Surface-induced aggregation of ferritin. Concentration dependence of adsorption onto a hydrophobic surface

The isotherm of ferritin adsorption onto a hydrophobic surface was studied by transmission electron microscopy. Adsorbed ferritin was found to be distributed in molecular clusters. The adsorption process was diffusion-rate-limited after 20 h adsorption time at bulk concentrations below 1 mg/1. The clusters formed during the diffusion-rate-limited adsorption had a fractal dimension D approximately 1.0 when averaged over all clusters. The pair distribution function g(r) showed an increased probability of finding nearest neighbours at distances less than 30 nm. The surface concentration of adsorbed ferritin was weakly dependent on the bulk concentration of ferritin in the range 10 mg/1-10 g/1 and the average number of nearest neighbour molecules was constant in this concentration range. The mass distribution of adsorbed ferritin c(r) had a fractal dimension D = 1.8 at a bulk concentration of 10 g/l and a surface concentration corresponding to theta = 0.45 +/- 0.05. The pair correlation function g(r) showed decreasing probability of finding nearest neighbour molecules over long distances as in percolating clusters. The results indicate that ferritin adsorbs strongly to the surface at low surface concentrations and weakly at high surface concentrations. The stability of ferritin adsorption was correlated to the average number of nearest neighbour molecules, indicating a possibility that desorption is a critical supramolecular phenomenon.     

Computer simulation of surface-induced aggregation of ferritin.

Models are presented describing the transient mass-transport limited adsorption and cluster growth of ferritin at a solid surface. Computer simulations are carried out on a hexagonal lattice using a computer model that can be characterized as a two-dimensional stochastic cellular automaton allowing different rules regarding association, lateral interaction and dissociation to be incorporated in the model. The fractal dimensions of individual clusters were extracted from simulated aggregates and for similar rules found to be consistent with literature values on reversible diffusion-limited aggregation in two dimensions. The distribution of clusters versus free surface were shown to be affected by neighbor-dependent association probability. Low fractal dimension clusters were generated by a combination of strong lateral cohesion and neighbor-dependent dissociation to the bulk. By comparing computer simulated aggregation to experimental electron micrographs of adsorbed ferritin layers it is suggested that neighbor-dependent association, neighbor-dependent dissociation and lateral interactions are important factors in the complex dynamics of adsorbed protein layers.     

Nonlinear kinetics of ferritin adsorption.

The adsorption of ferritin at a methylized quartz surface was measured with off-null ellipsometry and transmission electron microscopy. An initial lag-phase was seen, followed by an accelerating adsorption leading to mass transport limitation of the reaction. The rate of adsorption then decreased at a surface concentration far below monolayer coverage, and a continuously decreasing rate of binding was seen. The slope of the binding rate was linear with the logarithm of time (fractal kinetics). The adsorbed ferritin molecules were distributed in clusters as seen by transmission electron microscopy. Clusters grown during the mass transport limited adsorption had crystalline structure at short range and low fractal dimensions (df = 0.89) over long range. Clusters grown during adsorption with fractal kinetics showed random structure at short range and a high fractal dimension df = 1.86 over all ranges. These findings indicate some new important mechanisms responsible for the complex kinetics of macromolecular reactions at solid-liquid interfaces. The results are discussed in relation to recently developed theories of self-organized criticality.     

Langmuir monolayer approaches to protein recognition through molecular imprinting

Surface plasmon resonance (SPR) spectroscopy and atomic force microscopy (AFM) have been employed to investigate ferritin adsorption to binary surfactant monolayers of cationic dioctadecyldimethylammonium bromide (DOMA) and non-ionic methyl stearate (SME). Surfactant molar ratios, miscibility, and lateral mobility were controlled to define the number, size, and distribution of "binding sites" for ferritin, which under the low ionic strength conditions investigated, adsorbed to the monolayers predominantly through electrostatic interactions. Successive adsorption/desorption cycles revealed that fluid monolayers, capable of laterally restructuring during the initial protein adsorption event, bound up to 60% more ferritin (dependent on SME:DOMA ratios) as compared to monolayers that were immobilized on a hydrophobic support during this first adsorption step. The enhanced binding of ferritin to fluid monolayers was accentuated in films having non-ionic SME as the principal component. These findings support the premise that the surfactants reorganize to form favorable interactions with an adsorbing protein, leading to protein specific charge patterns, or templates, in the films. Template assessment, however, was complicated by the presence of an irreversibly bound protein fraction, which AFM revealed to be locally ordered protein clusters.     

