High-resolution 2D 1H-15N NMR characterization of persistent structural alterations of proteins induced by interactions with silica nanoparticles

The binding of protein to solid surfaces often induces changes in the structure, and to investigate these matters we have selected two different protein-nanoparticle systems. The first system concerns the enzyme human carbonic anhydrase II which binds essentially irreversibly to the nanoparticles, and the second system concerns human carbonic anhydrase I which alternate between the adsorbed and free state upon interaction with nanoparticles. Application of the TROSY pulse sequence has allowed high-resolution NMR analysis for both of the protein-nanoparticle systems. For HCAII it was possible to observe spectra of protein when bound to the nanoparticles. The results indicated that HCAII undergoes large rearrangements, forming an ensemble of molten globule-like structures on the surface. The spectra from the HCAI-nanoparticle system are dominated by HCAI molecules in solution. A comparative analysis of variations in intensity from 97 amide resonances in a 1H-15N TROSY spectrum revealed the effects from interaction with nanoparticle on the protein structure at amino acid resolution.     

Structure of a Complex Formed by a Protein and a Helical Aromatic Oligoamide Foldamer at 2.1 Å Resolution

In the search of molecules that could recognize sizeable areas of protein surfaces, a series of ten helical aromatic oligoamide foldamers was synthesized on solid phase. The foldamers comprise three to five monomers carrying various proteinogenic side chains, and exist as racemic mixtures of interconverting right‐handed and left‐handed helices. Functionalization of the foldamers by a nanomolar ligand of human carbonic anhydrase II (HCA) ensured that they would be held in close proximity to the protein surface. Foldamer–protein interactions were screened by circular dichroism (CD). One foldamer displayed intense CD bands indicating that a preferred helix handedness is induced upon interacting with the protein surface. The crystal structure of the complex between this foldamer and HCA could be resolved at 2.1 Å resolution and revealed a number of unanticipated protein–foldamer, foldamer–foldamer, and protein–protein interactions.     

圆二色性测定蛋白质在超细粒子上吸附的构象变化

研究了蛋白质在超细粒子固体表面吸附过程中构象的变化;选择的吸附剂粒径很小,可以直接应用圆二色性光谱测定蛋白质吸附层的二级结构变化;研究了pH、固体吸附表面在蛋白质吸附过程中对蛋白质构象的影响,得到了较好的实验数据,为进一步进行蛋白质吸附机理的理论研究提供了基础。     

Secondary ligands enhance affinity at a designed metal-binding site.

BACKGROUND: Specific interactions of metal ions with proteins are central to all life processes. The varied functions enabled by this cooperation are a consequence of strict control of the binding-site environment, particularly the number, type and geometry of metal-coordinating sidechains. Attempts to mimic these characteristics in the de novo design of metal-binding sites have thus far concentrated primarily on metal recruitment and not on affecting site function through systematic fine-tuning of the metal environment. RESULTS: A designed tetrahedral Zn(II)-binding site in a variant of the B1 domain of IgG-binding protein G has been expanded by introducing 'secondary ligands'. These interactions were engineered to stabilize the positions of the metal-coordinating histidine residues while retaining the desired coordination geometry. Each mutation increased the protein's affinity for metal, and combining two secondary ligands demonstrated that these enhancements are additive. These results mimic the effects of altering similar interactions observed in the native Zn(II)-binding site of carbonic anhydrase. In the B1 system, this enhanced affinity for metal is observed despite a substantial decrease in protein secondary structure. CONCLUSIONS: The intended effects of secondary ligand addition on metal affinity were observed in each mutant and demonstrated to be additive. Addition of metal also stabilized the protein's structure, partially offsetting the destabilizing effect of the mutations. These results represent a successful first attempt at designing an extended metal-binding site environment and illustrate the importance of including secondary interactions in the design of metal-binding sites.     

Biomaterials obtained by gelation of silica precursor with CO<Subscript>2</Subscript> saturated water containing a carbonic anhydrase enzyme

As part of an effort to develop biomaterials for the capture of CO₂ catalyzed by a carbonic anhydrase enzyme, the effects of an aqueous CO₂ saturated solution and a carbonic anhydrase on the gelation and texture of SiO₂ gels derived from tetramethoxysilane (TMOS), were studied. Both aqueous CO₂ and the enzyme were found to accelerate the gelation of silica, with a stronger effect when both the enzyme and CO₂ saturated aqueous water, were used. According to the gel texture data, aqueous CO₂ acted as an acid type catalyst, while the carbonic anhydrase acted as a weak base type catalyst. Moreover, a gel with a more granular visual aspect was obtained when both the enzyme and CO₂ saturated water were used. The latter characteristic was consistent with a double action of the enzyme, first as a gelation catalyst on the silica precursor, secondly as a reverse protonation catalyst which accelerated the back nucleation of CO₂ gas bubbles from aqueous HCO₃ ⁻ anions.     

