First, in model proteins containing chiefly short-ranged (local in sequence) contacts, cotranslational folding is shown to be significantly faster than direct folding from the denatured state.
In these instances, the availability of additional sequence contacts may have compensated for the disrupted interaction with PCAF Tyr640 caused by Arg8 modifications, which our kinetic studies revealed to affect peptide affinity.
This element lies in fragment 10, immediately upstream of the sequence contacted by the promoter in intron 1.
Our linear regression-based, parameter-free, sequence-derived GNM (L-pfSeqGNM) uses contact maps predicted from the sequence and models local, in the sequence, contact neighborhoods with the linear regression.
This technique allows clear resolution of the DNA sequences contacted by wH and ISM.
For example, if the number of aligned sequences is greater than the sum of the lengths of the two proteins, residue residue contact predictions are likely to be accurate if the coupling strength is 2 or greater, while if there are twice as many sequences, contact predictions are accurate above a coupling strength of 1.5 (the cutoff shown in Figure 1A).
Play can be graded along a gradient of intensity, going from gentle play, involving no body contact (e.g. play run) or a sequence of contact and/or no-contact patterns, to rough play (or rough and tumble), involving fighting with a series of body contact patterns normally performed in rapid succession (e.g. biting, pushing, pulling, rolling, falling on the ground) [26], [48].
In fact, by concatenating the rows in a contact map and creating a 1D sequence of contacts, the CMAPi algorithm can be mapped to a specific case of 1D sequence alignment with a complex, position-dependent gap penalty structure as defined by Equation (3). Figure 2 illustrates the mapping of a 2D contact map onto a 1D string.
In every realization (simulation run), the contact record was stepped through like an animation, creating exactly the same sequence of contacts in the course of every Monte Carlo realization, which we have termed a Groundhog Day technique, after the 1993 movie of the same name.
At the beginning of the mating sequence, antennal contacts allow males to assess key information (sex and relatedness) concerning the quality of the encountered partner and this helps them to decide whether to invest or not in vigorous courting displays.
We note that GNM and its variations use the local, in the sequence, residue residue contacts.
