Team:USTC/Modeling/a

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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]

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

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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 {{Template:USTCiGEM2010_header}}
-[[Known Conditions]]
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+<div id="transparent">
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+== Known Conditions ==
+This table illustrate some basic information of pdu shell protein family.[http://www.ncbi.nlm.nih.gov/pubmed/20417607]
+https://static.igem.org/mediawiki/2010/d/dc/USTC2010_known_conditions_table_1.jpg
+Table 1| Basic information of pdu shell protein family.
+https://static.igem.org/mediawiki/2010/2/2f/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 structures'''for 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]
+https://static.igem.org/mediawiki/2010/5/55/USTC2010_hypothesis_N_vertex.jpg     https://static.igem.org/mediawiki/2010/5/59/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:
+https://static.igem.org/mediawiki/2010/6/63/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 nm<sup>2</sup>
+*then the ''number'' of hexamer is 23936.353 nm<sup>2</sup>/31.8255 nm<sup>2</sup>=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
+https://static.igem.org/mediawiki/2010/1/1e/USTC2010_model_1_Result_of_composition.jpg
+https://static.igem.org/mediawiki/2010/6/66/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 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 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