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This latter feature permitted the unequivocal identification of divalent ion binding sites. Representative electron density for these data is shown in Fig.
The asymmetric unit was composed of two molecules hereon referred to as chain A and chain X that exhibited subtle structural differences.
This region of the M-box is involved in multiple long-range contacts that are centered around M5 and M6 in Core 2.
The apparent flexibility of M-box backbone in this region may support the previous observation that metal sites in Core 2 show relatively weaker phosphorothioate interference Symmetry related molecules form an inter-molecular kissing loops interaction to stabilize the P6 helix in this crystal form.
The P6 helix region of the molecule was disordered in the previous structural model. Intermolecular kissing loop interactions between symmetry related molecules appeared to stabilize the L6 loop Fig.
The loop-loop interaction involves 6 nucleotides G, C, U, U, G and U where G-U and G-C base pairs flank the central uridines and allow them to be stabilized by N3-O4 and O2-N3 interactions, respectively.
While it is likely that the relative orientation of these nucleotides with respect to the native M-box structure may be affected by this crystal contact, the increased order in this region resulted in improved electron density of the entire P6 helix region.
Guided by difference density calculated from 1. The two chains also differed modestly in the number of occupied metal sites Fig.
Three out of four sites in Core 1 M1, M2 and M3 showed nearly identical occupancies in both chains. Mn1 was coordinated via interactions to the RNA backbone with the non-bridging phosphate oxygens of G, C and A, at an average distance of 2.
Again, distances from the remaining coordinating water molecules averaged around 2. This interaction is likely to be functionally significant as previous phosphorothioate interference experiments had inferred the importance of this outer—sphere interaction Finally, the last remaining Core 1 cation site, Mn4, was coordinated by a single inner-sphere contact to a nonbridging phosphate oxygen of A72, and an outer-sphere contact to the N7 of A It is noteworthy that this site is likely to represent the weakest specific cation site in Core 1 since the anomalous density ranged from 3.
Consistent with this, position A72 had previously exhibited only moderate phosphorothioate interference.
Red positions denote sites of phosphorothioate interferences. Dashed lines denote key tertiary interactions. There are negligible structural differences in the backbone as well as individual nucleotide orientations.
Mn5 contacts the RNA though one inner-sphere interaction with the phosphate oxygen of A63 and multiple outer-sphere interactions with nucleobases of C77 and U Similarly, Mn6 is coordinated by a backbone phosphate oxygen of A80 and the O4 of U The two metal-coordinating atoms are 3.
In chain X however, this distance is 4. Previously, we had observed phosphorothioate interferences at positions C35, C36, C89, G91 and U in the M-box aptamer.
These positions together appeared to represent three putative metal sites, which we designated M7 through M9. One possible explanation is that they exhibit relatively low-affinity for metal ligand and therefore were unoccupied in the final crystal structure.
Alternatively, the putative M7-M9 sites might occupied with metals only during folding. Key coordinating functional groups are shown along with metal coordinating water molecules black.
Cation binding sites are visible as patches of relatively higher electronegativity. Closer examination of Mn7 Fig. Of these, the interaction with U alone is via the pro-Rp oxygen and was previously seen as a position of phosphorothioate interference.
Metal-ligand distances are in the range of 2. Three water molecules, at an average distance of 2. The combined orientations of the A, A, and U phosphates, towards formation of an electronegative cavity, appeared to help position adjacent nucleosides for key long-range interactions at the apex of the molecule.
For example, the nucleobase ring of A stacks against the GU85 base pair located in the backbone U-turn separating the P4 and P5 helices.
Similarly, A stacks against the AU base pair at the apex of the P5 helix and also forms an A-minor motif interaction with the P4 GC57 base pair, again stabilizing distant regions of the RNA.
Mn9 is coordinated by inner-sphere interactions with the pro-Rp oxygens of C35 and C36 Fig. Outer-sphere interactions with the phosphate oxygens of C from the adjacent turn of the P2 helix further stabilize this coordination.
C35 not only makes direct inner-sphere contacts with Mn9, but also stacks against A88, which is involved in an A-minor interaction to a P2 G:C base pair.
These different metal sites exhibit a concentration of electronegative charge as would be expected for specific cation binding sites Fig.
Most were observed in both RNA chains, although Mn11 was present only in chain A and Mn14 was only in chain X. The most interesting of these metal sites, Mn10, is present in the L5 loop and is coordinated via one backbone interaction with the pro-Rp oxygen of A and the N7 of G Fig.
Two outer-sphere interactions with pro-Rp oxygen of A and G further stabilize the coordination. Notably, A had previously shown to exhibit moderate phosphorothioate interference.
