2nr2
From Proteopedia
| Line 1: | Line 1: | ||
[[Image:2nr2.jpg|left|200px]] | [[Image:2nr2.jpg|left|200px]] | ||
| - | + | <!-- | |
| - | + | The line below this paragraph, containing "STRUCTURE_2nr2", creates the "Structure Box" on the page. | |
| - | + | You may change the PDB parameter (which sets the PDB file loaded into the applet) | |
| - | + | or the SCENE parameter (which sets the initial scene displayed when the page is loaded), | |
| - | + | or leave the SCENE parameter empty for the default display. | |
| - | + | --> | |
| - | + | {{STRUCTURE_2nr2| PDB=2nr2 | SCENE= }} | |
| - | + | ||
| - | + | ||
| - | }} | + | |
'''The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native states ensembles of proteins''' | '''The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native states ensembles of proteins''' | ||
| Line 30: | Line 27: | ||
[[Category: Varnai, P.]] | [[Category: Varnai, P.]] | ||
[[Category: Vendruscolo, M.]] | [[Category: Vendruscolo, M.]] | ||
| - | [[Category: | + | [[Category: Signaling protein]] |
| - | [[Category: | + | [[Category: Ubiquitin]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 09:48:25 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 06:48, 4 May 2008
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 Page seeded by OCA on Sun May 4 09:48:25 2008
