Residue-Specific Interactions of an Intrinsically Disordered Protein with Silica Nanoparticles and Their Quantitative Prediction

Abstract

Elucidation of the driving forces that govern interactions between nanoparticles and intrinsically disordered proteins (IDP) is important for the understanding of the effect of nanoparticles in living systems and for the design of new nanoparticle-based assays to monitor health and combat disease. The quantitative interaction profile of the intrinsically disordered transactivation domain of p53 and its mutants with anionic silica nanoparticles is reported at atomic resolution using nuclear magnetic spin relaxation experiments. These profiles are analyzed with a novel interaction model that is based on a quantitative nanoparticle affinity scale separately derived for the 20 natural amino acids. The results demonstrate how the interplay of attractive and repulsive Coulomb interactions with hydrophobic effects is responsible for the sequence-dependent binding of a disordered protein to nanoparticles.

Quantitative Binding Behavior of Intrinsically Disordered Proteins to Nanoparticle Surfaces at Individual Residue Level

“…Parameters λ j of Equation (1) represent the decay rates of the symmetric exponential decays associated with either electrostatic ( λ ± =13.2 number of residues) or hydrophobic ( λ 0 =4.2 number of residues) interactions, and were globally fitted based on the four IDP‐SNP interaction profiles (Figure E). It should be noted that the uncertainty in the interaction range λ j is relatively high, which explains how different interaction ranges for anionic and cationic residues were able to explain p53TAD data alone . Compared to the previous parametrization, the new FRIM is physically more realistic, more accurate, and much better transferable among a diverse set of IDPs.…”

“…Because IDP molecules constantly exchange between the surface‐bound state and the free state on a rapid timescale (>10 4 s −1 ), the slow‐down of their tumbling is manifested in an increase of the effective NMR transverse relaxation rate ( R 2 ) of each amide 15 N spin of the polypeptide backbone. The difference of residue‐specific 15 N‐ R 2 observed in the presence and absence of nanoparticles, termed Δ R 2 , provides a direct measure of the interaction strength between the nanoparticle and IDP residues …”

“…Δ R 2 differences of backbone 15 N‐ R 2 rates in the presence and absence of SNPs are plotted against the primary sequence for all four IDPs in Figure A–D. The interaction profile of each IDP is unique and displays large Δ R 2 modulations along the primary sequence, reflecting strong variations in the binding propensities in response to its specific amino‐acid sequence . The profiles of p53TAD and Pup both have several pronounced local maxima and minima.…”

“…To quantitatively determine the effect of individual residues on the Δ R 2 interaction profile, profiles of site‐directed mutants were measured (Figure ). The effect of Pro residue P27 in p53TAD is revealed when comparing the profile of wild‐type (WT) p53TAD with P27N mutant (Figure A), where Asn was used because of its very weak binding affinity . The difference between the two profiles, ΔΔ R 2 [p53TAD WT−P27N] (Figure B), shows a strong, but relatively localized effect, which can be approximated by a symmetric exponential centered at the mutation site.…”

“…For a quantitative understanding of these interaction profiles, we developed a generalization of the Free Residue Interaction Model (FRIM) (Figure , for details see SI). The model uses the inherent affinity a j of each amino‐acid type measured separately for all non‐negatively charged amino acids together with its interaction range λ j . The a j values, which are unitless amino‐acid specific quantities, are positive (negative) for attractive (repulsive) interactions.…”