Talk:Protein dynamics: Difference between revisions
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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. [[User:TheTweaker|TheTweaker]] ([[User talk:TheTweaker|talk]]) 06:27, 25 August 2009 (UTC) |
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. [[User:TheTweaker|TheTweaker]] ([[User talk:TheTweaker|talk]]) 06:27, 25 August 2009 (UTC) |
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Others are [[anharmonic]], such as sidechains that jump between separate discrete energy minima, or [[rotamer]]s. [[Neutron scattering]] is a direct method to observe these types of protein motions on the nanosecond to picosecond timescale. It is important to note however that neutron measurements are ensemble in nature, reflecting all scattering from the sample. Accordingly, there can be difficulties in connecting specific spectral features to specific motions. |
Others are [[anharmonic]], such as sidechains that jump between separate discrete energy minima, or [[rotamer]]s. [[Neutron scattering]] is a direct method to observe these types of protein motions on the nanosecond to picosecond timescale. It is important to note however that neutron measurements are ensemble in nature, reflecting all scattering from the sample. Accordingly, there can be difficulties in connecting specific spectral features to specific motions. |
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Relaxations in proteins in these timescales can be classified into two groups, solvent slaved and non-slaved.<ref name="Fenimore_2002">{{ |
Relaxations in proteins in these timescales can be classified into two groups, solvent slaved and non-slaved.<ref name="Fenimore_2002">{{cite journal | vauthors = Fenimore PW, Frauenfelder H, McMahon BH, Parak FG | title = Slaving: solvent fluctuations dominate protein dynamics and functions | journal = Proc. Natl. Acad. Sci. U.S.A. | volume = 99 | issue = 25 | pages = 16047–51 | year = 2002 | pmid = 12444262 | pmc = 138562 | doi = 10.1073/pnas.212637899 }}</ref> 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.<ref name="Fenimore_2002"/> It is important to note that water molecules in the hydration shell of a protein are considerably slowed relative to water in the bulk.<ref name="pmid23062349">{{cite journal | vauthors = Nickels JD, O'Neill H, Hong L, Tyagi M, Ehlers G, Weiss KL, Zhang Q, Yi Z, Mamontov E, Smith JC, Sokolov AP | title = Dynamics of protein and its hydration water: neutron scattering studies on fully deuterated GFP | journal = Biophys. J. | volume = 103 | issue = 7 | pages = 1566–75 | year = 2012 | pmid = 23062349 | pmc = 3471459 | doi = 10.1016/j.bpj.2012.08.046 }}</ref> |
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Indirect evidence for dynamics is also sometimes obtained from structural methods such as [[NMR spectroscopy]] with methods like [[Random Coil Index]] or [[X-ray crystallography]] using uncertainties in high-resolution electron density maps. Of particular note when diffraction data is collected at room temperature instead of the traditional cryogenic temperature (typically near 100 K).<ref> |
Indirect evidence for dynamics is also sometimes obtained from structural methods such as [[NMR spectroscopy]] with methods like [[Random Coil Index]] or [[X-ray crystallography]] using uncertainties in high-resolution electron density maps. Of particular note when diffraction data is collected at room temperature instead of the traditional cryogenic temperature (typically near 100 K).<ref> |
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{{cite journal | vauthors = Fraser JS, van den Bedem H, Samelson AJ, Lang PT, Holton JM, Echols N, Alber T | title = Accessing protein conformational ensembles using room-temperature X-ray crystallography | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 108 | issue = 39 | pages = 16247–16252 | year = 2011 | date = Sep 2011 | pmid = 21918110 | doi = 10.1073/pnas.1111325108 }}</ref> [[User:Jon33dn|Jon33dn]] ([[User talk:Jon33dn|talk]]) 00:34, 22 February 2015 (UTC) |
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Latest revision as of 02:11, 25 October 2024
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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
[edit]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 anharmonic, such as sidechains that jump between separate discrete energy minima, or rotamers. Neutron scattering is a direct method to observe these types of protein motions on the nanosecond to picosecond timescale. It is important to note however that neutron measurements are ensemble in nature, reflecting all scattering from the sample. Accordingly, there can be difficulties in connecting specific spectral features to specific motions.
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 NMR spectroscopy with methods like Random Coil Index or X-ray crystallography using uncertainties in high-resolution electron density maps. Of particular note when diffraction data is collected at room temperature instead of the traditional cryogenic temperature (typically near 100 K).[3] Jon33dn (talk) 00:34, 22 February 2015 (UTC)
References
- ^ a b Fenimore PW, Frauenfelder H, McMahon BH, Parak FG (2002). "Slaving: solvent fluctuations dominate protein dynamics and functions". Proc. Natl. Acad. Sci. U.S.A. 99 (25): 16047–51. doi:10.1073/pnas.212637899. PMC 138562. PMID 12444262.
- ^ Nickels JD, O'Neill H, Hong L, Tyagi M, Ehlers G, Weiss KL, Zhang Q, Yi Z, Mamontov E, Smith JC, Sokolov AP (2012). "Dynamics of protein and its hydration water: neutron scattering studies on fully deuterated GFP". Biophys. J. 103 (7): 1566–75. doi:10.1016/j.bpj.2012.08.046. PMC 3471459. 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. doi:10.1073/pnas.1111325108. 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)