Rapid characterization of protein chips using microwave-assisted protein tryptic digestion and MALDI mass spectrometry

We demonstrate that the microwave-assisted protein enzymatic digestion (MAPED) method can be successfully applied to the mass spectrometric characterization of proteins captured on the affinity surfaces of protein chips. The microwave-assisted on-chip tryptic digestion method was developed using a domestic microwave, completing the on-chip proteolysis reaction in minutes, whereas the previous on-chip digestion methods by incubation took hours of incubation time. For the model protein chips, antibody-presenting surfaces were prepared, where anti-α-tubulin1 and antibovine serum albumin (BSA) were immobilized on self-assembled monolayers. The resulting digestion efficiency, displaying sequence coverages of 30 and 14% for α-tubulin1 and BSA, respectively, was comparable to the previous time-consuming incubation studies. It allowed the characterization of immunosensed proteins by MASCOT search using peptide mass fingerprinting. In an example of this method for protein chip applications, BSA naturally involved in fetal bovine serum was unambiguously identified on a model protein chip by imaging mass spectrometry. This work shows that biomass spectrometry techniques can be implemented for surface mass spectrometry and biochip applications. Along with recent advances in imaging mass spectrometry, this technique will provide a new opportunity for high-speed, and thus high-throughput in the future, label-free mass spectrometric assays using protein arrays.     

Internal amino acid sequence analysis of proteins separated by gel electrophoresis after tryptic digestion in polyacrylamide matrix

Summary A method is described for obtaining peptide fragments for sequence analysis from microquantities of proteins separated by 1- or 2-dimensional polyacrylamide gel electrophoresis. After separation by electrophoresis, the proteins were stained with Coomassie Blue and excised. Proteolytic digestion with trypsin was performed directly in the polyacrylamide matrix. The resulting peptide fragments were eluted, separated by reversed phase HPLC, collected and sequenced in a gas phase sequencer. Excellent peptide recoveries allowed generation of extensive internal sequence information from picomole amounts of protein. The method thus overcomes the problem of obtaining amino acid sequence data from N-terminally blocked proteins and provides multiple, independent stretches of sequences that can be used to generate oligonucleotide probes for molecular cloning, to design synthetic peptides for inducing antibodies, and to search sequence databases for related proteins.     

Rheostatic control of tryptic digestion in a microscale fluidic system

Integrated fluidic systems that unite bottom-up and top-down proteomic approaches have the potential to deliver complete protein characterization. To circumvent fraction collection, as is conducted in current blended approaches, a technique to regulate digestion efficiency in a flow-through system is required. The present study examined the concept of regulating tryptic digestion in an immobilized enzyme reactor (IMER), incorporating mixed solvent systems for digestion acceleration. Using ovalbumin, cytochrome c, and myoglobin as protein standards, we demonstrate that tryptic digestion can be efficiently regulated between complete digestion and no digestion extremes by oscillating between 45 and 0% acetonitrile in the fluid stream. Solvent composition was tuned using programmable solvent waveforms in a closed system consisting of the IMER, a sample delivery stream, a dual gradient pumping system and a mass spectrometer. Operation in this rheostatic digestion mode provides access to novel peptide mass maps (due to substrate unfolding hysteresis) as well as the intact protein, in a reproducible and stable fashion. Although cycle times were on the order of 90 s for testing purposes, we show that regulated digestion is sufficiently rapid to be limited by solvent switching efficiency and kinetics of substrate unfolding/folding. Thus, regulated digestion should be useful in blending bottom-up and top-down proteomics in a single closed fluidic system.     

