Artificial antibody created by conformational reconstruction of the complementary-determining region on gold nanoparticles

Abstract

SignificanceMimicking protein-like specific interactions and functions has been a long-pursued goal in nanotechnology. The key challenge is to precisely organize nonfunctional surface groups on nanoparticles into specific 3D conformations to function in a concerted and orchestrated manner. Here, we develop a method to graft the complementary-determining regions of natural antibodies onto nanoparticles and reconstruct their “active” conformation to create nanoparticle-based artificial antibodies that recognize the corresponding antigens. Our work demonstrates that it is possible to create functions on nanoparticles by conformational engineering, namely tuning flexible surface groups into specific conformations. Our straightforward strategy could be used further to create other artificial antibodies for various applications and provides a new tool to understand the structure and folding of natural proteins.

How the Avidity of Polymerase Binding to the -35/-10 Promoter Sites Affects Gene Expression

“…This process, which was done without recourse to fitting, demonstrated that the -35 and -10 elements bind in a concerted manner that we postulated is caused by avidity. In this context, avidity implies that when RNAP is singly bound to either the -35 or -10 sites, it is much more likely (compared to unbound RNAP) to bind to the other site, similar to the boost in binding seen in bivalent antibodies (17) or multivalent systems (13,18,19). Surprisingly, we found that outside the -35/-10 pair, the other components of the promoter contributed independently to RNAP binding.…”

“…Finally, we end by zooming out from the particular context of transcription regulation and note that multivalent interactions are prevalent in all fields of biology (22), and our work suggests that differentiating between independent and dependent interactions may be key to not only characterizing overall binding affinities but to also understand the dynamics of a system (23). Such formulations may be essential when dissecting the much more complicated interactions in eukaryotic transcription where large complexes bind at multiple DNA loci (24,25) and more broadly in multivalent scaffolds and materials (12,13).…”

“…While this work focuses on RNAP-promoter binding, its implications extend to general regulatory architectures involving multiple tight-binding elements including transcriptional activators that make contact with RNAP (CRP in the lac promoter (9)), transcription factors that oligomerize (as recently identified for the xylE promoter (6)), and transcription factors that bind to multiple sites on the promoter (DNA looping mediated by the Lac repressor (10)). More generally, this approach of categorizing which binding elements behave independently (without resorting to fitting) can be applied to multivalent interactions in other biological contexts including novel materials, scaffolds, and synthetic switches (12,13).…”

Uncovering temporally sensitive targeting motifs for traumatic brain injury via phage display

“…Methodology to produce dAbs is time consuming and resource intensive due to difficulties maintaining stability after purification and degradation of affinity tags [27,28]. To address these limitations "synthetic antibody"-type constructs have been developed by taking advantage of the antigen binding qualities of the dAb HCDR3 [29][30][31][32]. These constructs are functional at an even smaller scale, as they are solely derived from the HCDR3 sequence and modified for stability.…”

“…These constructs are functional at an even smaller scale, as they are solely derived from the HCDR3 sequence and modified for stability. HCDR3 constructs have been shown to mimic the binding specificity and capacity of full-length antibodies for factors such as platelet aggregation and HIV-1 promoter at a fraction of the size [30,32] and demonstrate the ability to be integrated with nanoparticle engineering to facilitate protein-like functionality in the nanoparticle [29].…”