Also, O2 of A on the non-metal binding face coordinates a potassium ion. The ribose oxygen of G further interacts with N1 of A from the P2 helix.
The adenine rings of A and A stack against each other and interact on opposite faces with elements from L4 and P2. While the A nucleobase interacts with the C68 ribose oxygen from the L4 loop, the N6 of A lies within 2.
The G ribose oxygen further interacts with N1 of A, also located within the P2 helix. Mn11 is present in the P4 helix of the M-box aptamer, making one inner-sphere contact with the A60 phosphate oxygen Fig.
The remaining coordinations are satisfied by water molecules. Outer-sphere coordinations are also seen with the N7 groups of A60 and A61 and the phosphate oxygen of A In chain X, the altered backbone conformation in the P4 helix alters the placement of the nucleotides involved in coordinating Mn11, placing them too far away to be able to create a compact metal-coordinating pocket.
Mn12 lies at one end of the P2 helix, close to the L6 turn in the M-box aptamer. The N7 of G45 also makes an outer sphere contact with Mn The remaining coordinations are satisfied via water molecules, though only four of the five metal-chelating water molecules were modeled due to lack of clear density for one water molecule.
A46 forms multiple interactions with A as well as U on the same plane, with a distance of 2. U is positioned so as to make an outer-sphere contact to Mn12 via a water molecule.
In chain X, however, the location of Mn12 is different. This region of the RNA shows one more significant difference with regard to the structure of chain A.
A46 is splayed outwards from the P2 helix and instead of interacting with A on the plane of the nucleobase, it stacks against the adenine ring.
Also, the interaction between A46 and U are altered such that the N6 of A46 is positioned as far away as 5. Mn13 is present in the P6 helix, proximal to the L6 loop and is coordinated to the pro-Sp phosphate oxygens of G, A and U and two water molecules.
Hexa-coordination is completed by water from the other chain. Also noteworthy is an outer-sphere interaction with G29 from the other chain via a water molecule.
This observation suggests that this site is created due to proximity of the two chains of M-box in the crystal lattice and therefore not likely to be of functional relevance.
Mn14 is present in the central region of the P2 helix, coordinated by nucleotides A30 and G31 that stack against each other in the P2 helix.
The proximity of a symmetry related molecule in this region, lack of apparent metal-mediated tertiary contacts as well as lack of phosphorothioate interference data for the coordinating nucleotides seems to suggest that this site is not likely to be functionally relevant.
Mn 15 is coordinated via the N7 of G15 and is in close proximity to the pro-Sp oxygen of G Mn 16 is occupied only in chain X and is coordinated via the N7 of G and the ribose oxygen of A Metal ions play a critical role in RNA tertiary structure formation and often mediate long-range interactions between distant regions of the RNA.
It is therefore no surprise that, unlike other riboswitches that recognize a single ligand molecule, the M-box associates with several putative ligand molecules.
It is likely that the M-box relies on more than just a diffuse atmosphere of loosely associated ions for overall charge neutralization a function that can be performed by most positively charged ions regardless of valency and structural compaction; our data suggest that the M-box native state is dependent on formation of specific cation binding pockets.
These cation binding sites are likely to be responsible for sensory input during regulation by M-box riboswitches.
The challenge thus far has been to identify the dedicated cation-binding sites within the M-box, and assess the importance, affinity and specificity of each individual site with regards to M-box function.
Follow-up biochemical experiments confirmed the importance of these six sites and predicted three additional putative binding sites.
In the current study we have attempted to visualize the complete suite of specific cation binding sites in the M-box. This is especially challenging with lower resolution X-ray diffraction data.
This difference in affinity is however lost in the presence of 2. This observation confirms that along with a diffuse ionic atmosphere of loosely associated metal ions, which can be displaced by a higher concentration of monovalent ions, the M-box possesses a collection of specific cation binding sites which are likely to play a critical role in gene regulation.
Also, it confirms that the extent of compaction is similar in the presence of all three metal ions tested. Therefore Core 2 sites sites 5, 6 and 11 possibly represent regions of structural flexibility in the M-box, in contrast to our expectations for Core 1.
This is in agreement with previous phosphorothioate interference experiments where nucleotides constituting these sites 5 and 6 showed moderate to weak interferences at 0.
One particular caveat in using crystallographic structures as a means to understand atomic level details of RNA-metal interactions is that inherent properties of a particular metal ion may influence subtle structural alterations in the RNA itself.
This could suggest that folding of the M-box is influenced by formation of tertiary and long range contacts potentially prior to cation binding.
Such interactions may even conceptually resemble sites M10 and M12, which both include metal interactions to guanine N7 groups.
