Talk:Protein dynamics
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This topic really needs to have it's own page. The topic of protein dynamics is really quite a bit different (and broader) than the material discussed on the page for protein domain motion. TheTweaker (talk) 06:27, 25 August 2009 (UTC)
Suggestion to Local flexibility: atoms and residues
Portions of protein structures often deviate from the equilibrium state. Some such excursions are harmonic, such as stochastic fluctuations of chemical bonds and bond angles. Others are
Relaxations in proteins in these timescales can be classified into two groups, solvent slaved and non-slaved.[1] A example of non-slaved dynamics might me the rotation of methyl groups, while solvent slaved motions include hydrogen bond fluctuations and peptide backbone relaxations. It is proposed that the solvent is responsible for the activation enthalpy, whereas the protein and the hydration shell control the activation entropy through the energy landscape.[1] It is important to note that water molecules in the hydration shell of a protein are considerably slowed relative to water in the bulk.[2]
Indirect evidence for dynamics is also sometimes obtained from structural methods such as
References
- ^ PMID 12444262.
- PMID 23062349.
- ^
Fraser JS, van den Bedem H, Samelson AJ, Lang PT, Holton JM, Echols N, Alber T (Sep 2011). "Accessing protein conformational ensembles using room-temperature X-ray crystallography". Proceedings of the National Academy of Sciences of the United States of America. 108 (39): 16247–16252. PMID 21918110.)
{{cite journal}}: CS1 maint: date and year (link
- Thanks for suggesting this; I agree that this article could use some work. I was shocked to see it was only written in 2013! This looks like a good start to me, if not quite how I'd write it (coming from an NMR/simulation background). To my mind NMR is better established than neutron scattering in studying protein dynamics by relaxation (though I notice we have no article on the Lipari-Szabo formalism usually used to interpret these data on the ps-ns timescale), and it's usually presented that way in textbooks. So I'd prefer to list NMR and crystallography before neutron scattering. The second paragraph could be simplified - target audience is probably undergrads clicking through from a more basic article - and in particular I'd suggest explaining what "slaved" means, or using a more intuitive term like "coupled", as it's a bit of a term of art in this context. Other than that I think this is a good improvement.
- I also edited the existing article text a bit to be clearer about how NMR yields dynamics information (RCI somewhat conflates disorder with dynamics). Opabinia regalis (talk) 04:55, 23 February 2015 (UTC)