Chimeric single α-helical domains as rigid fusion protein connections for protein nanotechnology and structural biology

Abstract

Highlights d Three crystal structures and a cryo-EM structure of engineered fusion proteins d Rigid ER/K helix is used as a modular fusion protein linker d Crystal structure of a high-affinity calmodulin-binding peptide/calmodulin complex d Rigid fusion approach for structural biology and protein nanotechnology

Generalized Born Implicit Solvent Models Do Not Reproduce Secondary Structures of De Novo Designed Glu/Lys Peptides

“…Such motifs are found in all kingdoms of life and in ≈0.2–0.5% of all proteins and form stable α-helical structures in the absence of tertiary interactions. − As such, they are also called single α-helical domains (SAHs). Notably, MD simulations of these domains using different force fields and with explicit TIP3P water models have been able to reproduce the experimental helicities. ,− …”

“…Notably, MD simulations of these domains using different force fields and with explicit TIP3P water models have been able to reproduce the experimental helicities. 16 , 20 − 22 …”

“…Explicit solvent simulations give good results for similar peptides. ,− The recommendation to the protein designer currently would therefore be to use explicit solvent MD simulations. Inclusion of nonelectrostatic solvation terms may improve results and would be recommended for protein design applications with implicit solvent models.…”