Supplementary Material for Cole & Bystroff

Supplementary Material for

Alpha helical crossovers favor right-handed supersecondary structures by kinetic trapping. The phone cord effect in protein folding.

Cole B & Bystroff C. (2009) Alpha helical crossovers favor right-handed supersecondary structures by a kinetic trapping mechanism. The phone cord effect in protein folding. Protein Science 18(8) 1602 - 1608

Rensselaer Polytechnic Institute, Dept of Biology

Supplementary Figure 1.
Proposed late stage of the folding of knotted protein 1MXI. (a) Native structure, showing C-terminal helix (blue) inserted through helical crossover loop (green). (b) Proposed non-native folding intermediate with no knot, drawn using TOPS conventions. (c) C-terminal helix formation rotates hydrophobic loop against α5 crossover. (d) α7 is pulled through the loop as it forms, creating a knot.

Supplementary Figure 2. *

Proposed folding pathway for knotted protein 1YVE, chain I, using the phone cord effect. (see erratum in footnote) (a) Formation of a non-local 4-helix bundle, proposed by Taylor, followed by the collapse of the central segment against the 4-helix bundle (arrows). (b) Collapse of the C-terminal segment over contacting helices (red). (c) Proposed non-native folding intermediate with left-handed helical crossover (red - green - red). Small arrow shows direction of torque produced by the phone cord effect. (d) Formation of a helix drives the green loop towards a right-handed crossover. Large arrows show the rolling trajectory. Small arrow shows the direction of the torque. (e) Native structure. Large arrows show the rolling trajectory of the green loop over the magenta C-terminus, creating a knot.

Supplementary Table 1.

Handedness of all three-helix bundles. Listed are all 3-helix bundles within all-alpha class proteins, filtered for non-redundancy at the SCOP superfamily level. Columns as follows. PDB code/chain, R/L: right or Left handed super-helicity as defined by Eq 2. frac R: fraction of contacts found to be right-handed. accoring to Eq 1. Contacts: number of contacting pairs of C-alphas (distance < 8Å) between helix 1 and helix 3. Helix residue ranges: first and last residue, using PDB numbering.

Supplementary Movie 1.

South. Simultaneous angular shifts in ψ for a 8-residue peptide, from positive (extended) to negative (helical), through ψ =0°, pass through 3-10 helix on the way to α-helix. The chain does not cross itself.

Supplementary Movie 2.

North. Simultaneous angular shifts in ψ for a 8-residue peptide, from positive (extended) to negative (helical), through ψ =180°, The chain must cross itself.

Analysis of folding of 3-helix bundle by MD.

MD simulations by the Martin Gruebele group at UIUC show the phone cord effect in the formation of the 3-helix bundle villin headpiece protein.

Simulation: The forwards phone cord effect -- helix angles go South

Simulation: The backwards phone cord effect -- helix angles go North

*ERRATUM: In the published text this knotted protein is erroneously given as PDB code 1LVE, instead of 1YVE. The authors regret this typographical error and the subsequent mislabeling of the protein as "immunoglobin light chain", instead of its true identity "acetohydroxy acid isomeroreductase."

Supplementary Figure 1. Proposed late stage of the folding of knotted protein 1MXI. (a) Native structure, showing C-terminal helix (blue) inserted through helical crossover loop (green). (b) Proposed non-native folding intermediate with no knot, drawn using TOPS conventions. (c) C-terminal helix formation rotates hydrophobic loop against α5 crossover. (d) α7 is pulled through the loop as it forms, creating a knot.
Supplementary Figure 2. * Proposed folding pathway for knotted protein 1YVE, chain I, using the phone cord effect. (see erratum in footnote) (a) Formation of a non-local 4-helix bundle, proposed by Taylor, followed by the collapse of the central segment against the 4-helix bundle (arrows). (b) Collapse of the C-terminal segment over contacting helices (red). (c) Proposed non-native folding intermediate with left-handed helical crossover (red - green - red). Small arrow shows direction of torque produced by the phone cord effect. (d) Formation of a helix drives the green loop towards a right-handed crossover. Large arrows show the rolling trajectory. Small arrow shows the direction of the torque. (e) Native structure. Large arrows show the rolling trajectory of the green loop over the magenta C-terminus, creating a knot.
Supplementary Table 1. Handedness of all three-helix bundles. Listed are all 3-helix bundles within all-alpha class proteins, filtered for non-redundancy at the SCOP superfamily level. Columns as follows. PDB code/chain, R/L: right or Left handed super-helicity as defined by Eq 2. frac R: fraction of contacts found to be right-handed. accoring to Eq 1. Contacts: number of contacting pairs of C-alphas (distance < 8Å) between helix 1 and helix 3. Helix residue ranges: first and last residue, using PDB numbering.
Supplementary Movie 1. South. Simultaneous angular shifts in ψ for a 8-residue peptide, from positive (extended) to negative (helical), through ψ =0°, pass through 3-10 helix on the way to α-helix. The chain does not cross itself.
Supplementary Movie 2. North. Simultaneous angular shifts in ψ for a 8-residue peptide, from positive (extended) to negative (helical), through ψ =180°, The chain must cross itself.
Analysis of folding of 3-helix bundle by MD. MD simulations by the Martin Gruebele group at UIUC show the phone cord effect in the formation of the 3-helix bundle villin headpiece protein.
Simulation: The forwards phone cord effect -- helix angles go South
Simulation: The backwards phone cord effect -- helix angles go North