Alkaline Titrations of poly(dG-dC)·poly(dG-dC): Microemulsion Versus Solution Behavior

Abstract

PolyGC was titrated with a strong base in the presence of increasing concentrations of NaCl (from 0.00 to 0.60M) either in water solution or with the polynucleotide solubilized in the aqueous core of reverse micelles, i.e., the cationic quaternary water-in-oil microemulsion CTAB/n-hexane/n-pentanol/water. The results for matched samples in the two media were compared. CD and UV spectroscopies and, for the solution experiments, pH measurements were used to follow the course of deprotonation. In both media the primary effect of the addition of base was denaturation of the polynucleotide, reversible by back-titration with a strong acid.

In solution, the apparent pK_a of the transition decreases with increasing the salt concentration and a roughly linear dependence of pK_a on p[NaCl] has been found. A parallel monotonic decay with ionic strength has been found in solution for R_OH, defined as the number of hydroxyl ions required per monomeric unit of polyGC to reach half-transition. By contrast, in microemulsion, R_OH has been found to be independent of the NaCl concentration (and 10 to 50 times lower than in solution). This result is proposed as an indirect evidence of the independence of pK_a on the salt concentration in microemulsion, where the pH cannot be measured. A sort of buffering effect of the positive charges on the micellar wall and of their counter-ions on the ionic strength could well explain this discrepancy of behavior in the two media.     

PIG BRAIN GLUTAMINASE: PURIFICATION AND IDENTIFICATION OF DIFFERENT ENZYME FORMS

—Pig brain glutaminase (EC 3.5.1.2 L-glutamine amidohydrolase) has been purified about 5000-fold from acetone powder. Glutaminase exists in different molecular forms, dependent on the ionic composition of the buffer. The three main forms are similar to those of kidney glutaminase and therefore called the tris-HCl enzyme, the phosphate enzyme, and the phosphate-borate enzyme. The sedimentation coefficients, as estimated by sucrose gradient technique, are 7·3, 8·7, and 53, respectively. Glutaminase has a pH optimum of about 9, but the pH curves of the tris-HCl enzyme and the phosphate-borate enzyme have different shapes. The apparent pK₁ of the tris-HCl enzyme-substrate complex is similar to pK₂ of inorganic phosphate, the apparent pK₂ of both the tris-HCl and the phosphateborate enzyme complexes is similar to pK₂ of glutamine. By use of the electron microscope we were able to see the phosphate-borate enzyme.     

Prediction of Secondary Ionization of the Phosphate Group in Phosphotyrosine Peptides

A computational approach, based on a continuum molecular electrostatics model, for the calculation of the pK_a values of secondary ionization of the phosphate group in phenyl phosphate derivatives is described. The method uses the ESP atomic charges of the mono-anionic and di-anionic forms of the ionizable phosphate group, computed with the use of the density functional method, and applies a new concept of the model group, being the reference state for the pK_a calculations. Both conformational flexibility and tautomeric degrees of freedom are taken into account in the calculations. The method was parameterized using experimentally available pK_a values of four derivatives of phenyl phosphates, and phosphotyrosine. Subsequently this parameterization was used to predict pK_a of the phosphate group in a short peptide Gly-Gly-Tyr(P)-Ala, and in a longer peptide consisting of 12 residues, the latter in water, and in a complex with a protein—phospholipase. The agreement between the computed and the experimental pK_a values is better than ±0.3 pH units for the optimized solute dielectric constant of 11–13. This approach is promising and its extension to other phospho-amino acids is in progress.     

Highly perturbed pKa values in the unfolded state of hen egg white lysozyme

The majority of pK_a values in protein unfolded states are close to the amino acid model pK_a values, thus reflecting the weak intramolecular interactions present in the unfolded ensemble of most proteins. We have carried out thermal denaturation measurements on the WT and eight mutants of HEWL from pH 1.5 to pH 11.0 to examine the unfolded state pK_a values and the pH dependence of protein stability for this enzyme. The availability of accurate pK_a values for the folded state of HEWL and separate measurements of mutant-induced effects on the folded state pK_a values, allows us to estimate the pK_a values of seven acidic residues in the unfolded state of HEWL. Asp-48 and Asp-66 display pK_a values of 2.9 and 3.1 in our analysis, thus representing the most depressed unfolded state pK_a values observed to date. We observe a strong correlation between the folded state pK_a values and the unfolded state pK_a values of HEWL, thus suggesting that the unfolded state of HEWL possesses a large degree of native state characteristics.     

