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1.
Figure 8

Figure 8. From: Simultaneous Structure and Dynamics of a Membrane Protein using REDCRAFT: Membrane-bound form of Pf1 Coat Protein.

The dynamic profile of REDCRAFT in application to experimental data. The observed increase in error is consistent with that of simulated motion.

Paul Shealy, et al. J Magn Reson. 2010 November;207(1):8-16.
2.
Figure 3

Figure 3. From: Simultaneous Structure and Dynamics of a Membrane Protein using REDCRAFT: Membrane-bound form of Pf1 Coat Protein.

The dynamic profile of REDCRAFT for the static structure mbPf1 using simulated data. REDCRAFT’s computed error stays consistently below the expected experimental error. This is indicative of a well determined structure.

Paul Shealy, et al. J Magn Reson. 2010 November;207(1):8-16.
3.
Figure 7

Figure 7. From: Simultaneous Structure and Dynamics of a Membrane Protein using REDCRAFT: Membrane-bound form of Pf1 Coat Protein.

The structure of mbPf1 computed by REDCRAFT under the assumption of a static structure, using experimental data, is shown from different viewpoints in (a) and (b). The REDCRAFT structure (in green) is superimposed with the previously determined ensemble of NMR structures (in red).

Paul Shealy, et al. J Magn Reson. 2010 November;207(1):8-16.
4.
Figure 9

Figure 9. From: Simultaneous Structure and Dynamics of a Membrane Protein using REDCRAFT: Membrane-bound form of Pf1 Coat Protein.

Structure of fragments 4–13 and 20–45 determined individually using experimental data are shown in (a) and (b) respectively. The REDCRAFT structure is shown in green, with the previously reported NMR structures in red.

Paul Shealy, et al. J Magn Reson. 2010 November;207(1):8-16.
5.
Figure 2

Figure 2. From: Simultaneous Structure and Dynamics of a Membrane Protein using REDCRAFT: Membrane-bound form of Pf1 Coat Protein.

Ramachandran based dihedral constraints for a non-glycine (a) or a glycine (b) residue for use as REDCRAFT torsion angle constraints. Gray blocks represent the allowed torsion angles for consideration during REDCRAFT computations. The solution space for glycine differs due to its unique flexibility.

Paul Shealy, et al. J Magn Reson. 2010 November;207(1):8-16.
6.
Figure 4

Figure 4. From: Simultaneous Structure and Dynamics of a Membrane Protein using REDCRAFT: Membrane-bound form of Pf1 Coat Protein.

Structure from REDCRAFT (green) determined under the assumption of molecular rigidity, as compared to that of the actual structure (blue), shown from two different perspectives. The two structures are aligned by the transmembrane helix and display near parallel alignment of amphipathic helices.

Paul Shealy, et al. J Magn Reson. 2010 November;207(1):8-16.
7.
Figure 6

Figure 6. From: Simultaneous Structure and Dynamics of a Membrane Protein using REDCRAFT: Membrane-bound form of Pf1 Coat Protein.

The REDCRAFT structure (in green) computed using data from a protein undergoing internal dynamics is compared to the structures used to simulate a two-state jump (blue and purple). The structures are shown from different viewpoints in (a) and (b). These structures were aligned using the transmembrane helix.

Paul Shealy, et al. J Magn Reson. 2010 November;207(1):8-16.
8.
Figure 1

Figure 1. From: Simultaneous Structure and Dynamics of a Membrane Protein using REDCRAFT: Membrane-bound form of Pf1 Coat Protein.

The simulated two state motion of mbPf1, with the two states in blue (original model) and purple (second state model), as shown from two perspectives. The φ angle of the 19th residue is modified by 60°to produce the second model.

Paul Shealy, et al. J Magn Reson. 2010 November;207(1):8-16.
9.
Figure 5

Figure 5. From: Simultaneous Structure and Dynamics of a Membrane Protein using REDCRAFT: Membrane-bound form of Pf1 Coat Protein.

Dynamic profile from REDCRAFT using simulated data for the structure with internal dynamics. Motion is simulated at residue 19 and precedes a sudden jump in the REDCRAFT score, where it exceeds the experimental error. For mobile domains no single consistent order tensor exists, so the error grows during the analysis of these regions.

Paul Shealy, et al. J Magn Reson. 2010 November;207(1):8-16.

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