Two-component membrane material properties and domain formation from dissipative particle dynamics

The material parameters (area stretch modulus and bending rigidity) of two-component amphiphilic membranes are determined from dissipative particle dynamics simulations. The preferred area per molecule for each species is varied so as to produce homogeneous mixtures or nonhomogeneous mixtures that form domains. If the latter mixtures are composed of amphiphiles with the same tail length, but different preferred areas per molecule, their material parameters increase monotonically as a function of composition. By contrast, mixtures of amphiphiles that differ in both tail length and preferred area per molecule form both homogeneous and nonhomogeneous mixtures that both exhibit smaller values of their material properties compared to the corresponding pure systems. When the same nonhomogeneous mixtures of amphiphiles are assembled into planar membrane patches and vesicles, the resulting domain shapes are different when the bending rigidities of the domains are sufficiently different. Additionally, both bilayer and monolayer domains are observed in vesicles. We conclude that the evolution of the domain shapes is influenced by the high curvature of the vesicles in the simulation, a result that may be relevant for biological vesicle membranes.     

Targeted Protein Surface Sensors as a Tool for Analyzing Small Populations of Proteins in Biological Mixtures

Optical cross‐reactive sensor arrays (the so‐called chemical “noses/tongues”) have recently been demonstrated as a powerful tool for high‐throughput protein detecting and analysis. Nevertheless, applying this technology to biomarker detection is complicated by the difficulty of non‐selective sensors to operate in biological mixtures. Herein we demonstrate a step toward circumventing this limitation by using self‐assembled fluorescent receptors consisting of two distinct recognition motifs: specific and non‐specific. When combined in an array, binding cooperatively between the specific and non‐specific protein binders enables the system to discriminate among closely related isoform biomarkers even in the presence of serum proteins or within human urine.     

Use of electrophoretic techniques in determining the composition of seed storage proteins in alfalfa

Holoprotein molecular weights and polypeptide composition can be determined for complex mixtures of oligomeric proteins using two-dimensional electrophoretic techniques. The variety of two-dimensional analyses presented here is a reflection of the general usefulness of each method for the identification and characterization of the different classes of seed storage proteins in alfalfa. These techniques can be applied to studies of storage proteins in other seeds as well as non-seed storage proteins. The major seed storage proteins in alfalfa are medicagin (a legumin-like globulin), alfin (a vicilin-like globulin) and a family of lower molecular weight albumins (LMW1-3). These comprise 30%, 10%, and 20%, respectively, of the total extractable protein from cotyledons of mature seeds. Alfin is a heterogeneous oligomeric protein (Mr approximately 150,000) composed of polypeptides ranging in size from Mr 14,000 to 50,000 (alpha 1-alpha 6; 50,000, 38,000, 32,000, 20,000, 16,000 and 14,000, respectively). Medicagin is also a high molecular weight oligomeric protein, but requires high concentrations of salt for solubilisation. It is comprised of a family of individually distinct subunits, each composed of an acidic polypeptide (A1-A9; Mr 49,000 to 39,000) linked via disulphide bond(s) to a basic polypeptide (B1, B2, B3; Mr 24,000, 23,000 and 20,000, respectively). This pairing is highly specific and two families are recognizable on the basis of the B polypeptide (B3 or B1/B2). Subunits (Mr approximately 50,000-65,000) are assembled as trimers (8S) or larger oligomers (12S-15S) in mature seeds. The lower molecular weight albumins (LMW1-3) are acidic (pI less than 6), and consist of sets of disulphide-bonded polypeptides (Mr 15,000 and 11,000).     

