Biomolecular electrostatics with the linearized Poisson-Boltzmann equation.
Electrostatics plays a key role in many biological processes. The Poisson-Boltzmann equation (PBE) and its linearized form (LPBE) allow prediction of electrostatic effects for biomolecular systems. The discrepancies between the solutions of the PBE and those of the LPBE are well known for systems with a simple geometry, but much less for biomolecular systems. Results for high charge density systems show that there are limitations to the applicability of the LPBE at low ionic strength and, to a lesser extent, at higher ionic strength. For systems with a simple geometry, the onset of nonlinear effects has been shown to be governed by the ratio of the electric field over the Debye screening constant. This ratio is used in the present work to correct the LPBE results to reproduce fairly accurately those obtained from the PBE for systems with a simple geometry. Since the correction does not involve any geometrical parameter, it can be easily applied to real biomolecular systems. The error on the potential for the LPBE (compared to the PBE) spans few kT/q for the systems studied here and is greatly reduced by the correction. This allows for a more accurate evaluation of the electrostatic free energy of the systems.
Fogolari
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Dipartimento Scientifico Tecnologico, University of Verona, 37100 Verona, Italy.federico@nmr.sci.univr.it
Zuccato
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Esposito
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Viglino
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D000818:Animals; D051943:Antennapedia Homeodomain Protein; D055592:Biophysical Phenomena; D001703:Biophysics; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D018398:Homeodomain Proteins / Q000737:chemistry; D046911:Macromolecular Substances; D008954:Models, Biological; D008958:Models, Molecular; D009687:Nuclear Proteins; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D055672:Static Electricity; D013499:Surface Properties; D013816:Thermodynamics; D014157:Transcription Factors
D051943:Antennapedia Homeodomain Protein; D018398:Homeodomain Proteins; D046911:Macromolecular Substances; D009687:Nuclear Proteins; D014157:Transcription Factors; D004247:DNA