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Team:USTC/Modeling/a
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== Conclusion == | == Conclusion == | ||
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| + | '''Explanation''' about the size. | ||
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| + | * Typical size of a prokaryotes is 1~10 µm | ||
| + | |||
| + | * Diameter of a Pdu Microcompartment is 100nm=0.1 µm | ||
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| + | * Volume of a Pdu Microcompartment is 317018.839 nm<sup>3</sup> ~=320000 nm<sup>3</sup>=3.2*105 nm3=3.2*10<sup>-4</sup> µm<sup>3</sup> | ||
| + | |||
| + | * Bacterium, are about 2 µm long and 0.5 µm in diameter, with a cell volume of 0.6 - 0.7 µm<sup>3</sup> | ||
| + | |||
| + | => Conclusion: about '''1875''' Pdu microcompartment can fill a bacterial cell！ | ||
== Reference == | == Reference == | ||
Revision as of 03:25, 25 October 2010
Known Conditions
This table illustrate some basic information of pdu shell protein family.[http://www.ncbi.nlm.nih.gov/pubmed/20417607]
Table 1| Basic information of pdu shell protein family.
Figure 1| 3-dimension structure of the known shell proteins from Salmonella enterica . UPPER: pduU. [http://www.ncbi.nlm.nih.gov/pubmed/18786396] MIDDLE: pduA. [http://www.ncbi.nlm.nih.gov/pubmed/20870711] DOWN：pduT. [http://www.ncbi.nlm.nih.gov/pubmed/20870711 [3]]
Hypothesis
I）Pdu N is the vertex and its pentametic structuresfor its identity with a proved vertex pentametic protein---CcmL. [http://www.ncbi.nlm.nih.gov/pubmed/18292340]
II) Hexamers forms the facets, which comprises the building blocks of bacterial microcompartment shells. [http://www.ncbi.nlm.nih.gov/pubmed/17518518]
Figure 2| LEFT: A diagram showing the construction of a large icosahedron from many smaller hexagons and 12 pentagons at the vertices. The figure shown has a triangulation number (T) of 75 (29). RIGHT: Individual CsoS1A molecules, typical shell proteins, are differently in each hexamer.
III) Similarity of the shell proteins to the carboxysome [http://www.ncbi.nlm.nih.gov/pubmed/12923081] and carboxysome is believed to be in icosohedral shape.
Results
From the paper data of EM observation:
Then we decide to count the molecular copies of each structural basic element.
Relative abundance [http://www.ncbi.nlm.nih.gov/pubmed/12923081 [6]]
pdu -J:-A:-B':-B:-K:-T:-U=15:10:7:6:1:1:2
- the diameter of a hexamer is 7 nm
- the edge is 3.5 nm
- the area of a hexamer is 31.8255 nm2
- then the number of hexamer is 23936.353 nm2/31.8255 nm2=752.11
So. in total 752 hexamers
Because B, B' and T have two BMC domains, so they form trimer instead
(15t+10t+t+2t)/6+(7t+6t+t)/3=752 => t=77.8
Conclusion
Explanation about the size.
- Typical size of a prokaryotes is 1~10 µm
- Diameter of a Pdu Microcompartment is 100nm=0.1 µm
- Volume of a Pdu Microcompartment is 317018.839 nm3 ~=320000 nm3=3.2*105 nm3=3.2*10-4 µm3
- Bacterium, are about 2 µm long and 0.5 µm in diameter, with a cell volume of 0.6 - 0.7 µm3
=> Conclusion: about 1875 Pdu microcompartment can fill a bacterial cell！
Reference
[1] Martin J. Warren, et al. 2010. Synthesis of empty bacterial microcompartments, directed organelle protein incorporation, and evidence of filament-associated organelle movement. Molecular Cell. 2010 Apr 38 (2), 305–315
[2] Structure of the PduU shell protein from the Pdu microcompartment of Salmonella. Structure. 2008 Sep 16(9):1324-32
[3] Structural insights into the mechanisms of transport across the Salmonella enterica Pdu microcompartment shell. J Biol Chem. 2010 Sep: [Epub ahead of print]
[4] Atomic-level models of the bacterial carboxysome shell. Science. 2008 Feb, 319(5866):1083-6
[5] Structural analysis of CsoS1A and the protein shell of the Halothiobacillus neapolitanus carboxysome. PLoS Biol. 2007 Jun;5(6):e144.
[6] Protein content of polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol in Salmonella enterica serovar Typhimurium LT2. J Bacteriol. 2003 Sep;185(17):5086-95
