Editing Protein structure (section)

==Protein structure determination==
[[File:Protein structure examples.png|thumb|left|Examples of protein structures from the [[Protein Data Bank|PDB]] ]]
[[File:Rate of Protein Structure Determination-2014.png|thumb|400px|Rate of Protein Structure Determination by Method and Year]]
Around 90% of the protein structures available in the [[Protein Data Bank]] have been determined by [[X-ray crystallography]].<ref>{{cite journal | vauthors = Kendrew JC, Bodo G, Dintzis HM, Parrish RG, Wyckoff H, Phillips DC | title = A three-dimensional model of the myoglobin molecule obtained by x-ray analysis | journal = Nature | volume = 181 | issue = 4610 | pages = 662–666 | date = March 1958 | pmid = 13517261 | doi = 10.1038/181662a0 | s2cid = 4162786 | bibcode = 1958Natur.181..662K }}</ref> This method allows one to measure the three-dimensional (3-D) density distribution of [[electron]]s in the protein, in the [[crystallized]] state, and thereby [[infer]] the 3-D coordinates of all the [[atom]]s to be determined to a certain resolution. Roughly 7% of the known protein structures have been obtained by [[protein NMR|nuclear magnetic resonance]] (NMR) techniques.<ref>{{Cite web |date=2022-10-01 |title=PDB Statistics |url=https://www.rcsb.org/stats/summary}}</ref> For larger protein complexes, [[cryo-electron microscopy]] can determine protein structures. The resolution is typically lower than that of X-ray crystallography, or NMR, but the maximum resolution is steadily increasing. This technique is still a particularly valuable for very large protein complexes such as [[virus coat protein]]s and [[amyloid]] fibers.

General secondary structure composition can be determined via [[circular dichroism]]. [[Vibrational spectroscopy]] can also be used to characterize the conformation of peptides, polypeptides, and proteins.<ref name="pmid3541539">{{cite book | vauthors = Krimm S, Bandekar J | title = Advances in Protein Chemistry Volume 38 | chapter = Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins | journal = Adv. Protein Chem. | volume = 38 | pages = 181–364 | date = 1986 | pmid = 3541539 | doi = 10.1016/S0065-3233(08)60528-8|isbn = 9780120342389}}</ref> [[Two-dimensional infrared spectroscopy]] has become a valuable method to investigate the structures of flexible peptides and proteins that cannot be studied with other methods.<ref>{{cite journal | vauthors = Lessing J, Roy S, Reppert M, Baer M, Marx D, Jansen TL, Knoester J, Tokmakoff A | display-authors = 6 | title = Identifying residual structure in intrinsically disordered systems: a 2D IR spectroscopic study of the GVGXPGVG peptide | journal = Journal of the American Chemical Society | volume = 134 | issue = 11 | pages = 5032–5035 | date = March 2012 | pmid = 22356513 | doi = 10.1021/ja2114135 | hdl-access = free | hdl = 11370/ff19c09b-088a-48f0-afee-2111a9b19252 | url = https://pure.rug.nl/ws/files/6776580/2012JAmChemSocLessing.pdf }}<!--https://pure.rug.nl/ws/files/6776580/2012JAmChemSocLessing.pdf--></ref><ref>{{cite journal | vauthors = Jansen TL, Knoester J | title = Two-dimensional infrared population transfer spectroscopy for enhancing structural markers of proteins | journal = Biophysical Journal | volume = 94 | issue = 5 | pages = 1818–1825 | date = March 2008 | pmid = 17981904 | pmc = 2242754 | doi = 10.1529/biophysj.107.118851 | bibcode = 2008BpJ....94.1818J }}</ref> A more qualitative picture of protein structure is often obtained by [[proteolysis]], which is also useful to screen for more crystallizable protein samples. Novel implementations of this approach, including [[fast parallel proteolysis (FASTpp)]], can probe the structured fraction and its stability without the need for purification.<ref name="pmid23056252">{{cite journal | vauthors = Minde DP, Maurice MM, Rüdiger SG | title = Determining biophysical protein stability in lysates by a fast proteolysis assay, FASTpp | journal = PLOS ONE | volume = 7 | issue = 10 | pages = e46147 | date = 2012 | pmid = 23056252 | pmc = 3463568 | doi = 10.1371/journal.pone.0046147 | doi-access = free | bibcode = 2012PLoSO...746147M }}</ref> Once a protein's structure has been experimentally determined, further detailed studies can be done computationally, using [[Molecular dynamics|molecular dynamic]] simulations of that structure.<ref name="pmid28637405">{{cite journal | vauthors = Kumari I, Sandhu P, Ahmed M, Akhter Y | title = Molecular Dynamics Simulations, Challenges and Opportunities: A Biologist's Prospective | journal = Current Protein & Peptide Science | volume = 18 | issue = 11 | pages = 1163–1179 | date = August 2017 | pmid = 28637405 | doi = 10.2174/1389203718666170622074741 }}</ref>