Serum protein immunogenicity: implications for liver xenografting

The objectives of this study were threefold: (i) assess immunogenicity of donor plasma proteins following hepatic xenotransplantation, (ii) identify potential immunogens, and (iii) consider the implications of antibody formation against these plasma proteins in xenograft survival. We studied liver and heart xenografts in a concordant combination, hamster to rat. All grafts were examined at necropsy for evidence of rat immunoglobulin G (IgG) deposition. Cardiac xenografts were placed in recipients who had, or had not, been sensitized with hamster serum. Hepatic xenografts were placed in naive recipients to see if antibodies to hamster serum proteins could be eluted from the rejecting organ. Sera of immunized rats were examined for the presence of anti-hamster antibodies by immunoelectrophoresis and by Western blotting following sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) separation of hamster serum. Antibodies in sera of immunized rats were compared with those eluted from rejecting livers. Candidate antigens were identified by tandem mass spectrometry, sequence analysis, and reference to protein databases. Results showed that sera of immunized rats recognized a minimum of four different antigens in hamster serum by immunoelectrophoresis, and a minimum of seven by the more sensitive SDS-PAGE Western blot. IgG eluted from rejecting livers bound three of seven candidate antigens recognized by sera of the immunized animals. Sequence analysis searches revealed proteinase inhibitors in each of the three SDS-PAGE bands common to the above samples. All of these candidate proteinase inhibitor immunogens share a common catabolic fate, uptake via the lipoprotein-related protein (LRP/alpha 2-macroglobulin receptor (CD91). Sensitization to hamster serum proteins hastened cardiac xenograft rejection in 30-50% of recipients (depending on sensitization protocol). Vascular deposition of rat IgG occurred in all rejecting xenografts. Antibody binding to proteinase inhibitors could disturb their functional activity and contribute to the pathogenesis of delayed xenograft rejection.     

The fluorescent probe prodan characterizes the warfarin binding site on human serum albumin

Abstract— The fluorescent probe Prodan (6-propionyl-2-dimethyl-aminonaphthalene) binds with high affinity to human serum albumin (HSA). The spectral characteristics of the Prodan bound to the protein are very different from the free Prodan in solution. These differences allowed the spectra to be deconvoluted into log-normal bands in order to quantify the bound and unbound ligand and to calculate the binding constant at different temperatures. From such temperature dependence, we found the binding to be exothermic with a van't Hoff enthalpy of -22.8 kJ mol^-1. Thermodynamic analysis suggests that the in teraction may be mainly caused by hydrophobic forces and electrostatic interactions. The above analysis of the spectra and the measures of the fluorescence polarization during the successive presence of six specific drugs suggest that the Prodan binding site corresponds with the warfarin binding site on HSA, whereas under the present experimental conditions the other characteristic binding sites of HSA were not affected. Thus, this fluorescent probe provides a rapid and simple means for the characterization of a specific binding site on HSA and also for detecting potential or nonspecific drug-protein interactions.     

Radiopharmaceuticals for renal studies: Evaluation of protein binding

Determination of total in vitro protein binding was evaluated for the following radiopharmaceuticals:^99mTc-diethylenetriaminepentaacetic acid (DTPA),^99mTc-dimercaptosuccinic acid (DMSA),^99mTc-glucoheptonate (GH) and^99mTc-fosfomycin (PHO). For that they were incubated wtih human serum at 37°C. After three and sixty minutes of incubation, the bound fraction was evaluated by two different methods: gel filtration and precipitation with trichloroacetic acid (TCA). The percentage of the^99mTc-kidney agents bound by human serum proteins is different for each one. Determination by TCA precipitation always leads to higher results. For renal imaging agents (DMSA, GH and PHO) the percentage of binding by each serum proteic constituent was also evaluated by electrophoretic analysis. All proteic constituents of human serum bind with those radiopharmaceuticals but the percentage of binding is different in accordance with both the radiopharmaceutical and the proteic constituent.     