Silica nanoparticle size influences the structure and enzymatic activity of adsorbed lysozyme

Adsorption of chicken egg lysozyme on silica nanoparticles of various diameters has been studied. Special attention has been paid to the effect of nanoparticle size on the structure and function of the adsorbed protein molecules. Both adsorption patterns and protein structure and function are strongly dependent on the size of the nanoparticles. Formation of molecular complexes is observed for adsorption onto 4-nm silica. True adsorptive behavior is evident on 20- and 100-nm particles, with the former resulting in monolayer adsorption and the latter yielding multilayer adsorption. A decrease in the solution pH results in a decrease in lysozyme adsorption. A change of protein structure upon adsorption is observed, as characterized by a loss in alpha-helix content, and this is strongly dependent on the size of the nanoparticle and the solution pH. Generally, greater loss of alpha helicity was observed for the lysozyme adsorbed onto larger nanoparticles under otherwise similar conditions. The activity of lysozyme adsorbed onto silica nanoparticles is lower than that of the free protein, and the fraction of activity lost correlates well with the decrease in alpha-helix content. These results indicate that the size of the nanoparticle, perhaps because of the contributions of surface curvature, influences adsorbed protein structure and function.     

Structure of a 129Xe-cryptophane biosensor complexed with human carbonic anhydrase II

Cryptophanes represent an exciting class of xenon-encapsulating molecules that can be exploited as probes for nuclear magnetic resonance imaging. The 1.70 A resolution crystal structure of a cryptophane-derivatized benezenesulfonamide complexed with human carbonic anhydrase II shows how an encapsulated xenon atom can be directed to a specific biological target. The crystal structure confirms binding measurements indicating that the cryptophane cage does not strongly interact with the surface of the protein, which may enhance the sensitivity of 129Xe NMR spectroscopic measurements in solution.     

Surface tailoring for controlled protein adsorption: effect of topography at the nanometer scale and chemistry

Protein adsorption behavior is at the heart of many of today's research fields including biotechnology and materials science. With understanding of protein-surface interactions, control over the conformation and orientation of immobilized species may ultimately allow tailor-made surfaces to be generated. In this contribution protein-surface interactions have been examined with particular focus on surface curvature with and without surface chemistry effects. Silica spheres with diameters in the range 15-165 nm with both hydrophilic and hydrophobic surface chemistries have been used as model substrates. Two proteins differing in size and shape, bovine serum albumin (BSA) and bovine fibrinogen (Fg), have been used in model studies of protein binding with detailed secondary structure analysis being performed using infrared spectroscopy (IR) on surface-bound proteins. Although trends in binding affinity and saturation values were similar for both proteins, albumin is increasingly less ordered on larger substrates, while fibrinogen, in contrast, loses secondary structure to a greater extent when adsorbing onto particles with high surface curvature. These effects are compounded by surface chemistry, with both proteins becoming more denatured on hydrophobic surfaces. Both surface chemistry and topography play key roles in determining the structure of the bound proteins. A model of the binding characteristics of these two proteins onto surfaces having differing curvature and chemistry is presented. We propose that properties of an adsorbed protein layer may be guided through careful consideration of surface structure, allowing the fabrication of materials/surface coatings with tailored bioactivity.     

New antifouling silica hydrogel

In this work, a new antifouling silica hydrogel was developed for potential biomedical applications. A zwitterionic polymer, poly(carboxybetaine methacrylate) (pCBMA), was produced via atom-transfer radical polymerization and was appended to the hydrogel network in a two-step acid-base-catalyzed sol-gel process. The pCBMA silica aerogels were obtained by drying the hydrogels under supercritical conditions using CO(2). To understand the effect of pCBMA on the gel structure, pCBMA silica aerogels with different pCBMA contents were characterized using scanning electron microscopy (SEM), nuclear magnetic resonance (NMR) spectroscopy, and the surface area from Brauner-Emmet-Teller (BET) measurements. The antifouling property of pCBMA silica hydrogel to resist protein (fibrinogen) adsorption was measured using enzyme-linked immunosorbent assay (ELISA). SEM images revealed that the particle size and porosity of the silica network decreased at low pCBMA content and increased at above 33 wt % of the polymer. The presence of pCBMA increased the surface area of the material by 91% at a polymer content of 25 wt %. NMR results confirmed that pCBMA was incorporated completely into the silica structure at a polymer content below 20 wt %. A protein adsorption test revealed a reduction in fibrinogen adsorption by 83% at 25 wt % pCBMA content in the hydrogel compared to the fibrinogen adsorption in the unmodified silica hydrogel.     

