Fatma Briki, Jean Doucet, Catherine Etchebest Biophysical Journal

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A Procedure for Refining a Coiled Coil Protein Structure Using X-Ray Fiber Diffraction and Modeling Fatma Briki, Jean Doucet, Catherine Etchebest Biophysical Journal Volume 83, Issue 4, Pages 1774-1783 (October 2002) DOI: 10.1016/S0006-3495(02)73943-X Copyright © 2002 The Biophysical Society Terms and Conditions

Figure 1 Experimental fiber diffraction pattern from hard α-keratin in hair sample (A) (the fiber axis is vertical, called meridian). (1) the arc at 5.15Å spacing is directly related to the α-helix pitch projection along the coiled coil axis; (2) the broad spot at 9.8Å on the normal to the axis direction (equator) corresponds to the mean distance between α-helical axes, for comparison, a blow-up of the 5.15Å zone as used in the following calculated patterns is shown (B), along with a calculated pattern from an isolated experimental coiled coil (pdb code: 1D7M) (C); see the text for details. The dotted sharp arc on the simulated pattern indicates the 5Å position. Biophysical Journal 2002 83, 1774-1783DOI: (10.1016/S0006-3495(02)73943-X) Copyright © 2002 The Biophysical Society Terms and Conditions

Figure 2 Calculated patterns built from structures using different side chain positioning methods on an ideal coiled coil backbone conformation, all-g+ configuration of the side chains (A), side chains configured with SMD (B), Confmat (C), SCWRL (D), all-trans configuration (E). The dotted sharp arc indicates the 5Å position. Biophysical Journal 2002 83, 1774-1783DOI: (10.1016/S0006-3495(02)73943-X) Copyright © 2002 The Biophysical Society Terms and Conditions

Figure 3 Calculated χ1 distributions using different side chain positioning methods on an ideal coiled coil backbone conformation, SMD (A), Confmat (B), SCWRL (C). Biophysical Journal 2002 83, 1774-1783DOI: (10.1016/S0006-3495(02)73943-X) Copyright © 2002 The Biophysical Society Terms and Conditions

Figure 4 Calculated pattern from the experimental structure of the cortexillin coiled coil protein (pdb entry: 1D7M) (A), calculated patterns on the same backbone structure as in (A) but with the side chains configured using the different procedures (B) SMD, (C) Confmat, (D) SCWRL. Biophysical Journal 2002 83, 1774-1783DOI: (10.1016/S0006-3495(02)73943-X) Copyright © 2002 The Biophysical Society Terms and Conditions

Figure 5 trans configuration χ1 rate along two free molecular dynamics simulations from all-g+ initial structure (A) and RMSD from the initial structure along the MD calculation (B). Biophysical Journal 2002 83, 1774-1783DOI: (10.1016/S0006-3495(02)73943-X) Copyright © 2002 The Biophysical Society Terms and Conditions

Figure 6 Coiled coil side chain χ1 distribution from a selected molecular dynamics structure after the equilibration period (at 0.21ns). Biophysical Journal 2002 83, 1774-1783DOI: (10.1016/S0006-3495(02)73943-X) Copyright © 2002 The Biophysical Society Terms and Conditions

Figure 7 Calculated pattern from a selected MD structure 0.21ns (A), calculated patterns on the same backbone structure as in (A) but with the side chains configured using the different procedures (B) SMD, (C) Confmat, (D) SCWRL. Biophysical Journal 2002 83, 1774-1783DOI: (10.1016/S0006-3495(02)73943-X) Copyright © 2002 The Biophysical Society Terms and Conditions

Figure 8 Calculated pattern from a selected structure after 0.21ns backbone restrained molecular dynamics. Biophysical Journal 2002 83, 1774-1783DOI: (10.1016/S0006-3495(02)73943-X) Copyright © 2002 The Biophysical Society Terms and Conditions

Figure 9 Coiled coil side chain χ1 distribution from experimental cortexillin structure (A), side chains configured on the experimental cortexillin backbone using Confmat (B), SMD (C), SCWRL (D). Biophysical Journal 2002 83, 1774-1783DOI: (10.1016/S0006-3495(02)73943-X) Copyright © 2002 The Biophysical Society Terms and Conditions