Engineered nanoparticles enable deep proteomics studies at scale by leveraging tunable nano-bio interactions.

SignificanceDeep profiling of the plasma proteome at scale has been a challenge for traditional approaches. We achieve superior performance across the dimensions of precision, depth, and throughput using a panel of surface-functionalized superparamagnetic nanoparticles in comparison to conventional workflows for deep proteomics interrogation. Our automated workflow leverages competitive nanoparticle-protein binding equilibria that quantitatively compress the large dynamic range of proteomes to an accessible scale. Using machine learning, we dissect the contribution of individual physicochemical properties of nanoparticles to the composition of protein coronas. Our results suggest that nanoparticle functionalization can be tailored to protein sets. This work demonstrates the feasibility of deep, precise, unbiased plasma proteomics at a scale compatible with large-scale genomics enabling multiomic studies.

Formation of Copper(I) Oxide- and Copper(I) Cyanide-Polyacetonitrile Nanocomposites through Strong-Field Laser Processing of Acetonitrile Solutions of Copper(II) Acetate Dimer.

Irradiation studies of acetonitrile solutions of copper(II) acetate dimer ([Cu(OAc)2]2) using high energy, simultaneously spatially and temporally focused (SSTF) ultrashort laser pulses are reported. Under ambient conditions, irradiation for relatively short periods of time (10-20 s) selectively produces relatively small, narrowly size-dispersed (3.5 ± 0.7 nm) copper(I) oxide nanoparticles (Cu2O NPs) embedded in CuCN-polyacetonitrile polymers generated in situ by the laser. The Cu2O NPs become embedded in a CuCN-polyacetonitrile network as they form, stabilizing them and protecting the air-sensitive material from oxygen. Laser irradiation of acetonitrile causes fragmentation into transient radicals that initiate and terminate polymerization of acetonitrile. Control and mechanistic investigations reveal that HCN formed during laser irradiation reacts rapidly to reduce the Cu(II) centers in [Cu(OAc)2]2, leading to the formation of CuCN or, in the presence of water, Cu2O nanoparticles that bind and cross-link CuCN-polyacetonitrile chains. The acetate-bridged Cu(II) dimer unit is a required structural feature that functions to preorganize and direct the Cu(II) reduction and selective formation of CuCN and Cu2O nanoparticles. This study illustrates how rapid deposition of energy using shaped, ultrashort laser pulses can initiate multiple photolytic and thermal processes that lead to the selective formation of composite nanoparticle/polymer materials for applications in electronics and catalysis.

Gold Nanotriangle Formation through Strong-Field Laser Processing of Aqueous KAuCl4 and Postirradiation Reduction by Hydrogen Peroxide.

Femtosecond laser irradiation of aqueous KAuCl4 followed by postirradiation reduction with hydrogen peroxide (H2O2) is investigated as a new approach for the synthesis of gold nanotriangles (AuNTs) without any added surfactant molecules. Laser irradiation was applied for times ranging from 5 to 240 s, and postirradiation reduction of the solutions was monitored by UV-vis spectroscopy. Laser processing of aqueous KAuCl4 for 240 s, where the full reduction of Au(III) occurred during irradiation, produced spherical gold nanoparticles (AuNPs) with an average size of 11.4 ± 3.4 nm. Irradiation for shorter times (i.e., 15 s) resulted in the formation of laser-generated AuNP seeds (5.7 ± 1.8 nm) in equilibrium with unreacted KAuCl4 after termination of laser irradiation. The postirradiation reduction of these solutions by H2O2 produced a mixture of spherical and triangular AuNPs. Decreasing the laser irradiation time from 45 to 5 s significantly reduced the number of laser-generated Au seeds, the amount of H2O2 produced, and the rate of postirradiation reduction, resulting in the formation of a large number of AuNTs with sizes increasing from 29.5 ± 10.2 to 125 ± 43.2 nm. Postirradiation reduction is kinetically inhibited in the absence of laser-generated AuNP seeds.

Elucidating Strong Field Photochemical Reduction Mechanisms of Aqueous [AuCl4](-): Kinetics of Multiphoton Photolysis and Radical-Mediated Reduction.

Direct, multiphoton photolysis of aqueous metal complexes is found to play an important role in the formation of nanoparticles in solution by ultrafast laser irradiation. In situ absorption spectroscopy of aqueous [AuCl4](-) reveals two mechanisms of Au(0) nucleation: (1) direct multiphoton photolysis of [AuCl4](-) and (2) radical-mediated reduction of [AuCl4](-) upon multiphoton photolysis of water. Measurement of the reaction kinetics as a function of solution pH reveals zeroth-, first-, and second-order components. The radical-mediated process is found to be zeroth-order in [AuCl4](-) under acidic conditions, where the reaction rate is limited by the production of reactive radical species from water during each laser shot. Multiphoton photolysis is found to be first order in [AuCl4](-) at all pHs, whereas the autocatalytic reaction with H2O2, the photolytic reaction product of water, is second order.

