The intrinsic rate constants in diffusion-influenced reactions

Bolhuis, Peter G.; Wolde, Pieter Rein ten

doi:10.1039/c6fd00104a

Cited by 25 publications

(65 citation statements)

References 23 publications

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“…Another obvious use of our integrator is in studying self-assembly. Recently, several authors have highlighted the important role of diffusion in determining the selfassembly pathways of finite-sized structures in the absence of cooperative hydrodynamics 47,56 . Our integrator would enable this analysis to be extended to selfassembling systems with hydrodynamic interactions.…”

Section: Discussionmentioning

confidence: 99%

Geometric integrator for Langevin systems with quaternion-based rotational degrees of freedom and hydrodynamic interactions

Davidchack

Ouldridge

Tretyakov

2017

The Journal of Chemical Physics

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We introduce new Langevin-type equations describing the rotational and translational motion of rigid bodies interacting through conservative and non-conservative forces, and hydrodynamic coupling. In the absence of non-conservative forces the Langevin-type equations sample from the canonical ensemble. The rotational degrees of freedom are described using quaternions, the lengths of which are exactly preserved by the stochastic dynamics. For the proposed Langevin-type equations, we construct a weak 2nd order geometric integrator which preserves the main geometric features of the continuous dynamics. The integrator uses Verlet-type splitting for the deterministic part of Langevin equations appropriately combined with an exactly integrated Ornstein-Uhlenbeck process. Numerical experiments are presented to illustrate both the new Langevin model and the numerical method for it, as well as to demonstrate how inertia and the coupling of rotational and translational motion can introduce qualitatively distinct behaviours.

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Section: Discussionmentioning

confidence: 99%

Geometric integrator for Langevin systems with quaternion-based rotational degrees of freedom and hydrodynamic interactions

Davidchack

Ouldridge

Tretyakov

2017

The Journal of Chemical Physics

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“…Protein association and dissociation is essential for biologically relevant processes, such as cell signalling, DNA replication/transcription, cellular transport, immune response, gene editing [1], as well as for protein aggregation and self-assembly into structures with desired properties, e.g in food, colloids [2,3]. Moreover, knowledge of the kinetics and mechanisms of association is crucial for understanding and controlling biochemical network and cascade reactions of processive or distributive nature [4,5]. Yet, this kinetics is poorly understood even on the dimer level, and varies with the nature of the proteins [6].…”

Section: Introductionmentioning

confidence: 99%

Unbiased Atomistic Insight in the Mechanisms and Solvent Role for Globular Protein Dimer Dissociation

Brotzakis

Bolhuis

2018

Preprint

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Association and dissociation of proteins are fundamental processes in nature. While this process is simple to understand conceptually, the details of the underlying mechanism and role of the solvent are poorly understood. Here we investigate the mechanism and solvent role for the dissociation of the hydrophilic β-lactoglobulin dimer by employing transition path sampling. Analysis of the sampled path ensembles indicates that dissociation (and association) occurs via a variety of mechanisms: 1) a direct aligned dissociation 2) a hopping and rebinding transition followed by unbinding 3) a sliding transition before unbinding. Reaction coordinate and transition state analysis predicts that, besides native contact and vicinity salt-bridge interactions, solvent degrees of freedom play an important role in the dissociation process. Analysis of the structure and dynamics of the solvent molecules reveals that the dry native interface induces enhanced populations of both disordered hydration water and hydration water with higher tetrahedrality, mainly nearby hydrophobic residues. Bridging waters, hydrogen bonded to both proteins, support contacts, and exhibit a faster decay and reorientation dynamics in the transition state than in the native state interface, which renders the proteins more mobile and assists in rebinding. While not exhaustive, our sampling of rare unbiased reactive molecular dynamics trajectories shows in full detail how proteins can dissociate via complex pathways including (multiple) rebinding events. The atomistic insight obtained assists in further understanding and control of the dynamics of protein-protein interaction including the role of solvent.PACS numbers:

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“…To predict the power spectrum, we thus need the effective association rate k on and the effective dissociation rate k off . As described in the previous section, these rates can be computed in a single TIS/FFS simulation [22]. Using the computed values of the rate constants in combination with Eq.…”

Section: Power Spectrummentioning

confidence: 99%

“…13 analytically is not possible for the complex anisotropic potential used here. However, recently we have shown how in one TIS/FFS simulation both the association rate k on and the dissociation rate k off can be computed [22], which then allows us to obtain K eq from Eq. 12.…”

Section: B Bimolecular Reactionsmentioning

confidence: 99%

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Multiscale simulations of anisotropic particles combining molecular dynamics and Green’s function reaction dynamics

Vijaykumar

Ouldridge

Wolde

et al. 2017

The Journal of Chemical Physics

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The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Greens Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic Molecular Dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P.G. Bolhuis and P.R. ten Wolde, J. Chem. Phys. 43, 21: 214102 (2015)]. Here we extend this multiscale BD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm we discuss its performance. The rotational BD-GFRD multiscale method will open up the possibility for large scale simulations of e.g. protein signalling networks.

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The intrinsic rate constants in diffusion-influenced reactions

Cited by 25 publications

References 23 publications

Geometric integrator for Langevin systems with quaternion-based rotational degrees of freedom and hydrodynamic interactions

Geometric integrator for Langevin systems with quaternion-based rotational degrees of freedom and hydrodynamic interactions

Unbiased Atomistic Insight in the Mechanisms and Solvent Role for Globular Protein Dimer Dissociation

Multiscale simulations of anisotropic particles combining molecular dynamics and Green’s function reaction dynamics

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