The coiled-coil dimer is a widespread protein structural motif and, due to its designability, represents an attractive building block for assembling modular nanostructures. The specificity of coiled-coil dimer pairing is mainly based on hydrophobic and electrostatic interactions between residues at positions a, d, e, and g of the heptad repeat. Binding affinity, on the other hand, can also be affected by surface residues that face away from the dimerization interface. Here we show how design of the local helical propensity of interacting peptides can be used to tune the stabilities of coiled-coil dimers over a wide range. By designing intramolecular charge pairs, regions of high local helical propensity can be engineered to form trigger sequences, and dimer stability is adjusted without changing the peptide length or any of the directly interacting residues. This general principle is demonstrated by a change in thermal stability by more than 30 °C as a result of only two mutations outside the binding interface. The same approach was successfully used to modulate the stabilities in an orthogonal set of coiled-coils without affecting their binding preferences. The stability effects of local helical propensity and peptide charge are well described by a simple linear model, which should help improve current coiled-coil stability prediction algorithms. Our findings enable tuning the stabilities of coiled-coil-based building modules match a diverse range of applications in synthetic biology and nanomaterials.
COBISS.SI-ID: 6191642
Knots are some of the most remarkable topological features in nature. Self-assembly of knotted polymers without breaking or forming covalent bonds is challenging, as the chain needs to be threaded through previously formed loops in an exactly defined order. Here we describe principles to guide the folding of highly knotted single-chain DNA nanostructures as demonstrated on a nano-sized square pyramid. Folding of knots is encoded by the arrangement of modules of different stability based on derived topological and kinetic rules. Among DNA designs composed of the same modules and encoding the same topology, only the one with the folding pathway designed according to the "free-end" rule folds efficiently into the target structure. Besides high folding yield on slow annealing, this design also folds rapidly on temperature quenching and dilution from chemical denaturant. This strategy could be used to design folding of other knotted programmable polymers such as RNA or proteins.
COBISS.SI-ID: 5880858
Polipeptidi in polinukleotidi so naravni programabilni biopolimeri, ki se lahko sami sestavi v kompleksne terciarne strukture. V članku smo opisali sistem, na podobnem principu kot DNK nanostrukture, kjer smo za gradnike uporabili polipeptidne obvite vijačnice (CC) za izgradnjo proteinskih kletk, ki se same sestavijo in vitro ter in vivo. Pripravili in analizirali smo ) 20 kletk ki se zvijejo v tri poliedrske strukture - tetraeder, štiristransa piramida in trikotna prizma. Njihova stabilnost in kinetika zvitja sta bili podobni kot pri naravnih proteinih. Z uporabo metod SAXS, elektronske mikroskopije (EM) in biofizikalne analize smo potrdili pravilno zvitje. Dokazali smo tudi samosestavljanje tetraederske strukture v bakterijah, celicah sesalcev in miših brez prisotnosti vnetja. Pripravili smo platformo za modeliranje kletk v poljubnih oblikah.
COBISS.SI-ID: 6266906