Preparation of well-defined polystyrene/silica hybrid nanoparticles by ATRP

Immobilization of the atom transfer radical polymerization (ATRP) macroinitiators at the silica nanoparticle surfaces was achieved through surface modification with excess toluene-2,4-diisocynate (TDI), after which the residual isocyanate groups were converted into ATRP macroinitiators. Structurally well-defined polystyrene chains were grown from the nanoparticle surfaces to yield individual particles composed of a silica core and a well-defined, densely grafted outer polystyrene by ATRP, which was initiated by the as-synthesized silica-based macroinitiator. FTIR, NMR and gel permeation chro-matography (GPC) were used to characterize the polystyrene/silica hybrid particles.     

Molecular simulation to characterize the adsorption behavior of a fibrinogen gamma-chain fragment

Implants invoke inflammatory responses from the body even if they are chemically inert and nontoxic. It has been shown that a crucial precedent event in the inflammatory process is the spontaneous adsorption of fibrinogen (Fg) on implant surfaces, which is typically followed by the presence of phagocytic cells. Interactions between the phagocyte integrin Mac-1 and two short sequences within the fibrinogen gamma chain, gamma190-202 and gamma377-395, may partially explain phagocyte accumulation at implant surfaces. These two sequences are believed to form an integrin binding site that is inaccessible when Fg is in its soluble-state structure but then becomes available for Mac-1 binding following adsorption, presumably due to adsorption-induced conformational changes. The objective of this research was to theoretically investigate this possibility by using molecular dynamics simulations of the gamma-chain fragment of Fg over self-assembled monolayer (SAM) surfaces presenting different types of surface chemistry. The GROMACS software package was used to carry out the molecular simulations in an explicit solvation environment over a 5 ns period of time. The adsorption of the gamma-chain of fibrinogen was simulated on five types of SAM surfaces. The simulations showed that this protein fragment exhibits distinctly different adsorption behavior on the different surface chemistries. Although the trajectory files showed that significant conformational changes did not occur in this protein fragment over the time frame of the simulations, it was predicted that the protein does undergo substantial rotational and translational motions over the surface prior to stabilizing in various preferred orientations. This suggests that the kinetics of surface-induced conformational changes in a protein's structure might be much slower than the kinetics of orientational changes, thus enabling the principles of adsorption thermodynamics to be used to guide adsorbing proteins into defined orientations on surfaces before large conformational changes can occur. This finding may be very important for biomaterial surface design as it suggests that surface chemistry can potentially be used to directly control the orientation of adsorbing proteins in a manner that either presents or hides specific bioactive sites contained within a protein's structure, thereby providing a mechanism to control cellular responses to the adsorbed protein layer.     

Adsorption Behavior of Lysozyme and Tween 80 at Hydrophilic and Hydrophobic Silica–Water Interfaces

Nonionic surfactants such as Tween 80 are used commercially to minimize protein loss through adsorption and aggregation and preserve native structure and activity. However, the specific mechanisms underlying Tween action in this context are not well understood. Here, we describe the interaction of the well-characterized, globular protein lysozyme with Tween 80 at solid–water interfaces. Hydrophilic and silanized, hydrophobic silica surfaces were used as substrates for protein and surfactant adsorption, which was monitored in situ, with ellipsometry. The method of lysozyme and Tween introduction to the surfaces was varied in order to identify the separate roles of protein, surfactant, and the protein–surfactant complex in the observed interfacial behavior. At the hydrophobic surface, the presence of Tween in the protein solution resulted in a reduction in amount of protein adsorbed, while lysozyme adsorption at the hydrophilic surface was entirely unaffected by the presence of Tween. In addition, while a Tween pre-coat prevented lysozyme adsorption on the hydrophobic surface, such a pre-coat was completely ineffective in reducing adsorption on the hydrophilic surface. These observations were attributed to surface-dependent differences in Tween binding strength and emphasize the importance of the direct interaction between surfactant and solid surface relative to surfactant–protein association in solution in the modulation of protein adsorption by Tween 80.     

