User:Christian Kassebaum/Sandbox 2

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Description

is believed to be a crucial protein involved in magentoreception, a function that allows birds to visualize magnetic fields. In most animals where it is present, it is located within both the outer segments of the double cones and long-wavelength cones in the eye (2). It is evolutionarily related to DNA Photolyase proteins, however is shows no DNA repair activity (1). It shows a weak circadian oscillation and has strong up regulation during migratory seasons (2.2x upregulated) (2). It binds FAD at physiological conditions; a necessary function for its photochemical function (1). It has “a construct truncated at the C terminus by 28 residues that contains the photolyase homology region (PHR) that demonstrates spectra consistent with bound FAD^ox in the ground state” (1). There is high efficiency of conversion of FAD^ox to FADH^rad as well as the conversions of FADH^rad to FADH^-, meaning that it is sensitive to low light intensity (2).

Function

This protein’s proposed function is visualization of magnetic fields though magnetoreception forming radical a pair upon photo-excitation for light-dependent magentoreception. The mechanism of magentoreception is based upon the CIDNP (chemically induced dynamic nuclear polarization) concept, the description of which is beyond the scope of this analysis. It shows a very weak circadian oscillation regulation, unlike other cryptochromes such as Cry1 which show a much stronger circadian oscillation.

Composition & Function

This protein's gene has 1,584 base pairs corresponding to 527 amino acid residues (2). The photosensitizer in this system that contributes to the CIDNP function for this protein is flavin adenine dinucleotide, . Cryptochrome 4 contains a DNA photolyase homology domain, an FAD binding domain, and three or four tryptophan are thought to be involved in radical-pair formation known as the Trp-triad (Photolyase homology region and trp-triad) (1). The residue is adjacent to the N5 position of the FAD isoalloxazine ring which acts to promote the creation of a stable FADH^rad radicle (1). This function has been shown in cryptochrome 1 proteins which, normally having a Cys instead of a Asn residue at this point, have previously been mutated to have a Asn and exhibited an increase in quantum yield after this change. It is assumed that this function is present in Cryptochrome 4 and thus Asn 391 will lead to a selection of a stable FADH^rad state (1). is solvent exposed (a necessity for CIDNP function) and is located 3.9 angstrom away from (Add highlight of Tyr319). It is anchored in a solvent-filed cleft through a tightly bound water molecule bridging Tyr319 and Arg324 and Arg477. This Tyr319 is highly conserved in CRY4 proteins and shows significant importance in the outcome of quantum yields which will allow this protein to ruction at low intensities of light, a time which corresponds to the conditions under which many migratory birds may be traveling (1). It is currently believed that upon photo induction of the system, the trp-triad will transfer an electron to the bound FADH to produce FAD^rad and TrpH^rad+. The radical will then switch to Tyr319 (1). There are 3 structural domains within cryptochrome 4, the first being the N-terminal alpha beta domain connected via a long flexible linker to the second domain, an all-helical C-terminal domain. This is then adjacent to the initial residues of a divergent C-terminal tail.This C-terminal tail is oriented toward the FAD-binding cleft where blue light excitation of this FAD-binding cleft can lead to conformational changes in the C-terminal tail (1) (Try and find/highlight these sections?). Adjacent to the adenine moiety of FAD is a conserved pocket that is occupied by a glycerol molecule. This pocket is an evolutionary remnant that, in proteolyses, contains residues necessary for DNA repair. Currently, this pocket is lined by trp290/trp397 and his353/his357 (Highlight all of these). The His353 will hydrogen bond with ribitol side chain of FAD (1). Check pymole for structure. PBD is 6pu0.

Importance

Magentoreception is the ability of a bird to sense the Earth’s magnetic field and thus orient itself. Cryptochrome 4 is believed to be the instrumental protein that allows this function to take place in the bird. However, the exact way this process is carried out has not yet been determined. Thus far, the functional data from the protein does not line up with the observed behavior of birds in that, birds can easily orient themselves in full daylight where as studies suggest that cryptochrome 4 will be most active in low light intensity environments such as dawn and dusk. This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.