scholarly journals Accurate Quadrupolar NMR Relaxation Rates of Aqueous Cations from Classical Molecular Dynamics

2014 ◽  
Vol 118 (46) ◽  
pp. 13252-13257 ◽  
Author(s):  
Antoine Carof ◽  
Mathieu Salanne ◽  
Thibault Charpentier ◽  
Benjamin Rotenberg
Keyword(s):  
Molecular Dynamics ◽  
Nmr Relaxation ◽  
Relaxation Rates ◽  
Classical Molecular 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.

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.

scholarly journals Predicting NMR Relaxation of Proteins from Molecular Dynamics Simulations with Accurate Methyl Rotation Barriers

2020 ◽  
Author(s):  
Falk Hoffmann ◽  
Frans Mulder ◽  
Lars V. Schäfer
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Force Fields ◽  
Nmr Relaxation ◽  
Md Simulations ◽  
Quantitative Agreement ◽  
Relaxation Rates ◽  
Protein Force Fields ◽  
Dynamics Simulations ◽  
Methyl Rotation

The internal dynamics of proteins occurring on time scales from picoseconds to nanoseconds can be sensitively probed by nuclear magnetic resonance (NMR) spin relaxation experiments, as well as by molecular dynamics (MD) simulations. This complementarity offers unique opportunities, provided that the two methods are compared at a suitable level. Recently, several groups have used MD simulations to compute the spectral density of backbone and side-chain molecular motions, and to predict NMR relaxation rates from these. Unfortunately, in the case of methyl groups in protein side-chains, inaccurate energy barriers to methyl rotation were responsible for a systematic discrepancy in the computed relaxation rates, as demonstrated for the AMBER ff99SB*-ILDN force field (and related parameter sets), impairing quantitative agreement between simulations and experiments. However, correspondence could be regained by emending the MD force field with accurate coupled cluster quantum chemical calculations. Spurred by this positive result, we tested whether this approach could be generally applicable, in spite of the fact that different MD force fields employ different water models. Improved methyl group rotation barriers for the CHARMM36 and AMBER ff15ipq protein force fields were derived, such that the NMR relaxation data obtained from the MD simulations now also display very good agreement with experiment. Results herein showcase the performance of present-day MD force fields, and manifest their refined ability to accurately describe internal protein dynamics.

scholarly journals Predicting NMR Relaxation of Proteins from Molecular Dynamics Simulations with Accurate Methyl Rotation Barriers

2019 ◽  
Author(s):  
Falk Hoffmann ◽  
Frans Mulder ◽  
Lars V. Schäfer
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Force Fields ◽  
Nmr Relaxation ◽  
Md Simulations ◽  
Quantitative Agreement ◽  
Relaxation Rates ◽  
Protein Force Fields ◽  
Dynamics Simulations ◽  
Methyl Rotation

The internal dynamics of proteins occurring on time scales from picoseconds to nanoseconds can be sensitively probed by nuclear magnetic resonance (NMR) spin relaxation experiments, as well as by molecular dynamics (MD) simulations. This complementarity offers unique opportunities, provided that the two methods are compared at a suitable level. Recently, several groups have used MD simulations to compute the spectral density of backbone and side-chain molecular motions, and to predict NMR relaxation rates from these. Unfortunately, in the case of methyl groups in protein side-chains, inaccurate energy barriers to methyl rotation were responsible for a systematic discrepancy in the computed relaxation rates, as demonstrated for the AMBER ff99SB*-ILDN force field (and related parameter sets), impairing quantitative agreement between simulations and experiments. However, correspondence could be regained by emending the MD force field with accurate coupled cluster quantum chemical calculations. Spurred by this positive result, we tested whether this approach could be generally applicable, in spite of the fact that different MD force fields employ different water models. Improved methyl group rotation barriers for the CHARMM36 and AMBER ff15ipq protein force fields were derived, such that the NMR relaxation data obtained from the MD simulations now also display very good agreement with experiment. Results herein showcase the performance of present-day MD force fields, and manifest their refined ability to accurately describe internal protein dynamics.

scholarly journals Predicting NMR Relaxation of Proteins from Molecular Dynamics Simulations with Accurate Methyl Rotation Barriers

2019 ◽  
Author(s):  
Falk Hoffmann ◽  
Frans Mulder ◽  
Lars V. Schäfer
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Force Fields ◽  
Nmr Relaxation ◽  
Md Simulations ◽  
Quantitative Agreement ◽  
Relaxation Rates ◽  
Protein Force Fields ◽  
Dynamics Simulations ◽  
Methyl Rotation

The internal dynamics of proteins occurring on time scales from picoseconds to nanoseconds can be sensitively probed by nuclear magnetic resonance (NMR) spin relaxation experiments, as well as by molecular dynamics (MD) simulations. This complementarity offers unique opportunities, provided that the two methods are compared at a suitable level. Recently, several groups have used MD simulations to compute the spectral density of backbone and side-chain molecular motions, and to predict NMR relaxation rates from these. Unfortunately, in the case of methyl groups in protein side-chains, inaccurate energy barriers to methyl rotation were responsible for a systematic discrepancy in the computed relaxation rates, as demonstrated for the AMBER ff99SB*-ILDN force field (and related parameter sets), impairing quantitative agreement between simulations and experiments. However, correspondence could be regained by emending the MD force field with accurate coupled cluster quantum chemical calculations. Spurred by this positive result, we tested whether this approach could be generally applicable, in spite of the fact that different MD force fields employ different water models. Improved methyl group rotation barriers for the CHARMM36 and AMBER ff15ipq protein force fields were derived, such that the NMR relaxation data obtained from the MD simulations now also display very good agreement with experiment. Results herein showcase the performance of present-day MD force fields, and manifest their refined ability to accurately describe internal protein dynamics.