Interaction of fibrinogen with magnetite nanoparticles

The interaction between fibrinogen and magnetite nanoparticles in solution has been studied by the methods of spin labeling, ferromagnetic resonance, dynamic and Rayleigh light scattering. It is shown that protein molecules adsorb on the surface of nanoparticles to form multilayer protein covers. The number of molecules adsorbed on one nanoparticle amounts to ∼65 and the thickness of the adsorption layer amounts to ∼27 nm. Separate nanoparticles with fibrinogen covers (clusters) form aggregates due to interactions of the end D domains of fibrinogen. Under the influence of direct magnetic field, nanoparticles with adsorbed proteins form linear aggregates parallel to the force lines. It is shown that the rate of protein coagulation during the formation of fibrin gel under the action of thrombin on fibrinogen decreases ∼2 times in the presence of magnetite nanoparticles, and the magnitude of the average fiber mass/length ratio grows.     

Effects of excluded surface area and adsorbate clustering on surface adsorption of proteins. II. Kinetic models

Models for equilibrium surface adsorption of proteins have been recently proposed (Minton, A. P., 2000. Biophys. Chem. 86:239-247) in which negative cooperativity due to area exclusion by adsorbate molecules is compensated to a variable extent by the formation of a heterogeneous population of monolayer surface clusters of adsorbed protein molecules. In the present work this concept is extended to treat the kinetics of protein adsorption. It is postulated that clusters may grow via two distinct kinetic pathways. The first pathway is the diffusion of adsorbed monomer to the edge of a preexisting cluster and subsequent accretion. The second pathway consists of direct deposition of a monomer in solution onto the upper (solution-facing) surface of a preexisting cluster ("piggyback" deposition) and subsequent incorporation into the cluster. Results of calculations of the time course of adsorption, carried out for two different limiting models of cluster structure and energetics, show that in the absence of piggyback deposition, enhancement of the tendency of adsorbate to cluster can reduce, but not eliminate, the negative kinetic cooperativity due to surface area exclusion by adsorbate. Apparently noncooperative (Langmuir-like) and positively cooperative adsorption progress curves, qualitatively similar to those reported in several published experimental studies, require a significant fraction of total adsorption flux through the piggyback deposition pathway. According to the model developed here and in the above-mentioned reference, the formation of surface clusters should be a common concomitant of non-site-specific surface adsorption of proteins, and may provide an important mechanism for assembly of organized "protein machines" in vivo.     

Multilayer adsorption of lysozyme on a hydrophobic substrate.

Macromolecular adsorption is known to occur as a complex process, often in a series of steps. Several models are discussed in the literature which describe the microscopic structure of the adsorbate. In the present study we investigated the adsorption of hen egg white lysozyme on alkylated silicon oxide surfaces. A combination of fluorescence excitation in the evanescent field and fluorescence recovery after photobleaching allowed us to measure the amount of adsorbed fluorescent lysozyme and the equilibrium exchange kinetics with molecules in solution. We found that a model with at least three classes of adsorbed molecules is necessary to describe the experimental results. A first layer is formed by the molecules which adsorb within a short time after the beginning of the incubation. These molecules make up approximately 65% of the final coverage. They are quasi-irreversibly adsorbed and do not measurably exchange with bulk molecules within one day even at temperatures up to 55 degrees C. A second layer, which reaches equilibrium only after several hours of incubation, shows a pronounced exchange with bulk molecules. The on-off kinetics show a distinct temperature dependence from which an activation barrier of delta E approximately 22 kcal/mol is derived. A third layer of molecules that exchange rapidly with the bulk can be seen to comprise approximately 10% of the total coverage. The exchange rate is on the order of fractions of a second. The binding of the latter two classes of adsorbed molecules is exothermic. From the temperature dependence of the coverage, the binding enthalpy of the slowly exchanging layer was estimated to be delta Hads approximately 3.8 kcal/mol. The second and third class of molecules remain enzymatically active as a muramidase, which was tested by the lysis of the cell walls of Micrococcus lysodeiktikus. The molecules in the first layer, on the other hand, showed no enzymatic activity.     