Effect of background electrolyte on the estimation of protein hydrodynamic radius and net charge through capillary zone electrophoresis

Two physicochemical models are proposed for the estimation of both hydrodynamic radius and net charge of a protein when the capillary zone electrophoretic mobility at a given protocol, the set of pK of charged amino acids, and basic data from Protein Data Bank are available. These models also provide a rationale to interpret appropriately the effects of solvent properties on protein hydrodynamic radius and net charge. To illustrate the numerical predictions of these models, experimental data of electrophoretic mobility available in the literature for well-defined protocols are used. Five proteins are considered: lysozyme, staphylococcal nuclease, human carbonic anhydrase, bovine carbonic anhydrase, and human serum albumin. Numerical predictions of protein net charges through these models compare well with the results reported in the literature, including those found asymptotically through protein charge ladder techniques. Model calculations indicate that the hydrodynamic radius is sensitive to changes of the protein net charge and hence it cannot be assumed constant in general. Also, several limitations associated with models for estimating protein net charge and hydrodynamic radius from protein structure, amino acid sequence, and experimental electrophoretic mobility are provided and discussed. These conclusions also show clear requirements for further research.     

Using covalent dimers of human carbonic anhydrase II to model bivalency in immunoglobulins

This paper describes the development of a new bivalent system comprising synthetic dimers of carbonic anhydrase linked chemically through thiol groups of cysteine residues introduced by site-directed mutagenesis. These compounds serve as models with which to study the interaction of bivalent proteins with ligands presented at the surface of mixed self-assembled monolayers (SAMs). Monovalent carbonic anhydrase (CA) binds to benzenesulfonamide ligands presented on the surface of the SAM with K(d)(surf) = 89 nM. The synthetic bivalent proteins--inspired by the structure of immunoglobulins--bind bivalently to the sulfonamide-functionalized SAMs with low nanomolar avidities (K(d)(avidity,surf) = 1-3 nM); this difference represents a ~50-fold enhancement of bivalent over monovalent association. The paper describes dimers of CA having (i) different lengths of the covalent linker that joined the two proteins and (ii) different points of attachment of the linker to the protein (either near the active site (C133) or distal to the active site (C185)). Comparison of the thermodynamics of their interactions with SAMs presenting arylsulfonamide groups demonstrated that varying the length of the linker between the molecules of CA had virtually no effect on the rate of association, or on the avidity of these dimers with ligand-presenting surfaces. Varying the point of attachment of the linker between monomeric CA's also had almost no effect on the avidity of the dimers, although changing the point of attachment affected the rates of binding and unbinding. These observations indicate that the avidities of these bivalent proteins, and by inference the avidities of structurally similar bivalent proteins such as IgG, are unexpectedly insensitive to the structure of the linker connecting them.     

Forces between hydrophilic surfaces adsorbed with apolipoprotein AII alpha helices

To provide better understanding of how a protein secondary structure affects protein-protein and protein-surface interactions, forces between amphiphilic alpha-helical proteins (human apolipoprotein AII) adsorbed on a hydrophilic surface (mica) were measured using an interferometric surface force apparatus (SFA). Forces between surfaces with adsorbed layers of this protein are mainly composed of electrostatic double layer forces at large surface distances and of steric repulsive forces at small distances. We suggest that the amphiphilicity of the alpha-helix structure facilitates the formation of protein multilayers next to the mica surfaces. We found that protein-surface interaction is stronger than protein-protein interaction, probably due to the high negative charge density of the mica surface and the high positive charge of the protein at our experimental conditions. Ellipsometry was used to follow the adsorption kinetics of this protein on hydrophilic silica, and we observed that the adsorption rate is not only controlled by diffusion, but rather by the protein-surface interaction. Our results for dimeric apolipoprotein AII are similar to those we have reported for the monomeric apolipoprotein CI, which has a similar secondary structure but a different peptide sequence and net charge. Therefore, the observed force curves seem to be a consequence of the particular features of the amphiphilic alpha-helices.     

