Side-Chain Dynamics of the Trifluoroacetone Cysteine Derivative Characterized by19F NMR Relaxation and Molecular Dynamics Simulations

2019 ◽  
Vol 123 (17) ◽  
pp. 3665-3671 ◽  
Author(s):  
Suad Rashid ◽  
Brian L. Lee ◽  
Benjamin Wajda ◽  
Leo Spyracopoulos
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Nmr Relaxation ◽  
Side Chain ◽  
Chain Dynamics ◽  
Cysteine Derivative ◽  
Dynamics Simulations ◽  
Side Chain Dynamics

scholarly journals Analysis Of Side-chain Dynamics Of PhoB Dna Binding/transactivation Domain Using Molecular Dynamics Simulations

2009 ◽  
Vol 96 (3) ◽  
pp. 299a
Author(s):  
Tsutomu Yamane ◽  
Hideyasu Okamura ◽  
Yoshifumi Nishimura ◽  
Akinori Kidera ◽  
Mitsunori Ikeguchi
Keyword(s):  
Molecular Dynamics ◽  
Dna Binding ◽  
Molecular Dynamics Simulations ◽  
Side Chain ◽  
Transactivation Domain ◽  
Chain Dynamics ◽  
Dynamics Simulations ◽  
Side Chain Dynamics

Structure and Dynamics of Spherical and Rodlike Alkyl Ethoxylate Surfactant Micelles Investigated Using NMR Relaxation and Atomistic Molecular Dynamics Simulations

2019 ◽  
Author(s):  
Allison Edwards ◽  
Abdolreza Javidialesaadi ◽  
Katie Weigandt ◽  
George Stan ◽  
Charles Eads
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Nmr Relaxation ◽  
Cross Relaxation ◽  
Relaxation Rates ◽  
Surfactant Micelles ◽  
Cylindrical Micelles ◽  
Spherical Micelles ◽  
Dynamics Simulations ◽  
Relative Motions

We study molecular arrangements and dynamics in alkyl ethoxylate nonionic surfactant micelles by combining high field (600 and 700 MHz) NMR relaxation measurements with large-scale atomistic molecular dynamics simulations. For spherical micelles, but not for cylindrical micelles, cross relaxation rates are positive only for surfactant alkyl tail atoms connected to the hydrophilic head group. All cross relaxation rates are negative for cylindrical micelles. This effect is reproducible either by changing composition (ratios of the nonionic surfactants) or changing temperature of a single surfactant in order to change the micelle shape. We validate the micelle shape by SANS and use the results as a guide for our simulations. We calculate parameters that determine relaxation rates directly from simulated trajectories, without introducing specific functional forms. Results indicate that relative motions of nearby atoms are liquid-like, in agreement with 13C T1 measurements, though constrained by micelle morphology. Relative motions of distant atoms have slower components because the relative changes in distances and angles are smaller when the moving atoms are further apart. The slow, long-range motions appear to be responsible for the predominantly negative cross relaxation rates observed in NOESY spectra. The densities of atoms from positions 1 and 2 in the boundary region are lower in spherical micelles compared to cylindrical micelles. Correspondingly, motions in this region are less constrained by micelle morphology in the spherical compared to the cylindrical cases. The two effects of morphology lead to the unusual occurrence of positive cross relaxation involving positions 1 and 2 for spheres.

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