Discontinuous formation and desorption of clusters during particles adsorption at surfaces

A theoretical model was derived to describe the discontinuous formation and desorption of clusters during particle adsorption at surfaces. Two steps were investigated: (1) time-dependent adsorption, where we found that the initial slope and the limiting magnitude of an adsorption isotherm depend on the clusters' distribution. A higher magnitude of both the adsorption and desorption rates appear to contract the time scale and hence increase the initial slope. Decreasing the geometrical parameter, q, which represents the shape of an adsorbed cluster, enhances the growth of large clusters on the surface. (2) A concentration dependence model shows that the number of adsorbed molecules increases with increases in the value of n (nucleation capacity). Furthermore, higher rates of adsorption provide steeper initial slopes (higher affinity of, molecules to surface). Decreasing q from 2 to 1, i.e. from a circular to a linear cluster formation, slightly decreases the magnitude of the isotherms.     

Distribution functions, describing the binding of extended ligands with DNA molecules. Possible use for cases of DNA condensation

Due to noncooperative binding of ligands to DNA molecules, DNA molecules are in equilibrium with different numbers of adsorbed ligands. This equilibrium for a given concentration of the free ligand in the solution is characterized by the distribution function, which describes the probability of revealing the DNA molecule with a definite number of adsorbed ligands. If polycations act as ligands, DNA molecules with the number of ligands sufficient for neutralizing the charges on phosphates may undergo a phase transition. One example of this transition is the formation of liquid-crystalline dispersions during the binding of DNA to chitosan. We analyzed the binding of chitosan to DNA on the assumption that this binding is due to equilibrium adsorption. At a definite concentration of chitosan in solution, DNA molecules are in equilibrium with different numbers of adsorbed molecules of chitosan. If the number of adsorbed ligands exceeds some critical value, the DNA molecule covered with chitosan becomes capable of interacting with other DNA molecules. As a result of this interaction (attraction), liquid-crystalline dispersions can form. Equations describing the dependence of the concentration of DNA molecules on the concentration of the ligand in solution were derived. It was shown that, at given parameters of the model, it is possible to describe experimental data characterizing the formation of cholesteric liquid-crystalline dispersions. The analysis of the data makes it possible to reconstitute both the size of the binding site occupied by chitosan on the DNA and the energy of interaction of chitosan with DNA.     

Analysis of protein adsorption characteristics to nano-pore silica particles by using confocal laser scanning microscopy

The effect of average pore size of nano-pore silica particles on protein adsorption characteristics was determined experimentally by the dissociation constant and the adsorption capacity determined from the Langmuir equation. As the average pore size was increased from 2.2 to 45 nm, the BSA adsorption capacity increased from 16.8 to 84.3 mg/g-silica so as the equilibrium constant (from 2.6 to 9.4 mg/ml). Using confocal microscopy with fluorescence labeling, we could visualize the protein adsorption in situ and determine the minimum pore size required for efficient intraparticle adsorption. The confocal microscopy analysis revealed that BSA was adsorbed mainly on the surface of the particles with a smaller pore size, but diffused further into the interstitial surface when it was sufficiently large. It was concluded that for BSA whose Stoke's diameter is ca. 3.55 nm the minimum pore size of about 45 nm or larger was required for a sufficient adsorption capacity.     