For AUC and SHAPE reactions, DNA templates were amplified by PCR from B. RNA was prepared by in vitro transcription for 2. Your purchases also help protect forests, including trees traditionally used to make instruments.
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Learn More. That listing sold. Then, for good measure, I tried the same thing with my R, and that worked too.
The supplied version of Pro Tools supports older M Box and interfaces too, allowing you to switch between them though not to run them simultaneously.
Now here is the extra special thing I discovered by accident. I swapped back to the original M Box to check something, and when I loaded up Pro Tools and played the Session, I heard audio coming out of the headphones that were still plugged into the M Box 2 Pro.
This confused me because the M Box's lights were all on, as you would expect. A trip to Playback Engine in the Setups menu showed that Pro Tools had recognised both units, but the M Box 2 Pro was selected.
When I tried to select the M Box, Pro Tools came up with a screen I had only seen before on HD systems when swapping Playback Engines, advising me that Pro Tools would save and close the current Session before changing the Playback Engine and reopening the Session.
So I clicked Yes, expecting it to all go horridly wrong, and the Session reopened fine and ran through the M Box even though the M Box 2 Pro was still plugged in!
I wondered if Pro Tools would recognise my R in the same way, so I quit Pro Tools , plugged the R into the other Firewire socket on the back of the M Box 2 Pro, and loaded Pro Tools again — and that worked just as well, giving me a list of different Playback Engines to choose from in the Engine column.
The upshot of this is that it is now possible to swap from one interface to another at will. Just to be very cheeky I unplugged the Firewire interfaces whilst Pro Tools was still running but the Playback Engine thought that they were still connected, and when I tried to swap to one of them, Pro Tools closed and saved the Session fine but then came up with an error message that 'The selected Playback Engine didn't support the sample rate of I clicked the OK box and the Session didn't reopen, so I went back into the Playback Engine dialogue box and tried to re-select the M Box, which was still plugged in, but at that point Pro Tools had had enough and crashed.
An unfair test, I know, but I wanted to see what happened! Something that has bothered me about the M Box family to date is that the analogue outputs produce a lower level than those of the family and the HD interfaces.
On those interfaces I would expect that a tone file created at dBFS would produce an analogue output of 0dBu assuming that the Calibration option on the HD systems was set correctly; there is no Calibration option on the LE software.
The M Box family to date has produced a lower level around dB for a tone signal of dBFS. In broadcast settings, where you are dependent on external PPM metering for level monitoring, this has been a pain.
With its 'Pro' label, I hoped that the M Box 2 Pro might deliver a pro-level output, so I checked with my audio level meter and found that it didn't.
For a test tone of dBFS, the M Box 2 produced an analogue output level of dB. The original M Box produced an output of dB, whereas the R did produce an output level of 0dB.
I can only assume that the higher-level output cannot be achieved because of limitations on the amount of power the M Box 2 Pro can receive from the host down the Firewire cable.
I also wanted to see if the Pro label meant any improvements in the mic preamps, so I ran a test with speech. This can be quite telling on a mic preamp, especially in revealing its noise floor — you often need high gain settings for speech, especially in radio, when you often want to create a more intimate sound.
I first recorded using my original M Box with its Focusrite preamps, and then, without changing the mic position, swapped over to the M Box 2 Pro and recorded the same voice again.
To my ears, the M Box 2 Pro sounded smoother and fuller, and the 'silence' sounded less grainy. Main menu: Drag the description out of the way.
Tap the third button on the top to light it up, then press PLAY. It goes It will then say Tap the red LOCK button until the glass over it shatters.
Then press the button itself. Five more buttons will appear. The clue for them is the Tap the first two and the last one to copy that sequence.
Then press the red button again. Level 2: Notice the words RESERVE POWER — Enter into the combination lock and press the green button.
Drag the battery to the magnifying glass to turn the UV purple light on. They go in that order because of the number of dots around each of them.
So enter and press the the green button again to go to the next screen. Level 3: First, pull the lever to reveal the numbers Next hold the green button down and release it when the green light is on.
But once you manage it, a keypad will appear. Play with the lever until it breaks and then drag that piece to the right of the keypad. Turn on the keypad and enter Level 4: This is a grabber machine.
You need to enter 4-letter words to control it. Start with DOWN, then LEFT, DOWN, GRAB, BACK, DROP. Then OPEN. Drag the fuse to the left of the red lock button and press the button to clear the level.
Use it on the buttons to get a fuse. Place the fuse where the screwdriver was and slide it back in. Then, copy the pattern on the inside of the panel lid onto the light buttons and press the green button after it lights up.
Level 6: Pull the number pad down to reveal a screwdriver.