Preparation of molecular imprinted polymer with quaternary ammonium groups as recognition sites for separation of pig cyclophilin 18 and bovine serum albumin

We introduce a new type of molecular imprinted polymer (MIP) with immobilized assistant recognition polymer chains (ARPCs) to create effective recognition sites. In this work, cloned pig cyclophilin 18 (pCyP18) and BSA were used as templates, respectively. The template protein was selectively assembled with ARPCs from the library which consists of numerous limited length polymer chains with randomly distributed recognition sites of the quaternary ammonium cationic groups and immobilizing sites. The assemblies of protein and ARPCs were adsorbed by macroporous microspheres and immobilized by cross‐linking polymerization. After removing the templates, the two kinds of synthesized MIPs were used to adsorb cloned pCyP18 and BSA from protein mixtures respectively and both showed high selectivity. It confirms that this new method is suitable to separate proteins of both low and high molecular weight. The extended experiment on adsorption of natural pCyP18 from cytosol shows that the obtained MIP using cloned protein as template can be used to enrich natural protein of low content.     

Structural varieties of selectively mixed G‐ and C‐rich short DNA sequences studied with electrospray ionization mass spectrometry

Short guanine(G)‐repeat and cytosine(C)‐repeat DNA strands can self‐assemble to form four‐stranded G‐quadruplexes and i‐motifs, respectively. Herein, G‐rich and C‐rich strands with non‐G or non‐C terminal bases and different lengths of G‐ or C‐repeats are mixed selectively in pH 4.5 and 6.7 ammonium acetate buffer solutions and studied by electrospray ionization mass spectrometry (ESI‐MS). Various strand associations corresponding to bi‐, tri‐ and tetramolecular ions are observed in mass spectra, indicating that the formation of quadruplex structures is a random strand by strand association process. However, with increasing incubation time for the mixtures, initially associated hybrid tetramers will transform into self‐assembled conformations, which is mainly driven by the structural stability. The melting temperature values of self‐assembled quadruplexes suggest that the length of G‐repeats or C‐repeats shows more significant effect on the stability of quadruplex structures than that of terminal residues. Accordingly, we can obtain the self‐associated tetrameric species generated from the mixtures of various homologous G‐ or C‐strands efficiently by altering the length of G‐ or C‐repeats. Our studies demonstrate that ESI‐MS is a very direct, fast and sensitive tool to provide significant information on DNA strand associations and stoichiometric transitions, particularly for complex mixtures. Copyright © 2016 John Wiley & Sons, Ltd.     

Competitive adsorption of model charged proteins: the effect of total charge and charge distribution

The adsorption of mixtures of charged proteins on charged surfaces is studied using a molecular theory. The theory explicitly treats each of the molecular species in the system. The mixtures treated in this work are composed by two types of proteins, dissociated monovalent salt and solvent. The intermolecular and surface interactions include electrostatic, van der Waals and excluded volume. The theory is more general than the Poisson-Boltzmann approach since the size and shape of all the molecular components are explicitly treated. The studies presented in this work concentrate on the differences in competitive adsorption when the proteins in the mixtures differ in their total charge or in the spatial distribution of the charges within the proteins. In the cases of mixtures that differ in the number of charges it is found, as expected, that the particles with the larger charge adsorb in excess. The ratio of adsorbed proteins can vary by 3-5 orders of magnitude by varying the bulk salt concentration from 1 to 100 mM. This is the result of an increase on the adsorption of the proteins with larger charge and an even stronger decrease on the adsorption of the less charged particles. The simple model systems studied provide guidelines on how to separate charge ladder proteins and proteins with different charge distributions. In the case of proteins with the same total charge but different charge distribution, it is found that the partition of the proteins depends upon the bulk composition. However, in general the particles with the highest localized charge tend to adsorb more on the surfaces. The proteins are adsorbed in one or more layers. The structure of the second adsorbed layer is determined mostly by the bulk properties of the solution. In all cases it is found that in the range of salt concentrations studied the number of adsorbed ions from the salt is very large. This is due to competitive adsorption with the proteins and their very low bulk concentration compared to the salt. The limitations of the theory and directions for improvement of the approach as well as the model for the proteins are discussed.     