Triangular gold nanoplate growth by oriented attachment of Au seeds generated by strong field laser reduction.

The synthesis of surfactant-free Au nanoplates is desirable for the development of biocompatible therapeutics/diagnostics. Rapid Δ-function energy deposition by irradiation of aqueous KAuCl4 solution with a 5 s burst of intense shaped laser pulses, followed by slow addition of H2O2, results in selective formation of nanoplates with no additional reagents. The primary mechanism of nanoplate formation is found to be oriented attachment of the spherical seeds, which self-recrystallize to form crystalline Au nanoplates.

Enhanced Competition at the Nano-Bio Interface Enables Comprehensive Characterization of Protein Corona Dynamics and Deep Coverage of Proteomes.

Introducing engineered nanoparticles (NPs) into a biofluid such as blood plasma leads to the formation of a selective and reproducible protein corona at the particle-protein interface, driven by the relationship between protein-NP affinity and protein abundance. This enables scalable systems that leverage protein-nano interactions to overcome current limitations of deep plasma proteomics in large cohorts. Here the importance of the protein to NP-surface ratio (P/NP) is demonstrated and protein corona formation dynamics are modeled, which determine the competition between proteins for binding. Tuning the P/NP ratio significantly modulates the protein corona composition, enhancing depth and precision of a fully automated NP-based deep proteomic workflow (Proteograph). By increasing the binding competition on engineered NPs, 1.2-1.7× more proteins with 1% false discovery rate are identified on the surface of each NP, and up to 3× more proteins compared to a standard plasma proteomics workflow. Moreover, the data suggest P/NP plays a significant role in determining the in vivo fate of nanomaterials in biomedical applications. Together, the study showcases the importance of P/NP as a key design element for biomaterials and nanomedicine in vivo and as a powerful tuning strategy for accurate, large-scale NP-based deep proteomic studies.

Rapid, deep and precise profiling of the plasma proteome with multi-nanoparticle protein corona.

Large-scale, unbiased proteomics studies are constrained by the complexity of the plasma proteome. Here we report a highly parallel protein quantitation platform integrating nanoparticle (NP) protein coronas with liquid chromatography-mass spectrometry for efficient proteomic profiling. A protein corona is a protein layer adsorbed onto NPs upon contact with biofluids. Varying the physicochemical properties of engineered NPs translates to distinct protein corona patterns enabling differential and reproducible interrogation of biological samples, including deep sampling of the plasma proteome. Spike experiments confirm a linear signal response. The median coefficient of variation was 22%. We screened 43 NPs and selected a panel of 5, which detect more than 2,000 proteins from 141 plasma samples using a 96-well automated workflow in a pilot non-small cell lung cancer classification study. Our streamlined workflow combines depth of coverage and throughput with precise quantification based on unique interactions between proteins and NPs engineered for deep and scalable quantitative proteomic studies.

Metal dication cross-linked polymer network colloids as an approach to form and stabilize unusually small metal nanoparticles.

Reduction of Cu(II) cations immobilized as cross-linkers in polyacrylate network colloids produce relatively small (~3 nm) Cu metal particles which are further tuned to smaller size (~1.5 nm) by partially substituting Ca(+2) for Cu(+2) in the polymer network colloid.

Palladium metal nanoparticle size control through ion paired structures of [PdCl4]2- with protonated PDMAEMA.

The mean diameter of palladium metal particles produced by citrate reduction of the (H(+))(n) PDMAEMA/[PdCl(4)](2-) aqueous system increases from 1.4 nm to 5.0 nm as the pH decreases from 6.3 to 3.3 and the (H(+))(n) PDMAEMA/[PdCl(4)](2-) species undergo conversion from a cross linked polymer network to a single chain structure.

Anionically cross linked homopolymer colloids applied in formation of platinum nanoparticles.

Diprotonic sulfuric and succinic acids react efficiently with the tertiary amine sites in polydimethylaminoethylmethacrylate (PDMAEMA) to produce polymer colloid nano-particles held together by dinegatively charged anions that cross link the partially protonated PDMAEMA homopolymer. This procedure is used to encorporate [PtCl(6)](2-) as a cross linker into the framework of well defined polymer network colloid particles that have dual roles as nanoreactors and a source of protective polymer coating. Reduction of the cross linking [PtCl(6)](2-) groups produces platinum metal nano-particles (1.12(.25)nm) that are relatively small and narrowly dispersed. Formation of colloid particles by reaction of diprotic acids with homopolymers that have proton accepting centers provides a convenient intentional route to incorporate a variety of homopolymers into self assembled polymer network materials for applications as nanoreactors and transport systems.