Effects of pH on the kinetics of redox reactions in and around the cytochromebf complex in an isolated system

Rate-coefficients describing the electron transfer reactions between P700 and plastocyanin, between cytochromef in cytochromebf complexes and plastocyanin, and between decyl plastoquinol and cytochromebf complexes were determined as a function of pH in the range 4–10 from flash-induced absorbancy changes at four wavelengths. The reactions between P700 and plastocyanin, and between cytochromef and plastocyanin were optimised when there was electrostatic interaction between ionised acidic groups in plastocyanin with a pK_a of 4.3–4.7 and ionised basic constituents in P700 (assumed to be in the PSI-F subunit) and in cytochromef, with a pK_b of 8.9–9.4. The basic groups are thought to be lysine rather than arginine. This mechanism agrees with that inferred from effects of ionic strength changes on rate-coefficients. The relation between the second-order rate-coefficient for decyl plastoquinol oxidation by thebf complex and pH was characterised by a pK_a of 6.1. This is interpreted as showing that the anion radical form of that quinol, which has a pK_a of 6, and which becomes progressively protonated when pH is changed from 7 to 5, is essential to reduce cytochromeb-563 (low potential) during quinol oxidation. Above pH 9, permanent effects were observed on this rate-coefficient, which were absent in the reactions between P700, plastocyanin and cytochromef.     

pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4

The acid-base behavior of amino acids is an important subject of study due to their prominent role in enzyme catalysis, substrate binding and protein structure. Due to interactions with the protein environment, their pK_as can be shifted from their solution values and, if a protein has two stable conformations, it is possible for a residue to have different “microscopic”, conformation-dependent pK_a values. In those cases, interpretation of experimental measurements of the pK_a is complicated by the coupling between pH, protonation state and protein conformation. We explored these issues using Nitrophorin 4 (NP4), a protein that releases NO in a pH sensitive manner. At pH 5.5 NP4 is in a closed conformation where NO is tightly bound, while at pH 7.5 Asp30 becomes deprotonated, causing the conformation to change to an open state from which NO can easily escape. Using constant pH molecular dynamics we found two distinct microscopic Asp30 pK_as: 8.5 in the closed structure and 4.3 in the open structure. Using a four-state model, we then related the obtained microscopic values to the experimentally observed “apparent” pK_a, obtaining a value of 6.5, in excellent agreement with experimental data. This value must be interpreted as the pH at which the closed to open population transition takes place. More generally, our results show that it is possible to relate microscopic structure dependent pKa values to experimentally observed ensemble dependent apparent pK_as and that the insight gained in the relatively simple case of NP4 can be useful in several more complex cases involving a pH dependent transition, of great biochemical interest.     

Direct observation of multiple protonation states in recombinant human purple acid phosphatase

To date, most spectroscopic studies on mammalian purple acid phosphatases (PAPs) have been performed at a single pH, typically pH 5. The catalytic activity of these enzymes is, however, pH dependent, with optimal pH values of 5.5–6.2 (depending on the form). For example, the pH optimum of PAPs isolated as single polypeptides is around pH 5.5, which is substantially lower that of proteolytically cleaved PAPs (ca. pH 6.2). In addition, the catalytic activity of single polypeptide PAPs at their optimal pH values is four to fivefold lower than that of the proteolytically cleaved enzymes. In order to elucidate the chemical basis for the pH dependence of these enzymes, the spectroscopic properties of both the single polypeptide and proteolytically cleaved forms of recombinant human PAP (recHPAP) and their complexes with inhibitory anions have been examined over the pH range 4 to 8. The EPR spectra of both forms of recHPAP are pH dependent and show the presence of three species: an inactive low pH form (pH<pK _a,1), an active form (pK _a,1<pH<pK _a,2), and an inactive high pH form (pH>pK _a,2). The pK _a,1 values observed by EPR for the single polypeptide and proteolytically cleaved forms are similar to those previously observed in kinetics studies. The spectroscopic properties of the enzyme–phosphate complex (which should mimic the enzyme–substrate complex), the enzyme–fluoride complex, and the enzyme–fluoride–phosphate complex (which should mimic the ternary enzyme–substrate–hydroxide complex) were also examined. EPR spectra show that phosphate binds to the diiron center of the proteolytically cleaved form of the enzyme, but not to that of the single polypeptide form. EPR spectra also show that fluoride binds only to the low pH form of the enzymes, in which it presumably replaces a coordinated water molecule. The binding of fluoride and phosphate to form a ternary complex appears to be cooperative.Electronic Supplementary Material Supplementary material is available for this article at     

