Continuum electrostatics of biomolecular systems
1University of Oulu, Faculty of Science, Department of Biochemistry
2University of Oulu, Biocenter Oulu
|Online Access:||PDF Full Text (PDF, 1.2 MB)|
|Persistent link:|| http://urn.fi/urn:isbn:9789514287602
|Publish Date:|| 2008-04-08
|Thesis type:||Doctoral Dissertation
|Defence Note:||Academic dissertation to be presented, with the assent of the Faculty of Science of the University of Oulu, for public defence in Raahensali (Auditorium L10), Linnanmaa, on April 18th, 2008, at 12 noon
Associate Professor Mikko Karttunen
Professor Ilpo Vattulainen
Electrostatic interactions are very important in biomolecular systems. Electrostatic forces have received a great deal of attention due to their long-range nature and the trade-off between desolvation and interaction effects. It remains a challenging task to study and to predict the effects of electrostatic interactions in biomolecular systems. Computer simulation techniques that account for such interactions are an important tool for the study of biomolecular electrostatics.
This study is largely concerned with the role of electrostatic interactions in biomolecular systems and with developing novel models to estimate the strength of such interactions.
First, a novel formulation based upon continuum electrostatics to compute the electrostatic potential in and around two biomolecules in a solvent with ionic strength is presented. Many, if not all, current methods rely on the (non)linear Poisson-Boltzmann equation to include ionic strength. The present formulation, however, describes ionic strength through the inclusion of explicit ions, which considerably extends its applicability and validity range. The method relies on the boundary element method (BEM) and results in two very similar coupled integral equations valid on the dielectric boundaries of two molecules, respectively. This method can be employed to estimate the total electrostatic energy of two protein molecules at a given distance and orientation in an electrolyte solution with zero to moderately high ionic strength.
Secondly, to be able to study interactions between biomolecules and membranes, an alternative model partly based upon the analytical continuum electrostatics (ACE) method has been also formulated. It is desirable to develop a method for calculating the total solvation free energy that includes both electrostatic and non-polar energies. The difference between this model and other continuum methods is that instead of determining the electrostatic potential, the total electrostatic energy of the system is calculated by integrating the energy density of the electrostatic field. This novel approach is employed for the calculation of the total solvation free energy of a system consisting of two solutes, one of which could be an infinite slab representing a membrane surface.
Acta Universitatis Ouluensis. A, Scientiae rerum naturalium
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