Global and internal molecular dynamics of poly(acrylamide-co-allyl 2-acetamido-2-deoxy-D-glucopyranoside) glycopolymers from 13C NMR relaxation studies

1993 ◽  
Vol 71 (12) ◽  
pp. 1995-2006 ◽  
Author(s):  
René Roy ◽  
François D. Tropper ◽  
Antony J. Williams ◽  
Jean-Robert Brisson
Keyword(s):  
Molecular Dynamics ◽  
Spin Relaxation ◽  
Correlation Time ◽  
Relaxation Times ◽  
Nmr Relaxation ◽  
Relaxation Rates ◽  
Polymer Backbone ◽  
Model Free ◽  
Internal Motions ◽  
Poly Acrylamide

13C spin-lattice and spin–spin relaxation times and nuclear Overhauser enhancements have been used to examine the molecular dynamics of the α- (1) and β- (2) anomeric forms of poly(acrylamide-co-allyl 2-acetamido-2-deoxy-D-glucopyranoside) glycopolymers. The timescale of motions and the spatial restriction of these motions were determined by using various forms of the "model-free" approach. It is shown that the motions of the C—H vectors of the polymer backbone may be described by a scaled Lorentzian spectral density function, giving rise to an effective correlation time for overall tumbling. The temperature dependence of this correlation time suggests that the overall motion is dependent on viscosity. The overall motion of the polymer molecules is shown to be anisotropic in nature by including the spin–spin relaxation data in the analysis. The N-acetyl methyl and sugar hydroxymethyl (C6) groups exhibit internal motions. The activation energies associated with these internal motions are derived. The difference in relaxation rates between the α and β anomeric forms, though small, suggests that the motions of the sugar ring may be different for the two systems. This conclusion is supported by potential energy contour map calculations, which indicate that the β anomer (2) has almost twice the conformational flexibility of the α anomer (1).

scholarly journals Predicting NMR Relaxation of Proteins from Molecular Dynamics Simulations with Accurate Methyl Rotation Barriers

2019 ◽  
Author(s):  
Falk Hoffmann ◽  
Frans Mulder ◽  
Lars V. Schäfer
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Force Fields ◽  
Nmr Relaxation ◽  
Md Simulations ◽  
Quantitative Agreement ◽  
Relaxation Rates ◽  
Protein Force Fields ◽  
Dynamics Simulations ◽  
Methyl Rotation

The internal dynamics of proteins occurring on time scales from picoseconds to nanoseconds can be sensitively probed by nuclear magnetic resonance (NMR) spin relaxation experiments, as well as by molecular dynamics (MD) simulations. This complementarity offers unique opportunities, provided that the two methods are compared at a suitable level. Recently, several groups have used MD simulations to compute the spectral density of backbone and side-chain molecular motions, and to predict NMR relaxation rates from these. Unfortunately, in the case of methyl groups in protein side-chains, inaccurate energy barriers to methyl rotation were responsible for a systematic discrepancy in the computed relaxation rates, as demonstrated for the AMBER ff99SB*-ILDN force field (and related parameter sets), impairing quantitative agreement between simulations and experiments. However, correspondence could be regained by emending the MD force field with accurate coupled cluster quantum chemical calculations. Spurred by this positive result, we tested whether this approach could be generally applicable, in spite of the fact that different MD force fields employ different water models. Improved methyl group rotation barriers for the CHARMM36 and AMBER ff15ipq protein force fields were derived, such that the NMR relaxation data obtained from the MD simulations now also display very good agreement with experiment. Results herein showcase the performance of present-day MD force fields, and manifest their refined ability to accurately describe internal protein dynamics.

scholarly journals Predicting NMR Relaxation of Proteins from Molecular Dynamics Simulations with Accurate Methyl Rotation Barriers

2020 ◽  
Author(s):  
Falk Hoffmann ◽  
Frans Mulder ◽  
Lars V. Schäfer
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Force Fields ◽  
Nmr Relaxation ◽  
Md Simulations ◽  
Quantitative Agreement ◽  
Relaxation Rates ◽  
Protein Force Fields ◽  
Dynamics Simulations ◽  
Methyl Rotation

The internal dynamics of proteins occurring on time scales from picoseconds to nanoseconds can be sensitively probed by nuclear magnetic resonance (NMR) spin relaxation experiments, as well as by molecular dynamics (MD) simulations. This complementarity offers unique opportunities, provided that the two methods are compared at a suitable level. Recently, several groups have used MD simulations to compute the spectral density of backbone and side-chain molecular motions, and to predict NMR relaxation rates from these. Unfortunately, in the case of methyl groups in protein side-chains, inaccurate energy barriers to methyl rotation were responsible for a systematic discrepancy in the computed relaxation rates, as demonstrated for the AMBER ff99SB*-ILDN force field (and related parameter sets), impairing quantitative agreement between simulations and experiments. However, correspondence could be regained by emending the MD force field with accurate coupled cluster quantum chemical calculations. Spurred by this positive result, we tested whether this approach could be generally applicable, in spite of the fact that different MD force fields employ different water models. Improved methyl group rotation barriers for the CHARMM36 and AMBER ff15ipq protein force fields were derived, such that the NMR relaxation data obtained from the MD simulations now also display very good agreement with experiment. Results herein showcase the performance of present-day MD force fields, and manifest their refined ability to accurately describe internal protein dynamics.

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