Characterization of the Specific Interactions between Nanoparticles and Proteins at Residue-Resolution by Alanine Scanning Mutagenesis

Abstract

The interaction between nanoparticles and proteins is a central problem in the nano-bio-fields. However, it is still a great challenge to characterize the specific interaction between nanoparticles and proteins in structural details. Using the Goldbodies, the artificial antibodies created by grafting complementary-determining regions (CDRs) of natural antibodies onto gold nanoparticles, as the models, we manage to identify the key residues of the CDR peptides on gold nanoparticles for the specific interactions by alanine scanning mutagenesis. Each and every residue of the CDR peptides on two Goldbodies (which specifically bind with hen egg white lysozyme and epidermal growth factor receptor, respectively) is mutated to alanine one by one, generating a total of 18 single-mutants of the two Goldbodies. Experimental results reveal that the key residues of the CDR peptides for the specific interactions between the two Goldbodies and the corresponding antigens are exactly the same as those in the natural antibodies, thus proving that the correct conformations of the CDRs of natural antibodies have been successfully reconstructed on AuNPs. This is the first residue-resolution structural illustration for the specific interaction between a designed nanoparticle and a protein.

A Potential MDM2 Inhibitor Formed by Restoring the Native Conformation of the p53 α‐Helical Peptide on Gold Nanoparticles

“…While the conjugation of peptides onto AuNPs is simple, the conformational engineering of the peptides on AuNPs is not. Though we had restored the binding conformation of the CDR peptides of natural antibodies on AuNPs [3,7] . The CDR peptides are in relatively flexible loop conformation, which might tolerate some degree of deviation, as long as the right conformation could be induced after binding with the target.…”

“…Previously, we developed a conformational engineering technique that could reconstruct the binding conformation of the complementary‐determining region (CDR) fragment of natural antibodies on the surface of AuNPs, and restore the antigen‐recognition function of the original natural antibody, resulted in a novel type of AuNP‐based artificial antibody, denoted as Goldbody [3] . And the results of alanine scanning mutagenesis technique demonstrate that the key residues of the CDR peptides on Goldbody for antigen‐recognition are exactly the same as those in the natural antibody, thus proving that the correct native conformations of the CDRs of natural antibodies have been successfully reconstructed [7] . Furthermore, unlike natural antibodies, Goldbody has excellent stability, and avoids the common immunogenicity problem of natural antibodies.…”

“…Natural proteins, the best “NPs” emerged from billions of years of evolution, are far superior to any human‐made nanomaterials in the way that they recognize their binding partners specifically, with almost no non‐specific binding to other proteins in the very crowded bio‐environments. However, when human‐made nanomaterials enter bio‐systems, they almost unavoidably bind non‐specifically with any proteins presented, [4–6] while specific interactions are rarely observed [3,7–9] . The dramatic different performance between human‐made nanomaterials and proteins is due to the fact that proteins fold precisely into unique conformations with “irregular” yet well‐defined surfaces.…”

Toward the Specificity of Bare Nanomaterial Surfaces for Protein Corona Formation

“…The creation of protein-like nanoparticles represents the Holy Grail in nanoscience, where the crucial challenge is to endow nanoparticles with protein-like specificity and enabling the abiotic material to interplay with biological systems [ 142 , 143 ]. In this view, as nanoparticles and proteins are entities of the same size, protein–protein interactions could inspire our comprehension of the selectivity between biological interfaces and synthetic, abiotic objects.…”

In-Silico Alanine Scanning Analysis on the Catalytic Residues of a Novel Β-Glucosidase From Trichoderma Asperellum Uc1

“…The more negative the value, the stronger the interaction between the side chain of the enzyme and ligand [14]. The method was useful to demonstrate the binding of human growth hormone (hGH) to hGH-binding protein (hGHbp) [15], ligandbinding pocket for the human Vitamin D receptor [16], and complete alanine scanning of the Esherichia coli RbsB ribose binding protein involved in chemoreceptor signaling [17] amongst many others.…”