2b0f: Difference between revisions
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'''NMR Structure of the Human Rhinovirus 3C Protease (serotype 14) with covalently bound Ace-LEALFQ-ethylpropionate inhibitor''' | '''NMR Structure of the Human Rhinovirus 3C Protease (serotype 14) with covalently bound Ace-LEALFQ-ethylpropionate inhibitor''' | ||
==Overview== | |||
The human rhinovirus (HRV) is a positive sense RNA virus responsible for about 30% of "common colds". It relies on a 182 residue cysteine protease (3C) to proteolytically process its single gene product. Inhibition of this enzyme in vitro and in vivo has consistently demonstrated cessation of viral replication. This suggests that 3C protease inhibitors could serve as good drug candidates. However, significant proteolytic substrate diversity exists within the 110+ known rhinovirus serotypes. To investigate this variability we used NMR to solve the structure of the rhinovirus serotype 14 3C protease (subgenus B) covalently bound to a peptide (acetyl-LEALFQ-ethylpropionate) inhibitor. The inhibitor-bound structure was determined to an overall rmsd of 0.82 A (backbone atoms) and 1.49 A (all heavy atoms). Comparison with the X-ray structure of the serotype 2 HRV 3C protease from subgenus A (51% sequence identity) bound to the inhibitor ruprintrivir allowed the identification of conserved intermolecular interactions involved in proximal substrate binding as well as subgenus differences that might account for the variability observed in SAR studies. To better characterize the 3C protease and investigate the structural and dynamic differences between the apo and bound states we also solved the solution structure of the apo form. The apo structure has an overall rmsd of 1.07 +/- 0.17 A over backbone atoms, which is greater by 0.25 A than what is seen for the inhibited enzyme (2B0F.pdb). This increase is localized to the enzyme's C-terminal beta-barrel domain, which is responsible for recognizing and binding proteolytic substrates. Amide hydrogen exchange dynamics revealed dramatic differences between the two enzyme states. Furthermore, a number of residues exhibited exchange-broadened amide NMR signals in the apo state compared to the inhibited state. The majority of these residues are associated with proteolytic substrate interaction. | |||
==About this Structure== | ==About this Structure== | ||
2B0F is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_14 Human rhinovirus 14]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B0F OCA]. | 2B0F is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_14 Human rhinovirus 14]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B0F OCA]. | ||
==Reference== | |||
NMR solution structures of the apo and peptide-inhibited human rhinovirus 3C protease (Serotype 14): structural and dynamic comparison., Bjorndahl TC, Andrew LC, Semenchenko V, Wishart DS, Biochemistry. 2007 Nov 13;46(45):12945-58. Epub 2007 Oct 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17944485 17944485] | |||
[[Category: Human rhinovirus 14]] | [[Category: Human rhinovirus 14]] | ||
[[Category: Picornain 3C]] | [[Category: Picornain 3C]] | ||
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[[Category: Wishart, D S.]] | [[Category: Wishart, D S.]] | ||
[[Category: Beta barrel]] | [[Category: Beta barrel]] | ||
[[Category: Hydrolase]] | |||
[[Category: Protein-inhibitor complex]] | [[Category: Protein-inhibitor complex]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu May 22 22:19:48 2008'' | ||
Revision as of 22:19, 22 May 2008
NMR Structure of the Human Rhinovirus 3C Protease (serotype 14) with covalently bound Ace-LEALFQ-ethylpropionate inhibitor
OverviewOverview
The human rhinovirus (HRV) is a positive sense RNA virus responsible for about 30% of "common colds". It relies on a 182 residue cysteine protease (3C) to proteolytically process its single gene product. Inhibition of this enzyme in vitro and in vivo has consistently demonstrated cessation of viral replication. This suggests that 3C protease inhibitors could serve as good drug candidates. However, significant proteolytic substrate diversity exists within the 110+ known rhinovirus serotypes. To investigate this variability we used NMR to solve the structure of the rhinovirus serotype 14 3C protease (subgenus B) covalently bound to a peptide (acetyl-LEALFQ-ethylpropionate) inhibitor. The inhibitor-bound structure was determined to an overall rmsd of 0.82 A (backbone atoms) and 1.49 A (all heavy atoms). Comparison with the X-ray structure of the serotype 2 HRV 3C protease from subgenus A (51% sequence identity) bound to the inhibitor ruprintrivir allowed the identification of conserved intermolecular interactions involved in proximal substrate binding as well as subgenus differences that might account for the variability observed in SAR studies. To better characterize the 3C protease and investigate the structural and dynamic differences between the apo and bound states we also solved the solution structure of the apo form. The apo structure has an overall rmsd of 1.07 +/- 0.17 A over backbone atoms, which is greater by 0.25 A than what is seen for the inhibited enzyme (2B0F.pdb). This increase is localized to the enzyme's C-terminal beta-barrel domain, which is responsible for recognizing and binding proteolytic substrates. Amide hydrogen exchange dynamics revealed dramatic differences between the two enzyme states. Furthermore, a number of residues exhibited exchange-broadened amide NMR signals in the apo state compared to the inhibited state. The majority of these residues are associated with proteolytic substrate interaction.
About this StructureAbout this Structure
2B0F is a Single protein structure of sequence from Human rhinovirus 14. Full crystallographic information is available from OCA.
ReferenceReference
NMR solution structures of the apo and peptide-inhibited human rhinovirus 3C protease (Serotype 14): structural and dynamic comparison., Bjorndahl TC, Andrew LC, Semenchenko V, Wishart DS, Biochemistry. 2007 Nov 13;46(45):12945-58. Epub 2007 Oct 18. PMID:17944485 Page seeded by OCA on Thu May 22 22:19:48 2008