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<StructureSection load='' size='500' side='right' caption='myoglobin (PDB entry [[1u3d]])'  scene='58/585079/1u3d_magnet/19'>
<StructureSection load='' size='300' side='right' caption='cryptochrome (PDB entry [[1u3d]])'  scene='58/585079/1u3d_simple/1'>
'''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.
[[Image:1u3d.png|250px|left]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
'''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 Earth's magnetic poles.


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'''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.  
'''Birds, turtles, butterflies and other animals migrate''' with the help of the compasses built into their bodies. Drs. Schulten and Solov'yov described a mechanism taking place 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<ref>doi:10.1529/biophysj.106.097139</ref>.  


'''They hypothesize the birds perceive the effect of Earth's magnetic field by measuring the reaction dynamics of a process involving a pair of entangled electrons. When a bird''' first encounters blue light, the electrons separate in the many cryptochrome proteins, such that one free radical is found on a tryptophan amino acid, and the second free radical - originating from the same tryptophan - is found on a nearby FAD factor. When the blue light stimulation stops, the lone electron on FAD returns - in an irreversable reaction - to the tryptophan where it originated. The backtransfer, or return, of the lone electron to tryptophan, is partially a function of the angle the line between the two electrons makes relative to Earth's poles. The "''transition time''" from when the first cryptochrome returns to its unstimulated electron configuration until when all the cryptochrome protein's have returned, is one example of measurement of the reaction dynamics involving the back-transfer of the electron, and which is likely used by the bird to perceive its position relative to the earth's magnetic field.
More specifically, when the entangled electrons exist in the opposite-direction, or ''antiparallel spin'' state - as opposed to the alternative same-direction, ''parallel'' state - then the electron from FAD can return to tryptophan. The earth's magnetic field ''biases'' which spin state the electrons are found. Since, regardless of the orientation of the Earth's magnetic field, there will be some "extreme" cryptochrome protein that immediately return to the unstimulated state, therefore, by the orientation to Earth's magnetic field affecting the ''average'' rate (averaged over all the cryptochromes) at which the electron of FAD returns to tryptophan, it affects the transition time for the whole population to return to the unstimulated electron configuration, which the bird brain can use to determine its navigational trajectory.
Drs. Schulten and Solov'yov also introduce the involvement of a superoxide radical in order to increase the difference in time to about a millisecond for the back reaction electron transfer in different magnetic fields. By stabilizing the electron on FAD in the triplet state for as long as a millisecond when in the corresponding magnetic field, the difference in transition times (from one crytochrome until all the cryptochrome proteins return to the unstimulated state) reaches the magnitude consistent with prevalent timescales for signaling systems. A further condition of this model is that one rotational axis of the cryptochrome be restricted, which they say can easily be accomplished by tethering the cryptochrome to the cell membrane. And
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'''Molecular Tour:'''
'''Molecular Tour:'''


