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| - | [[Image:1ud7.gif|left|200px]] | + | {{Seed}} |
| | + | [[Image:1ud7.png|left|200px]] |
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| | {{STRUCTURE_1ud7| PDB=1ud7 | SCENE= }} | | {{STRUCTURE_1ud7| PDB=1ud7 | SCENE= }} |
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| - | '''SOLUTION STRUCTURE OF THE DESIGNED HYDROPHOBIC CORE MUTANT OF UBIQUITIN, 1D7'''
| + | ===SOLUTION STRUCTURE OF THE DESIGNED HYDROPHOBIC CORE MUTANT OF UBIQUITIN, 1D7=== |
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| - | ==Overview==
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| - | BACKGROUND: The recent merger of computation and protein design has resulted in a burst of success in the generation of novel proteins with native-like properties. A critical component of this coupling between theory and experiment is a detailed analysis of the structures and stabilities of designed proteins to assess and improve the accuracy of design algorithms. RESULTS: Here we report the solution structure of a hydrophobic core variant of ubiquitin, referred to as 1D7, which was designed with the core-repacking algorithm ROC. As a measure of conformational specificity, we also present amide exchange protection factors and backbone and sidechain dynamics. The results indicate that 1D7 is similar to wild-type (WT) ubiquitin in backbone structure and degree of conformational specificity. We also observe a good correlation between experimentally determined sidechain structures and those predicted by ROC. However, evaluation of the core sidechain conformations indicates that, in general, 1D7 has more sidechains in less statistically favorable conformations than WT. CONCLUSIONS: Our results provide an explanation for the lower stability of 1D7 compared to WT, and suggest modifications to design algorithms that may improve the accuracy with which structure and stability are predicted. The results also demonstrate that core packing can affect conformational flexibility in subtle ways that are likely to be important for the design of function and protein-ligand interactions.
| + | The line below this paragraph, {{ABSTRACT_PUBMED_10467150}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 10467150 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_10467150}} |
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| | ==About this Structure== | | ==About this Structure== |
| - | 1UD7 is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UD7 OCA]. | + | 1UD7 is a [[Single protein]] structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UD7 OCA]. |
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| | ==Reference== | | ==Reference== |
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| | [[Category: Designed core mutant]] | | [[Category: Designed core mutant]] |
| | [[Category: Ubiquitin]] | | [[Category: Ubiquitin]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 11:03:49 2008'' | + | |
| | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 18:37:22 2008'' |
Revision as of 15:37, 27 July 2008
Template:STRUCTURE 1ud7
SOLUTION STRUCTURE OF THE DESIGNED HYDROPHOBIC CORE MUTANT OF UBIQUITIN, 1D7
Template:ABSTRACT PUBMED 10467150
About this Structure
1UD7 is a Single protein structure. Full experimental information is available from OCA.
Reference
Solution structure and dynamics of a designed hydrophobic core variant of ubiquitin., Johnson EC, Lazar GA, Desjarlais JR, Handel TM, Structure. 1999 Aug 15;7(8):967-76. PMID:10467150
Page seeded by OCA on Sun Jul 27 18:37:22 2008
