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Metal-sensing regulatory metalloregulatory proteins coordinate metals with gene expression of transporters, metal-sequestering proteins, detoxification genes, and other factors.
Less studied are regulatory mechanisms for the most prevalent ions in the intracellular environment of a bacterium, namely potassium and magnesium, which are present at concentrations of approximately mM and 0.
This conformational change is coupled to the regulation of downstream genes. Understanding the molecular basis for these RNA-based mechanisms will provide important insights into metal-induced RNA folding pathways and reveal the general importance of magnesium homeostasis control strategies.
Metal ions share a complicated relationship with nucleic acids, playing a critical role in the formation of both secondary and tertiary structure.
In general, positively charged metal ions aid in neutralization of the highly negative RNA backbone, enabling the formation of complex bends, folds and long range contacts characteristic of complex RNA structures.
However, RNA-chelated ions have only been observed in small numbers; there are not enough ions to adequately shield the electronegative backbone by themselves.
Various degrees of interaction between metal ions and RNA have been reported, ranging from loose or indirect association to direct coordination of the metal ion.
The latter often involves the displacement of one or more water molecules from the inner hydration shell of the metal ion and substitution instead with functional groups from the RNA.
Less frequently, magnesium ions contact RNA nitrogens, such as the guanine N7 nitrogen It is through the cumulative effect of these interactions that many RNAs compact into their native conformational state.
These interactions have been well illustrated by classic structural studies of ribozymes such as the P4-P6 domain of the Group I intron and more recently, riboswitch RNAs.
Riboswitches are cis-acting regulatory RNAs in bacteria that associate with metabolites and regulate expression of downstream genes.
Most often, binding of the appropriate metabolite ligand is coupled to regulatory control of translation initiation or premature transcription termination, 15 , 16 , 17 , 18 , 19 although at least one riboswitch class controls the intracellular lifetime of its associated mRNA.
Additionally, two different riboswitch classes have been discovered, that respond not to metabolites, but instead to magnesium ions.
Indeed, recent biophysical data have suggested that divalent ions alone can promote a near native, compacted conformation for several riboswitch RNA classes, a structural configuration that resembles in part the final metabolite-bound state.
Understanding the basis for regulation by the M-box riboswitch will help reveal the underlying principles used by metal-sensing regulatory RNAs in bacteria and may lead to the molecular engineering of synthetic metalloregulatory RNAs as genetically encoded metal sensors.
Given the pivotal relationship between magnesium homeostasis mechanisms and bacterial pathogenesis, 26 , 27 , 7 analysis of the M-box riboswitch is also likely to provide clues into the mechanisms used by intracellular bacterial pathogens for modulation of the divalent ion conditions within the phagosome where they reside.
Equilibrium measurements of folding of the M-box aptamer tertiary structure by hydroxyl-radical footprinting and analytical ultracentrifugation revealed that divalent ions triggered a compacted tertiary conformation.
Also, the presence of cobalt III hexammine, which is isosteric with hexahydrated magnesium but is unable to make inner-sphere coordinations due to tight coordination of the amine ligands, did not elicit formation of the tertiary conformation.
Together, these results suggested that individual cation sites were specifically required for tertiary structure formation, including a requirement for inner-sphere coordinations to RNA.
From these data, it is unlikely that loosely associated, nonspecific cation interactions alone are responsible for the compacted native conformation.
Therefore, elucidating and characterizing specific cation binding sites is crucial for understanding the molecular mechanism of the M-box riboswitch.
One of the most successful methods for identifying specific RNA-metal interactions at high resolution is X-ray crystallography of metal-bound RNA complexes.
For example, an analysis of metal ions associated with the large ribosomal subunit revealed the presence of magnesium and 88 monovalent ions, most of which included at least one inner-sphere coordination to RNA atoms.
Similarly, a total of six well-ordered magnesiums were observed in a 2. However, the relative importance of each metal site is unclear from this structural model alone.
It is also possible that the folding pathway of the M-box RNA may involve specific cation sites in addition to those observed from the structural model.
Indeed, metal-RNA interactions are undoubtedly more dynamic than can be implied from a single structure, making it difficult to establish the functional relevance of individual cation binding sites from structural data alone.
A commonly used biochemical method for assessing the importance of individual metal ion binding sites is through substitution of phosphoryl oxygen atoms with sulfurs, 29 , 30 which exhibit a marked decrease in affinity for magnesium ions.
However, alternative explanations for such phosphorothioate substitutions are still possible, including perturbation of local structural features by the sulfur atom.
Previously, we searched for randomly substituted phosphorothioates that prevented magnesium-mediated compaction of the M-box RNA, 32 and observed remarkable agreement between sites of phosphorothioate interferences and the six magnesium sites observed in the prior structural model.
However, we also observed a small collection of phosphorothioate interferences within electronegative pockets that resembled cation sites, but which lacked metals in the structural model.
Based on this observation, we proposed a role for these sites as putative metal sites, perhaps operative during folding of the M-box RNA.
