Bluues: a program for the analysis of the electrostatic properties of proteins based on generalized Born radii.

Federico Fogolari,Vijaylakshmi Yarra,Alessandra Corazza,Paolo Viglino,Anusha Jalaru,Gennaro Esposito

doi:10.1186/1471-2105-13-s4-s18

Federico Fogolari, Vijaylakshmi Yarra + Show 4 more

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https://doi.org/10.1186/1471-2105-13-s4-s18

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Abstract

BackgroundThe Poisson-Boltzmann (PB) equation and its linear approximation have been widely used to describe biomolecular electrostatics. Generalized Born (GB) models offer a convenient computational approximation for the more fundamental approach based on the Poisson-Boltzmann equation, and allows estimation of pairwise contributions to electrostatic effects in the molecular context.ResultsWe have implemented in a single program most common analyses of the electrostatic properties of proteins. The program first computes generalized Born radii, via a surface integral and then it uses generalized Born radii (using a finite radius test particle) to perform electrostic analyses. In particular the ouput of the program entails, depending on user's requirement:1) the generalized Born radius of each atom;2) the electrostatic solvation free energy;3) the electrostatic forces on each atom (currently in a dvelopmental stage);4) the pH-dependent properties (total charge and pH-dependent free energy of folding in the pH range -2 to 18;5) the pKa of all ionizable groups;6) the electrostatic potential at the surface of the molecule;7) the electrostatic potential in a volume surrounding the molecule;ConclusionsAlthough at the expense of limited flexibility the program provides most common analyses with requirement of a single input file in PQR format. The results obtained are comparable to those obtained using state-of-the-art Poisson-Boltzmann solvers. A Linux executable with example input and output files is provided as supplementary material.

Highlights

The Poisson-Boltzmann (PB) equation and its linear approximation have been widely used to describe biomolecular electrostatics
Onufriev and coworkers have developed an analytical approximation to the exact potential inside and outside the low dielectric region of a sphere [6], that performs surprisingly well for the complex shape of proteins [7,8,9,10] and is more general than the generalized Born (GB) models
It is seen that the GBR6 model performs very well and that the gain in accuracy when linear combinations of a constant term and self-energies corresponding to radii an are used, with n ranging from 3 to 6 (LC5) and 3 to 10 (LC9), is limited

Summary

Introduction

The Poisson-Boltzmann (PB) equation and its linear approximation have been widely used to describe biomolecular electrostatics. Generalized Born (GB) models offer a convenient computational approximation for the more fundamental approach based on the Poisson-Boltzmann equation, and allows estimation of pairwise contributions to electrostatic effects in the molecular context. Generalized Born models Electrostatic effects arising due to the interaction of solute charges among themselevs and with solvent and ion charges, are of utmost importance for biomolecular structure and function. Recent reviews summarize the approach and highlight most interesting recent results [3,11,12,13,14] Central to these models is the estimation of polarization charge contributions to: i) the self-energy of each charge (embedded in the solute); ii) the interaction energy of each pair of charges.

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