Menu Content/Inhalt
Home
Staff - Tayefeh PDF  | Print |  E-mail

Computational Simulation and Analysis of the Kcv K+ Channel

Abstract

My studies deal with the computational modeling and simulation of biological proteins, in particular of the viral potassium channel Kcv. Among the methods I use are:

Molecular Dynamics Simulation
Based on classical mechanics, the motion of atoms is simulated. For large systems like mine, enormose computational power is required in order to perform these calculations. Hence, the calculations are not performed by ordinary desktop computers, not even by clusters of computers, but by massiv parallel SMP-machines with up to thousand CPUs (up to 32CPUs and 128GB RAM per node). Actually, the calculations were performed by the IBM Regatta installations "Jump" at Forschungszentrum Juelich and "HHLR (Hessischer Hochleistungsrechner)"at Hochschulrechenzentrum Darmstadt.
Improved Homology Modelling
While the atomic structure of Kcv is unknown, the homology modelling technique provides the mean to create models on atomic level. With this method, several models for Kcv were created, examined, simulated, and finally, with additional data from the simulation, refined.
3D Electrostatics (Poisson-Boltzmann)
In order to access the the electrostatic field around a protein, I used an advanced application of the Poisson-Boltzmann equation (Roux et al.). With this, it was possible to draw a 3D picture of the impact of protein-mutations on this property.

Methods

Hardware

As mentioned, my calculations need a huge amount of resources -storage and performance, respectively. Thus, I compiled the software for the usage with parallel-clusters. I used the IBM Regatta installations "Jump" at Forschungszentrum Juelich and "HHLR (Hessischer Hochleistungsrechner)" at Hochschulrechenzentrum Darmstadt for the most of my molecular dynamics calculations. Each node offers the power of up to 32 p690 processors and 128GB Shared Memory. Further, I made use of an Opteron-Cluster and na Xeon-Cluster, both run by CSC-Frankfurt. Our local computer-network provides high-performance SGI machines for sophisticated visualisation-studies, well-equipped HP-Itanium workstations and various single-/multiprocessor workstations equipped with Intel Pentium processors.

Software

Besides self-written codes in C, C++, Fortran, Tcl/Tk, Perl and tons of shell-scripts, I use various scientific software capable of performing molecular dynamics simulation, energy minimization, (bio)molecular modelling and stereochemestry evaluation and 3d-visualisation. Among my favored modelling software is Modeller and Charmm, while the simulations are carried out by NAMD. Please, refer to our links-section for a more complete list.


Publications / Scientific Contributions

Literature

    • Computational study of the Kcv potassium channel.
    • Sascha Tayefeh
    • PhD Thesis, Darmstadt, Techn. Univ., Diss. 2007
    • [Link to thesis]
    • Molecular dynamics simulation of the cytosolic mouth in Kcv-type potassium channels.
    • Tayefeh S, Kloss T, Thiel G, Hertel B, Moroni A, Kast SM
    • Biochemistry (46) 2007
    • [Link to abstract]
    • Elongation of outer transmembrane domain alters function of miniature K+ channel Kcv.
    • Hertel B, Tayefeh S, Mehmel M, Kast SM, Van Etten JL, Morini A, Thiel G
    • J. Membrane Biol. (210) 2006
    • [Link to abstract]
    • Botanik (Contribution: P.189, Fig 11-7)
    • Lüttge, Kluge, Bauer
    • Lehrbuch, 2005, 5.Auflage
    • Wiley-VCH Verlag GMBH und Co., Weinheim, ISBN 3-527-31179-3
    • [Link To Amazon]
    • Long-distance interactions within the potassium channel pore are revealed by molecular diversity of viral proteins.
    • Gazzarrini S, Kang M, Van Etten JL, Tayefeh S, Kast SM, DiFrancesco D, Thiel G, Moroni A.
    • J Biol Chem. (22) 2004
    • [Link to abstract]
    • Trafficking of the plant potassium inward rectifier KAT1 in guard cell protoplasts of Vicia faba.
    • Hurst AC, Meckel T, Tayefeh S, Thiel G, Homann U.
    • Plant J. (37) 2004
    • [Link to abstract]
    • Number of inward rectifying K+-Channels in dependence of the size of the plasmamembrane surface in guard cells of Vicia faba.
    • Tayefeh S
    • Technische Univesitaet Darmstadt, Diploma Thesis, 2003 Jul,
    • [Download complete thesis] (.PDF, german only, approx. 1,5MB)

