Abstract Temperature-dependence of protein dynamics can provide information on details of the free energy landscape by probing the characteristics of the potential responsible for the fluctuations. We have investigated the temperature-dependence of picosecond to nanosecond backbone dynamics at carbonyl carbon sites in chicken villin headpiece subdomain protein using a combination of three NMR relaxation rates: 13Câ?² longitudinal rate, and two cross-correlated rates involving dipolar and chemical shift anisotropy (CSA) relaxation mechanisms, 13Câ?²/13Câ?²-13Cα CSA/dipolar and 13Câ?²/13Câ?²â??15N CSA/dipolar. Order parameters have been extracted using the Lipari-Szabo model-free approach assuming a separation of the time scales of internal and molecular motions in the 2â??16°C temperature range. There is a gradual deviation from this assumption from lower to higher temperatures, such that above 16°C the separation of the time scales is inconsistent with the experimental data and, thus, the Lipari-Szabo formalism can not be applied. While there are variations among the residues, on the average the order parameters indicate a markedly steeper temperature dependence at backbone carbonyl carbons compared to that probed at amide nitrogens in an earlier study. This strongly advocates for probing sites other than amide nitrogen for accurate characterization of the potential and other thermodynamics characteristics of protein backbone.
Content Type Journal Article
Pages 1-9
DOI 10.1007/s10858-011-9500-x
Authors
Liliya Vugmeyster, Department of Chemistry and Environment and Natural Resources Institute, University of Alaska at Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA
Dmitry Ostrovsky, Department of Mathematical Sciences, University of Alaska at Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA
[Question from NMRWiki Q&A forum] bulk water relaxation dependence on temperature
bulk water relaxation dependence on temperature
Is liquid water's relaxation rate strongly dependent on temperature, and does anyone have a link to a good online article with the dependency equation?Thanks!
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[NMR paper] Temperature dependence of protein backbone motion from carbonyl 13C and amide 15N NMR
Temperature dependence of protein backbone motion from carbonyl 13C and amide 15N NMR relaxation.
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The NMR spin-lattice relaxation rate (R1) and the rotating-frame spin-lattice relaxation rate (R1rho) of amide 15N and carbonyl 13C (13C') of the uniformly 13C- and 15N-labeled ubiquitin were measured at different temperatures and field strengths to investigate the...
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[NMR paper] Temperature dependence of NMR order parameters and protein dynamics.
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The helical subdomain, HP36, of the F-actin-binding headpiece domain of chicken villin, is the smallest naturally occurring polypeptide that folds to a thermostable compact structure. Unconstrained molecular dynamics simulations and constrained molecular dynamics simulations using umbrella sampling are used to study the...
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[NMR paper] Dynamic NMR line-shape analysis demonstrates that the villin headpiece subdomain fold
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There is considerable interest in small proteins that fold very rapidly. These proteins have become attractive targets for both theoretical and computational studies. The...
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11-24-2010 09:01 PM
Backbone Amide Dynamics Studies of Apo-L75F-TrpR, a Temperature-Sensitive Mutant of t
Backbone Amide Dynamics Studies of Apo-L75F-TrpR, a Temperature-Sensitive Mutant of the Tryptophan Repressor Protein (TrpR): Comparison with the 15N NMR Relaxation Profiles of Wild-Type and A77V Mutant Apo-TrpR Repressors
http://pubs.acs.org//appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi100508u/aop/images/medium/bi-2010-00508u_0005.gifBiochemistry, Volume 0, Issue 0, Articles ASAP (As Soon As Publishable).
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08-31-2010 10:50 PM
Backbone amide dynamics studies of apo-L75F-TrpR, a temperature sensitive mutant of t
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Biochemistry. 2010 Aug 18;
Authors: Goel A, Tripet BP, Tyler RC, Nebert LD, Copie V
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08-21-2010 01:02 AM
Comparison of fast backbone dynamics at amide nitrogen and carbonyl sites in dematin
Abstract We perform a detailed comparison of fast backbone dynamics probed at amide nitrogen versus carbonyl carbon sites for dematin headpiece C-terminal domain (DHP) and its S74E mutant (DHPS74E). Carbonyl dynamics is probed via auto-correlated longitudinal rates and transverse Câ?²/Câ?²-Cα CSA/dipolar and Câ?²/Câ?²â??N CSA/dipolar cross-correlated rates, while 15N data are taken from a previous study. Resulting values of effective order parameters and internal correlation times support the conclusion that Câ?² relaxation reports on a different subset of fast motions compared to those...
Temperature dependence of fast carbonyl backbone dynamics in chicken villin headpiece subdomain
Linear Mode