Some hydrodynamic and optical properties of polyribonucleotides

The size and shape of four polyribonucleotides were studied by sedimentation and viscosity measurements. The results were correlated with their conformations based on optical activity studies. Polyriboadenylic acid in acidic solution dimerizes into two double-stranded forms, one with half-protonated bases and the other fully protonated. The fully protonated form is somewhat less asymmetrical than the half-protonated form. Polyriboguanylic acid in alkaline solution (near the second pK_a of guanine) undergoes a time-dependent disaggregation and the final form shows little base stacking. In acidic solution, it demonstrates a reversible transition near the first pK_a of guanine but without evidence of disaggregation. Polyribocytidylic acid undergoes a transition upon half protonation of the bases, but its molecular weight remains unchanged with pH. The results suggest that this polymer assumes a hairpin structure in acidic solution. Polyribouridylic acid has some degree of base stacking: at room temperature. A transition to a hairpin structure occurs at low temperature.     

Predicting diafiltration solution compositions for final ultrafiltration/diafiltration steps of monoclonal antibodies

Many liquid formulations for monoclonal antibodies (MAbs) require the final ultrafiltration/diafiltration step to operate at high protein concentrations, often at or above 100 g/L. When operating under these conditions, the excipient concentrations and pH of the final diafiltered retentate are frequently not equal to the corresponding excipient concentrations and pH of the diafiltration buffer. A model based on the Poisson-Boltzmann equation combined with volume exclusion was extended to predict both pH and excipient concentrations in the retentate for a given diafiltration buffer. This model was successfully applied to identify the diafiltration buffer composition required to achieve the desired pre-formulated bulk drug substance (retentate) conditions. Predictions were in good agreement with the experimental results, and reduced the number of experimental iterations needed to define the diafiltration buffer composition. Additionally, the predictive model was applied in a sensitivity analysis across ranges of protein charge, protein concentration, and diafiltration buffer pH and excipient concentration. This sensitivity analysis can facilitate the design of experiments for robustness testing, and allow for generalized predictions across classes of molecules such as MAbs.     

Purification of singly PEGylated α-lactalbumin using charged ultrafiltration membranes

One of the challenges in producing a PEGylated therapeutic protein is that the PEGylation reaction typically generates a mixture of both singly and multiply PEGylated species. The objective of this study was to examine the feasibility of using ultrafiltration for the purification of a singly PEGylated protein from the multiply PEGylated conjugates. Data were obtained with α‐lactalbumin that was PEGylated with a 20 kDa activated PEG, with the ultrafiltration performed over a range of pH and ionic strength using both unmodified and negatively charged composite regenerated cellulose membranes. Purification of the singly PEGylated α‐lactalbumin from the multiply PEGylated species was accomplished using a diafiltration process with a negatively charged membrane at pH 5 and an ionic strength of 0.4 mM, conditions that maximized the electrostatic exclusion of the multiply PEGylated species from the charged membrane. The diafiltration process provided more than 97% yield with greater than 20‐fold purification between the singly and doubly PEGylated proteins and nearly complete removal of the more heavily PEGylated species. The singly PEGylated α‐lactalbumin was recovered as a dilute filtrate solution, although this dilution could be eliminated using a cascade filtration or the final product could be re‐concentrated in a second ultrafiltration as part of the final formulation. These results demonstrate the feasibility of using ultrafiltration for the purification of singly PEGylated protein therapeutics. Biotechnol. Bioeng. 2011; 108:822–829. © 2010 Wiley Periodicals, Inc.     