Principal component analysis of mass spectra of peptides generated from the tryptic digestion of protein mixtures

Principal component analysis (PCA) has been used to analyse mass spectral peptide profiles obtained from the enzymatic digestion of standard protein mixtures. Scores and loadings plots clearly revealed peptide fragments that differentiated one protein mixture from another. Peptide map search results identified with a high degree of certainty any additional proteins in these mixtures. As a proof-of-concept this methodology was applied to hepatic protein mixtures obtained from rats treated with two hepatotoxic compounds: methapyriline and SB-219994. Liver proteins were extracted, pre-separated by one-dimensional polyacrylamide gel electrophoresis, subjected to tryptic digestion and analysed by mass spectrometry. Two up-regulated proteins, glutathione S-transferase with methapyrilene and peroxisomal bifunctional enzyme with SB-219994, were identified in this manner.     

PAA-derived gold nanorods for cellular targeting and photothermal therapy

A single-step LbL procedure to functionalize CTAB-capped GNRs via electrostatic self-assembly is reported. This approach allows for consistent biomolecule/GNR coupling using standard carboxyl-amine conjugation chemistry. The focus is on cancer-targeting biomolecule/GNR conjugates and selective photothermal destruction of cancer cells by GNR-mediated hyperthermia and NIR light. GNRs were conjugated to a single-chain antibody selective for colorectal carcinoma cells and used as probes to demonstrate photothermal therapy. Selective targeting and GNR uptake in antigen-expressing SW 1222 cells were observed using fluorescence microscopy. Selective photothermal therapy is demonstrated using SW 1222 cells, where >62% cell death was observed after cells are treated with targeted A33scFv-GNRs.     

Functional Fe3O4@ZnO magnetic nanoparticle-assisted enrichment and enzymatic digestion of phosphoproteins from saliva

Saliva contains various proteins, particularly abundant are phosphoproteins, that may be related to disease occurrences and that play significant roles in a biological system. Thus, medical diagnostics will benefit tremendously if disease-related protein biomarkers are discovered from saliva. In this paper, we propose and demonstrate an approach using functional zinc oxide coated iron oxide magnetic nanoparticles (Fe₃O₄@ZnO MNPs) as affinity probes to selectively enrich phosphoproteins from complex saliva samples and as microwave absorbers to assist the enrichment and subsequent tryptic digestion of trapped proteins under microwave heating. The target species trapped by MNPs were characterized by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) combined with protein database search. Entire analysis time was shortened to less than 20 min. The detection limit of this approach for a monophosphopeptide was as low as 250 pM (10 μL).     

Plasmonic gold nanocrosses with multidirectional excitation and strong photothermal effect

We report a facile chemical synthesis of well-defined gold nanocrosses through anisotropic growth along both <110> and <001>, whereas gold nanorods grow only along either <110> or <001>. The multiple branching was achieved by breaking the face-centered-cubic lattice symmetry of gold through copper-induced formation of single or double twins, and the resulting gold nanocrosses exhibited pronounced near-IR absorption with a great extension to the mid-IR region. As studied by discrete dipole approximation (DDA) simulations, the entire nanocross gets excited even when one of the branches is exposed to incident light. The above properties make them useful as octopus antennas for capturing near-IR light for effective photothermal destruction of cells. The cell damage process was analyzed using the Arrhenius model, and its intrinsic thermodynamic characteristics were determined quantitatively. Besides effective photothermal treatment and two-photon luminescence imaging, the near- and mid-IR-absorbing gold nanocrosses may also find applications in IR sensing, thermal imaging, telecommunications, and the like.     

Functionalized magnetic micro- and nanoparticles: optimization and application to micro-chip tryptic digestion

