From MarcsHomepage

I did my biology diploma in biophysics, the title is: "Simulation von Large-Scale Motions bei der Substratbindung von Rubisco".
It was part of a joint project of the Theoretical Biophysics Group and the Lehrstuhl für Biochemie der Pflanzen .

Molecular Modelling of Rubisco

Ribulose-1,5-bisphosphate-Carboxylase/Oxygenase(Rubisco for short) is the most common protein in the biosphere of the earth. It´s purpose is to catalyze the addition of carbon dioxide on a small sugar-molecule (Ribulose-1,5-bisphosphate), the most important step in the dark- reaction of photosynthesis.

My part of the work was the simulation and analysis of large conformational changes during the substrate-binding process with help of a newly developed GROMOS-based force-field (Schlitter et al.), which can simulate solvent-effects without simulating the solvent itself (thus leading to a tenfold increase in computation-speed compared to simulations with an explicit waterbox).


One of the fascinating parts of computer simulation of molecular processes is the fact that you get incredibly nice graphics ;-)

Here are some examples of what Rubisco looks like, together with some short interpretation of the structure and function of the molecule.
All pictures are made from the 8RUB.PDB-structure from the Brookhaven Protein-Database (afaik this structure has been replaced by a better one recently), and have been rendered using SwissPDBViewer/DeepView and Povray , both programs based on WIN95 running on my P133, 24 MB back in 1999.


If you are interested in some more in-depth-information about molecular modelling or Rubisco, this is definitely the wrong place, but you may look at the following papers, available from every university-library:

G.F. Wildner et al.: Rubisco, an Old Challenge with new perspectives, Z. Naturforsch. 51 c, 263-276 (1996)

W.F. van Gunsteren & H.J.C. Berendsen: Moleküldynamik-Computersimulationen; Methodik, Anwendungen und Perspektiven in der Chemie, Angew.Chem. 102 (1990) 1020-1055