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2fkx

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{{STRUCTURE_2fkx| PDB=2fkx | SCENE= }}
{{STRUCTURE_2fkx| PDB=2fkx | SCENE= }}
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'''Ribosomal protein s15 from thermus thermophilus, nmr recalculated structure'''
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===Ribosomal protein s15 from thermus thermophilus, nmr recalculated structure===
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==Overview==
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The interaction between the ribosomal protein S15 and its binding sites in the 16S RNA was examined from two points of view. First, the isolated protein S15 was studied by comparing NMR conformer sets, available in the PDB and recalculated using the CNS-ARIA protocol. Molecular dynamics (MD) trajectories were then recorded starting from a conformer of each set. The recalculation of the S15 NMR structure, as well as the recording of MD trajectories, reveals that several orientations of the N-terminal alpha-helix alpha1 with respect to the structure core are populated. MD trajectories of the complex between the ribosomal protein S15 and RNA were also recorded in the presence and absence of Mg(2+) ions. The Mg(2+) ions are hexacoordinated by water and RNA oxygens. The coordination spheres mainly interact with the RNA phosphodiester backbone, reducing the RNA mobility and inducing electrostatic screening. When the Mg(2+) ions are removed, the internal mobility of the RNA and of the protein increases at the interaction interface close to the RNA G-U/G-C motif as a result of a gap between the phosphate groups in the UUCG capping tetraloop and of the disruption of S15-RNA hydrogen bonds in that region. On the other hand, several S15-RNA hydrogen bonds are reinforced, and water bridges appear between the three-way junction region and S15. The network of hydrogen bonds observed in the loop between alpha1 and alpha2 is consequently reorganized. In the absence of Mg(2+), this network has the same pattern as the network observed in the isolated protein, where the helix alpha1 is mobile with respect to the protein core. The presence of Mg(2+) ions may thus play a role in stabilizing the orientation of the helix alpha1 of S15.
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(as it appears on PubMed at http://www.pubmed.gov), where 17259282 is the PubMed ID number.
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{{ABSTRACT_PUBMED_17259282}}
==About this Structure==
==About this Structure==
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2FKX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FKX OCA].
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2FKX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FKX OCA].
==Reference==
==Reference==
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[[Category: Rna-binding protein]]
[[Category: Rna-binding protein]]
[[Category: Rrna-binding protein]]
[[Category: Rrna-binding protein]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 08:36:49 2008''

Revision as of 05:36, 28 July 2008

Image:2fkx.png

Template:STRUCTURE 2fkx

Ribosomal protein s15 from thermus thermophilus, nmr recalculated structure

Template:ABSTRACT PUBMED 17259282

About this Structure

2FKX is a Single protein structure of sequence from Thermus thermophilus. Full experimental information is available from OCA.

Reference

The conformational landscape of the ribosomal protein S15 and its influence on the protein interaction with 16S RNA., Crety T, Malliavin TE, Biophys J. 2007 Apr 15;92(8):2647-65. Epub 2007 Jan 26. PMID:17259282

Page seeded by OCA on Mon Jul 28 08:36:49 2008

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