Theoretical analysis of excipient concentrations during the final ultrafiltration/diafiltration step of therapeutic antibody

Diafiltration of a protein solution into a new buffer is a common final step in biopharmaceutical manufacturing. However, the excipient concentrations in the retentate are not always equal to their corresponding concentrations in the new buffer (diafiltration buffer). This phenomenon was observed repeatedly during diafiltration of different therapeutic monoclonal antibodies in which the concentrations of histidine and either sorbitol or sucrose (depending on which was chosen for the diafiltration buffer) in the retentate were lower than in the diafiltration buffer. Experimental studies and theoretical analyses of the ultrafiltration/diafiltration (UF/DF) step were carried out to determine the primary causes of the phenomenon and to develop a mathematical model capable of predicting retentate excipient concentrations. The analyses showed that retentate histidine concentration was low primarily because of repulsive charge interactions between positively‐charged histidine molecules and positively‐charged protein molecules, and that volume exclusion effects were secondary for like‐charged molecules. The positively‐charged protein molecules generate an electrical potential that cause an uneven distribution of charged histidine molecules. This interaction was used to construct a mathematical model based on the Poisson‐Boltzmann equation. The model successfully predicted the final histidine concentration in the diafiltered product (retentate) from the UF/DF development and production runs, with good agreement across a wide range of protein and histidine concentrations for four therapeutic monoclonal antibodies. The concentrations of uncharged excipients (sorbitol or sucrose) were also successfully predicted using previously established models, with volume exclusion identified as the primary cause of differences in uncharged excipient concentrations in the retentate and diafiltration buffer. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Ion-exchange properties of the cell wall of reindeer lichen <Emphasis Type="Italic">Cladonia rangiferina</Emphasis>

Ion-exchange properties of cell walls were investigated in reindeer lichen Cladonia rangiferina (L.) F. H. Wigg. In order to isolate cell walls, we used living parts of podetia as well as young parts (four upper internodes of podetia) and old parts (from the 4th to the 8th internode). We studied functional dependences of cell wall ion-exchange capacity on pH in the range from 2 to 12 and constant ionic strength of solution equal to 10 mM. It was found that three-dimensional structure of C. rangiferina cell walls comprised three types of ionogenic groups, which determine ion-exchange properties of the cell walls. They are amino groups with pK_a of about 3, carboxyl groups with pK_a of about 7, and phenolic OH-groups with pK_a of about 10. The content of groups of each type and their ionization constants were determined, and it was shown that, in the cell walls of young parts, the content of amino groups and carboxylic groups was greater than in old parts of podetia (by 1.5 and 2.0 times, respectively). It was found that with age the content of nitrogen and the proportion of deacetylated amino groups in the cell walls changed from 34% (young parts of podetia) to 40% (old parts of podetia). It was shown that in C. rangiferina N-acetyl glucosamine and glucosamine are not the main monomers of cell wall polymers because both in thalli and in the cell walls isolated therefrom the content of total nitrogen was less than 1%.     

Intracellular pH homeostasis plays a role in the NaCl tolerance of Debaryomyces hansenii strains

The effects of NaCl stress on cell area and intracellular pH (pH_i) of individual cells of two Debaryomyces hansenii strains were investigated. Our results show that one of the strains was more NaCl tolerant than the other, as determined by the rate of growth initiation. Whereas NaCl stress caused similar cell shrinkages (30–35%), it caused different pH_i changes of the two D. hansenii strains; i.e., in the more NaCl-tolerant strain, pH_i homeostasis was maintained, whereas in the less NaCl-tolerant strain, intracellular acidification occurred. Thus, cell shrinkage could not explain the different intracellular acidifications in the two strains. Instead, we introduce the concept of yeasts having an intracellular pK_a (pK_a,i) value, since permeabilized D. hansenii cells had a very high buffer capacity at a certain pH. Our results demonstrate that the more NaCl-tolerant strain was better able to maintain its pK_a,i close to its pH_i homeostasis level during NaCl stress. In turn, these findings indicate that the closer a D. hansenii strain can keep its pK_a,i to its pH_i homeostasis level, the better it may manage NaCl stress. Furthermore, our results suggest that the NaCl-induced effects on pH_i were mainly due to hyperosmotic stress and not ionic stress.     

Kinetic study of electrodialysis of acetic acid and phosphate in fermentation broth

Ion fluxes of acetic acid and phosphate in the electrodialysis of a model fermentation broth were examined using a solution of acetic acid and potassium dihydrogenphosphate. As the molar fraction of the phosphate was increased the ion flux of the acetic acid decreased, which was as predicted theoretically. As the influent pH was increased the flux also increased notably, reached a maximum, and then decreased slightly. The maximum flux was obtained in a pH range from 5.2 (near pK_a) to 6.6. The pH at the exit of the electrodialyzer became markedly alkaline when the influent pH was in the range of 6 to 7 in the absence of the phosphate. The pH range shifted to the alkaline side and the degree of alkalinity reduced as the molar fraction of phosphate increased. This may be ascribed to the buffering effect of the phosphate. It is concluded that the optimum pH for the electrodialysis of an organic acid fermentation broth is around (pKa + 1), where a relatively high ion flux with high current efficiency and a small pH increase at the exit of the electrodialyzer are established.     

