1fme
From Proteopedia
(New page: 200px<br /><applet load="1fme" size="450" color="white" frame="true" align="right" spinBox="true" caption="1fme" /> '''SOLUTION STRUCTURE OF FSD-EY, A NOVEL PEPTID...) |
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| - | [[Image:1fme.jpg|left|200px]]<br /><applet load="1fme" size=" | + | [[Image:1fme.jpg|left|200px]]<br /><applet load="1fme" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1fme" /> | caption="1fme" /> | ||
'''SOLUTION STRUCTURE OF FSD-EY, A NOVEL PEPTIDE ASSUMING A BETA-BETA-ALPHA FOLD'''<br /> | '''SOLUTION STRUCTURE OF FSD-EY, A NOVEL PEPTIDE ASSUMING A BETA-BETA-ALPHA FOLD'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The computational redesign of the second zinc finger of Zif268 to produce | + | The computational redesign of the second zinc finger of Zif268 to produce a 28 residue peptide (FSD-1) that assumes a betabetaalpha fold without metal binding was recently reported. In order to explore the tolerance of this metal-free fold towards sequence variability, six additional peptides resulting from the ORBIT computational protein design process were synthesized and characterized. The experimental stabilities of five of these peptides are strongly correlated with the energies calculated by ORBIT. However, when a peptide with a mutation in the beta-turn is examined, the calculated stability does not accurately predict the experimentally determined stability. The NMR solution structure of a peptide incorporating this mutation (FSD-EY) reveals that the register between the beta-strands is different from the model structure used to select and score the sequences. FSD-EY has a type I' turn instead of the target EbaaagbE turn (rubredoxin knuckle). Two additional peptides that have improved side-chain to backbone hydrogen bonding and turn propensity for the target turn were characterized. Both are of stability comparable to that of FSD-1. These results demonstrate the robustness of the ORBIT protein design methods and underscore the need for continued improvements in negative design. |
==About this Structure== | ==About this Structure== | ||
| - | 1FME is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 1FME is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FME OCA]. |
==Reference== | ==Reference== | ||
The beta-beta-alpha fold: explorations in sequence space., Sarisky CA, Mayo SL, J Mol Biol. 2001 Apr 13;307(5):1411-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11292351 11292351] | The beta-beta-alpha fold: explorations in sequence space., Sarisky CA, Mayo SL, J Mol Biol. 2001 Apr 13;307(5):1411-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11292351 11292351] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Mayo, S | + | [[Category: Mayo, S L.]] |
| - | [[Category: Sarisky, C | + | [[Category: Sarisky, C A.]] |
[[Category: beta-beta-alpha]] | [[Category: beta-beta-alpha]] | ||
[[Category: designed protein]] | [[Category: designed protein]] | ||
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[[Category: zinc finger]] | [[Category: zinc finger]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:40:17 2008'' |
Revision as of 10:40, 21 February 2008
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SOLUTION STRUCTURE OF FSD-EY, A NOVEL PEPTIDE ASSUMING A BETA-BETA-ALPHA FOLD
Overview
The computational redesign of the second zinc finger of Zif268 to produce a 28 residue peptide (FSD-1) that assumes a betabetaalpha fold without metal binding was recently reported. In order to explore the tolerance of this metal-free fold towards sequence variability, six additional peptides resulting from the ORBIT computational protein design process were synthesized and characterized. The experimental stabilities of five of these peptides are strongly correlated with the energies calculated by ORBIT. However, when a peptide with a mutation in the beta-turn is examined, the calculated stability does not accurately predict the experimentally determined stability. The NMR solution structure of a peptide incorporating this mutation (FSD-EY) reveals that the register between the beta-strands is different from the model structure used to select and score the sequences. FSD-EY has a type I' turn instead of the target EbaaagbE turn (rubredoxin knuckle). Two additional peptides that have improved side-chain to backbone hydrogen bonding and turn propensity for the target turn were characterized. Both are of stability comparable to that of FSD-1. These results demonstrate the robustness of the ORBIT protein design methods and underscore the need for continued improvements in negative design.
About this Structure
1FME is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
The beta-beta-alpha fold: explorations in sequence space., Sarisky CA, Mayo SL, J Mol Biol. 2001 Apr 13;307(5):1411-8. PMID:11292351
Page seeded by OCA on Thu Feb 21 12:40:17 2008
