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This Sandbox is Reserved from January through July 31, 2018 for use in the course HLSC322: Principles of Genetics and Genomics taught by Genevieve Houston-Ludlam at the University of Maryland, College Park, USA. This reservation includes Sandbox Reserved 1311 through Sandbox Reserved 1430.

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Contents 1 Bacteriorhodopsin 2 Structure 3 Function 4 References

Bacteriorhodopsin

Bacteriorhodopsin is a photoreceptor protein found in Archaea. It arises in the species Halobacterium salinarum, an organism belonging to extremely salinated environments with light as an available energy source ^[1].

When in the presence of light energy and protons, the protein undergoes a five-part conformational change and pumps protons out of the cell, creating an electrochemical gradient with a more negative intracellular environment ^[2]. During this process, water is used to bind to the protein; no other outside molecules are necessary ^[3].

While the single-celled Archaea to which the protein belongs do not have eyes or sensory vision as other organisms do, the protein is a homolog to other rhodopsin proteins, such as the sensory molecule in humans ^[4].

Structure

The protein's main structure is that stretch lengthwise across the membrane of the cell. The inside of the molecule is hydrophilic, which allows for protons to be transported without issue ^[5].

Light energy and protonation of the molecule leads to a complex system of isomerization that releases a proton outside of the membrane. The is at the center of the protein and is bound to the alpha helices. In bacterial rhodopsin, the retinal functions as a proton pump by a conformation from all trans to cis-13. The goes from cis to trans when the retinal is hit by light, and this change pumps protons out of the cell ^[6].

Due to the bonding patterns and placement of the retinal molecule, when the conformational change occurs the entire protein changes to move protons ^[7].

Bacteriorhodopsin has multiple key residues in its structure: one end of bond to water molecules to increase stability and alter the shape of the molecule during the conformational changes. Lys-216 is the residual also responsible the bond with the alpha helix structure. holds the proton that is lost and replaced through the process ^[8]. While deprotonated, the molecule is much less stable. Therefore the lost proton is quickly replaced, allowing the mechanism to be more efficient even though it sends protons against the concentration gradient ^[9].

It is not fully known how the conformational changes and residues lead to the proton pumping capability itself ^[10].

Function

Bacteriorhodopsin's activity in the presence of photons and the gradient it creates is used mainly to power the cell's process of ATP synthesis; each protein is grouped in an collection of three molecules which cover a large portion of the cell surface to create the effect of what is known as the purple membrane ^[11].

References

1. ↑ Bacteriorhodopsin. http://www.biochem.mpg.de/523002/Protein_BR (accessed Feb 12, 2018).
2. ↑ Ernst OP, Lodowski DT, Elstner M, Hegemann P, Brown LS, Kandori H. Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev. 2014 Jan 8;114(1):126-63. doi: 10.1021/cr4003769. Epub 2013 Dec 23. PMID:24364740 doi:http://dx.doi.org/10.1021/cr4003769
3. ↑ Terango, M. Bacteriorhodopsin. https://collab.its.virginia.edu/access/content/group/f85bed6c-45d2-4b18-b868-6a2353586804/2/Ch09_Terango_M_Bacteriorhodopsin-_-/Ch09_Terango_M_Bacteriorhodopsin_Bacteriorhodopsin.html (accessed Feb 12, 2018).
4. ↑ Terango, M. Bacteriorhodopsin. https://collab.its.virginia.edu/access/content/group/f85bed6c-45d2-4b18-b868-6a2353586804/2/Ch09_Terango_M_Bacteriorhodopsin-_-/Ch09_Terango_M_Bacteriorhodopsin_Bacteriorhodopsin.html (accessed Feb 12, 2018).
5. ↑ Terango, M. Bacteriorhodopsin. https://collab.its.virginia.edu/access/content/group/f85bed6c-45d2-4b18-b868-6a2353586804/2/Ch09_Terango_M_Bacteriorhodopsin-_-/Ch09_Terango_M_Bacteriorhodopsin_Bacteriorhodopsin.html (accessed Feb 12, 2018).
6. ↑ Ernst OP, Lodowski DT, Elstner M, Hegemann P, Brown LS, Kandori H. Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev. 2014 Jan 8;114(1):126-63. doi: 10.1021/cr4003769. Epub 2013 Dec 23. PMID:24364740 doi:http://dx.doi.org/10.1021/cr4003769
7. ↑ Terango, M. Bacteriorhodopsin. https://collab.its.virginia.edu/access/content/group/f85bed6c-45d2-4b18-b868-6a2353586804/2/Ch09_Terango_M_Bacteriorhodopsin-_-/Ch09_Terango_M_Bacteriorhodopsin_Bacteriorhodopsin.html (accessed Feb 12, 2018).
8. ↑ Goodsell, D. Bacteriorhodopsin, 2002. PDB-101. http://pdb101.rcsb.org/motm/27 (accessed Feb 12, 2018).
9. ↑ Terango, M. Bacteriorhodopsin. https://collab.its.virginia.edu/access/content/group/f85bed6c-45d2-4b18-b868-6a2353586804/2/Ch09_Terango_M_Bacteriorhodopsin-_-/Ch09_Terango_M_Bacteriorhodopsin_Bacteriorhodopsin.html (accessed Feb 12, 2018).
10. ↑ Goodsell, D. Bacteriorhodopsin, 2002. PDB-101. http://pdb101.rcsb.org/motm/27 (accessed Feb 12, 2018).
11. ↑ Goodsell, D. Bacteriorhodopsin, 2002. PDB-101. http://pdb101.rcsb.org/motm/27 (accessed Feb 12, 2018).