Activation of the cisplatin and transplatin complexes in solution with constant pH and concentration of chloride anions; quantum chemical study

The thermodynamics of cisplatin and transplatin hydration is studied within the model of constant pH solution. Several implicit solvation models were chosen for the determination of pK_a and pK constants of the hydration reactions. The polarizable dielectric model (DPCM), integral equation formalism polarizable model (IEFPCM), and polarizable conductor model (CPCM) were combined with the ‘united atom model for Hartree-Fock’ (UAHF) method for cavity construction and the B3LYP/6-31++G(2dp,2pd) level of calculations for the determination of electronic energies. The results were compared with the COSMO-RS and SM8 model developed by Truhlar (with M06 and MPWX functionals and the charge model CM4). The RMS difference between experimental and calculated pK_a values of cis/transplatin, water, HCl, and NH₄⁺ was used to evaluate accuracy of calculations. The DPCM model was confirmed to perform the best. The predicted pK_a constants were used in Legendre transformation for the estimation of the ΔG’ energies in the constant-pH model. The dependence of the pK constant on pH is plotted and compared with experimental value at pH=7.4. The influence of various chloride concentrations on the molar fractions of dissolved forms of cisplatin is examined for the DPCM model. The increased ratio of cisplatin active aqua-forms is clearly visible for 4 mM chloride solution in comparison with 104 mM Cl^- concentration.     

Mechanism of Long-Chain Free Fatty Acid Protonation at the Membrane-Water Interface

Long-chain free fatty acids (FFAs) play an important role in several physiological and pathological processes such as lipid fusion, adjustments of membrane permeability and fluidity, and the regulation of enzyme and protein activities. FFA-facilitated membrane proton transport (flip-flop) and FFA-dependent proton transport by membrane proteins (e.g., mitochondrial uncoupling proteins) are governed by the difference between FFA’s intrinsic pK_a value and the pH in the immediate membrane vicinity. Thus far, a quantitative understanding of the process has been hampered, because the pK_a value shifts upon moving the FFA from the aqueous solution into the membrane. For the same FFA, pK_a values between 5 and 10.5 were reported. Here, we systematically evaluated the dependence of pK_a values on chain length and number of double bonds by measuring the ζ-potential of liposomes reconstituted with FFA at different pH values. The experimentally obtained intrinsic pK_a values (6.25, 6.93, and 7.28 for DOPC membranes) increased with FFA chain length (C16, C18, and C20), indicating that the hydrophobic energy of transfer into the bilayer is an important pK_a determinant. The observed pK_a decrease in DOPC with increasing number of FFA double bonds (7.28, 6.49, 6.16, and 6.13 for C20:0, C20:1, C20:2, and C20:4, respectively) is in line with a decrease in transfer energy. Molecular dynamic simulations revealed that the ionized carboxylic group of the FFAs occupied a fixed position in the bilayer independent of chain length, underlining the importance of Born energy. We conclude that pK_a is determined by the interplay between the energetic costs for 1) burying the charged moiety into the lipid bilayer and 2) transferring the hydrophobic protonated FFA into the bilayer.     

Affinity labeling of rabbit skeletal muscle phosphorylase kinase by 5′-(p-fluorosulfonylbenzoyl)adenosine

Simple mixing of acid purified histones H₃ and H₄ in equimolar quantities at low ionic strength near pH 7 does not yield the tetramer but rather a high M_r aggregate. Dialysis of acid extracted total or core histones into 2 M NaCl 150 mM phosphate (pH 7.4) followed by fractionation of the histone complexes at lower ionic strength (150 mM NaCl) results in an H₃H₄ tetramer of a structure identical to that derived from salt-extracted histones. Dialysis of acid extracted total or core histones directly into the lower ionic strength buffer with subsequent fractionation, results in H₃H₄ tetramer of closely similar structure.     

