Difference between revisions of "Diploma"

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= Biophysics =
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I did my biology diploma in biophysics, the title is: "Simulation von Large-Scale Motions bei der Substratbindung von Rubisco".<br /> It was part of a joint project of the [http://www.bph.ruhr-uni-bochum.de/~juergen/ Theoretical Biophysics Group] and the [http://www.bpf.ruhr-uni-bochum.de Lehrstuhl für Biochemie der Pflanzen] .
 
 
I did my biology diploma in biophysics, the title is: "Simulation von Large-Scale Motions bei der Substratbindung von Rubisco".<br /> It was part of a joint project of the [http://www.bph.ruhr-uni-bochum.de/~juergen/ Theoretical Biophysics Group] of PD.Dr. J. Schlitter and Prof.Dr. G.F.Wildner from the [http://www.bpf.ruhr-uni-bochum.de Lehrstuhl für Biochemie der Pflanzen] .
 
  
 
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== Molecular Modelling of Rubisco ==
 
== Molecular Modelling of Rubisco ==
  
[http://en.wikipedia.org/wiki/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.
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[http://xkcd.com/1039/ Ribulose-1,5-bisphosphate-Carboxylase/Oxygenase][http://en.wikipedia.org/wiki/RuBisCO  (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).
 
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).
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Here are some examples of what Rubisco looks like, together with some short interpretation of the structure and function of the molecule.<br /> All pictures are made from the 8RUB.PDB-structure from the [http://www.rcsb.org Brookhaven Protein-Database] (afaik this structure has been replaced by a better one recently), and have been rendered using [http://www.expasy.ch/spdbv/mainpage.html SwissPDBViewer/DeepView] and [http://www.povray.org/ Povray] , both programs based on WIN95 running on my P133, 24 MB back in 1999.
 
Here are some examples of what Rubisco looks like, together with some short interpretation of the structure and function of the molecule.<br /> All pictures are made from the 8RUB.PDB-structure from the [http://www.rcsb.org Brookhaven Protein-Database] (afaik this structure has been replaced by a better one recently), and have been rendered using [http://www.expasy.ch/spdbv/mainpage.html SwissPDBViewer/DeepView] and [http://www.povray.org/ Povray] , both programs based on WIN95 running on my P133, 24 MB back in 1999.
 
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{|
<gallery>
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|[[Image:rubisco1.png|none|[[help:contents|Rubisco]]]]
[[Image:rubisco1.png|[[help:contents|Rubisco]]]]
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|[[Image:rubisco2.png|none|[[help:contents|Rubisco]]]]
[[Image:rubisco2.png|[[help:contents|Rubisco]]]]
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|}
</gallery
 
For more information regarding molecular modelling programs visit my [[Free Molecular Modelling Programs|Molecular Modelling Review]]-Page
 
  
 
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If you are interested in some more in-depth-information about molecular modelling or Rubisco, this might probably be the wrong place, but you may look at some of the links on my main-page, or get the following papers from every university-library:
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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)
 
G.F. Wildner et al.: Rubisco, an Old Challenge with new perspectives, Z. Naturforsch. 51 c, 263-276 (1996)
  
 
W.F. van Gunsteren &amp; H.J.C. Berendsen: Moleküldynamik-Computersimulationen; Methodik, Anwendungen und Perspektiven in der Chemie, Angew.Chem. 102 (1990) 1020-1055
 
W.F. van Gunsteren &amp; H.J.C. Berendsen: Moleküldynamik-Computersimulationen; Methodik, Anwendungen und Perspektiven in der Chemie, Angew.Chem. 102 (1990) 1020-1055
 
</gallery>
 

Revision as of 21:21, 8 October 2019

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).


Pictures

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.

Rubisco
Rubisco

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