Biochemical visualization

 

The field of molecular biology and biochemistry represents an equally diverse landscape as macroscopic landscapes and the opportunities for visualizations are endless.

Below is shown a protein from PDB and visualized using parametric modeling of membrane lipids and protein placement.

In membrane visualization of

Structure of the mannose transporter of the bacterial phosphotransferase system.

Liu, X., Zeng, J., Huang, K., Wang, J.

(2019) Cell Res 29: 680-682


WARNING: Here comes some biochemical size data.
Below is a model of 166 random color-coded base-pairs in a DNA double helix wrapped around an invisible histone protein complex. The whole thing is called a nucleosome and is part of the packing of DNA in cromosomes of higher order organisms (eucariotes). The diameter of the nucleosome is around 11 nm or approximately one hundred thousands of a mm. The diameter of the DNA double helix is 2 nm. The distance between a 360 degree loop of helix along the central axis is 10 base-pairs and 3.4 nm. The distance along the axis between the minor grove is 1/2 the distance of the major grove which corresponds to the angles of 120- and 240 degrees in the inner and outer angle of complementary base-pairs in DNA. A-T base pairs are symbolized as Light-green/dark-green and G-C base pairs as light-red/dark-red (or the other way around). The sequence is random but complementary.

It was made using procedural precision modeling in Blender and rendered using real-time renderer EEVEE.

Below the above “nucleosome” DNA helix is unwound using physics simulation.

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