BROMOC suite: Monte Carlo/Brownian dynamics suite for studies of ion permeation and DNA transport in biological and artificial pores with effective potentials

Biase, Pablo M. De; Markosyan, Suren; Noskov, Sergei Y.

doi:10.1002/jcc.23799

Cited by 11 publications

(19 citation statements)

References 23 publications

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“…The intrinsic electrostatic potential results from the charged residues embedded in the interior walls of the protein and can significantly influence the transport of ions and water molecules through the pore. 46,48,57,120 In the following section we aim to describe the most salient features of this potential and the extent of its influence over the entire investigated concentration range (Fig. 4).…”

Section: Electrostatic Potential and Energymentioning

confidence: 99%

“…The computational approaches most widely used to study nanofluidic transport in ion channels or biological nanopores comprise discrete methods such as molecular dynamics (MD) [44][45][46][47][48][49][50][51] and Brownian dynamics (BD), [52][53][54][55][56][57][58] and mean-field (continuum) methods based on solving the Poisson-Boltzmann (PB) equations 59,60 and Poisson-Nernst-Planck (PNP) equations. [61][62][63] The latter two can be coupled with the Navier-Stokes (NS) equation to include electro-osmotically or pressure driven fluid flow.…”

Section: Introductionmentioning

confidence: 99%

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Accurate modeling of a biological nanopore with an extended continuum framework

et al. 2020

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Section: Electrostatic Potential and Energymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Accurate modeling of a biological nanopore with an extended continuum framework

et al. 2020

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“…Grand-Canonical Monte-Carlo/Brownian Dynamics (GCMC/BD) represents an attractive computational approach for simulating the permeation process through wide channels over long time scales [76, 84–89]. The approach consists of generating the trajectory of the ions as a function of time by numerically integrating the stochastic equation of motions using effective potential functions to calculate the microscopic forces acting on mobile particles in the system.…”

Section: Vdac Structure and Permeation Propertiesmentioning

confidence: 99%

Current state of theoretical and experimental studies of the voltage-dependent anion channel (VDAC)

Noskov

Rostovtseva

Chamberlin

et al. 2016

Biochimica et Biophysica Acta (BBA) - Biomembranes

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Voltage-dependent anion channel (VDAC), the major channel of the mitochondrial outer membrane provides a controlled pathway for respiratory metabolites in and out of the mitochondria. In spite of the wealth of experimental data from structural, biochemical, and biophysical investigations, the exact mechanisms governing selective ion and metabolite transport, especially the role of titratable charged residues and interactions with soluble cytosolic proteins, remain hotly debated in the field. The computational advances hold a promise to provide a much sought-after solution to many of the scientific disputes around solute and ion transport through VDAC and hence, across the mitochondrial outer membrane. In this review, we examine how Molecular Dynamics, Free Energy, and Brownian Dynamics simulations of the large β-barrel channel, VDAC, advanced our understanding. We will provide a short overview of non-conventional techniques and also discuss examples of how the modeling excursions into VDAC biophysics prospectively aid experimental efforts.

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“…Many software packages are available for studying a variety of problems related to bimolecular association. For example, MacroDox, UHBD, BrownDye Simulation of Diffusional Association (SDA), BD_BOX, BROMOC, ReaDDy, Smoldyn, SEEKR, and BDpack are used to probe ligand–protein associations with a flexible or rigid biomolecular model (Madura et al, 1995 ; Northrup et al, 1999 ; Huber and McCammon, 2010 ; Długosz et al, 2011 ; Schöneberg and Noé, 2013 ; De Biase et al, 2015 ; Martinez et al, 2015 ; Saadat and Khomami, 2015 ; Andrews, 2017 ; Votapka et al, 2017 ). Our group has been developing the GeomBD program, which focuses on using BD to investigate inter-enzyme intermediate transfer and substrate association on surface environments in biosensor and nanoenzyme structures (Roberts and Chang, 2015 , 2016 ).…”

Section: Introductionmentioning

confidence: 99%

Molecular Mechanics Study of Flow and Surface Influence in Ligand–Protein Association

Kaushik

Chang

2021

Front. Mol. Biosci.

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Ligand–protein association is the first and critical step for many biological and chemical processes. This study investigated the molecular association processes under different environments. In biology, cells have different compartments where ligand–protein binding may occur on a membrane. In experiments involving ligand–protein binding, such as the surface plasmon resonance and continuous flow biosynthesis, a substrate flow and surface are required in experimental settings. As compared with a simple binding condition, which includes only the ligand, protein, and solvent, the association rate and processes may be affected by additional ligand transporting forces and other intermolecular interactions between the ligand and environmental objects. We evaluated these environmental factors by using a ligand xk263 binding to HIV protease (HIVp) with atomistic details. Using Brownian dynamics simulations, we modeled xk263 and HIVp association time and probability when a system has xk263 diffusion flux and a non-polar self-assembled monolayer surface. We also examined different protein orientations and accessible surfaces for xk263. To allow xk263 to access to the dimer interface of immobilized HIVp, we simulated the system by placing the protein 20Å above the surface because immobilizing HIVp on a surface prevented xk263 from contacting with the interface. The non-specific interactions increased the binding probability while the association time remained unchanged. When the xk263 diffusion flux increased, the effective xk263 concentration around HIVp, xk263–HIVp association time and binding probability decreased non-linearly regardless of interacting with the self-assembled monolayer surface or not. The work sheds light on the effects of the solvent flow and surface environment on ligand–protein associations and provides a perspective on experimental design.

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BROMOC suite: Monte Carlo/Brownian dynamics suite for studies of ion permeation and DNA transport in biological and artificial pores with effective potentials

Cited by 11 publications

References 23 publications

Accurate modeling of a biological nanopore with an extended continuum framework

Accurate modeling of a biological nanopore with an extended continuum framework

Current state of theoretical and experimental studies of the voltage-dependent anion channel (VDAC)

Molecular Mechanics Study of Flow and Surface Influence in Ligand–Protein Association

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