Use of EDTA to minimize ionic strength dependent frequency shifts in the <Superscript>1</Superscript>H NMR spectra of urine

The ¹H NMR spectrum of urine exhibits a large number of detectable metabolites and is, therefore, highly suitable for the study of perturbations caused by disease, toxicity, nutrition or environmental factors in humans and animals. However, variations in the chemical shifts and intensities due to altered pH and ionic strength present a challenge in NMR-based studies. With a view towards understanding and minimizing the effects of these variations, we have extensively studied the effects of ionic strength and pH on the chemical shifts of common urine metabolites and their possible reduction using EDTA (ethylenediaminetetraacetic acid). ¹H NMR chemical shifts for alanine, citrate, creatinine, dimethylamine, glycine, histidine, hippurate, formate and the internal reference, TSP (trimethylsilylpropionic acid-d₄, sodium salt) obtained under different conditions were used to assess each effect individually. EDTA minimizes the frequency shifts of the metabolites that have a propensity for metal binding. Chelation of such metal ions is evident from the appearance of signals from EDTA complexed to divalent metal ions such as calcium and magnesium. Not surprisingly, increasing the buffer concentration or buffer volume also minimizes pH dependent frequency shifts. The combination of EDTA and an appropriate buffer effectively minimizes both pH dependent frequency shifts and ionic strength dependent intensity variations in urine NMR spectra. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A new approach to the investigation on the tonogenic groups of root cell walls

Acid-base properties of wheat, lupin, pea root cell walls were investigated. The roots of etiolated and green plants of different age were analysed by the potentiometric method. The ion exchange capacity of root cell walls (S_i) was estimated at various pH values (pH_i 2 to pH_i 12) and constant ion strength of the solution (10 mM). To analyse polysigmoid curves pH_i =f (S_i), Gregor's equation was used. It was shown that Gregor's model fits fairly well the experimental data. The total quantities of cation-exchange (S_t ^cat) and anion-exchange (S_t ^an) groups were determined in the root cell walls. It was shown that the quantity of anion exchange groups is varied through a small range (60–185 μmol/g dry wt.) in plant species tested, and that the S_t ^cat differs widely from 550 to 1300 μmol/g dry wt. For leguininous plants the quantity of acidic groups (fixed anions) is nearly twice as large as that for cereals. It was found that in seedlings as well as in plants, there are 3 cation-exchange groups and one anion-exchange group in root cell walls. The quantity of functional groups of each type (S^j) was estimated, and the corresponding values of n^j and pK_a ^j were calculated. It can be assumed that the groups with the pK_a ¹ ≈ 3.2 are amine groups, the ones with PK_a ² ≈ 5 are groups of galacturonic acid, the ones with pK_a ≈ 7.5 are the carboxyl groups of the second species, and the ones with pK_a ⁴ ≈ 40 are the phenolic groups. The values of dissociation constants (pK_a ^j) and S^j indicate that the root cell walls of wheat, lupin and pea are identical in qualitative structure of ionogenic groups but vary in the quantity of each ionogenic group. It was demonstrated that the summarized quantity of carboxyl groups (S² + S³) should be connected directly with the pH gradient in the extracellar space at the membrane surface. The gradient arises from ion-exchange reactions between cations of an outer medium and protons of the ionized carboxyl groups of the cell walls. The results suggest that, S_t ^cat and S_t ^an allow the quantitative estimation of ion exchange properties of the cell walls. The resulting parameters (S^j, pK_a ^j and n^j) allow prediction of changes in an ionic composition of a medium that bathes the cell membrane, during the first step of mineral nutrition uptake. This revised version was published online in June 2006 with corrections to the Cover Date.     

Mechanistic studies of electrophilic protease inhibitors of full length hepatic C virus (HCV) NS3

The inhibition mechanism of electrophilic peptide-based protease inhibitors of full-length hepatitis C virus (HCV) NS3 has been investigated by determining the K_i-values for a series of compounds differing in the electrophilicity and acidity of the C-terminal residue at pH-values above and below the pK_a of the catalytic histidine (6.85) and at two different ionic strengths. Electrophilic compounds with a pentafluoroethyl ketone group showed stronger inhibition at pH 8 than pH 6, as expected for a mechanism requiring an unprotonated catalytic histidine. However, the difference was only significant at high ionic strength. In contrast, electrophilic compounds with an acidic C-terminal group or a cyclic P1 residue showed a lower inhibitory effect at pH 8 than at pH 6, inconsistent with a mechanism-based inhibition. Moreover, all electrophilic compounds had an unexpectedly strong inhibition at pH 6, when mechanism-based inhibition is unlikely. The results suggest that for some of the electrophilic compounds the reactive group may not be properly positioned in the active site and that binding of these inhibitors is a result of non-covalent interactions. The nature of these interactions is discussed.