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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. These reactions included: 30 pmol DNA template and buffer containing 30 mM Tris-HCl pH 8.
Reactions were terminated with loading dye containing 8M urea. Eluted RNAs were then ethanol precipitated and re-suspended in water.
Experiments performed at high concentrations of monovalent ions included 4M KCl in the 2X SHAPE buffer. An extension reaction was then performed using Transcriptor reverse transcriptase Roche , as described previously Samples were subjected to PAGE separation, and all polyacrylamide gels were visualized and quantified as described previously 9.
Analytical Ultra Centrifugation was performed essentially as described previously 9 using a Beckman AUC XL-I with absorbance optics.
Absorbance measurements at nm were collected during centrifugation in an An60Ti rotor at 42, rpm for at least 4 hours. Density and viscosity calculations for each buffer was made using SEDNTERP.
Since no density and viscosity values for MnCl 2 are included in the SEDNTERP program, this buffer component was excluded from the analysis.
Since MnCl 2 was present at submmillimolar concentrations, data analysis was not significantly impacted by this exclusion.
Divalent ions titrations were performed in buffer containing 10 mM Tris-HCl pH 7. Data were analyzed using SedFt v9. The template for these reactions included the sequence of the B.
Following phenol:chloroform extraction and ethanol precipitation of the PCR product, in vitro T7 transcription reactions were set up as described above.
The resultant RNA products encompassed nucleotides of the B. Immediately downstream of the aptamer was an unpaired adenine nucleotide and the glmS ribozyme e.
This resulted in clear separation of the M-box RNA from the glmS RNA fragment. The band corresponding to M-box RNA was excised and the RNA recovered by passive elution.
Irregular crystals for the M-box RNA were obtained using hanging drop vapor diffusion by mixing 1. To obtain better quality crystals, an optimization was performed using an additive screen Hampton Research where 1.
Rod-shaped crystals were obtained in the presence of 50 mM ammonium sulfate as the additive. Crystals were picked from the crystallization drop and directly flash frozen in liquid nitrogen.
Another crystal from the same drop yielded higher resolution data 1. Data statistics are compiled in Table 1. M-box crystals from the same crystallization drop often displayed non-isomorphism.
This phenomenon has been noted in the past for crystals of the P4-P6 domain of group I intron X-ray diffraction data was indexed, integrated, and scaled using HKL Molecular replacement was performed against the 2.
The resulting solution showed good statistics with a Z score of Using this solution as a search model, molecular replacement was performed against the 1.
Rigid body refinement followed by simulated annealing was performed using phenix. Iterative model building using Coot along with refinement phenix.
Positive electron density in the F o -F c map was used for the assignment of water molecules. An anomalous difference fourier map created using sfall 45 was generated using the model and the 2.
The final model was refined to an Rfactor of Refinement statistics are shown in Table 1. Electrostatic potential calculations was performed using pdb2pqr 48 to prepare input files for APBS and APBS 49 and visualization was done using Pymol.
Illustrations were made using UCSF Chimera Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication.
As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form.
Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Coordinates and structure factors have been deposited in the Protein Data Bank with accession number 3PDR. National Center for Biotechnology Information , U.
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Journal List HHS Author Manuscripts PMC J Mol Biol. Author manuscript; available in PMC Apr 8. PMCID: PMC NIHMSID: NIHMS Arati Ramesh , Catherine A.
Wakeman , and Wade C. Author information Copyright and License information Disclaimer. Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, , USA.
Corresponding authors. Copyright notice. The publisher's final edited version of this article is available at J Mol Biol. See other articles in PMC that cite the published article.
Abstract The M-box riboswitch couples intracellular magnesium levels to expression of bacterial metal transport genes. Keywords: riboswitch, magnesium-RNA interaction, RNA folding, RNA structure, manganese, X-ray crystallography.
Open in a separate window. MATERIALS AND METHODS RNA preparation For AUC and SHAPE reactions, DNA templates were amplified by PCR from B. Crystallization and X-ray Data Collection Irregular crystals for the M-box RNA were obtained using hanging drop vapor diffusion by mixing 1.
Table 1 Data collection, refinement and stereochemistry. Structure determination X-ray diffraction data was indexed, integrated, and scaled using HKL Footnotes Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication.
Accession Numbers Coordinates and structure factors have been deposited in the Protein Data Bank with accession number 3PDR.
