Electrostatics plays major role in molecular biology because practically all atoms carry partial charge while being situated at Angstroms distances. In addition, the electrostatic force is a long-range force, in contrast with other forces present in molecular biology, and thus frequently guides many reactions involving charged molecules and ligands. However, modeling electrostatic potential and computing electrostatic energies is not trivial task because biological macromolecules are large objects existing in water phase. To overcome the complexity of such a system one applies continuum electrostatics to deliver the electrostatic potential distribution and the corresponding electrostatic energy components. Essential component of such modeling is the representation of the dielectric property of the system being investigated and here we report development of Gaussian approach to deliver a smooth dielectric function. We argue that Gaussian-based dielectric function provides more realistic description of macromolecular system and results in better predictions as benchmarked against various experimental data. Furthermore we report a parallelized DelPhi, which speed is more than 100 times faster than the sequential DelPhi while delivering the same potential and energies. Several applications are outlined as well showing the importance of electrostatics in modeling biological systems. Specific attention is given to modeling the role of electrostatics in kinesin/dynein-microtubules systems.

 

Prof. Emil Alexov is the head of the Computational Biophysics and Bioinformatics Laboratory at Clemson University, South Carolina, USA. His interests cover the areas of electrostatic energy calculation of biomolecules, understanding diseases, mechanisms of molecular motors, etc. Prof. Alexov currently serves on the Editorial Boards of many international scientific journals, including the International Journal of Molecular Sciences and the Communications in Computational Physics. He also serves on panels at the National Institutes of Health and the National Science Foundation.