ELECTROSTATICS STUDY OF A SINGLE-STRANDED DNA: A PROSPECTIVE FOR SINGLE MOLECULE SEQUENCING

2014 ◽  
Vol 09 (01) ◽  
pp. 105-114
Author(s):  
MOHAMMAD J. I. A. SAUDE ◽  
BASHIR I. MORSHED
Keyword(s):  
Dna Sequencing ◽  
Single Molecule ◽  
Electrostatic Potential ◽  
Molecular Electrostatic Potential ◽  
Special Issue ◽  
Single Stranded Dna ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation ◽  
Dynamics Simulations ◽  
Nucleotide Bases

Single molecule DNA sequencing requires new approaches to identify nucleotide bases. Using molecular dynamics simulations, we investigate the intrinsic electrostatics of single-stranded DNA by solving the nonlinear Poisson–Boltzmann equation. The results show variations of the molecular electrostatic potential (MEP) within 3 nm from the center of the sugar backbone, with suitably differentiable variations at 1.4 nm distance. MEP variations among four nucleotide bases are the most significant near ~ 33.7° and ~ 326.3° angular orientation, while the influences of the neighboring bases on MEPs become insignificant after the 3rd-nearest neighbors. This analysis shows potential for direct electronic sequencing of individual DNA molecules. [Formula: see text]Special Issue Comment: This paper about DNA sequencing based on molecular electrostatic potential maps of the DNA in the channel is related to the Special Issue articles about: measuring enzymes,32 and solving single molecules' trajectories with the RDF approach33 and with the QuB software.34

The effect of undulations on the electrostatic potential in a polyelectrolyte system

1994 ◽  
Vol 348 (1687) ◽  
pp. 209-228 ◽  
Keyword(s):  
Boundary Condition ◽  
Integral Equation ◽  
Electrostatic Potential ◽  
Perturbation Technique ◽  
Cylindrical Symmetry ◽  
Potential Applications ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation ◽  
The Green Function ◽  
Constant Charge

I consider the effect of macromolecular undulation on the electrostatic potential around a rod-like molecule. This effort is set to demonstrate the use of a particular perturbation technique through application to a geometrical system of general colloidal interest. The Poisson—Boltzmann equation together with a constant charge boundary condition on the well defined surface of an undulating cylinder is reformulated in integral equation form by use of Green’s theorem. A perturbation solution appropriate to the deformed boundary can be extracted when the Green function is approximated by that relevant to a reference, undeformed cylinder. Numerical results demonstrate that undulation causes significant deviations (increases) in electrochemical properties from expected behaviour, assuming rigid cylindrical symmetry. By considering the total free energy of the system it is found that electrostatics tend to diminish the extent of the undulations. The predicted deviations are briefly discussed in light of measured intermolecular electrostatic forces acting in a condensed phase of close-packed DNA. The perturbation technique has potential applications to mathematically similar problems occurring in hydrodynamics.

The interaction of two charged spheres in the Poisson–Boltzmann equation

1981 ◽  
Vol 59 (13) ◽  
pp. 1860-1864 ◽  
Author(s):  
Joseph E. Ledbetter ◽  
Thomas L. Croxton ◽  
Donald A. McQuarrie
Keyword(s):  
Boltzmann Equation ◽  
Charge Density ◽  
Surface Charge ◽  
Electrostatic Potential ◽  
Surface Charge Density ◽  
Ionic Solution ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation ◽  
Good Agreement ◽  
Charged Spheres

The Poisson–Boltzmann equation for two large charged spheres immersed in an ionic solution with either constant surface charge density or constant surface potential is solved numerically. The repulsion between the spheres is calculated from the electrostatic potential in the double layer surrounding the spheres. Good agreement between this numerically calculated force and the force computed using the Derjaguin formula for spheres with constant surface charge density is found at small separations of the spheres.

scholarly journals Direct Observation of Topoisomerase IA Gate Dynamics

2018 ◽  
Author(s):  
Maria Mills ◽  
Yuk-Ching Tse-Dinh ◽  
Keir C. Neuman
Keyword(s):  
Single Molecule ◽  
Conformational Changes ◽  
Mechanistic Model ◽  
Cellular Functions ◽  
Single Stranded Dna ◽  
Gate Opening ◽  
Type Ia ◽  
Dna Strand ◽  
Dynamics Simulations ◽  
Strand Passage

AbstractType IA topoisomerases cleave single-stranded DNA and relieve negative supercoils in discrete steps corresponding to the passage of the intact DNA strand through the cleaved strand. Although it is assumed type IA topoisomerases accomplish this strand passage via a protein-mediated DNA gate, opening of this gate has never been observed. We developed a single-molecule assay to directly measure gate opening of the E. coli type IA topoisomerases I and III. We found that following cleavage of single-stranded DNA, the protein gate opens by as much as 6.6 nm and can close against forces in excess of 16 pN. Key differences in the cleavage, ligation and gate dynamics of these two enzymes provide insights into their different cellular functions. The single-molecule results are broadly consistent with conformational changes obtained from molecular dynamics simulations. These results allow us to develop a mechanistic model of type IA topoisomerase-ssDNA interactions.

scholarly journals Modeling the Opening SARS-CoV-2 Spike: an Investigation of its Dynamic Electro-Geometric Properties

2020 ◽  
Author(s):  
Anna Kucherova ◽  
Selma Strango ◽  
Shahar Sukenik ◽  
Maxime Theillard
Keyword(s):  
High Fidelity ◽  
Geometric Properties ◽  
New Class ◽  
Multiple Length Scales ◽  
Pharmacological Studies ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation ◽  
Numerical Solver ◽  
Dynamics Simulations ◽  
Electrostatic Calculations