Giedroc DP, Arunkumar AI. Metal sensor proteins: nature's metalloregulated allosteric switches. Learn More. That listing sold. Check out the similar listings below.
Digidesign MBox 2 Mini USB Audio Interface Pro Audio Interfaces Digidesign. Follow this Product. Listings Price Guide Reviews.
Buy Used. Having broken away from the shackles of the USB 1. The M Box 2 Pro can be powered via the Firewire interface if you use a six-pin cable, or with the included power supply if your host computer offers a four-pin Firewire interface.
There's also a lot that hasn't changed with the M Box 2 Pro, such as the Pro Tools software, so I won't spend too much time going over that here.
For more information and background knowledge, read the Pro Tools 7 review in the January issue, the M Box 2 review in the November issue, the R review in the October issue and the original M Box review back in the June issue.
The M Box 2 Pro is a little bigger than the M Box 2, and only slightly heavier, at 1. It follows the same basic design, though Digidesign have wisely dropped the handle idea they introduced on the M Box 2.
I don't know anyone who uses an M Box 2 who has kept the handle on — the way it sticks out makes the M Box 2 very awkward to store.
The M Box 2 Pro still has input selection buttons that are slightly confusing, in that the word 'Line' doesn't appear on them — to access the Line input you select Mic and Pad.
The original M Box with its LEDs on the input selection was completely clear, even if the 'feature' of it defaulting to mic input was a pain.
Digidesign have maintained the separate monitor output that they introduced on the M Box 2, and have brought back the proper separate line outputs that the original M Box had but the M Box 2 didn't; these have also multiplied, giving six analogue outputs.
The Mix control has gone and so the Low Latency monitoring feature is handled by the Pro Tools software, just as it is with the and R interfaces.
This addresses one of the other 'cons' in our M Box 2 review, as Low Latency recording now applies to the digital inputs as well as the analogue ins.
Alternatively, it means you can have two sets of headphones attached and have them at different volumes.
I know a number of users who will find that feature very useful. A nice 'pro' touch is the addition of external word clock sync, both in and out, so it is now possible to digitally lock an M Box 2 Pro system to an external clock, which is something that even the M Box 2 Pro's bigger brothers the and R can't do.
Finally, Digidesign have added a footswitch socket, but the small print includes a note saying this feature won't be available at launch; apparently support is 'expected' in , but I am not going to hold my breath on that one!
According to Digidesign's compatibility charts, system requirements and the range of compatible machines for the M Box 2 and M Box 2 Pro are very similar.
One good piece of news for Mac users is that the former's lack of support for phantom power with first-generation 1. In addition, the 1GHz and 1.
The Windows laptop charts, meanwhile, show that a few machines that are on the M Box 2 list have not got approval for the M Box 2 Pro, such as the IBM Thinkpad T43 and, of course, Firewire is not standard on all Windows machines.
Digidesign had already released a revision version of the M Box 2 Pro software two days before the M Box 2 Pro was released, but the supplied Pro Tools 7.
I have DV Toolkit 2 on my Powerbook, so I installed the Digitranslator and MP3 update options to make sure I had the latest versions of these extras.
The software, of course, is essentially Pro Tools 7 , and so looks no different to the 7. The M Box 2 Pro also comes with the Ignition Pack and Digidesign's instrument plug-in Xpand!
One of the first things I wanted to check was whether the Pro Tools software shipped with the M Box 2 Pro would run the other LE hardware as well, or whether 7.
Now, order them according to the rainbow ROYGBIV , so it goes Red, Green, Blue — or Enter that into the keypad to clear the level.
Drag it to the cut wire to fix it. This next part is super annoying. You have to press the big green power button until the first dial lines up with the light.
Then continue and go through each one. Yeah, frustrating. Once you do it, the numbers for the code is hidden in plain sight. Enter and press the small green button to complete the level.
Level 8: Drag the gear on the lower left to the slot on the upper right and press the red button to turn on the screen. It says RANDOMIZE.
Just punch in random numbers and eventually it should work and show you the numbers So the key is the word RANDOMIZE.
Give each letter a number from 1 to 9. Enter Now the 0 button appears and you can enter ! You need to figure out which buttons to press to power up the keypad.
Once the keypad is powered on, slide the home button back down and reveal the numbers Enter those into the keypad to complete the level.
Level This is like a memory game. You need to match all the pairs of icons. Just keep trying till you get it. After that, press the KEY button to begin as it instructs.
It will give you six different sequences of symbols to copy. 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.