Toward an Accurate Modeling of Hydrodynamic Effects on the Translational and Rotational Dynamics of Biomolecules in Many-Body Systems

Długosz, Maciej; Antosiewicz, Jan

doi:10.1021/acs.jpcb.5b04675

Cited by 16 publications

(35 citation statements)

References 48 publications

(169 reference statements)

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“…These findings identify a specific way that confinement affects the interactions between particles and points to a previously unidentified mechanism that may play a role in signal transduction and other processes near the membrane of biological cells. (1)(2)(3)(4)(5). Quantitative accuracy for diffusion rates of different sized particles has also been obtained with Stokesian dynamics (SD) simulations (6).…”

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confidence: 90%

Effects of confinement on models of intracellular macromolecular dynamics

Chow

Skolnick

2015

Proc. Natl. Acad. Sci. U.S.A.

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The motions of particles in a viscous fluid confined within a spherical cell have been simulated using Brownian and Stokesian dynamics simulations. High volume fractions mimicking the crowded interior of biological cells were used. Importantly, although confinement yields an overall slowdown in motion, the qualitative effects of motion in the interior of the cell can be effectively modeled as if the system were an infinite periodic system. However, we observe layering of particles at the cell wall due to steric interactions in the confined space. Motions of nearby particles are also strongly correlated at the cell wall, and these correlations increase when hydrodynamic interactions are modeled. Further, particles near the cell wall have a tendency to remain near the cell wall. A consequence of these effects is that the mean contact time between particles is longer at the cell wall than in the interior of the cell. These findings identify a specific way that confinement affects the interactions between particles and points to a previously unidentified mechanism that may play a role in signal transduction and other processes near the membrane of biological cells.B rownian dynamics (BD) simulations have been used to help qualitatively understand the motions and interactions of proteins and other macromolecules inside biological cells (1-5). Quantitative accuracy for diffusion rates of different sized particles has also been obtained with Stokesian dynamics (SD) simulations (6). In all these studies, a small portion of the interior of the cell is simulated, generally using a periodic simulation box that effectively mimics the motion in an unconfined, infinite system. However, in actual cells, macromolecules diffuse in a confined space and also interact with the cell wall, even at long range. These features may play an important role in the motion of macromolecules within the cell.As a first step toward developing and understanding coarse grained models of entire biological cells, we performed BD simulations, with and without hydrodynamic interactions (HIs), of monodisperse particle suspensions in a confined space, mimicking a biological cell. We also performed SD simulations, which include short-range HIs, called lubrication forces. SD is considered to be more accurate for high volume fraction systems such as the crowded interiors of biological cells. Our goal is to understand the effect of confinement on macromolecular diffusion inside biological cells. Near the cell wall, we hypothesize increased correlated particle motions (1, 6). Away from the wall, we are interested in the extent to which models and simulation methods can neglect the cell wall and effects of confinement.Previous theoretical and experimental studies have shown that diffusion slows down near planar membranes and that this is due to HI (7). Most studies of diffusion in confined spaces have addressed simple geometries such as parallel walls, in part for their simplicity and in part for their application to microfluidic devices (8-10). Other methods...

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confidence: 90%

Effects of confinement on models of intracellular macromolecular dynamics

Chow

Skolnick

2015

Proc. Natl. Acad. Sci. U.S.A.

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“…We realize that usage of pairwise additive Rotne–Prager hydrodynamic tensors to model hydrodynamic interactions is a rather crude approximation. However, employment of more sophisticated description of the hydrodynamic interactions , can hardly be used in Brownian dynamics simulations in three-dimensional Cartesian space , because it would make the time necessary to complete the results unacceptably long. On the other hand, even our simplified Brownian dynamics approach is useful and enables reliable interpretation of experimental data …”

Section: Materials and Methodsmentioning

confidence: 99%

Searching for Hydrodynamic Orienting Effects in the Association of Tri-N-acetylglucosamine with Hen Egg-White Lysozyme

2021

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Using stopped-flow fluorometry, we determined rate constants for the formation of diffusional encounter complexes of tri- N -acetylglucosamine (NAG 3 ) with hen egg-white lysozyme ( k a WT ) and its double mutant Asp48Asn/Lys116Gln ( k a MT ). We defined binding anisotropy, κ ≡ ( k a WT – k a MT )/( k a WT + k a MT ), and determined its ionic strength dependence. Our goal was to check if this ionic strength dependence provides information about the orienting hydrodynamic effects in the ligand-binding process. We also computed ionic strength dependence of the binding anisotropy from Brownian dynamics simulations using simple models of the lysozyme–NAG 3 system. The results of our experiments indicate that in the case of lysozyme and NAG 3 such hydrodynamic orienting effects are rather negligible. On the other hand, the results of our Brownian dynamics simulations prove that there exist molecular systems for which such orienting effects are substantial. However, the ionic strength dependence of the rate constants for the wild-type and modified systems do not exhibit any qualitative features that would allow us to conclude the presence of hydrodynamic orienting effects from stopped-flow experiments alone. Nevertheless, the results of our simulations suggest the presence of hydrodynamic orienting effects in the receptor–ligand association when the anisotropy of binding depends on the solvent viscosity.

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“…Currently, there are methods that allow one to accurately describe short-and long-range behaviors of hydrodynamic interactions between complex molecules modeled as clusters of spherical elements with the many-body character of hydrodynamic interactions taken into account. 48,49 However, because mobility tensors are strongly dependent on mutual distances between diffusing molecules and their mutual orientations, Brownian dynamics simulations employing these methods would be extremely computationally expensive and cannot be used at present without simplifications. 50 On the other hand, even our simplified Brownian dynamics approach leads to some useful conclusions, as described below.…”

Section: ■ Materials and Experimental Methodsmentioning

confidence: 99%

Diffusional Encounter Rate Constants for Xanthone and 2-Naphthoic Acid by Flash Photolysis Experiments and Brownian Dynamics Simulations: Substantial Effects of Polarizability of the Triplet State

2019

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Diffusional encounter rate constants, for xanthone and 2-naphthoic acid molecules in their triplet states with xanthone or 2-naphthoic acid molecules in their triplet or singlet states, were determined using nanosecond laser flash photolysis spectroscopy. Simultaneously, Brownian dynamics simulations were used to compute these rate constants for assumed models of encountering molecules. Altogether, a global fit to transient absorption progress curves, reporting populations of triplet state xanthone and triplet state 2-naphthoic acid molecules, allowed us to determine six diffusional encounter rate constants from our experiments. The most important result of this study is the detection of substantial effects of the electric polarizability of molecules in their triplet state, visible for xanthone triplet and 2-naphthoic acid ground states, a homo triplet–triplet annihilation of 2-naphthoic acid, and a hetero triplet–triplet annihilation for xanthone and 2-naphthoic acid.

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Toward an Accurate Modeling of Hydrodynamic Effects on the Translational and Rotational Dynamics of Biomolecules in Many-Body Systems

Cited by 16 publications

References 48 publications

Effects of confinement on models of intracellular macromolecular dynamics

Effects of confinement on models of intracellular macromolecular dynamics

Searching for Hydrodynamic Orienting Effects in the Association of Tri-N-acetylglucosamine with Hen Egg-White Lysozyme

Diffusional Encounter Rate Constants for Xanthone and 2-Naphthoic Acid by Flash Photolysis Experiments and Brownian Dynamics Simulations: Substantial Effects of Polarizability of the Triplet State

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