Ordering surfaces on the nanoscale: implications for protein adsorption

Monolayer-protected metal nanoparticles (MPMNs) are a newly discovered class of nanoparticles with an ordered, striped domain structure that can be readily manipulated by altering the ratio of the hydrophobic to hydrophilic ligands. This property makes them uniquely suited to systematic studies of the role of nanostructuring on biomolecule adsorption, a phenomenon of paramount importance in biomaterials design. In this work, we examine the interaction of the simple, globular protein cytochrome C (Cyt C) with MPMN surfaces using experimental protein assays and computational molecular dynamics simulations. Experimental assays revealed that adsorption of Cyt C generally increased with increasing surface polar ligand content, indicative of the dominance of hydrophilic interactions in Cyt C-MPMN binding. Protein-surface adsorption enthalpies calculated from computational simulations employing rigid-backbone coarse-grained Cyt C and MPMN models indicate a monotonic increase in adsorption enthalpy with respect to MPMN surface polarity. These results are in qualitative agreement with experimental results and suggest that Cyt C does not undergo significant structural disruption upon adsorption to MPMN surfaces. Coarse-grained and atomistic simulations furthermore elucidated the important role of lysine in facilitating Cyt C adsorption to MPMN surfaces. The amphipathic character of the lysine side chain enables it to form close contacts with both polar and nonpolar surface ligands simultaneously, rendering it especially important for interactions with surfaces composed of adjacent nanoscale chemical domains. The importance of these structural characteristics of lysine suggests that proteins may be engineered to specifically interact with nanomaterials by targeted incorporation of unnatural amino acids possessing dual affinity to differing chemical motifs.     

Method for computing protein binding affinity

A Monte Carlo method is given to compute the binding affinity of a ligand to a protein. The method involves extending configuration space by a discrete variable indicating whether the ligand is bound to the protein and a special Monte Carlo move, which allows transitions between the unbound and bound states. Provided that an accurate protein structure is given, that the protein-ligand binding site is known, and that an accurate chemical force field together with a continuum solvation model is used, this method provides a quantitative estimate of the free energy of binding.     

Multicomponent membranes on solid substrates: Interfaces for protein binding

Even though lipid membranes deposited on a solid support are now used for more than 20 years as a model system for cellular membranes, their potential has, as yet, not been fully exploited. Only in recent years, the composition of solid supported membranes became more and more complex, which is a prerequisite for the elucidation of biologically relevant protein adsorption processes. Multicomponent bilayers resemble the heterogeneity of the biological membrane, which is composed of hundreds of different lipids varying in their headgroup and acyl chain composition. The development of a multitude of elaborated surface sensitive techniques allows to study the phase behavior of these membranes and their interaction with proteins, some of which will be highlighted in this review.     

Study of binding of warfarin to serum albumins by high-performance liquid chromatography

The binding of warfarin to human serum albumin and bovine serum albumin, respectively, was studied by high-performance liquid chromatography (HPLC). Based upon the Hummel - Dreyer method, two techniques were developed: the internal calibration and the external calibration. The results obtained by the HPLC method and those obtained by the classical method (equilibrium dialysis) were compared. The external calibration method seems to be superior to others for its simplicity, speed and convenience.     

Ultrafast protein splicing is common among cyanobacterial split inteins: implications for protein engineering

We describe the first systematic study of a family of inteins, the split DnaE inteins from cyanobacteria. By measuring in vivo splicing efficiencies and in vitro kinetics, we demonstrate that several inteins can catalyze protein trans-splicing in tens of seconds rather than hours, as is commonly observed for this autoprocessing protein family. Furthermore, we show that when artificially fused, these inteins can be used for rapid generation of protein α-thioesters for expressed protein ligation. This comprehensive survey of split inteins provides indispensable information for the development and improvement of intein-based tools for chemical biology.     

