NMR Ensembles of Models: Difference between revisions
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== | ==Structure Determination by NMR== | ||
About 6% of the entries in the [[Protein Data Bank]] were determined by nuclear magnetic resonance in solution (NMR) as of October 2024. 83% were determined by [[X-ray crystallography]], 10% by [[electron cryomicroscopy]], and <1% by other methods. NMR can only be used for relatively small macromolecules (see [[#Median_Size_of_Published_NMR_Structures|below]]). | |||
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NMR spectroscopy is based on the ability of a nucleus with a spin of 1/2 (e.g. <sup>1</sup>H, <sup>13</sup>C, <sup>15</sup>N, <sup>31</sup>P) to adopt two different orientations in a magnetic field. The distribution of nuclei between the two states can be changed by subjecting them to a short pulse of radiation with a frequency commensurate with the energy difference between them. Monitoring the magnetic signals in the subsequent decay can yield dynamic information about the orientation and spacing of the nuclei, which provide restraints that can be turned into structural information<ref>Quoted from page 22 of the book ''Molecular Biology of Assemblies and Machines'' by Steven, Baumeister, Johnson and Perham, [https://www.crcpress.com/Molecular-Biology-of-Assemblies-and-Machines/Steven-Baumeister-Johnson-Perham/9780815341666 Garland/CRC Press, 2016].</ref>. | |||
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The primary data yielded by NMR analysis is mostly local and more recently global geometric information about atoms within the structure. Typically, these include distance between pairs of atoms, dihedral angles (typically backbone φ angles and some side-chain χ1 angles) and sometimes global information such as the orientation of a given bond with respect to a fixed axis of the molecule. These data are used as "restraints" to reconstruct 3D models which are compatible with the NMR data. All calculations are performed directly in the physical space, starting with a random conformation of the macromolecule, which is progressively folded to satisfy the restraints. Typically, several runs are performed, starting from different initial conformations, in order to check that the calculation converges onto a single solution. The result is thus an ensemble of models, the distribution of which gives a measure of the precision of the NMR structure. | The primary data yielded by NMR analysis is mostly local and more recently global geometric information about atoms within the structure. Typically, these include distance between pairs of atoms, dihedral angles (typically backbone φ angles and some side-chain χ1 angles) and sometimes global information such as the orientation of a given bond with respect to a fixed axis of the molecule. These data are used as "restraints" to reconstruct 3D models which are compatible with the NMR data. All calculations are performed directly in the physical space, starting with a random conformation of the macromolecule, which is progressively folded to satisfy the restraints. Typically, several runs are performed, starting from different initial conformations, in order to check that the calculation converges onto a single solution. The result is thus an ensemble of models, the distribution of which gives a measure of the precision of the NMR structure. | ||
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Model building for NMR experiments typically starts with the complete protein or nucleic acid chain, including [[Hydrogen in macromolecular models|hydrogen atoms]]. The distance restraints are then applied. The resulting model usually includes the entire protein and nucleic acid chains, unlike [[X-ray crystallography|X-ray crystallographic]] models that often lack the ends, and even loops in the middle of chains, due to [[Disorder|disorder]] in protein crystals. | Model building for NMR experiments typically starts with the complete protein or nucleic acid chain, including [[Hydrogen in macromolecular models|hydrogen atoms]]. The distance restraints are then applied. The resulting model usually includes the entire protein and nucleic acid chains, unlike [[X-ray crystallography|X-ray crystallographic]] models that often lack the ends, and even loops in the middle of chains, due to [[Disorder|disorder]] in protein crystals. | ||
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''<ref>[http://www.pdb.org/pdb/static.do?p=general_information/about_pdb/nature_of_3d_structural_data.html Nature of 3D Structural Data | Macromolecular structure determination by NMR is done at high protein concentrations in aqueous solution, and thus requires that the molecule be highly soluble. For more information, see ''NMR in Wikipedia''<ref>[http://en.wikipedia.org/wiki/Nuclear_magnetic_resonance NMR in Wikipedia]</ref> | ||
and ''Nature of 3D Structural Data at PDB''<ref>[https://web.archive.org/web/20110415074813/http://www.pdb.org/pdb/static.do?p=general_information/about_pdb/nature_of_3d_structural_data.html Nature of 3D Structural Data (archived copy)]</ref>. | |||
==Displaying NMR Models== | ==Displaying NMR Models== | ||
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===Individual Models=== | ===Individual Models=== | ||
Proteopedia shows only the first model by default, while it says ''Displaying simplified model''. After you click the <font color="orange">orange '''load full'''</font> button, all models will be displayed. | |||
In order to view individual models, click on ''JSmol'' or ''Jmol_S'' (lower right corner below the molecule) to '''open Jmol's menu'''. There, use the '''All N models''' item (where N is the total number of models in the ensemble). For example, clicking on 1.1: 1 will display only model 1, and the menu will now say ''model 1/N''. You can also use Jmol's menu to change the rendering and coloring. | In order to view individual models, click on ''JSmol'' or ''Jmol_S'' (lower right corner below the molecule) to '''open Jmol's menu'''. There, use the '''All N models''' item (where N is the total number of models in the ensemble). For example, clicking on 1.1: 1 will display only model 1, and the menu will now say ''model 1/N''. You can also use Jmol's menu to change the rendering and coloring. | ||
[[FirstGlance in Jmol]] also shows model 1 by default, but you can click on ''View All Models''. | |||
===Animating NMR Ensembles=== | ===Animating NMR Ensembles=== | ||
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==See Also== | ==See Also== | ||
*[[X-ray crystallography]] | *[[X-ray crystallography]] | ||
*[[Empirical models]] | |||
==References and Websites== | ==References and Websites== | ||