A method to construct the dynamic landscape of a bio-membrane with experiment and simulation

AbstractBiomolecular function is based on a complex hierarchy of molecular motions. While biophysical methods can reveal details of specific motions, a concept for the comprehensive description of molecular dynamics over a wide range of correlation times has been unattainable. Here, we report an approach to construct the dynamic landscape of biomolecules, which describes the aggregate influence of multiple motions acting on various timescales and on multiple positions in the molecule. To this end, we use 13C NMR relaxation and molecular dynamics simulation data for the characterization of fully hydrated palmitoyl-oleoyl-phosphatidylcholine bilayers. We combine dynamics detector methodology with a new frame analysis of motion that yields site-specific amplitudes of motion, separated both by type and timescale of motion. In this study, we show that this separation allows the detailed description of the dynamic landscape, which yields vast differences in motional amplitudes and correlation times depending on molecular position.

Download Full-text

A method to construct the dynamic landscape of a bio-membrane with experiment and simulation

10.21203/rs.3.rs-645823/v1 ◽

2021 ◽

Author(s):

Albert Smith ◽

Alexander Vogel ◽

Oskar Engberg ◽

Peter Hildebrand ◽

Daniel Huster

Keyword(s):

Molecular Dynamics ◽

Lipid Membranes ◽

Nmr Relaxation ◽

Dynamics Simulation ◽

Molecular Systems ◽

Biological Interface ◽

Novel Approach ◽

Wide Range ◽

Dynamic Landscape

Abstract Biomolecular function is based on a complex hierarchy of molecular motions. While biophysical methods can reveal details of specific motions, a concept for the comprehensive description of molecular dynamics over a wide range of correlation times has been unattainable. Here, we report a novel approach to construct the dynamic landscape of biomolecules, which describes the aggregate influence of multiple motions acting on various timescales and on multiple positions in the molecule. To this end, we use NMR relaxation and molecular dynamics simulation data for the characterization of lipid membranes, the most important biological interface. We develop a dynamics detector method that yields site-specific amplitudes, separated both by type and timescale of motion. This separation allows the detailed description of the dynamic landscape, which reveals vast differences in motion depending on molecular position. More generally, the method is applicable to a broad range of molecular systems, and can be adapted to other timescale-sensitive techniques.

Download Full-text

Characterization of the internal motions of Escherichia coli ribonuclease HI by a combination of 15N-NMR relaxation analysis and molecular dynamics simulation: examination of dynamic models

Biochemistry ◽

10.1021/bi00020a003 ◽

1995 ◽

Vol 34 (20) ◽

pp. 6587-6601 ◽

Cited By ~ 36

Author(s):

Kazuhiko Yamasaki ◽

Minoru Saito ◽

Motohisa Oobatake ◽

Shigenori Kanaya

Keyword(s):

Escherichia Coli ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamic Models ◽

Nmr Relaxation ◽

Dynamics Simulation ◽

15N Nmr ◽

Internal Motions ◽

15N Nmr Relaxation

Download Full-text

Silver nitrate in aqueous solution and as molten salt: A molecular dynamics simulation and NMR relaxation study

Canadian Journal of Chemistry ◽

10.1139/v94-290 ◽

1994 ◽

Vol 72 (11) ◽

pp. 2278-2285 ◽

Cited By ~ 14

Author(s):

Aatto Laaksonen ◽

Helena Kovacs

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Silver Nitrate ◽

Nmr Relaxation ◽

Md Simulations ◽

Dynamics Simulation ◽

Correlation Times ◽

Nitrate Ion ◽

Relaxation Measurements ◽

Dynamics Simulations

Using molecular dynamics simulations, the motion and intermolecular interactions of the ions of silver nitrate are studied in aqueous solution and compared to the results obtained from simulations of molten AgNO3. The particularly interesting and experimentally frequently studied modes of reorientational motion (in-plane and end-over-end) of the planar nitrate ion have been determined from the simulation results. In accordance with earlier experimental results, the correlation times for the end-over-end rotation in aqueous solution are longer than those for the in-plane rotation, while the opposite is found to hold in the melt. In addition, the rotational motion of the nitrate ion in aqueous solution is experimentally studied using 14N relaxation measurements. Good agreement is found between the reorientational correlation times obtained from MD simulations and from NMR relaxation measurements.

Download Full-text