Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints

Journal of Chemical Theory and Computation, Год журнала: 2025, Номер unknown

Опубликована: Март 5, 2025

Coiled-coil proteins provide an excellent scaffold for multistate de novo protein design due to their established sequence-to-structure relationships and ability switch conformations in response external stimuli, such as changes pH or temperature. However, the computational of coiled-coil assemblies is challenging, it requires accurate estimates free energy differences between multiple alternative conformations. Here, we demonstrate how this challenge can be tackled using metadynamics simulations with orientational, positional conformational restraints. We show that, even subtle sequence variations, our protocol predict preferred topology dimers trimers, oligomerization states dimers, tetramers, well switching behavior a pH-dependent system. Our approach provides method predicting stability designs offers new framework computing binding energies protein-protein multiprotein complexes.

Язык: Английский

De Novo Design of Parallel and Antiparallel A₃B₃ Heterohexameric α-Helical Barrels

Biochemistry, Год журнала: 2025, Номер unknown

Опубликована: Апрель 14, 2025

The de novo design of α-helical coiled-coil peptides is advanced. Using established sequence-to-structure relationships, it possible to generate various assemblies with predictable numbers and orientations helices. Here, we target new assemblies, namely, A3B3 heterohexamer barrels. These designs are based on pairs sequences three heptad repeats (abcdefg), programmed a = Leu, d Ile, e Ala, g Ser, b c Glu make the acidic (A) chains Lys in basic (B) chains. rules ensure that desired oligomeric state stoichiometry readily achieved. However, controlling orientation neighboring helices (parallel or antiparallel) less straightforward. Surprisingly, find assembly helix sensitive length overhang between To study this, cyclically permutated peptide (the register) were analyzed. Peptides starting at (g-register) form parallel 6-helix barrel solution an X-ray crystal structure, whereas b- c-register antiparallel complex. In lieu experimental structures for peptides, AlphaFold-Multimer used predict atomistic models. considerably more sampling than default value required match models data, as many confidently predicted plausible generated incorrect orientations. This work reveals previously unknown influence register helical provides insights modeling oligopeptide complexes AlphaFold.

Язык: Английский