scholarly journals On the Use of Side‐Chain NMR Relaxation Data to Derive Structural and Dynamical Information on Proteins: A Case Study Using Hen Lysozyme

ChemBioChem ◽  
2020 ◽  
Author(s):  
Lorna J. Smith ◽  
Wilfred F. Gunsteren ◽  
Niels Hansen
Keyword(s):  
Nmr Relaxation ◽  
Side Chain ◽  
Relaxation Data ◽  
Dynamical Information

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.

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 New Scheme for Extracting Molecular Dynamics from Spectra: Case Study on Vibrationally Highly Excited Acetylene

1994 ◽  
Vol 14 (1-3) ◽  
pp. 183-190 ◽  
Author(s):  
Kaoru Yamanouchi ◽  
Jun Miyawaki ◽  
Soji Tsuchiya ◽  
David M. Jonas ◽  
Robert W. Field
Keyword(s):  
Molecular Dynamics ◽  
Statistical Analysis ◽  
Spectroscopic Analysis ◽  
Polyatomic Molecules ◽  
Complex Spectrum ◽  
Hierarchical Analysis ◽  
Efficient Procedure ◽  
Dispersed Fluorescence ◽  
Dynamical Information

Three types of analyses: generalized conventional spectroscopic analysis, statistical analysis, and hierarchical analysis, by which we aim to extract dynamical information from the complex spectrum of small polyatomic molecules are reviewed by referring to recent studies on vibrationally highly excited acetylene. A convolution analysis, one type of hierarchical analysis, is performed on the dispersed fluorescence spectrum of acetylene to demonstrate its practical applicability. Based on previous studies, as well as on the convolution analysis, a systematic and efficient procedure to treat such complex spectra is discussed.

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
Sign in / Sign up

Export Citation Format

Share Document