AbstractThe recent COVID-19 pandemic has brought about a surge of crowd-sourced initiatives aimed at simulating the proteins of the SARS-CoV-2 virus. A bottleneck currently exists in translating these simulations into tangible predictions that can be leveraged for pharmacological studies. Here we report on extensive electrostatic calculations done on an exascale simulation of the opening of the SARS-CoV-2 spike protein, performed by the Folding@home initiative. We compute the electric potential as the solution of the non-linear Poisson-Boltzmann equation using a parallel sharp numerical solver. The inherent multiple length scales present in the geometry and solution are reproduced using highly adaptive Octree grids. We analyze our results focusing on the electro-geometric properties of the receptor-binding domain and its vicinity. This work paves the way for a new class of hybrid computational and data-enabled approaches, where molecular dynamics simulations are combined with continuum modeling to produce high-fidelity computational measurements serving as a basis for protein bio-mechanism investigations.

Analytical resolution of the Poisson–Boltzmann equation for a cylindrical polyion immersed in an electrolyte solution: using the optimal linearization method

2019 ◽  
Vol 97 (6) ◽  
pp. 656-661
Author(s):  
Leila Djebbara ◽  
Mohammed Habchi ◽  
Abdalhak Boussaid
Keyword(s):  
Boltzmann Equation ◽  
Electrolyte Solution ◽  
Electrostatic Potential ◽  
Analytical Calculation ◽  
Linearization Method ◽  
General Potential ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation ◽  
Analytical Resolution ◽  
Potential Conditions

By using the optimal linearization method (OLM), the potential of the electrical double layer created by a highly charged cylindrical polyion immersed in an electrolyte reservoir, which is represented by the so-called Poisson–Boltzmann equation (PBE), has been solved analytically under general potential conditions. For this system, three regions must be considered. The first one is in the near-neighborhood of the polyion and it is deprived of coions because of the repulsion phenomenon between the polyion and the coions, as proposed by Fuoss et al. (Proc. Natl. Acad. Sci. 37, 579 (1951). doi: 10.1073/pnas.37.9.579 ). For the second region, where the potential is slightly lower, we propose an OLM for solving the PBE. In the last region, where the potential is sufficiently low, the approximation of Debye–Hückel is adopted. This method allowed us to overcome some shortcomings in the analytical calculation of the electrostatic potential created by a polyion in an electrolyte solution.

scholarly journals CONTINUUM ELECTROSTATICS INVESTIGATION OF IONIC MICELLES USING ATOMISTIC MODELS

2021 ◽  
Vol 87 (6) ◽  
pp. 55-69
Author(s):  
Vladimir Farafonov ◽  
Alexander Lebed ◽  
Nikolay Mchedlov-Petrossyan
Keyword(s):  
Electrostatic Potential ◽  
Sodium Dodecyl ◽  
Theoretical Models ◽  
Ionic Surfactant ◽  
Surfactant Micelle ◽  
Surfactant Micelles ◽  
Atomistic Models ◽  
Ionic Micelles ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation

The key parameter related to the structure of the electric double layer of ionic surfactant micelles – electrostatic potential – is considered. A brief overview of experimental methods and theoretical models for estimating electrostatic potential- is given. The calculating method for the electrostatic potential based on a numerical solution of the Poisson-Boltzmann equation using an atomistic model of anionic surfactant micelle - is proposed. The parameters necessary for the construction of atomistic models - are obtained from molecular dynamic modeling.  The electrostatic potentials for the micelles of sodium dodecyl sulfate and cetyltrimethylammonium bromide at different ionic strengths - were calculated by this method. The results are discussed in comparison with the values calculated in the simplified model, the Ohshima – Healy – White equation.

scholarly journals Electron transfer pathways in a multiheme cytochrome MtrF

2017 ◽  
Vol 114 (11) ◽  
pp. 2916-2921 ◽  
Author(s):  
Hiroshi C. Watanabe ◽  
Yuki Yamashita ◽  
Hiroshi Ishikita
Keyword(s):  
Electron Transfer ◽  
Binding Sites ◽  
Heme Binding ◽  
Binding Domains ◽  
Poisson Boltzmann ◽  
Electron Transfer Pathways ◽  
Poisson Boltzmann Equation ◽  
Dynamics Simulations ◽  
Flavin Binding ◽  
Multiheme Cytochrome

In MtrF, an outer-membrane multiheme cytochrome, the 10 heme groups are arranged in heme binding domains II and IV along the pseudo-C2 axis, forming the electron transfer (ET) pathways. Previous reports based on molecular dynamics simulations showed that the redox potential (Em) values for the heme pairs located in symmetrical positions in domains II and IV were similar, forming bidirectional ET pathways [Breuer M, Zarzycki P, Blumberger J, Rosso KM (2012) J Am Chem Soc 134(24):9868–9871]. Here, we present the Em values of the 10 hemes in MtrF, solving the linear Poisson–Boltzmann equation and considering the protonation states of all titratable residues and heme propionic groups. In contrast to previous studies, the Em values indicated that the ET is more likely to be downhill from domain IV to II because of localization of acidic residues in domain IV. Reduction of hemes in MtrF lowered the Em values, resulting in switching to alternative downhill ET pathways that extended to the flavin binding sites. These findings present an explanation of how MtrF serves as an electron donor to extracellular substrates.

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