I’ve always been intrigued by vibrant iridescent colors. In nature, iridescence is caused by structural coloration, which is the production of color by nanostructure surfaces that interfere with visible light, sometimes in combination with pigments.

Another fascinating phenomenon is dynamic coloring in some animals including cephalopods such as squid are able to vary their colors rapidly for both camouflage and signaling. The mechanisms include reversible proteins which can be switched between two configurations. The configuration of reflectin proteins in chromatophore cells in the skin of the Doryteuthis pealeii squid is controlled by electric charge. When charge is absent, the proteins stack together tightly, forming a thin, more reflective layer; when charge is present, the molecules stack more loosely, forming a thicker layer. Since chromatophores contain multiple reflectin layers, the switch changes the layer spacing and hence the color of light that is reflected. Additionally, within the chromatocytes, where the pigment resides in nanostructured granules, we find the lens protein Ω- crystallin interfacing tightly with pigment molecules.

Protein Analysis

Pick any protein (from any organism) of your interest that has a 3D structure

Briefly describe the protein you selected and why you selected it.

• Identity the amino acid sequence of your protein.

  • How long is it? What is the most frequent amino acid?

  • How many protein sequence homologs are there for your protein?

    Hint: Use the pBLAST tool to search for homologs and ClustalOmega to align and visualize them.

  • Does your protein belong to any protein family?

• Identify the structure page of your protein in RCSB

  • When was the structure solved? Is it a good quality structure?

  • Are there any other molecules in the solved structure apart from protein?

  • Does your protein belong to any structure classification family?

• Open the structure of your protein in any 3D molecule visualization software

  • Visualize the protein as "cartoon", "ribbon" and "ball and stick".

  • Color the protein by secondary structure. Does it have more helices or sheets?

  • Color the protein by residue type. What can you tell about the distribution of hydrophobic vs hydrophilic residues?

  • Visualize the surface of the protein. Does it have any "holes" (aka binding pockets)?

References

Williams, T.L., Senft, S.L., Yeo, J. et al. Dynamic pigmentary and structural coloration within cephalopod chromatophore organs. Nat Commun 10, 1004 (2019). https://doi.org/10.1038/s41467-019-08891-x