NMR Ensembles of Models
CaveatCaveat
I wrote the initial content for this page based on discussions I've had with NMR spectroscopists and crystallographers. Be warned that I am far from an expert, and have never done either NMR spectroscopy nor crystallography. Until this page is vetted by an expert, its content should be considered provisional, not authoritative! Eric Martz 01:25, 26 June 2008 (IDT)
Structure Determination by NMRStructure Determination by NMR
About 14% of the entries in the Protein Data Bank were determined by nuclear magnetic resonance in solution (NMR) as of mid-2008. 85% were determined by X-ray crystallography, and <1% by other methods. NMR can only be used for relatively small macromolecules (see below).
Macromolecular structure determination by NMR is done in aqueous solution, and thus requires that the molecule be soluble. For more information, see Nature of 3D Structural Data[1] and NMR in Wikipedia[2].
NMR Experiments Yield Multiple ModelsNMR Experiments Yield Multiple Models
When a macromolecular structure is determined by nuclear magnetic resonance (NMR) in solution, the result is an ensemble of multiple molecular models, each of which is consistent with the experimental data. The results of an NMR experiment are a large number of inter-atomic distance restraints, which are consistent with multiple models. This is in contrast to the result of an X-ray crystallographic experiment, which is a single model that best fits the empirical electron density. (In some cases where the resolution is very high, the model may include alternative positions for some atoms.)
The number of NMR models published depends upon the experiment and is up to the authors, and varies between 2 and over 100. The first model in the ensemble has no special significance.
Meaning of the Variation Between ModelsMeaning of the Variation Between Models
The variation between models in the ensemble can mean either of two things. The variation can represent actual flexibility and thermal motion that occurred during the NMR measurements in solution, typically at room temperature. Alternatively, the variation can simply mean uncertainty in the atomic positions, namely, that an inadequate number of restraints were available to determine the positions of some atoms. Unfortunately, there is nothing comparable to the B value or Temperature value that quantitates the uncertainty of the position of each atom in crystallographic results. Hence, the only way to find out what the meaning of the variation between models is to contact the experimenters who authored the published ensemble of models.
Using appropriate methodologies, it is possible to determine both the average structure and its dynamic movements[3].
Reliability of NMR ModelsReliability of NMR Models
NMR models are more likely to contain major errors [4] than are crystallographic models that have good Resolution and Free R values.
The Most-Representative ModelThe Most-Representative Model
The most representative model is the model closest to the average model. A server called Olderado reports the most representative model.
The Minimized Average ModelThe Minimized Average Model
It is common to average the models from an NMR experiment, but in order for the result to be realistic, it must undergo some energy minimization in order to adjust covalent bond lengths and angles. The result is called a minimized average model. Sometimes, authors publish both the ensemble and the minimized average. For example 2bbm appears to be the minimized average for the ensemble of 21 models in 2bbn, but without reading the original publication or contacting the authors, it is difficult to be sure (since the header of the PDB file does not say).
Median Size of Published NMR StructuresMedian Size of Published NMR Structures
Solution NMR is unable to determine atomic resolution protein structures for molecules in excess of about 30,000 Daltons. In fact, the median mass of NMR structures published in the Protein Data Bank is about 9 kD, with 90% less than 19 kD [5]. In contrast, the median mass of crystallographically determined structures is 45 kD, with 90% <145 kD.
Alignment of ModelsAlignment of Models
NMR models are typically aligned by the authors before publication. However, there are some exceptions.
Literature CitedLiterature Cited
- ↑ Nature of 3D Structural Data
- ↑ http://en.wikipedia.org/wiki/Nuclear_magnetic_resonance NMR in Wikipedia]
- ↑ Simultaneous determination of protein structure and dynamics. Kresten Lindorff-Larsen, Robert B. Best, Mark A. DePristo, Christopher M. Dobson, and Michele Vendruscolo (2005). Nature 433:128. PMID:15650731.
- ↑ Traditional biomolecular structure determination by NMR spectroscopy allows for major errors. Sander B. Nabuurs, Chris. A. E. M. Spronk, Geerten W. Vuister, and Gert Vriend. (2006). PLoS Computational Biology 2: Open Access Full Text Precis. DOI: 10.1371/journal.pcbi.0020009
- ↑ At Protein Explorer: [http://proteinexplorer.org/gpsi/chardata.htm Size and Redundancy of 43,000 Entries in the Protein Data Bank] (as of April 2007)