Structural and Energetic Nonuniformities of Pyrocarbon-Mineral Adsorbents

Several series of pyrocarbon-mineral adsorbents (carbosils) were studied using the nitrogen adsorption method to compute structural and energetic parameters within the scope of overall adsorption isotherm approximation applying a regularization procedure with consideration for surface heterogeneity. A portion of pyrocarbon deposits (graphene clusters) fills mesopores of the oxide supports, but another portion represents relatively large nonporous pyrocarbon globules formed on the outer surfaces of the oxide matrices. Contributions of these two types of pyrocarbon deposits depend on the nature of oxide matrices and carbonized precursors. The characteristics of pyrocarbon formed on the silica (silica gel, fumed silica) surfaces differ from those for deposits prepared on the surfaces of titania/silica and alumina/silica or by the pyrolysis of metal acetylacetonates (Zr(AcAc)(4), TiO(AcAc)(2), Ni(AcAc)(2), Zn(AcAc)(2), Cr(AcAc)(3), Co(AcAc)(2)) on mesoporous silica gel. The structural and energetic characteristics estimated using the adsorption method with consideration for the adsorbent heterogeneity are fruitful for comparative analysis of the (1)H NMR spectra of water adsorbed on carbosils from the gas phase or unfrozen in the aqueous suspensions at T < 273 K. Copyright 2001 Academic Press.     

Adsorption of fibrinogen on a biomedical-grade stainless steel 316LVM surface: a PM-IRRAS study of the adsorption thermodynamics, kinetics and secondary structure changes

Polarization-modulation infrared reflection-absorption spectroscopy (PM-IRRAS) was employed to investigate the interaction of serum protein fibrinogen with a biomedical-grade 316LVM stainless steel surface, in terms of the adsorption thermodynamics, kinetics and secondary structure changes of the protein. Apparent Gibbs energy of adsorption values indicated a highly spontaneous and strong adsorption of fibrinogen onto the surface. The kinetics of fibrinogen adsorption were successfully modeled using a pseudo first-order kinetic model. Deconvolution of the amide I bands indicated that the adsorption of fibrinogen on 316LVM results in significant changes in the protein's secondary structure that occur predominantly within the first minute of adsorption. Among the investigated structures, the alpha-helix structure undergoes the smallest changes, while the beta-sheet and beta-turns structures undergo significant changes. It was shown that lateral interactions between the adsorbed molecules do not play a role in controlling the secondary structure changes. An increase in temperature induced changes in the secondary structure of the protein, characterized by a loss of the alpha-helical content and its transformation into the beta-turns structure.     

Thermodynamic Parameters for the Association of Fluorinated Benzenesulfonamides with Bovine Carbonic Anhydrase II

This paper describes a calorimetric study of the association of a series of seven fluorinated benzenesulfonamide ligands (C₆H_nF_5?nSO₂NH₂) with bovine carbonic anhydrase II (BCA). Quantitative structure–activity relationships between the free energy, enthalpy, and entropy of binding and pK_a and log P of the ligands allowed the evaluation of the thermodynamic parameters in terms of the two independent effects of fluorination on the ligand: its electrostatic potential and its hydrophobicity. The parameters were partitioned to the three different structural interactions between the ligand and BCA: the Zn^II cofactor–sulfonamide bond (≈65 % of the free energy of binding), the hydrogen bonds between the ligand and BCA (≈10 %), and the contacts between the phenyl ring of the ligand and BCA (≈25 %). Calorimetry revealed that all of the ligands studied bind in a 1:1 stoichiometry with BCA; this result was confirmed by ¹⁹F NMR spectroscopy and X‐ray crystallography (for complexes with human carbonic anhydrase II).     

Research of protein adsorption on the different surface topography of the zinc oxide

The effect of the surface topography on the protein adsorption process is of great significance for designing biomaterial surfaces and the biocompatibility for specific biomedical applications. In this work, we have systematically investigated the mono‐protein adsorption kinetics of bovine serum albumin (BSA) and fibrinogen (Fg) adsorbed on the four different surface topographies (nanoparticles (NPs), nanorods (NRs), nanosheets (NSs) and nanobeams (NBs) of Zinc oxide (ZnO), respectively. The competition of multi‐protein adsorbed on them has been studied as well. Results showed that each protein had a singular process of adsorption that fitted well by Spreading Particle Model (SPM). It confirmed that ZnO NRs compared with other samples had more adsorption sites, which could provide more opportunities for the interaction between material and protein molecules. In addition, the Fg compared to the BSA could be more tightly adsorbed to the surface, both of which existed slight conformational changes by Fourier transform infrared (FTIR) and circular dichroism spectra (CD). Taken together, all these consequences well demonstrated that NRs may have wider applications in designing biomaterial surfaces and the biocompatibility for implanted biomaterials. Copyright © 2014 John Wiley & Sons, Ltd.