An additional method for investigating magnesium sites is through substitution with manganese. Typically, manganese can substitute for magnesium; however, the ability of manganese to bind to a particular RNA site may not necessarily prove it to be a magnesium site as the two ions exhibit different chemical characteristics 33 , 34 , 35 , These data also reveal a higher resolution structural model, at 1.
From the sum of all of these data we gain a more thorough understanding of the specific magnesium sites that are formed within the M-box tertiary structure, which are likely to play a critical role during metal-responsive regulation by M-box RNAs.
Divalent metal ions associate closely with RNA, occupying specific sites and serving to neutralize negatively charged pockets in the RNA. This charge neutralization likely stabilizes tertiary contacts and folding of the RNA.
However, in this study we wanted to compare the folding characteristics of M-box in the presence of different ions and elaborate on the interactions of other divalent ions with the M-box using structural probing techniques.
This compares to a value of 0. The Hill coefficients for these fits, however, showed similar values ranging from 4.
This suggests that the M-box may bind different metal ions with similar degrees of cooperativity but with varying affinity.
Circles that are yellow, green, red, and blue correspond to C, U, A, and G, respectively. Dashed lines indicate key tertiary contacts.
Reactions are shown for d physiological mM and e high 2. Curve-fitting analysis indicates an EC 50 value of 0. This difference is eliminated in the presence of high concentrations of monovalent ions.
These data show that in the presence of molar concentration of monovalents, all three divalents induce compaction of the M-box RNA at nearly identical concentrations.
Together, these results suggest that the M-box compacted state can be induced by multiple divalent ions, albeit at different concentrations.
However, metal-induced folding of the M-box RNA was similar for the different divalents in the context of high monovalent ions, suggesting that a common minimal number of divalent cation sites were required when low affinity metal interactions could be outcompeted by monovalent ions.
While this substitution resulted in the formation of crystals, the addition of 50 mM ammonium sulfate as an additive significantly improved diffraction quality.
The previously reported 2. This compacted native state appeared to be stabilized by multiple long-range nucleoside and base stacking interactions.
Four of these cation sites Mg1-Mg4 are located within a common region at the base of the molecule where the three helical elements converge.
The remaining two cation sites were located within an internal bulge of the P4 helix. Core 1 appears to stabilize key interhelical interactions at the portion where the three helices converged.
Core 2 may assist orientation of the L4 terminal loop to permit key long-range interactions. However, additional phosphorothioate interferences were identified at positions other than within the binding sites for M1-M6.
Several of these sites, which exhibited a similar overall strength of phosphorothioate interference, were found to be located within electronegative cavities reminiscent of the other cation binding pockets.
From these data we proposed the presence of three additional metal binding sites M7-M9. It is possible that these electronegative cavities represent relatively low occupancy sites and therefore were not observed in the 2.
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.
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You have to do them pretty quickly, before the timer runs out. Then it will give you a password. Press the first button of the password again and then it will give you a new one.
A diamond button will appear and now you can enter the real password. Secret Level Level 11 : Notice it says NUMBER ONE.
Drag the level 1 button to the first empty slot and it will turn into 11! Press on it to access level Now, look at the four number buttons.
Now look at the words NO POWER. The N and the E flicker, so you get OPOWR. Translate those into numbers and you get Press the buttons in that order.
A battery slot will appear. Pull the little metal piece in the lower left corner to the left to get a battery-shaped metal panel to appear.
Notice that each square has a corner cut off. So it goes Move the battery to the slot at the bottom. Now you have another clue:?
This is related to Pi, which is 3. Press the buttons in order of Press the red lock button to complete the secret level!
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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. I don't own an M Box 2 so I was unable to compare the preamps in that model.
The headphone outputs are satisfactory, and I had no problems driving both low-impedance and high-impedance headphones with them. Whilst recording I noticed a nice feature of the input section's peak level lights.
The peak level lights go green at around dBFS, so acting as a 'signal present' indicator. Then comes the clever bit: the lights go orange at around This is a very neat touch.
You can use the conventional TRS balanced jack inputs, but the M Box 2 Pro also includes an RIAA phono preamp, with two phono sockets for connecting a turntable.
You select the phono preamp by pressing the Phono button on the front panel to the right of the Aux input level. Digi have also thoughtfully included an earth terminal, which most turntables need to stop them from humming.
The Startup Guide is a little confusing here, in that it states 'Plug in your turntable, mixer, or similar outputs into the Aux In Phono inputs L and R '.
However, taking a mixer output into the phono inputs would overload the inputs, which are specifically designed to accommodate the output straight from the turntable cartridge and process it via the RIAA EQ curve as well.
Unlike any of the other interfaces in the current Pro Tools LE range, the M Box 2 Pro has the facility to use word clock, both in and out, so it is now possible to lock up a Pro Tools LE system to external word clock, which is not available even on the or R.
Both of these do limit the flexibility of the M Box 2 Pro, but the external word clock feature is nevertheless a major step forward in the Pro Tools LE product range.
This is a new feature in the software, and offered only when the M Box 2 Pro is in use. Digidesign have finally released the portable Firewire-based interface that many people felt the M Box 2 should have been.
The M Box 2 Pro packs a lot into a small box, and Digi have tried to please a broad range of users with this new version. My only real disappointment is that there aren't four mic preamps.