The Poisson–Boltzmann equation for biomolecular electrostatics: a tool for structural biology

Fogolari, Federico; Brigo, Alessandro; Molinari, Henríette

doi:10.1002/jmr.577

Cited by 523 publications

(444 citation statements)

References 173 publications

(167 reference statements)

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“…[1][2][3][4] Several different computational techniques have been developed in the last two decades, such as finite difference ͑FD͒ methods, [5][6][7] finite element ͑FE͒ methods, 8,9 and boundary element methods ͑BEMs͒. 10,11 In most applications, the stationary solutions of the PBE under fixed conformations were used for calculating the electrostatic potential or solvation energy.…”

Section: Introductionmentioning

confidence: 99%

Computation of electrostatic forces between solvated molecules determined by the Poisson–Boltzmann equation using a boundary element method

Zhang

McCammon

2005

The Journal of Chemical Physics

102

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A rigorous approach is proposed to calculate the electrostatic forces among an arbitrary number of solvated molecules in ionic solution determined by the linearized Poisson-Boltzmann equation. The variational principle is used and implemented in the frame of a boundary element method ͑BEM͒. This approach does not require the calculation of the Maxwell stress tensor on the molecular surface, therefore it totally avoids the hypersingularity problem in the direct BEM whenever one needs to calculate the gradient of the surface potential or the stress tensor. This method provides an accurate and efficient way to calculate the full intermolecular electrostatic interaction energy and force, which could potentially be used in Brownian dynamics simulation of biomolecular association. The method has been tested on some simple cases to demonstrate its reliability and efficiency, and parts of the results are compared with analytical results and with those obtained by some known methods such as adaptive Poisson-Boltzmann solver.

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Section: Introductionmentioning

confidence: 99%

Computation of electrostatic forces between solvated molecules determined by the Poisson–Boltzmann equation using a boundary element method

Zhang

McCammon

2005

The Journal of Chemical Physics

102

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“…We have determined the effects of solvation on the interaction energy by solving the nonlinear Poisson-Boltzmann equation using finite element method (39). The displacement threshold and nonbonded cutoffs were set to 0.1 Å and 12.0 Å.…”

Section: Methodsmentioning

confidence: 99%

Role of large thermal fluctuations and magnesium ions in t-RNA selectivity of the ribosome

Guo

Gibson

Sitha

et al. 2011

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

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The fidelity of translation selection begins with the base pairing of codon-anticodon complex between the m-RNA and tRNAs. Binding of cognate and near-cognate tRNAs induces 30S subunit of the ribosome to wrap around the ternary complex, EF-Tu(GTP)aa-tRNA. We have proposed that large thermal fluctuations play a crucial role in the selection process. To test this conjecture, we have developed a theoretical technique to determine the probability that the ternary complex, as a result of large thermal fluctuations, forms contacts leading to stabilization of the GTPase activated state. We argue that the configurational searches for such processes are in the tail end of the probability distribution and show that the probability for this event is localized around the most likely configuration. Small variations in the repositioning of cognate relative to near-cognate complexes lead to rate enhancement of the cognate complex. The binding energies of over a dozen unique site-bound magnesium structural motifs are investigated and provide insights into the nature of interaction of divalent metal ions with the ribosome.rare events | magnesium binding sites | biomolecular machinery

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“…To calculate this force, the electrostatic potential was determined using the Poisson-Boltzmann equation [7,31] that describes an electric field around the immobile charges with account of free ions:…”

Section: Simulation Of Electrostatic Interactionsmentioning

confidence: 99%

Computer Simulation of Protein-Protein Association in Photosynthesis

Kovalenko

Abaturova

Diakonova

et al. 2011

Math. Model. Nat. Phenom.

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Abstract. The paper is devoted to the method of computer simulation of protein interactions taking part in photosynthetic electron transport reactions. Using this method we have studied kinetic characteristics of protein-protein complex formation for four pairs of proteins involved in photosynthesis at a variety of ionic strength values. Computer simulations describe non-monotonic dependences of complex formation rates on the ionic strength as the result of long-range electrostatic interactions. Calculations confirm that the decrease in the association second order rate constant at low values of the ionic strength is caused by the protein pairs spending more time in "wrong" orientations which do not satisfy the docking conditions and so do not form the final complex capable of the electron transfer.

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The Poisson–Boltzmann equation for biomolecular electrostatics: a tool for structural biology

Cited by 523 publications

References 173 publications

Computation of electrostatic forces between solvated molecules determined by the Poisson–Boltzmann equation using a boundary element method

Computation of electrostatic forces between solvated molecules determined by the Poisson–Boltzmann equation using a boundary element method

Role of large thermal fluctuations and magnesium ions in t-RNA selectivity of the ribosome

Computer Simulation of Protein-Protein Association in Photosynthesis

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