Population-based heteropolymer design to mimic protein mixtures

Abstract

Biological fluids, the most complex blends, have compositions that constantly vary and cannot be molecularly defined1. Despite these uncertainties, proteins fluctuate, fold, function and evolve as programmed2–4. We propose that in addition to the known monomeric sequence requirements, protein sequences encode multi-pair interactions at the segmental level to navigate random encounters5,6; synthetic heteropolymers capable of emulating such interactions can replicate how proteins behave in biological fluids individually and collectively. Here, we extracted the chemical characteristics and sequential arrangement along a protein chain at the segmental level from natural protein libraries and used the information to design heteropolymer ensembles as mixtures of disordered, partially folded and folded proteins. For each heteropolymer ensemble, the level of segmental similarity to that of natural proteins determines its ability to replicate many functions of biological fluids including assisting protein folding during translation, preserving the viability of fetal bovine serum without refrigeration, enhancing the thermal stability of proteins and behaving like synthetic cytosol under biologically relevant conditions. Molecular studies further translated protein sequence information at the segmental level into intermolecular interactions with a defined range, degree of diversity and temporal and spatial availability. This framework provides valuable guiding principles to synthetically realize protein properties, engineer bio/abiotic hybrid materials and, ultimately, realize matter-to-life transformations.

Sequence Patterning, Morphology, and Dispersity in Single-Chain Nanoparticles: Insights from Simulation and Machine Learning

“…While prior work has leveraged assembly protocols to bias structure formation (e.g., toward globular morphologies), here we show that dispersity outcomes (either SCNP size or nanostructural environments) might be manipulated either by setting particular precursor parameters or by tailoring sequences. Furthermore, with many demonstrations of using statistical ensembles of chains in functional materials, − it will be interesting to consider how distributions of chains can be designed to achieve target properties. Approaches to navigate such design tasks, particularly in the context of experimentally verifiable systems will be needed.…”

Protein‐Inspired Control over Synthetic Polymer Folding for Structured Functional Nanoparticles in Water

“…In their latest work, random copolymer mixtures with precise monomer ratios were synthesized to carry out specific functions. [25] Here, the random copolymers proved to be capable of assisting protein folding, enhancing the thermal stability of proteins, and acting as a synthetic substitute for the cytosol. In these studies, it was shown that complex, biologically relevant functions can be conducted by random copolymers without a defined primary sequence but instead consisting of a mixture of individual polymer chains only similar in their average monomer composition.…”

“…The random copolymers distributed themselves in the lipid bilayer, forming bilayer‐spanning segments, allowing for proton transport through the bilayer. In their latest work, random copolymer mixtures with precise monomer ratios were synthesized to carry out specific functions [25] . Here, the random copolymers proved to be capable of assisting protein folding, enhancing the thermal stability of proteins, and acting as a synthetic substitute for the cytosol.…”

“…Random copolymers have also been successfully used for the stabilization of proteins, in particular by the group of Xu. [25,214,215] Xu and coworkers designed random heteropolymers (RHPs) based on methacrylate monomers, being hydrophilic poly(ethylene glycol) methacrylate (PEGMA), hydrophobic methyl methacrylate (MMA) and 2-ethylhexylmethacrylate (2-EHMA), and the negatively charged 3-sulfopropyl methacrylate potassium salt (3-SPMA) in a specific ratio to perfectly compliment the exposed hydrophilic, hydrophobic, and positively charges surfaces areas of membrane proteins, respectively, see Figure 21. [214] Complexation between either oligopeptide/proton symporter PepTso or water channel aquaporin Z (AqpZ) with the random copolymers in water occurred successfully, resulting in the proper folding and stabilization of the membrane proteins in cell-free environments.…”

“…[13] Variations in the polymer's length and microstructure has allowed the formation of nanoparticles of different shapes and sizes. [14,15] Typically, one polymeric nanoparticle consists of one polymer chain, which is referred to by different names such as single chain polymeric nanoparticles (SCPN [5,13] or SCNP [2,16,17] ), unimolecular [18,19] or unimer [20,21] micelles, organic nanoparticles, [22,23] random heteropolymers, [24,25] or even amphiphilic folded copolymers. [26] The formation of polymeric nanoparticles bears resemblance to the folding of proteins in nature.…”