The simultaneous analysis of proteins, lipids, and diterpenoid resins found in cultural objects

We report a GC-MS method for the simultaneous analysis of proteins oil, and diterpenoid resins found in cultural objects. The method was initially designed for protein analysis of protenaceous paints and adhesives and involves acid hydrolysis as the first step. The amino acids in the protein hydrolysates, thus obtained, are treated with propan-l-ol/ hydrogen chloride and then pentafluoropropionic anhydride. The procedure was found also to yield the propyl esters of fatty acids derived from lipids and diterpenoid acids derived from natural resins, and thus allows the choice of a single method for the analysis of artists media which contain either oil s or proteins or mixtures of both proteins and oils or even resins. Thus natural mixtures such as egg yolk and also mixtures made by the artist such as animal glue/seed oil emulsions can be analysed. Coupled with FTIR analysis of paints and the staining of cross sections, to indicate layer structure the method can help to elucidate the paints and adhesives used by artists.     

Phase behavior and 3D structure of strongly attractive microsphere-nanoparticle mixtures

We investigate the phase behavior and 3D structure of strongly attractive mixtures of silica microspheres and polystyrene nanoparticles. These binary mixtures are electrostatically tuned to promote a repulsion between like-charged (microsphere-microsphere and nanoparticle-nanoparticle) species and a strong attraction between oppositely charged (microsphere-nanoparticle) species. Using confocal fluorescence scanning microscopy, we directly observe the 3D structure of colloidal phases assembled from these mixtures as a function of varying composition. In the absence of nanoparticle additions, the charged-stabilized microspheres assemble into a polycrystalline array upon sedimentation. With increasing nanoparticle volume fraction, nanoparticle bridges form between microspheres, inducing their flocculation. At even higher nanoparticle volume fractions, the microspheres become well coated with nanoparticles, leading to their charge reversal and subsequent restabilization. We demonstrate how this fluid-gel-fluid transition can be utilized to control the morphology of the colloidal phases formed under gravity-driven sedimentation.     

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.     

A Supramolecular Chiral Auxiliary Approach: “Remote Control” of Stereochemistry at a Hierarchically Assembled Dimeric Helicate

Dimeric hierarchically‐assembled titanium(IV) helicates are in solvent‐dependent equilibrium with the corresponding monomers. Statistically formed mixtures of such complexes bearing chiral stereocontrolling ligands and achiral diene‐substituted ligands show high diastereoselectivity and reasonable enantioselectivity in the Diels–Alder reaction with maleimides if the reaction proceeds with the dimer but not with the monomer. Thus, solvent dependent switching between the monomer and dimer enables on/off switching of the enantioselectivity.     

The protein "glass" transition and the role of the solvent

Hydrated proteins undergo a change in their dynamical properties in the neighborhood of a temperature. The change of dynamics has been likened to glass transition of glass-forming substances because similar properties were found. However, a complete understanding of the conformation fluctuations of hydrated proteins and their relation to the dynamics of the solvent is still not available, possibly due to the protein molecules being more complex than ordinary glass-formers. For this reason, we turn our attention to the experimental findings of the dynamics of mixtures of water with simpler glass-formers (small molecules and polymers). Two major relaxation processes have been observed in these aqueous mixtures. One is the structural alpha-relaxation of the hydrophilic glass-former hydrogen bonded to the water, which is responsible for glass transition. The other one is the local secondary beta-relaxation of water in the mixture. Remarkably, these two relaxation processes in aqueous mixtures have analogues in hydrated proteins with the same properties. The conformation fluctuations of the protein and the relaxation of the solvent in hydrated proteins behave like the alpha-relaxation of the hydrophilic glass-former hydrogen bonded to the water and the beta-relaxation of water in other aqueous mixtures, respectively. At low temperatures, the Arrhenius activation energy of the relaxation time of the solvent in a hydrated protein is almost the same as that of the beta-relaxation of water in the glassy states of aqueous mixtures. The Arrhenius T-dependence of the solvent relaxation times no longer holds at temperatures that exceed the "glass" transition temperature of the hydrated protein, defined as the temperature at which the conformation relaxation time is very long. This behavior of the solvent in hydrated proteins is similar to that found in the beta-relaxation of water in aqueous mixtures when crossing the glass transition temperature of the mixture (Capaccioli, S.; Ngai, K. L.; Shinyashiki, N. J. Phys. Chem. B 2007, 111, 8197). Furthermore, the same dynamics were found in mixtures of two van der Waals glass-formers, which are even simpler systems than aqueous mixtures because of the absence of hydrogen bonding. The experimental data of these ideal mixtures of van der Waals glass-formers have been given a satisfactory theoretical explanation. Since the properties of hydrated proteins, aqueous mixtures, and the mixtures of van der Waals liquids are similar, we transfer the theoretical understanding gained in the study of the last system sequentially to the two other increasingly more complex systems.     

