ensembles_of_Models | 5 NMR models]]' scene=''>
@@ Line 4: / Line 5: @@
 <table><tr><td colspan='2'>[[2ru7]] is a 4 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RU7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RU7 FirstGlance]. <br>
 </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2rsk|2rsk]]</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=2ru7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ru7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ru7 RCSB], [http://www.ebi.ac.uk/pdbsum/2ru7 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=2ru7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ru7 OCA], [http://pdbe.org/2ru7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ru7 RCSB], [http://www.ebi.ac.uk/pdbsum/2ru7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ru7 ProSAT]</span></td></tr>
 </table>
 == Disease ==
@@ Line 18: / Line 19: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2ru7" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>

2ru7

From Proteopedia

Revision as of 01:09, 5 August 2016

Refined structure of RNA aptamer in complex with the partial binding peptide of prion protein

Structural highlights

Disease

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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