The preparation of an easily replaceable protease microreactor for micro-chip application is described. Magnetic particles coated with poly(N-isopropylacrylamide), polystyrene, poly(2-hydroxyethyl methacrylate-co-ethylene dimethacrylate), poly(glycidyl methacrylate), [(2-amino-ethyl)hydroxymethylen]biphosphonic acid, or alginic acid with immobilized trypsin were utilized for heterogeneous digestion. The properties were optimized, with the constraint of allowing immobilization in a microchannel by a magnetic field gradient. To obtain the highest digestion efficiency, sub-micrometer spheres were organized by an inhomogeneous external magnetic field perpendicularly to the direction of the channel. Kinetic parameters of the enzyme reactor immobilized in micro-chip capillary (micro-chip immobilized magnetic enzyme reactor (IMER)) were determined. The capability of the proteolytic reactor was demonstrated by five model (glyco)proteins ranging in molecular mass from 4.3 to 150 kDa. Digestion efficiency of proteins in various conformations was investigated using SDS-PAGE, HPCE, RP-HPLC, and MS. The compatibility of the micro-chip IMER system with total and limited proteolysis of high-molecular-weight (glyco)proteins was confirmed. It opens the route to automated, high-throughput proteomic micro-chip devices.     

Implications of partial tryptic digestion in organic-aqueous solvent systems for bottom-up proteome analysis

For bottom-up MS, the digestion step is critical and is typically performed with trypsin. Solvent-assisted digestion in 80% acetonitrile has previously been shown to improve protein sequence coverage at shorter digestion times. This has been attributed to enhanced enzyme digestion efficiency in this solvent. However, our results demonstrate that tryptic digestion in 80% acetonitrile is less efficient than that of conventional (aqueous) digestion. This is a consequence of decreased enzyme activity beyond ∼40% acetonitrile, increased enzyme autolysis and lower protein solubility in 80% acetonitrile. We observe multiple missed cleavages and reduced concentration of fully cleaved digestion products. Nonetheless we confirm, through room temperature solvent-assisted digestion, a consistent improvement in protein sequence coverage when analyzed by mass spectrometry. These results are explained through the increased number of unique digestion products available for detection. Thus, while solvent-assisted digestion has clear merits for proteome analysis, one should be aware of the inefficiency of protein digestion though this protocol, particularly with absolute protein quantitation experiments.     

Nanoliter-volume protein enrichment, tryptic digestion, and partial separation based on isoelectric points by CE for MALDI mass spectral analysis

Sequence-specific proteolysis is an important part of protein identification by MS. Digestion of protein is commonly performed in-solution, in sample vials with volumes ranging from milli- to microliters. When digestion is performed with a sample volume below 1 microL, handling of solution and potential sample loss via adsorption become significant issues. In this report, a proof of concept for the digestion of a small volume protein solution inside a capillary was demonstrated using a discontinuous buffer system previously studied (Nesbitt, C. A., et al. J. Chromatogr. A 2005, 1073, 175-180). Upon voltage application, a pH junction was created by the discontinuous buffer. Using myoglobin as an example, the protein molecules were enriched at the junction with an estimated volume of a few nanoliters. A protease, trypsin, was then introduced to myoglobin at the junction by coenrichment to induce in-capillary digestion. The voltage application was then suspended to provide the necessary time (2 h) for the proteolysis to proceed. When completed, voltage application was resumed, and the discontinuous buffer reconcentrated the peptides formed from digestion. Importantly, the refocused peptides appeared to roughly elute according to their pIs, resulting in a partial separation. Direct sample deposition from capillary was performed to facilitate mass spectral analysis by MALDI. The partial separation, according to pI, offered the potential benefits of MALDI MS signal enhancement and provided supplementary pI information for peptide identity assignment.     

Microlens formation in microgel/gold colloid composite materials via photothermal patterning