Interaction of urea with amino acids: implications for urea-induced protein denaturation

The molecular mechanism of urea-induced protein denaturation is not yet fully understood. Mainly two opposing mechanisms are controversially discussed, according to which either hydrophobic, or polar interactions are the dominant driving force. To resolve this question, we have investigated the interactions between urea and all 20 amino acids by comprehensive molecular dynamics simulations of 22 tripeptides. Calculation of atomic contact frequencies between the amino acids and solvent molecules revealed a clear profile of solvation preferences by either water or urea. Almost all amino acids showed preference for contacts with urea molecules, whereas charged and polar amino acids were found to have slight preferences for contact with water molecules. Particularly strong preference for contacts to urea were seen for aromatic and apolar side-chains, as well as for the protein backbone of all amino acids. Further, protein-urea hydrogen bonds were found to be significantly weaker than protein-water or water-water hydrogen bonds. Our results suggest that hydrophobic interactions are the dominant driving force, while hydrogen bonds between urea and the protein backbone contribute markedly to the overall energetics by avoiding unfavorable unsatisfied hydrogen bond sites on the backbone. In summary, we suggest a combined mechanism that unifies the two current and seemingly opposing views.     

Circumventing the problems caused by protein diversity in microarrays: implications for protein interaction networks

Protein microarrays provide a well-controlled, high-throughput way to uncover protein-protein interactions. One problem with this and other standardized assays, however, is that proteins vary considerably with respect to their physical properties. If a simple threshold-based approach is used to define protein-protein interactions, the resulting binary networks can be strongly biased. Here, we investigate the extent to which even closely related protein interaction domains vary when printed as microarrays. We find that, when a collection of well behaved, monomeric Src homology 2 (SH2) domains are printed at the same concentration, they vary by up to 50-fold with respect to the resulting surface density of active protein. When a threshold-based binding assay is performed on these domains using fluorescently labeled phosphopeptides, a misleading picture of the underlying biophysical interactions emerges. This problem can be circumvented, however, by obtaining saturation binding curves for each protein-peptide interaction. Importantly, the equilibrium dissociation constants obtained from these curves are independent of the surface density of active protein. We submit that an increased emphasis should be placed on obtaining quantitative information from protein microarrays and that this should serve as a more general goal in all efforts to define large-scale protein interaction networks.     

A perturbed pK(a) at the binding site of the nicotinic acetylcholine receptor: implications for nicotine binding

A series of tethered quaternary ammonium derivatives of Tyr have been incorporated into the binding site of the nicotinic acetylcholine receptor (nAChR) using the in vivo nonsense suppression method, producing constitutively active (self-gating) receptors. We have incorporated primary, secondary, and tertiary amine tethered agonists to give receptors whose constitutive activity can be modulated by pH. Lowering the pH protonates the tethered amine, giving it a positive charge and allowing it to reversibly activate the receptor. Tertiary and secondary tethered amines, TyrO3T and TyrO3S, have been successfully incorporated at alpha149 in the nAChR. Constitutive currents at pH 5.5 are 6 times those at pH 9.0. The pKa of TyrO3T in the binding site appears to be 6 or lower, differing substantially from its pKa in solution ( approximately 9.3). This local pKa perturbation has substantial implications for pharmacological research on the nAChR: of the tertiary agonists considered, noracetylcholine experiences this pKa perturbation, while nicotine does not.     

Capillary electrophoresis of liposomes functionalized for protein binding

CE enabled assessing the attachment of hexa-histidine-tagged proteins to functionalized phospholipid liposomes. The liposomes were made of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, phosphatidyl-ethanolamine, cholesterol and distearoyl-glycero-3-phosphoethanolamine-N-methoxy(polyethylene glycol) in a molar ratio of 29:26:40:5. The unilamellar vesicles, which had an average diameter of 170 nm, were labelled by inclusion of FITC-dextran for fluorescence detection. CE was carried out in poly(vinyl alcohol) (PVA)-coated capillaries at 25 degrees C with a BGE consisting of Tris-HCl (50 mM, pH 8.0). For conjugation of the liposomes with the proteins (soluble synthetic receptor fragments with molecular mass of 60 and 70 kDa, respectively), Ni(2+) was implanted into the vesicle surface by an anchor lipid containing a nitrilotriacetate acid (NTA) group as complexation agent for the metal ions. The difference in surface charge enabled the separation of the different species of interest by CE: plain vesicles, vesicles functionalised with Ni-NTA, vesicle-protein complexes and the species formed upon removal of the Ni-ions by complexation with EDTA. Loss of the Ni-ions resulted in the release of the proteins and the reappearance of the plain Ni-free NTA-liposome species in the electropherograms.     

