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麻花13

新虫 (小有名气)

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注册: 2011-07-14
专业: 生物化学

[交流] 有一个idea,寻求想在“信号转达”方面做一番事业的伙伴已有1人参与

Anticipation for construction of platform of visible signal transdruction pathway

In biochemistry, millions of proteins and small molecules are in involved in the enormous system called singal transdruction which is hard to be described with consideration to systematicness and accuracy.
Thus, a new description pattern was designed. AutoCAD software was used to draw involved in signal transdruction. Here, the example of composite including 7TM receptor, Gs protein and adenylyl cyclases is as Figure 1

Figure 1. Complex of 7TM receptor, Gs protein and adenylyl cyclases described by new pattern
AutoCAD software was used. The pink curve represent inner membrane of cells and the yellow curve represent outer membrane

Through function in AutoCAD called “layer”, the complex was descriped in the levels by turns: motif, sub-region, region, domain, subunit and protein, as figure 2, figure 3, figure 4, figure 5, figure 6, and figure 7 show. If one structure doesn't exist or hasn’t been found in certern level, the structure loss location in this level is filled with the structure in upper level.

Figure 2 The complex description in motif level
Because of being the most commen and beautiful image in nature, regular hexagons were used to construct primary sturcture of the complex. Regular hexagons which were arranged in forms of being portait and transversal by turns represent motifs, containing N and C terminatio, found in proteins. Three foms of conjection between two regular hexagons appeared in the pattern: when two regular hexagons contacted with each through one line or shared one edge, the two motifs they represent were indicated to contact with each other through covalent bond, and when two regular hexagons shared one point, the two motifs were refered to conneted through non- covalent bond. It should be note that regular hexagons occuring in figure don't represent all the motifs existing in proteins of reality, and units addition in this level would coutinue with much more discoveries. In this figure, motifs and their conjugation are described in white.

Figure 3 The complex description in sub-region level
The category of sub-region level contains N and C terminatio in proteins, small structure such as pocket located in functional region, and conjugated motifs between two subunits or proteins, or the conjugation between proteins and membrane. In this figure, sub-region and their connection are describe in light blue.

Figure 4 The complex description in sub-region level
The category of region level contains N and C terminatio in proteins, functional region such as binding site, catalytic site and so on that were involved in the primary interactions in/between molecules, and conjugated motifs between two subunits or proteins, or the conjugation between proteins and membrane. In this figure, regions and their connection are described in green.

Figure 5 The complex description in domain level
From this level, block diagrams start to get rid of regular hexagon with exception of N and C terminatio tail. In this figure, domains in one protein or subunit and their connection are described in red.

Figure 6 The complex description in domain level
From this level, block diagrams get rid of regular hexagon at all. In figure, block diagram connect with each other by shareing points rather than through line or by shareing edge, and this indicates that the connection between subunits is non-covalent bond with exception disulfide bond sometimes. In this figure, subunits in one protein are described in light brown

Figure 7 The complex description in protein level
In this figure, proteins in the complex are described in ivory white

By means of AutoCAD, the complex was depicted in different layers according to different levels, and these several layers were combined into one picture axs figure 1 has shown.
The visible platform is expected to be constructed in this patten that one can view kinds of signal transduction in different levels from motifs to whole protein complex.
Still further, a dynamic and visible data bank online deserves to anticipiation in future. In each level, every unit, as a node in the whole web, can be added, edited, and arranged by scientist all over the world, and with efforts of biochemist on earth, it is believable that the whole signal transduction pathway system can be described in detail one day

[ Last edited by 麻花13 on 2012-2-12 at 19:08 ]

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