Tertiary Structure-Based Prediction of How ATRP Initiators React with Proteins

Abstract

The growth of polymers from the surface of proteins via controlled radical polymerization depends on the attachment of small molecule initiators to amino acid residues. Our ability to control and harness the power of polymer-based protein engineering is reliant on the accuracy of prediction where and how fast atom transfer radical polymerization (ATRP) initiators will react with a protein surface. We performed a systematic characterization of the reaction between a bromine-functionalized N-hydroxysuccinimide amine-reactive ATRP initiator and the amino groups in lysozyme and chymotrypsin. The tertiary structures of the proteins were used to predict computationally α-amino group and lysine side-chain accessibility and analyze the chemical and structural environment of the amino groups. To predict reactivity from accessibility calculations, a probe radius that resembled the size of the initiator molecule was used. Experimental data showed that the rate of initiator–protein modification at each amine site was related to surface accessibility but not the pK a of amino groups. Further refinements of the prediction of where the initiator modified the protein and in what sequence were achieved by considering the local environment of each amino group.

Advanced Materials by Atom Transfer Radical Polymerization

“…Differences in polymer–protein hybrid behavior were manifested in enzyme activity assays, indicating that responsive polymer–protein block copolymers of varied structures, architectures, and solution behavior can be used to control bioconjugate activity . The conjugates exhibited dramatic increases in enzyme stability over a wide range of temperatures indicating that one can manipulate enzyme kinetics and stability using polymer‐based protein engineering …”

A guide to maximizing the therapeutic potential of protein–polymer conjugates by rational design

“…Russell, Matyjaszewski, and co-workers studied conjugation of ATRP initiators to lysozyme and chymotrypsin, and concluded that a lysine must be sufficiently exposed; in addition, the microenvironment such as the presence of adjacent lysine and local charge affects the reactivity. 36 Bernardes, Jiménez-Osés, and co-workers used a sulfonyl acrylate reagent to selectively modify a single lysine in five different proteins (human serum albumin, synaptotagmin-I C2A domain, lysozyme, annexin-V, and trastuzumab). 37 High reactivity of the reagent allowed the most acidic lysine to be selectively modified at pH 8, and the conjugation reached complete conversion using equimolar amounts of the reagent.…”

Mapping protein–polymer conformations in bioconjugates with atomic precision

“…S3 † ). The number of polymers is estimated based on predicted reactivities 37 and conjugation sites observed by MALDI-TOF (Table S2 † ). CD gives the mean density of secondary structural elements (α-helices, β-strands, and coils) in a given system.…”