The potent anti-HIV protein cyanovirin-N contains two novel carbohydrate binding sites that selectively bind to Man(8) D1D3 and Man(9) with nanomolar affinity: implications for binding to the HIV envelope protein gp120.

Cyanovirin-N (CVN) is a monomeric 11 kDa cyanobacterial protein that potently inactivates diverse strains of human immunodeficiency virus (HIV) at the level of cell fusion by virtue of high affinity interactions with the surface envelope glycoprotein gp120. Several lines of evidence have suggested that CVN-gp120 interactions are in part mediated by N-linked complex carbohydrates present on gp120, but experimental evidence has been lacking. To this end we screened a comprehensive panel of carbohydrates which represent structurally the N-linked carbohydrates found on gp120 for their ability to inhibit the fusion-blocking activity of CVN in a quantitative HIV-1 envelope-mediated cell fusion assay. Our results show that CVN specifically recognizes with nanomolar affinity Man(9)GlcNAc(2) and the D1D3 isomer of Man(8)GlcNAc(2). Nonlinear least squares best fitting of titration data generated using the cell fusion assay show that CVN binds to gp120 with an equilibrium association constant (K(a)) of 2.4 (+/- 0.1) x 10(7) M(-1) and an apparent stoichiometry of 2 equiv of CVN per gp120, Man(8)GlcNAc(2) D1D3 acts as a divalent ligand (2 CVN:1 Man(8)) with a K(a) of 5.4 (+/- 0.5) x 10(7) M(-1), and Man(9)GlcNAc(2) functions as a trivalent ligand (3 CVN:1 Man(9)) with a K(a) of 1.3 (+/- 0.3) x 10(8) M(-1). Isothermal titration calorimetry experiments of CVN binding to Man(9)GlcNAc(2) at micromolar concentrations confirmed the nanomolar affinity (K(a) = 1.5 (+/- 0.9) x 10(8) M(-1)), and the fitted data indicated a stoichiometry equal to approximately one (1 Man(9):1 CVN). The 1:1 stoichiometry at micromolar concentrations suggested that CVN has not only a high affinity binding site-relevant to the studies at nM concentrations-but a lower affinity site as well that facilitates cross-linking of CVN-oligomannose at micromolar concentrations or higher. The specificity of CVN for Man(8) D1D3 and Man(9) over the D1D2 isomer of Man(8) indicated that the minimum structure required for high affinity binding comprises Manalpha1 --> 2Manalpha. By following the (1)H-(15)N correlation spectrum of (15)N-labeled CVN upon titration with this disaccharide, we unambiguously demonstrate that CVN recognizes and binds to the disaccharide Manalpha1 --> 2Manalpha via two distinct binding sites of differing affinities located on opposite ends of the protein. The high affinity site has a K(a) of 7.2 (+/- 4) x 10(6) M(-1) and the low affinity site a K(a) of 6.8 (+/- 4) x 10(5) M(-1) as determined by isothermal titration calorimetry. Mapped surfaces of the carbohydrate binding sites are presented, and implications for binding to gp120 are discussed.     

