Increased Rigidity of Eglin c at Acidic pH:  Evidence from NMR Spin Relaxation and MD Simulations†

Biochemistry ◽  
2003 ◽  
Vol 42 (47) ◽  
pp. 13856-13868 ◽  
Author(s):  
Hao Hu ◽  
Michael W. Clarkson ◽  
Jan Hermans ◽  
Andrew L. Lee
Keyword(s):  
Spin Relaxation ◽  
Md Simulations ◽  
Acidic Ph ◽  
Eglin C ◽  
Nmr Spin Relaxation

scholarly journals Effects of Hydrogen Bonding on the Rotational Dynamics of Water-Like Molecules in Liquids: Insights from Molecular Dynamics Simulations

2020 ◽  
Vol 73 (8) ◽  
pp. 734
Author(s):  
W. A. Monika Madhavi ◽  
Samantha Weerasinghe ◽  
Konstantin I. Momot
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Hydrogen Sulfide ◽  
Spin Relaxation ◽  
Rotational Diffusion ◽  
Molecular Geometry ◽  
Md Simulations ◽  
Water Molecules ◽  
Molecular Reorientation ◽  
Nmr Spin Relaxation

Rotational motion of molecules plays an important role in determining NMR spin relaxation properties of liquids. The textbook theory of NMR spin relaxation predominantly uses the assumption that the reorientational dynamics of molecules is described by a continuous time rotational diffusion random walk with a single rotational diffusion coefficient. Previously we and others have shown that reorientation of water molecules on the timescales of picoseconds is not consistent with the Debye rotational-diffusion model. In particular, multiple timescales of molecular reorientation were observed in liquid water. This was attributed to the hydrogen bonding network in water and the consequent presence of collective rearrangements of the molecular network. In order to better understand the origins of the complex reorientational behaviour of water molecules, we carried out molecular dynamics (MD) simulations of a liquid that has a similar molecular geometry to water but does not form hydrogen bonds: hydrogen sulfide. These simulations were carried out at T=208K and p=1 atm (~5K below the boiling point). Ensemble-averaged Legendre polynomial functions of hydrogen sulfide exhibited a Gaussian decay on the sub-picosecond timescale but, unlike water, did not exhibit oscillatory behaviour. We attribute these differences to hydrogen sulfide’s absence of hydrogen bonding.

scholarly journals Ab-Initio Prediction of NMR Spin-Relaxation Parameters from MD Simulations

2020 ◽  
Vol 118 (3) ◽  
pp. 520a
Author(s):  
Po-Chia Chen ◽  
Maggy Hologne ◽  
Olivier Walker ◽  
Janosch Hennig
Keyword(s):  
Ab Initio ◽  
Spin Relaxation ◽  
Md Simulations ◽  
Relaxation Parameters ◽  
Ab Initio Prediction ◽  
Nmr Spin Relaxation

scholarly journals Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation

2008 ◽  
Vol 71 (2) ◽  
pp. 684-694 ◽  
Author(s):  
Nikola Trbovic ◽  
Byungchan Kim ◽  
Richard A. Friesner ◽  
Arthur G. Palmer
Keyword(s):  
Structural Analysis ◽  
Protein Dynamics ◽  
Spin Relaxation ◽  
Md Simulations ◽  
Nmr Spin Relaxation

Active site dynamics in NADH oxidase from Thermus thermophilus studied by NMR spin relaxation

2011 ◽  
Vol 51 (1-2) ◽  
pp. 71-82 ◽  
Author(s):  
Teresa Miletti ◽  
Patrick J. Farber ◽  
Anthony Mittermaier
Keyword(s):  
Spin Relaxation ◽  
Active Site ◽  
Nadh Oxidase ◽  
Thermus Thermophilus ◽  
Nmr Spin Relaxation

Broadband Dynamics of Ubiquitin by Anionic and Cationic Nanoparticle Assisted NMR Spin Relaxation

2020 ◽  
Vol 133 (1) ◽  
pp. 150-154
Author(s):  
Stacey Wardenfelt ◽  
Xinyao Xiang ◽  
Mouzhe Xie ◽  
Lei Yu ◽  
Lei Bruschweiler‐Li ◽  
...  
Keyword(s):  
Spin Relaxation ◽  
Nmr Spin Relaxation

The eigenmode perspective of NMR spin relaxation in proteins

2013 ◽  
Vol 139 (22) ◽  
pp. 225104 ◽  
Author(s):  
Yury E. Shapiro ◽  
Eva Meirovitch
Keyword(s):  
Spin Relaxation ◽  
Nmr Spin Relaxation
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