2NR2

The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native states ensembles of proteins

2NR2 の概要

• エントリーDOI: 10.2210/pdb2nr2/pdb
• 関連するPDBエントリー: 1D3Z 1UBQ 1XQQ
• 分子名称: Ubiquitin (1 entity in total)
• 機能のキーワード: signaling protein, ubiquitin
• 由来する生物種: Homo sapiens (human)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 8576.83

構造登録者

Richter, B.,Gsponer, J.,Varnai, P.,Salvatella, X.,Vendruscolo, M. (登録日: 2006-11-01, 公開日: 2007-05-08, 最終更新日: 2023-12-27)

主引用文献

Richter, B.,Gsponer, J.,Varnai, P.,Salvatella, X.,Vendruscolo, M.
The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins
J.Biomol.Nmr, 37:117-135, 2007

PubMed Abstract: 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.

PubMed: 17225069
DOI: 10.1007/s10858-006-9117-7

実験手法

SOLUTION NMR