A mathematical analysis using fractals for binding interactions of nuclear estrogen receptors occurring on biosensor surfaces

A mathematical approach using fractal concepts is presented for modeling the binding and dissociation interactions between analytes and nuclear estrogen receptors (ER) occurring on surface plasmon resonance biosensor chip surfaces. A kinetic knowledge of the binding interactions mediated by ER would help in better understanding the carcinogenicity of these steroidogenic compounds and assist in modulating these reactions. The fractal approach is applied to analyte-ER interaction data obtained from literature. Numerical values obtained for the binding and dissociation rate coefficients are linked to the degree of roughness or heterogeneity (fractal dimension, D(f)) present on the biosensor surface. For example, a single-fractal analysis is used to describe the binding and dissociation phases for the binding of estradiol and ERalpha in solution to clone 31 protein immobilized on a biosensor chip (C-S. Suen et al., 1998, J. Biol. Chem. 273(42), 27645-27653). The binding and the dissociation rate coefficients are 27.57 and 8.813, respectively, and the corresponding fractal dimensions are 1.986 and 2.268, respectively. In some examples dual-fractal models were employed to obtain a better fit of either the association or the dissociation phases or for both. Predictive relationships are developed for (a) the binding and the dissociation rate coefficients as a function of their respective fractal dimensions and (b) the ratio K(A) (= k/k(d)) as a function of the ratio of the fractal dimensions (D(f)/D(fd)). The analysis should provide further physical insights into the ER-mediated interactions occurring on biosensor and other surfaces.     

Monomolecular layer formation of ferritin molecules on an amphiphilic cyclodextrin derivative at the air/water interface

A monomolecular layer of ferritin molecules was formed by adsorption from the subphase onto a Langmuir film of an amphiphilic beta-cyclodextrin (beta-CD) derivative at the air/water interface. The course of the adsorption of ferritin molecules was monitored by measuring the surface pressure and the resulting film was observed by transmission electron microscopy (TEM). These results show the potential of the amphiphilic CD derivative to work as a milder template for protein molecules at the air/water interface.     

Proton-dependent dissociation equilibrium of hemoglobin. 2. Surface pressure measurements in monolayers of horse hemoglobin (III).

The molecular weight of hemoglobin (III) in monolayers on aqueous subsolutions has been determined by measuring the surface pressure as a function of the protein surface concentration. The dissociation equilibrium between tetrameric and dimeric hemoglobin (III) was determined for spread as well as adsorbed monolayers. The results were compared with analogous measurements in solution. It was found that the numerical value and the pH dependence of the dissociation constant were similar both in the bulk and in the surface phase of the solution. From these findings it was concluded that the native conformation of hemoglobin (III) is retained after adsorption at aqueous surface.     

Small-angle neutron scattering study of the structure of protein/detergent complexes

Small-angle neutron scattering (SANS) was used to study the structure of protein/sodium dodecylsulfate complexes. Two water soluble proteins, bovine serum albumin (BSA) and ovalbumin (OVA), were used. The protein concentration was kept constant at 1 wt %, and protein/detergent wt ratio varied between 1/1, 1/1.5, 1/2 and 1/3. Absolute intensities of SANS distributions were analyzed by a fractal model. Analyses of large Q portions of SANS distributions established that sodium dodecylsulfate (SDS) molecules bound to a protein/SDS complex form micelle-like clusters. On the other hand, analyses of small Q portions of SANS distributions clearly showed that the arrangement of micelle-like clusters resembles a fractal packing of spheres. We showed that a protein/SDS complex can be characterized by four parameters extracted from the scattering experiment, namely, the average micelle size and its aggregation number, the fractal dimension characterizing the conformation of the micellar chains, the correlation length giving the extent of the unfolded polypeptide chains, and the numbers of micelle-like clusters in the complex.     