Talks

    • Understanding Potassium Channel Function by Atomistic Molecular Dynamics Simulation
    • Tayefeh S, Thiel G, Kast SM
    • 20. Darmstädter Modellig Workshop in Erlangen, 2006 Erlangen, Germany
    • Computational Methods Provide Insight Into The Mechanism of K+-Channels
    • Tayefeh S, Thiel G, Kast SM
    • Internal Seminar, 2006, Institute of Botany, Technische Universität Darmstadt, Germany
    • Model development and simulation of Kcv mutants
    • Tayefeh S, Thiel G, Kast SM
    • Viral Ion Channel Meeting, 26-29 Oct 2005, Gargnano (Brescia), Italy
    • Model development and simulation of Kcv mutants
    • Tayefeh S, Thiel G, Kast SM
    • Internal Seminar, 2005, Theroetical Physical Chemistry (AG F. Müller-Plathe), Technische Universität Darmstadt, Germany
    • Modeling and molecular dynamics of a miniature viral potassium channel
    • Tayefeh S, Thiel G, Kast SM
    • Summer-School, 2005, Hirschegg, Austria
    • Cycling of K+-Channels in Guard Cells
    • Tayefeh S, Thiel G, Hoffman U
    • Rhein-Main Kolloquim, 2004, Frankfurt, Germany

Poster

    • Computational Study of the Kcv potassium channel
    • Tayefeh S, Kloss T, Thiel G, Kast SM
    • 21. Darmstädter Modelling Workshop, 2007, Erlangen, Germany
    • Comparative computational study of miniature potassium channel mutants
    • Tayefeh S, Kloss T, Thiel G, Kast SM
    • Rhein-Main Modelling Workshop, 2006, Darmstadt, Germany
    • Comparative computational study of miniature potassium channel mutants
    • Tayefeh S, Kloss T, Thiel G, Kast SM
    • Bunsen-Tagung, 2006, Erlangen, Germany
    • Comparative computational study of miniature potassium channel mutants
    • Tayefeh S, Kloss T, Thiel G, Kast SM
    • 20. Darmstädter Modelling Workshop, 2006, Erlangen, Germany
    • Modeling and molecular dynamics of a miniature viral potassium channel
    • Tayefeh S, Hertel B, Thiel G, Kast SM
    • Bunsen-Tagung, 2005, Frankfurt, Germany
    • Modeling and molecular dynamics of a miniature viral potassium channel
    • Tayefeh S, Hertel B, Thiel G, Kast SM
    • 19. Darmstädter Modelling Workshop, 2005, Erlangen, Germany

Teaching

    • Vertiefungspraktikum Computergestützte Biologie (Praktikumsleiter)
    • S. Tayefeh for Prof. Dr. G. Thiel
    • Dept. Of Biology, Technische Universität Darmstadt, 2006-2007.
    • Übungen: Allgemeinen Chemie (Seminarleiter)
    • Prof. Dr. J. Schneider (WS03/04) / Prof. Dr. R. Schäfer (SS04,WS04/05, WS05/06) / Prof. Dr. H. Vogel (SS05)
    • Dept. Of Chemistry, Technische Universität Darmstadt, 2003-2006.
    • Pflanzenphysiologisches Grosspraktikum (HiWi)
    • Prof. Dr. M. Kluge
    • Dept. Of Biology, Technische Universität Darmstadt, 1996, 1998.
    • Praktikum Morphologie der Pfanzen (HiWi)
    • Dr. R. Schlichting
    • Dept. Of Biology, Technische Universität Darmstadt, 1996, 1998-1999.
Last Updated ( Tuesday, 30 October 2007 )
 
[ Back ]