| "Modeling of SAM-1 Riboswitch (apo state)" |
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Experimental Mass
30,100 Da |
| Experimental Details for BID: 1SAMRR |
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| Experiment ID: 42
In addition, this experiment links to experiment(s):
43
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| Collected at: ALS BL 12.3.1 |
| Contributors:
Rambo, R.P.
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Batey, R.T.
,
Stoddard, C.D.
,
Montange, R.K.
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| SAM-1 riboswitch binds a small metabolite (SAM). Crystal structures of bound and unbound states demonstrate nearly identical structures unlike in solution where SAXS data showed two distinct states of the riboswitch. The riboswitch appears to occupy a single bound state in the presence of SAM identical to the crystal structure whereas in the absence of SAM, the riboswitch appears to occupy many conformational states. Based on the X-ray crystal structure, SAXS data in the absence of SAM-1 was used as a modeling constraint in torsion angle molecular dynamic simulations. Results demonstrate a scissoring of the riboswitch for opening the metabolite binding site.
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| RNA samples were prepared maximally at 2 to 3 mg/ml and serially diluted at four different concentrations.
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Dmax → 82 Å
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Guinier Rg → 24.16 Å
Real Space Rg → 24.82 Å
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The Guinier plot is used to estimate the radius of gyration, Rg, which is taken from the slope of a line observed at low scattering angles (typically in the range where q* Rg < 1.3). This should be in reasonable agreement with the real space Rg.
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The Kratky plot is used to visually assess the degree of "unfoldedness" of a protein or RNA sample. The plot of a well-behaved folded protein approaches the baseline at high q values creating a parabolic shape similar to that for the Electron Pair Distribution Plot.
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A ENSEMBLE model was determined using the following:
| Simulation Method | FIRST, FRODA and CNS |
| Simulation Algorithm | limited torsion angle dynamics |
| Ensemble Size | 5000 |
| Selection Method | Genetic Algorithm |
| Member Size | 13 |
| Scoring Function | chi |
| Score | 1.0 |
Ensemble Fit
The red line is the calculated SAXS profile from the ENSEMBLE model scaled to the experimental SAXS curve (cyan).
Supportive Diagnostic Figure for ENSEMBLE Selection
Fig: Histogram analysis of EOM selection displaying four major distributions that represent four major structural classes of the SAM-1 riboswitch in solution (unbound). The varying conformational states suggest the riboswitch occupies many states in the unbound state.
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| Additional Experimental Details |
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| Title Modeling of SAM-1 Riboswitch (apo state) |
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| Description SAM-1 riboswitch binds a small metabolite (SAM). Crystal structures of bound and unbound states demonstrate nearly identical structures unlike in solution where SAXS data showed two distinct states of the riboswitch. The riboswitch appears to occupy a single bound state in the presence of SAM identical to the crystal structure whereas in the absence of SAM, the riboswitch appears to occupy many conformational states. Based on the X-ray crystal structure, SAXS data in the absence of SAM-1 was used as a modeling constraint in torsion angle molecular dynamic simulations. Results demonstrate a scissoring of the riboswitch for opening the metabolite binding site.
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| Publication Free state conformational sampling of the SAM-I riboswitch aptamer domain. Structure. 2010 Jul 14;18(7):787-97
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| Contributors
Rambo, R.P.
,
Batey, R.T.
,
Stoddard, C.D.
,
Montange, R.K.
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| Genomics and Proteomics
The experiment is
composed of a single gene/ORF
Abbreviated name: SAM1RSWTCH
Annotation:
SAM-1 aptamer domain from Thermoanearobacter tengocongensis metF-H2
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GGCUUAUCAA
GAGAGGUGGA
GGGACUGGCC
CGAGAAACCC
GGCAACCAGA
AAUGGUGCCG
AAUUCCUGCA
GCGGAAACGU
UGAAAGAUGA
GCCA
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| category | Residue composition (%) |
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| Nucleotides |
G (33.0) C (22.3) A (30.9) U (13.8) T (0.0) |
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| Mass: 30,796 Da | Total residues: 94 |
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