The Biochemistry of Channelrhodopsin
The primary structure of channelrhodopsins consists of 19 distinct amino acids, all but cysteine. The specific properties of each amino acid contributes to the secondary structure, as hydrophilic amino acids position themselves in such a way to contact the cytoplasm, while hydrophobic ones prefer to be in contact with the cellular membrane. The alternation of hydrophobic and hydrophilic amino acids tends to contribute to a helical shape, explaining the abundance of alpha helices in the protein. Channelrhodopsins are made up of seven alpha helices, meant to transverse the cellular membrane. Because the protein solely consists of alpha helices, it tends to be longer, has less surface area and is more tubular, supporting the idea that it is meant to bridge the cellular membrane. The hydrogen bonding between the polar molecules helps to form these helical shapes, contributing to the overall shape. The lack of cysteine amino acids means the lack of disulfide bridges, as the protein does not need disulfide bridges to connect across the ion channel. The presence of a disulfide bridge would likely interfere with the the transmission of ions across the cellular membrane, therefore, cysteine is not present.
In addition, the molecule, as a whole, contains very few charged particles - allowing it to function as a cation gate. The lack of charge does not force ions to either side. It simply opens and lets the pressure of diffusion force the cations in or out of the cell. One important thing to note is the molecule in the middle of the protein. This molecule, all-trans-retinal, is an aldehyde derivative of vitamin A, key to the protein's sensitivity to light - especially blue light (480nm). When blue light hits the all-trans-retinal, it undergoes a conformational change into 13-cis-retinal, and allows ions to pass through channelrhodopsin. The protein does not filter which kinds of cations are allowed through, but rather, allows all positively charged ions to pass.