Team:USTC/Modeling/a

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== Known Conditions ==
== Known Conditions ==
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Table 1| Basic information of pdu shell protein family.
Table 1| Basic information of pdu shell protein family.
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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]]
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]]
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== Hypothesis ==
== Hypothesis ==
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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.
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.
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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'''.
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== Results ==
== Results ==
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From the paper data of EM observation:
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https://static.igem.org/mediawiki/2010/6/63/USTC2010_model_a_result_Equation_1.jpg
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Then we decide to count the '''molecular copies''' of each structural basic element.
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Relative '''abundance''' [http://www.ncbi.nlm.nih.gov/pubmed/12923081 [6]]
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pdu -J:-A:-B':-B:-K:-T:-U=15:10:7:6:1:1:2
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*the diameter of a hexamer is 7 nm
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*the edge is 3.5 nm
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*the ''area'' of a hexamer is 31.8255 nm<sup>2</sup>
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*then the ''number'' of hexamer is 23936.353 nm<sup>2</sup>/31.8255 nm<sup>2</sup>=752.11
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So. in total 752 hexamers
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Because B, B' and T have '''two''' BMC domains, so they form '''trimer''' instead
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(15t+10t+t+2t)/6+(7t+6t+t)/3=752 => t=77.8
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https://static.igem.org/mediawiki/2010/1/1e/USTC2010_model_1_Result_of_composition.jpg
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https://static.igem.org/mediawiki/2010/6/66/USTC2010_model_a_Result_of_composition.jpg
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Table 2| The distribution of shell proteins in microcompartment.
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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
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* 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>
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* 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>
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=> Conclusion:　about '''1875'''　Pdu microcompartments can fill a bacterial cell！
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== Reference ==
== Reference ==
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[5] Structural analysis of CsoS1A and the protein shell of the Halothiobacillus neapolitanus carboxysome. ''PLoS Biol.'' 2007 Jun;'''5'''(6):e144.
[5] Structural analysis of CsoS1A and the protein shell of the Halothiobacillus neapolitanus carboxysome. ''PLoS Biol.'' 2007 Jun;'''5'''(6):e144.
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[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

Latest revision as of 02:07, 28 October 2010

An Integrated Platform Based on Bacterial Microcompartment for de novo Proteinaceous Artificial Organelles


Known Conditions

This table illustrate some basic information of pdu shell protein family.[http://www.ncbi.nlm.nih.gov/pubmed/20417607]


USTC2010_known_conditions_table_1.jpg

Table 1| Basic information of pdu shell protein family.


USTC2010_known_conditions_figure_1.jpg

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]

USTC2010_hypothesis_N_vertex.jpg USTC2010_Hypothesis_Hexamer.jpg

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:

USTC2010_model_a_result_Equation_1.jpg


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

USTC2010_model_1_Result_of_composition.jpg

USTC2010_model_a_Result_of_composition.jpg

Table 2| The distribution of shell proteins in microcompartment.


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 microcompartments 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

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