However, side-chain grafting is limited by the availability of scaffolds with compatible backbone for a given epitope structure and offers no route to modify backbone structure to improve mimicry or binding affinity.
DNA flexibility over the extent of a single codon (i.e., codon linkage flexibility) was defined by the total sum conformational state, or sum TRX score, for the four phosphate (P) linkages on the leading strand DNA sugar phosphate backbone for a given codon (fig. 1 A).
For a given backbone and number of grafts per backbone, the compatibilizing efficiency of the graft copolymer first increases with increasing graft length.
The probability of circuit k to implement a given dynamic j = { G+, G-, P+(T+), P+ T-), P-(T+), P- T-)} described by the backbone sequence i can, thus, be calculated as: (11) where Ψ ijk is the number of equal dynamical outcomes j for a given backbone i in the k- th FFL and T jk the total number of backbone sequences implementing dynamic j.
We will define the protein template t′ to include the protein backbone, as well as the side-chains of all residues that are fixed and are not subject to rotamer-based modeling; let E t ′(B c ) be the template energy of the system for a given backbone B c. Let i r denote rotamer identity r at residue position i.
Because of our normalization, our PTM values for a given peptide backbone are not necessarily independent of each other.
For a given initial backbone conformation, the magnitude of the two flanking rotation angles θ1,2 and θ2,3 can thus be defined as a function of the magnitude of the primary rotation angle θ1,3.
The idealized backbone curves were used to develop a set of empirical equations that were able to reproduce the bilinearized backbone curve of a given pier.
This allows to calculate the probability for a given set of parameters to implement a certain backbone sequence i as (10) For a given FFL topology it is possible to find different sets of parameters compatible with such topology but implementing different dynamics among the six possibilities.
For a given backbone/graft composition, graft copolymers having fewer and longer grafts were more efficient at compatibilizing and stabilizing the co-continuous morphology.
For example, with folding, a given sequence should have the specified backbone rather than an alternative as its most stable state and also present a gap between this state and unfolded or misfolded states.