We report on the nature of photothermally patterned regions inside self-assembled hydrogel nanoparticle materials containing coassembled colloidal Au. These composite materials are prepared from approximately 226-nm diameter particles composed of the environmentally responsive polymer, poly(N-isopropylacrylamide) (pNIPAm). Upon centrifugation to achieve a proper volume fraction, these close-packed assemblies display a sharp Bragg diffraction peak in the midvisible region of the spectrum and can be reversibly converted into a nondiffracting glassy material as the temperature is raised above the characteristic phase transition temperature of the polymer. The addition of 16-nm colloidal Au prior to centrifugation allows the homogeneous distribution of metal nanoparticles throughout the close-packed material. Localized heating is then possible upon excitation of the Au plasmon absorption with a frequency doubled Nd:YAG laser (lambda = 532 nm). Such localized heating events lead to patterned regions of ordered crystalline phases inside of bulk glassy phases. We illustrate that the nature of the locally patterned area results in the formation of a microlens due to density/refractive index gradient in the patterned crystalline region. The Gaussian power distribution of the incident beam is thought to be a contributing factor in the microlens formation. Microlens formation is shown by observing interference patterns similar to Newton's rings, which change over time as the region is formed. A true hallmark of the lens is also demonstrated by focusing an image through the patterned structure.     

Multilayer coating of gold nanorods for combined stability and biocompatibility

Engineering plasmonic nanostructures that simultaneously achieve high colloidal stability, high photothermal stability, low non-specific binding to biological specimens, and low toxicity is of significant interest to research in bionanotechnology. Using gold nanorods, we solved this problem by encapsulating them with a multilayer structure, silica, hydrophobic ligands, and amphiphilic-polymers. In comparison with nanorods covered with the conventional surface chemistries, such as surfactants, polyelectrolytes, thiolated polymers, and silica shells alone, the new nanorods remain single in various solutions and show remarkable stability against laser irradiation. We further demonstrated specific targeting and effective treatment of prostate tumor cells using nanorod-aptamer bioconjugates. This exquisitely formulated nanoencapsulation technology could potentially help stabilize other plasmonic nanostructures that are not in the most thermodynamically or chemically stable states, and should open exciting opportunities in nanotechnology-based imaging and therapeutics.     

Synthesis of different-sized gold nanostars for Raman bioimaging and photothermal therapy in cancer nanotheranostics

Gold nanoparticles(AuNPs) have been attractive for nanomedicine because of their pronounced optical properties.Here,we customerized the methods to synthesize two types of gold nanostars,Au nanostars-1 and Au nanostars-2,which have different spire lengths and optical properties,and also spherical AuNPs.Compared to nanospheres,gold nanostars were less toxic to a variety of cells,including macrophages.Au nanostars-1 and Au nanostars-2 also manifested a similar pattern of tissue distribution upon in vivo administration in mice to that of nanospheres,and but reveled less liver retention than nanospheres.Due to their strong absorption in the near-infrared(NIR),Au nanostars-2 induced a strong hyperthermia effect in vitro upon excitation at 808 nm,and elicited a robust photothermal therapy(PTT) efficacy in ablating tumors in a mouse model of orthotopic breast cancer using 4T1 breast cancer cells.Meanwhile,Au nanostars-1 showed a great capability to enhance the Raman signal through surface-enhanced Raman spectroscopy(SERS) in 4T1 cells.Our combined results opened a new avenue to develop Au nanostars for cancer imaging and therapy.     

Cancer cell imaging and photothermal therapy in the near-infrared region by using gold nanorods

Due to strong electric fields at the surface, the absorption and scattering of electromagnetic radiation by noble metal nanoparticles are strongly enhanced. These unique properties provide the potential of designing novel optically active reagents for simultaneous molecular imaging and photothermal cancer therapy. It is desirable to use agents that are active in the near-infrared (NIR) region of the radiation spectrum to minimize the light extinction by intrinsic chromophores in native tissue. Gold nanorods with suitable aspect ratios (length divided by width) can absorb and scatter strongly in the NIR region (650-900 nm). In the present work, we provide an in vitro demonstration of gold nanorods as novel contrast agents for both molecular imaging and photothermal cancer therapy. Nanorods are synthesized and conjugated to anti-epidermal growth factor receptor (anti-EGFR) monoclonal antibodies and incubated in cell cultures with a nonmalignant epithelial cell line (HaCat) and two malignant oral epithelial cell lines (HOC 313 clone 8 and HSC 3). The anti-EGFR antibody-conjugated nanorods bind specifically to the surface of the malignant-type cells with a much higher affinity due to the overexpressed EGFR on the cytoplasmic membrane of the malignant cells. As a result of the strongly scattered red light from gold nanorods in dark field, observed using a laboratory microscope, the malignant cells are clearly visualized and diagnosed from the nonmalignant cells. It is found that, after exposure to continuous red laser at 800 nm, malignant cells require about half the laser energy to be photothermally destroyed than the nonmalignant cells. Thus, both efficient cancer cell diagnostics and selective photothermal therapy are realized at the same time.     

