scholarly journals Fitting Side-Chain NMR Relaxation Data Using Molecular Simulations

2021 ◽  
Author(s):  
Felix Kümmerer ◽  
Simone Orioli ◽  
David Harding-Larsen ◽  
Falk Hoffmann ◽  
Yulian Gavrilov ◽  
...  
Keyword(s):  
Molecular Simulations ◽  
Nmr Relaxation ◽  
Side Chain ◽  
Relaxation Data

scholarly journals Fitting side-chain NMR relaxation data using molecular simulations

2020 ◽  
Author(s):  
Felix Kümmerer ◽  
Simone Orioli ◽  
David Harding-Larsen ◽  
Falk Hoffmann ◽  
Yulian Gavrilov ◽  
...  
Keyword(s):  
Nmr Relaxation ◽  
Side Chain ◽  
T4 Lysozyme ◽  
Molecular Models ◽  
Static Properties ◽  
Relaxation Data ◽  
Structure And Dynamics ◽  
Relaxation Measurements ◽  
Average Block ◽  
Dynamics Simulations

AbstractProteins display a wealth of dynamical motions that can be probed using both experiments and simulations. We present an approach to integrate side chain NMR relaxation measurements with molecular dynamics simulations to study the structure and dynamics of these motions. The approach, which we term ABSURDer (Average Block Selection Using Relaxation Data with Entropy Restraints) can be used to find a set of trajectories that are in agreement with relaxation measurements. We apply the method to deuterium relaxation measurements in T4 lysozyme, and show how it can be used to integrate the accuracy of the NMR measurements with the molecular models of protein dynamics afforded by the simulations. We show how fitting of dynamic quantities leads to improved agreement with static properties, and highlight areas needed for further improvements of the approach.

Quantitative interpretation of NMR relaxation data

1989 ◽  
Vol 84 (1) ◽  
pp. 134-152 ◽  
Author(s):  
Kenneth P Whittall ◽  
Alexander L MacKay
Keyword(s):  
Nmr Relaxation ◽  
Quantitative Interpretation ◽  
Relaxation Data

scholarly journals Upen2DTool: A Uniform PENalty Matlab tool for inversion of 2D NMR relaxation data

SoftwareX ◽  
2019 ◽  
Vol 10 ◽  
pp. 100302
Author(s):  
V. Bortolotti ◽  
L. Brizi ◽  
P. Fantazzini ◽  
G. Landi ◽  
F. Zama
Keyword(s):  
Nmr Relaxation ◽  
2D Nmr ◽  
Relaxation Data
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