JMS/sandbox22

spinqualitylabelsall models cryptochrome (PDB entry 1u3d) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D       Extraordinary Proteins. Extreme lifestyles sometimes require sensing the earth's magnetic field. Trytophan and aspartic acid residues may be key to an organism's ability to pick up where it is relative to the earth's poles. Birds, turtles, butterflies and other animals migrate with the help of the compasses built into their bodies. Little is known about the mechanistic nature of these compasses, and to fill the gap in knowledge, theoretical biophysicists Drs. Schulten and Solov'yov describe a nanomechanism within the birds' retina tissue, inside the rod cells, inside cryptochrome proteins known to process blue light for entraining circadian cycles, but now perhaps also deserving to be known as the seat of these organism's ability to sense magnetic fields. Molecular Tour: The cryptochrome protein absorbs a single photon of blue light of 2.7 eV, exciting either of the FAD ligand's two nitrogen atoms, because they are involved in resonance (and shown in halos, as are the all the relevant atoms). This FAD nitrogen atom is protonated by a nearby aspartic amino acid (the proximate donors shown with halos), and the electron hole is filled through a series of electron transfers from the three tryptophan amino acids (the nitrogen donors shown with halos). Notably, as seen in this alternative view, FAD and the three tryptophans form a chain from the protein's inside to its outside. At this stage, where FAD is in its active signaling state, the extra electron on FAD and lone electron on the final tryptophan amino acid (324) have formed a radical pair (location of the electrons shown with halos). The pair is entangled, such that they spin in opposite or same directions. But only when they spin in the opposite directions, can the extra electron on FAD tunnel back to the hole left in tryptophan 324. Researchers Klaus Schulten at University Illinois at Urbana Champaign and Ilya Solov'yov, now at the University of Southern Denmark, connect this system to the fascinating ability of many birds, and other flying species, to migrate while sensing the earth's magnetic field. Through simulations, they show that where the bird's cryptochrome compass's "FAD-trp324 needle" (shown as a dotted line) is aligned with the line extending between the earth's poles, the entangled electrons will 'on average' spend more time spinning the same direction, and therefore by delaying the electrons return to trp324, FAD will 'on average' be in its signalling mode for longer. this is similar to what is known for nitrogen vacancy centers. cornell also see march 2017 molecule of the month by david goodsell. Therefore, as a possible explanation, because many cryptochrome proteins are involved in registering blue light photons - millions of proteins per cell, and many cells across the retina, a change in the average time spent in the signalling state - "the transition rate" - is perhaps measured by the brain as the time until 50% of the cells do not have active FAD molecules. By moving its head about in different directions, a bird can find position at which the signalling last longest. That places the bird along the world's north-south pole axis.

showing asp390 (or 387 in cry2) that is critical for photoreception - no homo or heteroassociation showing the substitution of tucker which results in cry2oligo BLUE 374 weak as full, weaker, but still constitute as phr. DARK 387 is never bound.

References:

• Cryptochrome and Magnetic Sensing, Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign

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Joseph M. Steinberger