Halorhodopsin is a light-gated ion pump, specific for chloride ions, found in archaea, known as halobacteria. It is a seven-transmembrane protein of the retinylidene protein family, homologous to the light-driven proton pump bacteriorhodopsin, and similar in tertiary structure (but not primary sequence structure) to vertebrate rhodopsins, the pigments that sense light in the retina. Halorhodopsin also shares sequence similarity to channelrhodopsin, another light-driven ion channel. Halorhodopsin contains the essential light-isomerizable vitamin A derivative all-trans-retinal. Due to the intense attention on solving the structure and function of this molecule, halorhodopsin is one of the few membrane proteins whose crystal structure is known.
Halorhodopsin uses the energy of green/yellow light to move chloride ions into the cell, overcoming the membrane potential. Beside chlorides it transports other halides and nitrates into the cell. Potassium chloride uptake by cells helps to maintain osmotic balance during cell growth. By performing the same task, light-driven anion pumps can considerably reduce the use of metabolic energy. Halorhodopsin has been the subject of much study and its structure is accurately known. Its properties are similar to those of bacteriorhodopsin, and these two light-driven ion pumps transport cations and anions in opposite directions.
Halorhodopsin isoforms can be found in multiple species of halobacteria, including Hbt. salinarum, and Nbt. pharaonis. Much ongoing research is exploring these differences, and using them to parse apart the photocycle and pump properties. After bacteriorhodopsin, halorhodopsin may be the best type I (microbial) opsin studied. Peak absorbance of the halorhodopsin retinal complex is about 570 nm.
Just as the blue-light activated ion channel channelrhodopsin-2 opens up the ability to activate excitable cells (such as neurons, muscle cells, pancreatic cells, and immune cells) with brief pulses of blue light, halorhodopsin opens up the ability to silence excitable cells with brief pulses of yellow light. Thus halorhodopsin and channelrhodopsin together enable multiple-color optical activation, silencing, and desynchronization of neural activity, creating a powerful neuroengineering toolbox. 
Halorhodopsin from Natronomonas (NpHR) has been used to achieve inhibition of action potentials in neurons in mammalian systems. Since light activation of NpHR leads to an influx of chloride ions which is a part of the natural process for generating hyperpolarization, NpHR induced inhibition works very well in neurons. Original NpHR channels when expressed in mammalian cells, showed a tendency to get accumulated in the Endoplasmic reticulum of the cells. To overcome the sub-cellular localization issues, an ER export motif was added to the NpHR sequence. This modified NpHR (called eNpHR2.0) was utilized successfully to drive aggregate-free, high level expression of NpHR in vivo. However, even the modified form of NpHR showed poor localization at the cell membrane. To achieve higher membrane-localization it was further modified by addition of a golgi export signal and membrane trafficking signal from a potassium channel (Kir2.1). The addition of Kir2.1 signal significantly improved the membrane localization of NpHR and this engineered form of NpHR was labeled eNpHR3.0 
As a research tool
- Zhang F, Wang L, Brauner M, Liewald J, Kay K, Watzke N, Wood P, Bamberg E, Nagel G, Gottschalk A, Deisseroth K (April 2007). "Multimodal fast optical interrogation of neural circuitry". Nature 446 (7136): 633–639. doi:10.1038/nature05744. PMID 17410168.
- Han X, Boyden ES (March 2007). "Multiple-color optical activation, silencing, and desynchronization of neural activity, with single-spike temporal resolution". PLoS ONE 2: e299. doi:10.1371/journal.pone.0000299. PMC 1808431. PMID 17375185.
- Gradinaru, V., Thompson, K.R., Deisseroth, K. (2008). "eNpHR: A Natronomonas halorhodopsin enhanced for optogenetic applications". Brain Cell Biology 36: 129–139. doi:10.1007/s11068-008-9027-6. PMC 2588488. PMID 18677566.
- Gradinaru, Viviana; Mogri, M.; Thompson, K.R.; Henderson, J.M.; Deisseroth, K (2009). "Optical deconstruction of parkinsonian neural circuitry". Science 324 (5925): 354–359. doi:10.1126/science.1167093. PMID 19299587.
- Gradinaru, Viviana; Feng Zhang; Charu Ramakrishnan; Joanna Mattis; Rohit Prakash; Ilka Diester; Inbal Goshen; Kimberly R. Thompson; Karl Deisseroth (2010). "Molecular and Cellular Approaches for Diversifying and Extending Optogenetics". Cell 141 (1): 154–165. doi:10.1016/j.cell.2010.02.037. PMID 20303157.
- Synthetic Neurobiology Group, MIT: Halorhodopsin mediating optical silencing of neurons
- Halorhodopsin at the US National Library of Medicine Medical Subject Headings (MeSH)
- Optogenetics Resource Center
- OpenOptogenetics.org, an open wiki about optogenetics.
- UMich Orientation of Proteins in Membranes families/superfamily-6 - Structures and orientations of bacterial rhodopsins in membrane