Polyelectrolyte-mediated protein adsorption: fluorescent protein binding to individual polyelectrolyte nanospheres

We have used confocal fluorescence microscopy with single molecule sensitivity to characterize uptake and release of fluorescent protein (mEosFP) molecules by individual spherical polyelectrolyte brush (SPB) nanoparticles that were immobilized on a glass surface. The SPB particles consisted of a solid core particle of 100 nm diameter onto which long polyelectrolyte chains were affixed. They could be loaded with up to 30 000 mEosFP molecules in a solvent of low ionic strength. The concentration dependence of protein loading can be described with a simple bimolecular binding model, characterized by an equilibrium dissociation coefficient of 0.5 microM. Essentially complete release of the bound proteins was observed after increasing the ionic strength by adding 250 mM NaCl to the solvent. Fluorescence emission spectra and time-resolved fluorescence intensity decays were measured on individual, mEosFP-loaded SPB nanoparticles, and also on the dissolved mEosFP before and after adsorption. These results indicate that the mEosFP molecules remained structurally intact in this procedure. Hence, the present investigation demonstrates unambiguously that polyelectrolyte-mediated protein adsorption onto SPB particles presents a viable process for protein immobilization.     

Competitive binding of methanol and propane for water via matrix-isolation spectroscopy: implications for inhibition of clathrate nucleation

Methanol is a well-known thermodynamic inhibitor of clathrate hydrate formation. The interactions responsible for the inhibition, however, are not well-identified. Propane is a relatively simple hydrocarbon that forms a clathrate hydrate under mild conditions. This paper reports data about the interaction of methanol with water-propane complex. Methanol, water, and propane are isolated in carbon tetrachloride, and the interaction is probed with infrared spectroscopy. Water is known to interact with propane via the oxygen lone pairs and the propane methylene hydrogens. Experimental evidence indicates that methanol hydrogen bonds to water via donation of the hydroxyl hydrogen (K = 4.4 × 10(2)). Methanol does not have a direct interaction with propane. These results are consistent with an inhibitory mechanism in which methanol competes with propane for the oxygen atom of water.     

Kinetics of protein binding in solid-phase immunoassays: theory

In a solid-phase immunoassay, binding between an antigen and its specific antibody takes place at the boundary of a liquid and a solid phase. One of the reactants (receptor) is immobilized on a surface. The other reactant (ligand) is initially free in solution. We present a theory describing the kinetics of immunochemical reaction in such a system. A single essential restriction of the theory is the assumption that the reaction conditions are uniform along the binding surface. In general, the reaction rate as a function of time can be obtained numerically as a solution of a nonlinear integral equation. For some special cases, analytical solutions are available. Various immunoassay geometries are considered, in particular, the case when the reaction is carried out on a microspot.     

Protein:Ligand binding free energies: A stringent test for computational protein design

A computational protein design method is extended to allow Monte Carlo simulations where two ligands are titrated into a protein binding pocket, yielding binding free energy differences. These provide a stringent test of the physical model, including the energy surface and sidechain rotamer definition. As a test, we consider tyrosyl‐tRNA synthetase (TyrRS), which has been extensively redesigned experimentally. We consider its specificity for its substrate l ‐tyrosine (l ‐Tyr), compared to the analogs d ‐Tyr, p‐acetyl‐, and p‐azido‐phenylalanine (ac‐Phe, az‐Phe). We simulate l ‐ and d ‐Tyr binding to TyrRS and six mutants, and compare the structures and binding free energies to a more rigorous “MD/GBSA” procedure: molecular dynamics with explicit solvent for structures and a Generalized Born + Surface Area model for binding free energies. Next, we consider l ‐Tyr, ac‐ and az‐Phe binding to six other TyrRS variants. The titration results are sensitive to the precise rotamer definition, which involves a short energy minimization for each sidechain pair to help relax bad contacts induced by the discrete rotamer set. However, when designed mutant structures are rescored with a standard GBSA energy model, results agree well with the more rigorous MD/GBSA. As a third test, we redesign three amino acid positions in the substrate coordination sphere, with either l ‐Tyr or d ‐Tyr as the ligand. For two, we obtain good agreement with experiment, recovering the wildtype residue when l ‐Tyr is the ligand and a d ‐Tyr specific mutant when d ‐Tyr is the ligand. For the third, we recover His with either ligand, instead of wildtype Gln. © 2015 Wiley Periodicals, Inc.