GroPBS: Fast Solver for Implicit Electrostatics of Biomolecules.

Beitrag in einer Fachzeitschrift
(Originalarbeit)


Details zur Publikation

Autor(en): Bertelshofer F, Sun L, Greiner G, Böckmann R
Zeitschrift: Frontiers in bioengineering and biotechnology
Jahr der Veröffentlichung: 2015
Band: 3
Seitenbereich: 186
ISSN: 2296-4185
Sprache: Englisch


Abstract


Knowledge about the electrostatic potential on the surface of biomolecules or biomembranes under physiological conditions is an important step in the attempt to characterize the physico-chemical properties of these molecules and, in particular, also their interactions with each other. Additionally, knowledge about solution electrostatics may also guide the design of molecules with specified properties. However, explicit water models come at a high computational cost, rendering them unsuitable for large design studies or for docking purposes. Implicit models with the water phase treated as a continuum require the numerical solution of the Poisson-Boltzmann equation (PBE). Here, we present a new flexible program for the numerical solution of the PBE, allowing for different geometries, and the explicit and implicit inclusion of membranes. It involves a discretization of space and the computation of the molecular surface. The PBE is solved using finite differences, the resulting set of equations is solved using a Gauss-Seidel method. It is shown for the example of the sucrose transporter ScrY that the implicit inclusion of a surrounding membrane has a strong effect also on the electrostatics within the pore region and, thus, needs to be carefully considered, e.g., in design studies on membrane proteins.



FAU-Autoren / FAU-Herausgeber

Kranz, Franziska
Lehrstuhl für Informatik 9 (Graphische Datenverarbeitung)
Böckmann, Rainer Prof. Dr.
Professur für Computational Biology
Greiner, Günther Prof. Dr.
Lehrstuhl für Informatik 9 (Graphische Datenverarbeitung)
Sun, Liping
Professur für Computational Biology


Zitierweisen

APA:
Bertelshofer, F., Sun, L., Greiner, G., & Böckmann, R. (2015). GroPBS: Fast Solver for Implicit Electrostatics of Biomolecules. Frontiers in bioengineering and biotechnology, 3, 186. https://dx.doi.org/10.3389/fbioe.2015.00186

MLA:
Bertelshofer, Franziska, et al. "GroPBS: Fast Solver for Implicit Electrostatics of Biomolecules." Frontiers in bioengineering and biotechnology 3 (2015): 186.

BibTeX: 

Zuletzt aktualisiert 2018-18-10 um 04:23