An analysis of protein abundance suppression in data dependent liquid chromatography and tandem mass spectrometry with tryptic peptide mixtures of five known proteins

Reverse phase liquid chromatography (RPLC) has been widely used in proteomics research for peptide separation. When protein samples are separated by RPLC and identified with electrospray ion trap mass spectrometry (ESI-MS), the signals of high-abundance proteins may suppress those of low-abundance proteins, a phenomenon known as abundance suppression. To what degree the abundance suppression correlates to the number of tryptic peptides in the high-abundance proteins has not been carefully investigated. We tried to answer this question by studying the mixtures digested from five known proteins. The numbers of identified tryptic peptides (longer than five amino acids) of the five proteins ranged from 12 to 47. Four different peptide mixtures with 10- to 100-fold abundance differences of five known proteins were separated by RPLC and identified by ESI-MS. Our results showed that abundance suppression was related to the tryptic peptide numbers in the high-abundance protein. Within a 100-fold protein abundance difference range, tryptic peptide number in the low-abundance proteins could be suppressed up to seven times by high-abundance proteins. The procedure we suggest here can help to identify low-abundance proteins co-purified with their high-abundance binding protein. The result can also help to identify specific high-abundance proteins for removal by immunoaffinity.     

Image subtraction approach to screening one-bead-one-compound combinatorial libraries with complex protein mixtures

To screen one-bead-one-compound (OBOC) combinatorial bead libraries,(1) one generally uses tagged purified protein as the screening probe. Compound beads that interact with the purified protein are then identified, for example, via an enzyme-linked colorimetric assay, and isolated for structure determination. In this report, we demonstrate a rapid and efficient method to screen OBOC combinatorial libraries utilizing two protein mixtures as screening probes, and by comparing optical images of the beads stained by one protein mixture but not the other, ligand beads unique to one of the two protein mixtures can be identified. The significance of this method is that it allows for rapid selection of ligands directed against proteins unique to one mixture while screening out positive beads resulting from proteins common to both mixtures as well as beads that are positive as a result of interactions with chemical and protein components found in the assay itself. The method is fast, efficient, and uses off-the-shelf equipment.     

Nanoflow LC/IMS-MS and LC/IMS-CID/MS of protein mixtures

A simple ion trap/ion mobility/time-of-flight (TOF) mass spectrometer has been coupled with nanoflow liquid chromatography to examine the feasibility of analyzing mixtures of intact proteins. In this approach proteins are separated using reversed-phase chromatography. As components elute from the column, they are electrosprayed into the gas phase and separated again in a drift tube prior to being dispersed and analyzed in a TOF mass spectrometer. The mobilities of ions through a buffer gas depend upon their collision cross sections and charge states; separation based on these gas-phase parameters provides a new means of simplifying mass spectra and characterizing mixtures. Additionally it is possible to induce dissociation at the exit of the drift tube and examine the fragmentation patterns of specific protein ion charge states and conformations. The approach is demonstrated by examining a simple three-component mixture containing ubiquitin, cytochrome c, and myoglobin and several larger prepared protein mixtures. The potential of this approach for use in proteomic applications is considered.     

Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation.

We have demonstrated the use of per-methyl esterification of peptides for relative quantification of proteins between two mixtures of proteins and automated de novo sequence derivation on the same dataset. Protein mixtures for comparison were digested to peptides and resultant peptides methylated using either d0- or d3-methanol. Methyl esterification of peptides converted carboxylic acids, such as are present on the side chains of aspartic and glutamic acid as well as the carboxyl terminus, to their corresponding methyl esters. The separate d0- and d3-methylated peptide mixtures were combined and the mixture subjected to microcapillary high performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS). Parent proteins of methylated peptides were identified by correlative database searching of peptide tandem mass spectra. Ratios of proteins in the two original mixtures could be calculated by normalization of the area under the curve for identical charge states of d0- to d3-methylated peptides. An algorithm was developed that derived, without intervention, peptide sequence de novo by comparison of tandem mass spectra of d0- and d3-peptide methyl esters.     

