Related ArticlesLocalized and collective motions in HET-s(218-289) fibrils from combined NMR relaxation and MD simulation.
Angew Chem Int Ed Engl. 2019 May 09;:
Authors: Smith AA, Ernst M, Riniker S, Meier BH
Abstract
Nuclear magnetic resonance (NMR) relaxation data and molecular dynamics (MD) simulations are combined to characterize the dynamics of the fungal prion HET-s(218-289) in its amyloid form. NMR data is analyzed with the dynamics detector method, which yields timescale-specific information. An analogous analysis is performed on MD trajectories. Because we can verify specific MD predictions as agreeing with the NMR data, we use MD for further interpretation of NMR results: we derive, for the different timescales, cross-correlation coefficients to quantify the correlation of the motion between different residues. Short timescales are the result of very local motions, while longer timescales are found for longer-range correlated motion. Similar trends on ns- and ?s-timescales suggest that ?s motion in fibrils is the result of motion correlated over many fibril layers.
PMID: 31070275 [PubMed - as supplied by publisher]
A combined EPR and MD simulation study of a nitroxyl spin label with restricted internal mobility sensitive to protein dynamics
From The DNP-NMR Blog:
A combined EPR and MD simulation study of a nitroxyl spin label with restricted internal mobility sensitive to protein dynamics
p.p1 {margin: 0.0px 0.0px 0.0px 36.0px; text-indent: -36.0px; font: 12.0px Helvetica}
Oganesyan, V.S., et al., A combined EPR and MD simulation study of a nitroxyl spin label with restricted internal mobility sensitive to protein dynamics. J. Magn. Reson., 2017. 274: p. 24-35.
www.sciencedirect.com/science/article/pii/S1090780716302270
nmrlearner
News from NMR blogs
0
02-20-2017 03:39 PM
[NMR paper] A combined EPR and MD simulation study of a nitroxyl spin label with restricted internal mobility sensitive to protein dynamics
A combined EPR and MD simulation study of a nitroxyl spin label with restricted internal mobility sensitive to protein dynamics
Publication date: January 2017
Source:Journal of Magnetic Resonance, Volume 274</br>
Author(s): Vasily S. Oganesyan, Fatima Chami, Gaye F. White, Andrew J. Thomson</br>
EPR studies combined with fully atomistic Molecular Dynamics (MD) simulations and an MD-EPR simulation method provide evidence for intrinsic low rotameric mobility of a nitroxyl spin label, Rn, compared to the more widely employed label MTSL (R1). Both experimental...
nmrlearner
Journal club
0
11-19-2016 08:35 PM
[NMR paper] Pressure-induced structural transition of mature HIV-1 Protease from a combined NMR/MD simulation approach.
Pressure-induced structural transition of mature HIV-1 Protease from a combined NMR/MD simulation approach.
Related Articles Pressure-induced structural transition of mature HIV-1 Protease from a combined NMR/MD simulation approach.
Proteins. 2015 Sep 18;
Authors: Roche J, Louis JM, Bax A, Best RB
Abstract
We investigate the pressure-induced structural changes in the mature human immunodeficiency virus type 1 protease dimer (HIV-1 PR), using residual dipolar coupling (RDC) measurements in a weakly oriented solution. (1) DNH RDCs...
nmrlearner
Journal club
0
09-20-2015 12:56 PM
[NMR paper] NMR evidence for slow collective motions in cyanometmyoglobin.
NMR evidence for slow collective motions in cyanometmyoglobin.
Related Articles NMR evidence for slow collective motions in cyanometmyoglobin.
Nat Struct Biol. 1997 Apr;4(4):292-7
Authors: Tolman JR, Flanagan JM, Kennedy MA, Prestegard JH
Residual dipolar couplings observed in NMR spectra at very high magnetic fields have been measured to a high degree of accuracy for the paramagnetic protein cyanometmyoglobin. Deviations of these measurements from predictions based on available crystallographic and solution structures are largely systematic...
nmrlearner
Journal club
0
08-22-2010 03:31 PM
[NMR paper] NMR evidence for slow collective motions in cyanometmyoglobin.
NMR evidence for slow collective motions in cyanometmyoglobin.
Related Articles NMR evidence for slow collective motions in cyanometmyoglobin.
Nat Struct Biol. 1997 Apr;4(4):292-7
Authors: Tolman JR, Flanagan JM, Kennedy MA, Prestegard JH
Residual dipolar couplings observed in NMR spectra at very high magnetic fields have been measured to a high degree of accuracy for the paramagnetic protein cyanometmyoglobin. Deviations of these measurements from predictions based on available crystallographic and solution structures are largely systematic...
nmrlearner
Journal club
0
08-22-2010 03:03 PM
[NMR paper] Collective NMR relaxation model applied to protein dynamics.
Collective NMR relaxation model applied to protein dynamics.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/-PMGifs-Toolbar-topub.gif Related Articles Collective NMR relaxation model applied to protein dynamics.
Phys Rev Lett. 1994 Feb 7;72(6):940-943
Authors: Brüschweiler R, Case DA
nmrlearner
Journal club
0
08-22-2010 03:33 AM
[NMR paper] Collective NMR relaxation model applied to protein dynamics.
Collective NMR relaxation model applied to protein dynamics.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/-PMGifs-Toolbar-topub.gif Related Articles Collective NMR relaxation model applied to protein dynamics.
Phys Rev Lett. 1994 Feb 7;72(6):940-943
Authors: Brüschweiler R, Case DA
Localized and collective motions in HET-s(218-289) fibrils from combined NMR relaxation and MD simulation.
Linear Mode