Probing the micelle/water interface by rapid laser-induced proton pulse

The laser-induced pH jump (Gutman, M. and Huppert, D.J. (1979) Biochem. Biophys. Methods 1, 9–19) has a time resolution capable of measuring the diffusion-controlled rate constant of proton binding. In the present study we employed this technique for measuring the kinetics of protonation-deprotonation of surface groups of macromolecules.The heterogeneous surface of proteins excludes them from serving as a simple model, therefore we used micelles of a neutral detergent (Brij 58) as a high molecular weight structure. The charge was varied by the addition of a low concentration of sodium dodecyl sulfate and the surface group with which the protons react was an adsorbed pH indicator (bromocresol green or neutral red).The dissociation of a proton from adsorbed bromocresol green is slower than that from free indicator. This effect is attributed to the enhanced stabilization of the acid form of the indicator in the pallisade region of the micelle. The $\text{p}\text{K}$ shift of bromocresol green adsorbed on neutral micelles is thus quantitatively accounted for by the decreased rate of proton dissociation. Indicators such as neutral red, which are more lipid soluble in their alkaline form, do not exhibit such decelerated proton dissociation in their adsorbed state nor a $\text{p}\text{K}$ shift on adsorption to neutral micelles.The protonation of an indicator is a diffusion-controlled reaction, whether it is free in solution or adsorbed on micelles. By varying the electric charge of the micelle this rate can be accelerated or decelerated depending on the total charge of the micelle. The micellar charge calculated from this method was corroborated by other measurements which rely only on equilibrium parameters.The high time resulation of the pH jump is exemplified by the ability to estimate the diffusion coefficient of protons through the hydrated shell of the micelle.     

The protein coating of asbestos bodies

1. Asbestos bodies were isolated from human lungs and the amino acid composition of the protein content was determined. 2. The hydroxyproline, glycine, leucine and phenylalanine values indicate that the protein in the coating cannot be principally collagen. 3. Albumin can be adsorbed on chrysotile asbestos as a monolayer but more than a monolayer is adsorbed if iron is also adsorbed. 4. Ferritin is adsorbed on chrysotile to give a thick layer. 5. The amino acid composition and adsorption studies are discussed in the light of the suggestions that the protein coating of asbestos is collagen (Beattie, 1961) or ferritin (Davis, 1964).     

KDBI: Kinetic Data of Bio-molecular Interactions database

Understanding of cellular processes and underlying molecular events requires knowledge about different aspects of molecular interactions, networks of molecules and pathways in addition to the sequence, structure and function of individual molecules involved. Databases of interacting molecules, pathways and related chemical reaction equations have been developed. The kinetic data for these interactions, which is important for mechanistic investigation, quantitative study and simulation of cellular processes and events, is not provided in the existing databases. We introduce a new database of Kinetic Data of Bio-molecular Interactions (KDBI) aimed at providing experimentally determined kinetic data of protein-protein, protein-RNA, protein-DNA, protein-ligand, RNA-ligand, DNA-ligand binding or reaction events described in the literature. KDBI contains information about binding or reaction event, participating molecules (name, synonyms, molecular formula, classification, SWISS-PROT AC or CAS number), binding or reaction equation, kinetic data and related references. The kinetic data is in terms of one or a combination of the following quantities as given in the literature of a particular event: association/dissociation or on/off rate constant, first/second/third/. order rate constant, equilibrium rate constant, catalytic rate constant, equilibrium association/dissociation constant, inhibition constant and binding affinity constant. Each entry can be retrieved through protein or nucleic acid or ligand name, SWISS-PROT AC number, ligand CAS number and full-text search of a binding or reaction event. KDBI currently contains 8273 entries of biomolecular binding or reaction events involving 1380 proteins, 143 nucleic acids and 1395 small molecules. Hyperlinks are provided for accessing references in Medline and available 3D structures in PDB and NDB. This database can be accessed at http://xin.cz3.nus.edu.sg/group/kdbi/kdbi.asp.     