Klaus Schulten of the UIUC and Illia Solov'yov, now at the University of Southern Denmark, hypothesize that the FAD factor and just several residues of a crytochrome protein is all it takes to register the magnetic field of the earth. The <scene name='58/585079/1u3d_magnet/2'>"magnetic core"</scene> they describe involves the <scene name='58/585079/1u3d_magnet/15'>FAD factor, three tryptophan residues, as well as the aspartic residues which neighbor the FAD factor</scene>. When light in the blue range hits the FAD factor it becomes excited, with the excitement diffused over its <scene name='58/585079/1u3d_magnet/8'>aromatic ring system</scene> (the atoms involved in resonance are shown with halos). Then, one of the <scene name='58/585079/1u3d_magnet/16'>three neighboring aspartic acid residues</scene> donates a hydrogen proton from its hydroxyl group (the proximate ones shown with halos). The FAD factor then receives an electron from the neighboring tryptophan, from the tryptophan's nitrogen atom (shown in halo). The proton and electron that FAD received are attached to one of the nitrogen atoms on its ring (shown with a halo). Next, this tryptophan received an electron from its <scene name='58/585079/1u3d_magnet/17'>neighboring tryptophan</scene>, and then the second tryptophan received an electron from its neighbor, a third tryptophan. Finally, the third tryptophan loses a proton to a neighboring element. ''At this stage, the magnetic core contains an entangled pair of free radicals.'' The FAD factor contains a <scene name='58/585079/1u3d_magnet/18'>free radical on the adjacent carbon atom</scene> (shown with a halo), as does the third tryptophan residue on its donating nitrogen atom(shown with a halo).<br>  
The <scene name='58/585079/1u3d_magnet/19'>cryptochrome protein</scene> absorbs a single photon of blue light of 2.7 eV, exciting either of the FAD ligand's two nitrogen atoms, which are involved in resonance (and shown in halos, as are the <scene name='58/585079/1u3d_magnet/24'>all the relevant atoms</scene>). 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  <scene name='58/585079/1u3d_magnet/21'>form a chain</scene> 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) <scene name='58/585079/1u3d_magnet/25'>have formed a radical pair</scene> (location of the electrons shown with halos). The pair is entangled, but only when they spin in the opposite directions, can the extra electron on FAD return and fill 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 <scene name='58/585079/1u3d_magnet/23'>"FAD-trp324 needle"</scene> (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 in the same direction, and therefore by delaying the electrons return to trp324, FAD will 'on average' be in its signalling mode for longer.
 
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.
 
<!--
this is similar to what is known for <scene name='58/585079/Diamond/3'>nitrogen vacancy centers</scene>.
showing the <scene name='58/585079/Diamond/4'>molecular symmetry</scene>.
-->
 
<!--
<scene name='58/585079/1u3d_magnet/30'>cornell</scene>
also see march 2017 molecule of the month by david goodsell.
 
Mechanistically, the propensity of the electrons to spin in one direction or the other is affected by a local magnetic field, which is in this case primarily determined by the nuclear spins of several <scene name='58/585079/1u3d_magnet/22'>key nitrogen and hydrogen atoms</scene> (naming, as in fig. 5 of Schulten et al., 2007), the current spin state of the entangled electrons, '''and the external magnetic field (emanating from earth)'''. Only when the line between FAD and trp324 is parallel to the line connecting the north and south poles, is the earth's (external) magnetic field biasing the electrons spins to the same direction (parallel;triplet) spinning. Otherwise, the nuclear spins are the main determinants, and the the spins are approximately equivalently likely to be in the same or opposite directions.
-->
 
<!--
(But how a bird know whether it is facing due north or south is a question which cannot be figured out using this protein compass, the research emphasize in their study).  
<scene name='58/585079/1u3d_magnet/26'>showing asp390 (or 387 in cry2) that is critical for photoreception - no homo or heteroassociation</scene>
<scene name='58/585079/1u3d_magnet/27'>showing the substitution of tucker which results in cry2oligo</scene>
<scene name='58/585079/1u3d_magnet/28'>BLUE 374 weak as full, weaker, but still constitute as phr. DARK 387 is never bound.</scene>
-->


</StructureSection>
</StructureSection>

Latest revision as of 23:31, 16 June 2019

     

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 Earth's magnetic poles.

Birds, turtles, butterflies and other animals migrate with the help of the compasses built into their bodies. Drs. Schulten and Solov'yov described a mechanism taking place 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[1].

Molecular Tour:

The absorbs a single photon of blue light of 2.7 eV, exciting either of the FAD ligand's two nitrogen atoms, which are involved in resonance (and shown in halos, as are the ). 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 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) (location of the electrons shown with halos). The pair is entangled, but only when they spin in the opposite directions, can the extra electron on FAD return and fill 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 (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 in the same direction, and therefore by delaying the electrons return to trp324, FAD will 'on average' be in its signalling mode for longer.

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.



cryptochrome (PDB entry 1u3d)

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References:References:

  1. ↑ Solov'yov IA, Chandler DE, Schulten K. Magnetic field effects in Arabidopsis thaliana cryptochrome-1. Biophys J. 2007 Apr 15;92(8):2711-26. Epub 2007 Jan 26. PMID:17259272 doi:http://dx.doi.org/10.1529/biophysj.106.097139

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