NMR Ensembles of Models: Difference between revisions
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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. | 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. | ||
Protein chains commonly have more variation between models at the ends than in the middle. An example is [[2ryu]]. | |||
Using appropriate methodologies, it is possible to determine both the average structure and its dynamic movements<ref>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:[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15650731 15650731].</ref>. | Using appropriate methodologies, it is possible to determine both the average structure and its dynamic movements<ref>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:[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15650731 15650731].</ref>. | ||