Adsorption of glycinin and β-conglycinin on silica and cellulose: surface interactions as a function of denaturation, pH, and electrolytes

Soybean proteins have found uses in different nonfood applications due to their interesting properties. We report on the kinetics and extent of adsorption on silica and cellulose surfaces of glycinin and β-conglycinin, the main proteins present in soy. Quartz crystal microgravimetry (QCM) experiments indicate that soy protein adsorption is strongly affected by changes in the physicochemical environment. The affinity of glycinin and the mass adsorbed on silica and cellulose increases (by ca. 13 and 89%, respectively) with solution ionic strength (as it increases from 0 to 100 mM NaCl) due to screening of electrostatic interactions. In contrast, β-conglycinin adsorbs on the same substrates to a lower extent and the addition of electrolyte reduces adsorption (by 25 and 57%, respectively). The addition of 10 mM 2-mercaptoethanol, a denaturing agent, reduces the adsorption of both proteins with a significant effect for glycinin. This observation is explained by the cleavage of disulfide bonds which allows unfolding of the molecules and promotes dissociation into subunits that favors more compact adsorbed layer structures. In addition, adsorption of glycinin onto cellulose decreases with lowering the pH from neutral to pH 3 due to dissociation of the macromolecules, resulting in flatter adsorbed layers. The respective adsorption isotherms fit a Langmuir model and QCM shifts in energy dissipation and frequency reveal multiple-step kinetic processes indicative of changes in adlayer structure.     

Direct electrochemistry of hemoglobin in gold nanowire array

Gold nanowire array has been proven to be efficient support matrixes for the immobilization of hemoglobin (Hb). The vertically oriented nanowire array provides an ordered well-defined 3D structure with nanowire density approximately 5 x 10(8)cm(2). The adsorption of ferritin onto the nanowire surface was visualized by transmission electron microscopy. When Hb was adsorbed, UV-vis absorption and Fourier transform infrared (FT-IR) spectra show no obvious denaturation of Hb in the nanowire array. The Hb-modified nanowire array exerted direct electron transfer and gave a well-defined, nearly reversible redox couple with formal potential of -0.225 V. The quantity of electroactive Hb varied with the changing of the morphology of the electrode and found to increase with the increasing of the nanowire length. Comparisons of voltammetric and quartz crystal microbalance measurements show that 70% of the Hb molecules adsorbed are electroactive when the length of the nanowire was 2 microm. Both of the Hb-modified nanowire array and the unmodified nanowire array demonstrate good electrocatalytic reduction ability for hydrogen peroxide. With the adsorption of glucose oxidase onto the bare nanowire surface, sensitive and selective glucose biosensors can be fabricated.     

Phage SPP1 reversible adsorption to Bacillus subtilis cell wall teichoic acids accelerates virus recognition of membrane receptor YueB

Bacteriophage SPP1 targets the host cell membrane protein YueB to irreversibly adsorb and infect Bacillus subtilis. Interestingly, SPP1 still binds to the surface of yueB mutants, although in a completely reversible way. We evaluated here the relevance of a reversible step in SPP1 adsorption and identified the receptor(s) involved. We show that reversible adsorption is impaired in B. subtilis mutants defective in the glucosylation pathway of teichoic acids or displaying a modified chemical composition of these polymers. The results indicate that glucosylated poly(glycerolphosphate) cell wall teichoic acid is the major target for SPP1 reversible binding. Interaction with this polymer is characterized by a fast adsorption rate showing low-temperature dependence, followed by a rapid establishment of an equilibrium state between adsorbed and free phages. This equilibrium is basically determined by the rate of phage dissociation, which exhibits a strong dependence on temperature compatible with an Arrhenius law. This allowed us to determine an activation energy of 22.6 kcal/mol for phage release. Finally, we show that SPP1 reversible interaction strongly accelerates irreversible binding to YueB. Our results support a model in which fast SPP1 adsorption to and desorption from teichoic acids allows SPP1 to scan the bacterial surface for rapid YueB recognition.