Accurate and efficient protein sequence design through learning concise local environment of residues.

MOTIVATION: Computational protein sequence design has been widely applied in rational protein engineering and increasing the design accuracy and efficiency is highly desired. RESULTS: Here, we present ProDESIGN-LE, an accurate and efficient approach to protein sequence design. ProDESIGN-LE adopts a concise but informative representation of the residue's local environment and trains a transformer to learn the correlation between local environment of residues and their amino acid types. For a target backbone structure, ProDESIGN-LE uses the transformer to assign an appropriate residue type for each position based on its local environment within this structure, eventually acquiring a designed sequence with all residues fitting well with their local environments. We applied ProDESIGN-LE to design sequences for 68 naturally occurring and 129 hallucinated proteins within 20 s per protein on average. The designed proteins have their predicted structures perfectly resembling the target structures with a state-of-the-art average TM-score exceeding 0.80. We further experimentally validated ProDESIGN-LE by designing five sequences for an enzyme, chloramphenicol O-acetyltransferase type III (CAT III), and recombinantly expressing the proteins in Escherichia coli. Of these proteins, three exhibited excellent solubility, and one yielded monomeric species with circular dichroism spectra consistent with the natural CAT III protein. AVAILABILITY AND IMPLEMENTATION: The source code of ProDESIGN-LE is available at https://github.com/bigict/ProDESIGN-LE.

Systematic design and application of unimolecular star-like block copolymer micelles: a coarse-grained simulation study.

Unimolecular polymeric micelles have several features, such as thermodynamic stability, small particle size, biocompatibility, and the ability to internalize hydrophobic molecules. These micelles have recently attracted significant attention in various applications, such as nano-reactors, catalysis, and drug delivery. However, few attempts have explored the formation mechanisms and conditions of unimolecular micelles due to limited experimental techniques. In this study, a unimolecular micelle system formed from ß-cyclodextrin-graft-{poly(lactide)-block-poly(2-(dimethylamino) ethyl multimethacrylate)-block-poly[oligo (2-ethyl-2-oxazoline) methacrylate]} ß-CD-g-(PLA-b-PDMAEMA-b-PEtOxMA) star-like block copolymers in aqueous media was investigated by dissipative particle dynamics (DPD) to explore the formation process of unimolecular micelles. The simulation results showed that using longer hydrophobic or pH-sensitive chains, shorter hydrophilic backbones, smaller hydrophilic side chain grafting density, and fewer polymer arms resulted in micellar aggregation. Furthermore, this unimolecular polymeric micelle could be used for encapsulating gold nanoparticles, whose mesoscopic structure was also explored. The gold nanoparticles tended to distribute in the middle layer formed by PDMAEMA, and the unimolecular micelles were capable of impeding gold nanoparticle aggregation. This study could help understand the formation mechanism of unimolecular micelles formed from star-like block copolymers in dilute solutions and offer a theoretical guide to the design and preparation of promising unimolecular polymeric micelles with targeting properties.

pH-responsive micelles based on (PCL)2(PDEA-b-PPEGMA)2 miktoarm polymer: controlled synthesis, characterization, and application as anticancer drug carrier.

Amphiphilic A2(BC)2 miktoarm star polymers [poly(ϵ-caprolactone)]2-[poly(2-(diethylamino)ethyl methacrylate)-b- poly(poly(ethylene glycol) methyl ether methacrylate)]2 [(PCL)2(PDEA-b-PPEGMA)2] were developed by a combination of ring opening polymerization (ROP) and continuous activators regenerated by electron transfer atom transfer radical polymerization (ARGET ATRP). The critical micelle concentration (CMC) values were extremely low (0.0024 to 0.0043 mg/mL), depending on the architecture of the polymers. The self-assembled empty and doxorubicin (DOX)-loaded micelles were spherical in morphologies, and the average sizes were about 63 and 110 nm. The release of DOX at pH 5.0 was much faster than that at pH 6.5 and pH 7.4. Moreover, DOX-loaded micelles could effectively inhibit the growth of cancer cells HepG2 with IC50 of 2.0 µg/mL. Intracellular uptake demonstrated that DOX was delivered into the cells effectively after the cells were incubated with DOX-loaded micelles. Therefore, the pH-sensitive (PCL)2(PDEA-b-PPEGMA)2 micelles could be a prospective candidate as anticancer drug carrier for hydrophobic drugs with sustained release behavior.

Amphiphilic miktoarm star copolymer (PCL)3-(PDEAEMA-b-PPEGMA)3 as pH-sensitive micelles in the delivery of anticancer drug.

Well-defined A3(BC)3 type amphiphilic miktoarm star polymers poly(ε-caprolactone)3-[poly(2-(diethylamino)ethyl methacrylate)-b-poly(poly(ethylene glycol) methyl ether methacrylate)]3 [(PCL)3-(PDEAEMA-b-PPEGMA)3] and their pH-sensitive self-assembled polymeric micelles were developed as anticancer vehicles for improved cancer therapy. These miktoarm star polymers were synthesized by a combination of ring opening polymerization (ROP) and continuous activators regenerated by electron transfer atom transfer radical polymerization (ARGET ATRP) and characterized by GPC and 1H NMR measurement. The CMC values of the miktoarm star polymers in aqueous solution were extremely low (0.0029-0.0035 mg mL-1), suggesting that the micelles are relatively stable in solution. The self-assembled blank and doxorubicin (DOX)-loaded micelles were spherical in morphology with average sizes of 110-240 nm depending on the architecture of the copolymers, which were determined by transmission electron microscopy (TEM) and dynamic light scattering (DLS). When decreasing pH from 7.4 to 5.0, the micelles underwent globule-uneven-extended conformational transitions, and in vitro drug release rates were significantly accelerated, owing to the swelling of micelles at lower pH conditions caused by the protonation of tertiary amine groups of DEAEMA. Moreover, the drug release profiles at different pH values were well fitted by a semi-empirical equation. The in vitro cytotoxicity of DOX-loaded micelles against HepG2 cells suggested that DOX-loaded (PCL)3-(PDEAEMA-b-PPEGMA)3 micelles exhibited similar anti-tumor activities to free DOX, with at least 80% decrease in cell viability after 48 h incubation. Intracellular uptake demonstrated that DOX was delivered into the cells effectively after the cells were incubated with DOX-loaded micelles. The results demonstrated that the pH-responsive (PCL)3-(PDEAEMA-b-PPEGMA)3 micelles could be used as latent vehicles for delivering hydrophobic anticancer drugs with controlled and sustained release behavior.