Fig 1.
(A) Schematic of CATCH peptide sequence and sidechain structure for CATCH(6K+) in blue, (6E-) in red and (6D-) in orange, (B) Front view of CATCH(6K+/6E-) and CATCH(6K+/6D-) fibril showing two stacked bilayer starting structures built in PACKMOL and rendered in Chimera.[10,11] Sidechain structures are represented using sticks and colored based on the schematic from (A). Backbones are represented using black arrows and are directed into or out of the page. (C) Side view of CATCH(6K+/6E-) and CATCH(6K+/6D-) system.
Fig 2.
Morphology of CATCH(6K+/6E-) and CATCH(6K+/6D-) co-assemblies.
(A) Cryogenic TEM micrographs of CATCH(6K+/6E-) and CATCH(6K+/6D-) in the sol state (1 mM total peptide). (B) Cryogenic SEM micrographs of CATCH(6K+/6E-) and CATCH(6K+/6D-) in the gel state (12 mM total peptide).
Fig 3.
Snapshots of (A-B) CATCH(6K+/6E-) and (C-D) CATCH(6K+/6D-) bilayers before and after 200 ns of simulation. Final structure of CATCH(6K+/6E-) and CATCH(6K+/6D-) have an average twist of -3.55 and -2.22° between neighboring peptides, respectively.
Fig 4.
Contact map for (A) CATCH(6K+/6E-) and (B) CATCH(6K+/6D-). Contacts are counted for all atoms in each single bilayer system and grouped by residue. Contacts between two atoms were determined using a distance cutoff of 7Å. Values reported are averaged over three independent MD simulations.
Table 1.
Summary of hydrogen bonding and LIE analysis for CATCH single bilayer structures.
Hydrogen bonds and salt bridges were calculated using geometric criteria: an angle cutoff of 135° and a distance cutoff of 3.0Å. Salt bridges were defined to be between the hydrogens on lysine’s ammonium group and the oxygens on glutamic acid or on aspartic acid’s α-carboxylic acid group. Salt bridge VDW and ELE interactions were calculated between the atoms on the lysine’s ammonium group and the atoms on glutamic acid and aspartic acid’s carboxylic acid group. VDW interactions between charged residues are calculated using the LIE approach and exclude backbone atoms. Values listed are averaged over three independent simulations.
Fig 5.
Snapshots of (A-B) CATCH(6K+/6E-) and (C-D) CATCH(6K+/6D-) two stacked bilayers before and after 200 ns of simulation. Distances between the second and third layer of each structure are indicated.
Table 2.
Summary of MMGBSA and LIE analysis for CATCH two stacked bilayer structures.
MMGBSA values for VDW and ELE energies are calculated by considering the interactions between the top bilayer and the bottom bilayer. LIE values for VDW energies are calculated by considering only the sidechain-sidechain interactions between the charged residues on the top bilayer and the bottom bilayer. Values listed are averaged over three independent simulations.
Fig 6.
DMD Snapshots of (A) CATCH(6K+/6E-) and (B) CATCH(6K+/6D-) over the course of a 16 μs DMD simulation. Cationic peptides containing lysine are represented in teal. Anionic peptides containing aspartic acid are represented in orange, while anionic peptides containing glutamic acid are represented in red. (C) Chronological snapshots of oligomer growth, conformation change, and elongation of a β-barrel in the CATCH(6K+/6D-) simulation.
Fig 7.
(A) Quantitative assessment of hydrogen bond formation over DMD simulation. (B) Analysis of free peptide depletion (orange), oligomerization (purple), and fibrillization (black).
Table 3.
Summary of DSSP analysis for each CATCH single peptide REMD simulation.
Average secondary content over all frames for each residue are reported. Helix is the sum of the averages for 3–10, alpha, and pi helices. The total value is the sum of the averages over each CATCH single peptide.