Improved Technologies Now Routinely Provide Protein NMR Structures Useful for Molecular Replacement
By Binchen Mao, R. Guan, Gaetano T. Montelione. 2011
39 citations recorded by the source corpus.
Summary Molecular replacement (MR) is widely used for addressing the phase problem in X-ray crystallography. Historically, crystallographers have had limited success using NMR structures as MR search models. Here we report a comprehensive investigation of the utility of protein NMR ensembles as MR search models, using data for 25 pairs of X-ray and NMR structures solved and refined using modern NMR methods. Starting from NMR ensembles prepared by an improved protocol, FindCore, correct MR solutions were obtained for 22 targets. Based on these solutions, automatic model rebuilding could be done successfully. Rosetta refinement of NMR structures provided MR solutions for another two proteins. We also demonstrate that such properly prepared NMR ensembles and X-ray crystal structures have similar performance when used as MR search models for homologous structures, particularly for targets with sequence identity > 40%.
Subfields: Materials Chemistry, Molecular Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Materials Chemistry
- Andriy Kryshtafovych
- Yang Zhang
- Randy J. Read
- Torsten Schwede
- Gaetano T. Montelione
- Paul D. Adams
- Krzysztof Fidelis
- Pavel V. Afonine
In Molecular Biology
- Andriy Kryshtafovych
- Yang Zhang
- Torsten Schwede
- Randy J. Read
- David Baker
- Gaetano T. Montelione
- Krzysztof Fidelis
- Anna Tramontano
Citations in the corpus
- Critical Assessment of Methods of Protein Structure Prediction (CASP) – Progress and New directions in Round XI (2016, background): “25,26 Larger proteins present a much greater challenge mostly due to the well-known limitations of short transverse spin relaxation rates, broad NMR linewidths, and chemical shift degeneracy.”
- The Protein Structure Initiative: achievements and visions for the future (2012, background): “It has been a powerful and successful driving force for a wide range of method developments that have been realized only by collecting homogeneous, fully-documented data across large numbers of protein samples and structures (see for example [10,21,26,74-81]).”
- phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta (2012, methodology): “Qian et al. [29], Ramelot et al. [30], DiMaio et al. [28] and Mao et al. [6] have shown that Rosetta structure modeling can be used to improve homology models to make them more useful for finding their locations in a crystallographic cell, the first step in molecular replacement.”
- Automatic NOESY assignment in CS-RASREC-Rosetta (2014, methodology): “In the following, we demonstrate autoNOE-Rosetta on two protein targets from the North East Structural Genomics Consortium.”
- Protein structure determination by combining sparse NMR data with evolutionary couplings (2015, unknown): “Python code to identify high-confidence ECs is in Supplementary Data 1.”