Degradation of protein in nanoplasma generated around gold nanoparticles in solution by laser irradiation

We developed a method of protein degradation in an aqueous solution containing gold nanoparticles by irradiation of a pulse laser. In the present study, lysozyme was used as an example. Lysozyme degradation proceeded most efficiently when a pH of the solution was adjusted so that it was at the isoelectric point. The scheme of the lysozyme degradation is as follows: (1) Lysozyme molecules in the solution are neutralized and adsorbed on the gold nanoparticles with its pH value adjusted at the isoelectric point, (2) nanoplasma is generated in the close vicinity of a gold nanoparticle which is excited by an intense 532-nm laser, (3) lysozyme molecules in the nanoplasma are degraded into small fragments. Lysozyme degradation does not proceed efficiently at a pH value deviated from the isoelectric point because the lysozyme molecules are dissolved uniformly so that only a small portion of the lysozyme molecules are located in the vicinity of gold nanoparticles which create the nanoplasma.     

Analysis of pulsed laser plasmon-assisted photothermal heating and bubble generation at the nanoscale

A study is presented of photothermal effects associated with nanosecond-pulsed laser-illuminated subwavelength metallic nanoparticles in aqueous solutions. Computational electromagnetic and fluid analysis are used to model fundamental aspects of the photothermal process taking into account energy conversion within the nanoparticle at plasmon resonance, heat transfer to the fluid, homogeneous bubble nucleation, and the dynamic behaviour of the bubble and surrounding fluid. Various nanoparticle geometries are modelled including spheres, nanorods and tori. The analysis demonstrates that the laser intensity and pulse duration can be tuned to achieve controllable bubble generation without exceeding the melting temperature of the particle. The analysis also shows that the particle geometry can be tuned to optimize photothermal energy conversion for bubble generation at wavelengths that span the UV to NIR spectrum. Multiparticle systems are studied and a cooperative heating effect is demonstrated for particles that are within a few radii of each other. This provides more robust bubble generation using substantially reduced laser energy as compared to single-particle systems. The modelling approach is discussed in detail and should be of considerable use in the development of new photothermal applications.     

Analysis of missed cleavage sites, tryptophan oxidation and N-terminal pyroglutamylation after in-gel tryptic digestion

Peptide mass fingerprinting is a powerful tool for the identification of proteins. Trypsin is the most widely used enzyme for this purpose. Therefore, 104 protein digests from human Jurkat T cells and Mycobacterium were analyzed considering missed cleavage sites, tryptophan oxidation and N-terminal pyroglutamylation. About 90% of the matched peptides with missed cleavage sites could be classified into three groups: (i) lysine and arginine with a neighbouring proline on the carboxy-terminal side, (ii) neighboring lysines/arginines, and (iii) lysines and arginines with an aspartic acid or glutamic acid residue on either the amino- or carboxy-terminal side. The first group is already accounted for by search programs. The number of missed cleavage sites can be increased without reducing the precision of the database search by taking the other two groups into consideration. Peptides with tryptophan were observed in non, singly (+16 Da) and doubly (+32 Da) oxidized forms. The higher oxidized form was only observed with lower intensity in the presence of the lower oxidized form. Peptides with N-terminal glutamine were found always as pyroglutamate (-17 Da), and in the majority of cases in pairs with unmodified glutamine. These data can be used for the refinement of protein searches by peptide mass fingerprinting.