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The positive sign indicates an unfavorable contribution to folding.
Due to the highly electronegative charges on the InsP6, the electrostatic interactions make unfavorable contribution to ligand binding.
In this way, using solely sequence information, we generate for a given sequence a corrected score which takes into account both the relative propensities of the amino acids and the unfavorable contribution of non-contiguous prolines to prion formation.
(Note that since the entire DSA length has 18 carbons, in each case, there is also an unfavorable contribution to ΔΔ G from exposure to solvent of the remaining methylenes on the polar end of the chain).
Our position-independent model accounts for the positive contribution of Q and N to prion induction, but also for the favorable contribution given by S and Y, and for the unfavorable contribution of C, E or W, among others (see Table 1).
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Based on these, energetically favorable and unfavorable contributions to the binding affinity can be assessed on an atomic level.
Both models consider that the loops make unfavorable contributions to the free energy of the pseudoknot.
The reason to predict both sequence-specific and non-specific binding residues is that the main determinants of specificity are the unfavorable contributions of "wrong" base pairs and specific binding will also require a large non-specific contribution to the binding free energy to achieve sufficient binding affinity [ 38].
The interaction between soluble CD4 and full-length, monomeric gp120 is characterized by a high affinity (Kd = 4 nM), wherein a highly favorable Δ H is observed; this favorable enthalpy change is however compensated by a significant unfavorable entropic contribution.
As is typical for this type of interactions, complex formation between HP1 and K9me3-modified peptides is mediated by a strong favorable enthalpy, with a slightly unfavorable entropic contribution.
It can be seen that the formation of the binary complexes at 25 °C is enthalpy driven in all cases: large enthalpic contributions overcome the large unfavorable entropic contributions to the binding.
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