2nr2
From Proteopedia
(New page: 200px<br /> <applet load="2nr2" size="450" color="white" frame="true" align="right" spinBox="true" caption="2nr2" /> '''The MUMO (minimal under-restraining minimal...) |
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'''The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native states ensembles of proteins'''<br /> | '''The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native states ensembles of proteins'''<br /> | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2NR2 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http:// | + | 2NR2 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NR2 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: ubiquitin]] | [[Category: ubiquitin]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 15:21:23 2008'' |
Revision as of 13:21, 23 January 2008
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The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native states ensembles of proteins
Overview
While reliable procedures for determining the conformations of proteins, are available, methods for generating ensembles of structures that also, reflect their flexibility are much less well established. Here we present, a systematic assessment of the ability of ensemble-averaged molecular, dynamics simulations with ensemble-averaged NMR restraints to, simultaneously reproduce the average structure of proteins and their, associated dynamics. We discuss the effects that under-restraining, (overfitting) and over-restraining (underfitting) have on the structures, generated in ensemble-averaged molecular simulations. We then introduce, the MUMO (minimal under-restraining minimal over-restraining) method, a, procedure in which different observables are averaged over a different, number of molecules. As both over-restraining and under-restraining are, significantly reduced in the MUMO method, it is possible to generate, ensembles of conformations that accurately characterize both the structure, and the dynamics of native states of proteins. The application of the MUMO, method to the protein ubiquitin yields a high-resolution structural, ensemble with an RDC Q-factor of 0.19.
About this Structure
2NR2 is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
Reference
The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins., Richter B, Gsponer J, Varnai P, Salvatella X, Vendruscolo M, J Biomol NMR. 2007 Feb;37(2):117-35. Epub 2007 Jan 16. PMID:17225069
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