Functionalized porous silicon surfaces as MALDI-MS substrates for protein identification studies

Alkyl monolayer modified porous silicon functional surfaces are employed for selective binding of proteins from complex mixtures (through washing of the deposited mixture spot using appropriate buffer) and MALDI-MS is used to detect the components retained on the surface.     

Bioelectrochemically functional nanohybrids through co-assembling of proteins and surfactants onto carbon nanotubes: facilitated electron transfer of assembled proteins with enhanced faradic response

Preparation and bioelectrochemical properties of functional nanohybrids through co-assembling of hemeproteins (i.e., horseradish peroxidase, hemoglobin, myoglobin and cytochrome c) and surfactants onto carbon nanotubes (CNTs) are described. The prepared protein-surfactant-CNT nanohybrids are found to possess facilitated interfacial electron transfer of the proteins with enhanced faradic responses. The enhancements are ascribed for the first time to the properties of the surfactants for facilitation of protein electrochemistry and the improved portion of electroactive proteins assembled, of which the latter assignment is closely associated with the electrochemical and structural properties of the nanotubes and the three-dimensional architecture of the CNT film confined onto the glassy carbon electrode. It is proposed that the single and/or small bundles of the nanotubes in the CNT film electrode can be rationally functionalized with surfactants to be functional nanoelectrodes capable of facilitating electron transfer of proteins. The three-dimensional confinement of these functional nanowires onto the GC electrode essentially increases the portion of electroactive proteins assembled in the nanohybrids. These properties of the protein-surfactant-CNT nanohybrids, combined with the bioelectrochemical catalytic activity, could make them useful for development of bioelectronic devices and investigation of protein electrochemistry at functional interfaces.     

Recent developments of nanoparticle-based enrichment methods for mass spectrometric analysis in proteomics

In proteome research, rapid and effective separation strategies are essential for successful protein identification due to the broad dynamic range of proteins in biological samples. Some important proteins are often expressed in ultra low abundance, thus making the pre-concentration procedure before mass spectrometric analysis prerequisite. The main purpose of enrichment is to isolate target molecules from complex mixtures to reduce sample complexity and facilitate the subsequent analyzing steps. The introd...     

Cross-linked, heterogeneous colloidosomes exhibit pH-induced morphogenesis

Inspired by morphogenesis in biology, we present a strategy for developing functional 3D materials with the capacity to morph based on environmental cues. We utilized local mechanical stresses to cause global shape changes in colloidosomes. Colloidosomes were assembled from pH-sensitive calcium alginate particles (CAPs) with high and low swelling ratios. Colloidosomes were subsequently cross-linked via diamine compounds with varying carbon chain lengths. New colloidosome isoforms were generated from heterogeneous mixtures of CAPs, which resulted in nonuniform stresses. Our study demonstrated that coordinated networks of heterogeneous subunits may be used to design programmable materials.     

Generic pathways to stability in concentrated protein mixtures

We present a series of experimental results that disclose the crucial role of ionic strength and partial volume fractions in the control of the phase behaviour of binary protein mixtures. Our findings can be understood as that the ionic strength determines the relative contribution of the entropy of the protein counter-ions to the overall thermodynamics of the system. Associative phase separation and crystallization observed at, respectively, low and high ionic strength are suppressed at intermediate salt concentrations, where the entropy gain upon releasing the counter-ions from the double layer of the proteins is negligible and the entropy loss upon confining the counter-ions within the protein crystal phase significant. Moreover, we find that the partial volume fraction of the protein prone to crystallize determines the crystallization boundary and that the presence of other proteins strongly delays crystallization, leading to temporarily stable mixtures. These findings suggest that stability in more complex protein mixtures, such as the cytosol, relates to the ionic strength and protein composition rather than to protein specific properties.