Hydrogen in macromolecular models: Difference between revisions
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[[Image:Protein Hydrogens in electron Density 1yk4 Y13.jpg|thumb|left|320px|Experimental difference density peaks for hydrogen atoms at 0.69A resolution: [[1yk4]] Tyr 13]] | [[Image:Protein Hydrogens in electron Density 1yk4 Y13.jpg|thumb|left|320px|Experimental difference density peaks for hydrogen atoms at 0.69A resolution: [[1yk4]] Tyr 13]] | ||
Approximately 50% of the atoms in a protein are hydrogen. However, hydrogen atoms are absent from most molecular models. Most crystals do not have sufficient resolution (1.0 Ångstroms or better is needed) to determine the positions of hydrogen atoms directly. It is easy to add hydrogens to macromolecular models, but the results are only as good as the molecular models themselves. | Approximately 50% of the atoms in a protein are hydrogen. However, hydrogen atoms are absent from most molecular models. Most crystals do not have sufficient [[resolution]] (1.0 Ångstroms or better is needed) to determine the positions of hydrogen atoms directly. It is easy to add hydrogens to macromolecular models, but the results are only as good as the molecular models themselves. | ||
==Absence of Hydrogen Atoms in Most Macromolecular Models== | ==Absence of Hydrogen Atoms in Most Macromolecular Models== | ||
Hydrogen atoms are absent from most molecular models in Proteopedia, which come mostly from the [[Protein Data Bank]]. This is because most macromolecular crystals do not have sufficient [[resolution]] to determine the positions of hydrogen atoms. However it is easy to [[#Adding Hydrogens|add hydrogen atoms]], and in fact it is a good idea, because it [[#Model Validation??|helps to correct and validate]] the molecular model. | Hydrogen atoms are absent from most molecular models in Proteopedia, which come mostly from the [[Protein Data Bank]]. 83% of models in the [[Protein Data Bank]] lack hydrogen atoms (in May, 2024). This is because most macromolecular crystals do not have sufficient [[resolution]] to determine the positions of hydrogen atoms. However it is easy to [[#Adding Hydrogens|add hydrogen atoms]], and in fact it is a good idea, because it [[#Model Validation??|helps to correct and validate]] the molecular model. | ||
Although their positions are not well defined empirically in the electron density maps from typical macromolecular crystals, sometimes [[#Adding Hydrogens|hydrogens are added]] to X-ray crystallographic models before they are deposited in the Protein Data Bank. This is the choice of the authors of the [[PDB file]]. Hydrogens are usually present in PDB files resulting from [[NMR]] analysis, and usually present in [[theoretical models]]. | Although their positions are not well defined empirically in the electron density maps from typical macromolecular crystals, sometimes [[#Adding Hydrogens|hydrogens are added]] to X-ray crystallographic models before they are deposited in the Protein Data Bank. This is the choice of the authors of the [[PDB file]]. Hydrogens are usually present in PDB files resulting from [[NMR]] analysis, and usually present in [[theoretical models]]. | ||
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*'''Example: Some hydrogens from theory''': The X-ray file [[1lfa]] (1.8 A resolution; an integrin adhesion protein domain) contains 312 waters each with 2 hydrogens (so 624 water hydrogens), plus 639 protein hydrogens for 2,939 non-hydrogen protein atoms, which account for only about 22% (639/~2,939) of the hydrogens actually present in this protein. The protein hydrogens in the model are the polar hydrogens: one hydrogen on each main chain nitrogen (three hydrogens/amino terminal nitrogen), and hydrogens on sidechain oxygens or nitrogens in Ser, Thr, Tyr, Lys, Arg, His, Asn, and Gln. None of the hydrogens covalently bonded to carbons are present. The hydrogens which are present are required for the molecular dynamics stages of refinement of the X-ray model in the popular crystallographic refinement program X-PLOR; some authors strip them out before submitting a [[PDB file]] and others leave them in. The [[Protein Data Bank]] accepts X-ray models either way, according to the preference of the depositor. | *'''Example: Some hydrogens from theory''': The X-ray file [[1lfa]] (1.8 A resolution; an integrin adhesion protein domain) contains 312 waters each with 2 hydrogens (so 624 water hydrogens), plus 639 protein hydrogens for 2,939 non-hydrogen protein atoms, which account for only about 22% (639/~2,939) of the hydrogens actually present in this protein. The protein hydrogens in the model are the polar hydrogens: one hydrogen on each main chain nitrogen (three hydrogens/amino terminal nitrogen), and hydrogens on sidechain oxygens or nitrogens in Ser, Thr, Tyr, Lys, Arg, His, Asn, and Gln. None of the hydrogens covalently bonded to carbons are present. The hydrogens which are present are required for the molecular dynamics stages of refinement of the X-ray model in the popular crystallographic refinement program X-PLOR; some authors strip them out before submitting a [[PDB file]] and others leave them in. The [[Protein Data Bank]] accepts X-ray models either way, according to the preference of the depositor. | ||
*'''Example: All hydrogens from theory''': | *'''Example: All hydrogens from theory''': [[4gl2]], a 2013 [[X-ray crystallographic]] model of a protein-RNA complex, has all hydrogens, yet at its [[resolution]] of 3.56 Å, no hydrogens could have been resolved in the electron density map. | ||
===Hydrogens in NMR Models=== | ===Hydrogens in NMR Models=== | ||