Thermodynamic analysis of partially folded states of myoglobin in presence of 2,2,2-trifluoroethanol

The thermal denaturation of myoglobin was studied in the presence of 2,2,2-trifluoroethanol (TFE) at various pH values using differential scanning calorimetry and UV–visible spectroscopy. The most obvious effect of TFE was lowering the transition temperature up to 1.5 mol · kg⁻¹, beyond which no thermal transitions were observed. The protein conformation was analysed by fluorescence and circular dichroism measurements. Quantitative binding of ANS to the TFE induced molten globule state of myoglobin was studied by using isothermal titration calorimetry. The results enable quantitative estimation of the binding strength of ANS with the molten globule state of myoglobin along with the enthalpic and entropic contributions to the binding process. The results suggest occurrence of common structural features of the molten globule states of proteins offering two types of binding sites to ANS molecules which are a widely used fluorescence probe to characterise partially folded states of proteins.     

2,2,2-trifluoroethanol-induced molten globule state of concanavalin a and energetics of 8-anilinonaphthalene sulfonate binding: calorimetric and spectroscopic investigation

The interaction of 2,2,2-trifluoroethanol (TFE) with concanavalin A has been investigated by using a combination of differential scanning calorimetry, isothermal titration calorimetry (ITC), circular dichroism (CD), and fluorescence spectroscopy at pH 2.5 and 5.2. All of the calorimetric transitions at both the pH values were found to be irreversible. In the presence of 4 mol kg(-1) TFE at pH 2.5, concanavalin A is observed to be in a partially folded state with significant loss of native tertiary structure. The loss of specific side chain interactions in the transition from native to the TFE-induced partially folded state is demonstrated by the loss of cooperative thermal transition and reduction of the CD bands in the aromatic region. Acrylamide quenching, 8-anilinonaphthalene sulfonate (ANS) binding, and energy transfer also suggest that in the presence of 4 mol kg(-1) TFE at pH 2.5 concanavalin A is in a molten globule state. ITC has been used for the first time to characterize the energetics of ANS binding to the molten globule state. ITC results indicate that the binding of ANS to the molten globule state and acid-induced state at pH 2.5 displays heterogeneity with two classes of non-interacting binding sites. The results provide insights into the role of hydrophobic and electrostatic interactions in the binding of ANS to concanavalin A. The results also demonstrate that ITC can be used to characterize the partially folded states of the protein both qualitatively and quantitatively.     

Thermodynamic insights into the binding of ANS with the salt induced molten globule states of cytochrome c

The molten globule (MG) state or the A-state of cytochrome c (cyt c) has been induced by addition of salts sodium perchlorate (NaClO₄), sodium thiocyanate (NaSCN), and sodium sulphate (Na₂SO₄) at pH 2.0. Isothermal titration calorimetry (ITC) has been used for determining the energetics of binding of 8-anilino naphthalene sulphonate (ANS) to the salt induced A-state of cyt c, and the accompanying thermodynamic parameters have been analyzed to elucidate the nature of the interactions between ANS and the A-state of cyt c. Temperature dependent studies of the binding process reveal that the binding is not a two state process and there are more than a single type of interactions involved. Addition of a bulky salt tetraethylammonium bromide (TEAB) increases the stoichiometry of binding significantly, with a reduction in the binding affinity at a higher concentration. The results provide quantitative information on the binding of ANS to the salt induced molten globule states of cyt c. It is further inferred that the binding involves a combination of hydrophobic and electrostatic interactions.     

Protein structure information from mass spectrometry? Selective titration of arginine residues by sulfonates

Noncovalently bound complexes between basic sites of peptides/proteins and sulfonates are studied using Matrix Assisted Laser Desorption/Ionization (MALDI) Mass Spectrometry. Reactive sulfonate dyes such as Cibacron Blue F3G-A are known to bind to protonated amino groups on the exterior of a protein. In this work, we examine a wide range of other sulfonates with distinctly simpler structure and more predictable reactivity. Naphthalene-sulfonic acid derivatives were found to bind to arginine only, as opposed to expected binding to all basic sites (Arg, Lys and His). Detailed control experiments were designed to unambigously confirm this selectivity and to rule out nonspecific adduct formation in the gas phase. The data show that the number of complex adducts found equals the number of accessible arginine sites on the surface of folded peptides and proteins, plus the N-terminus. Lys and His are not complexed nor are buried residues with hindered access. MALDI-MS can therefore provide fast information related to the exposed surface of these biomolecules. Additional titration experiments with 1-anilino-naphthalene-8-sulfonic acid (ANS) revealed that this fluorescent dye, which was often hypothesized to bind to so-called molten globule states of proteins, behaved exactly like all other naphthalene-sulfonic acids. ANS binding thus occurs largely through the sulfonate group.     

Modulation of lysozyme charge influences interaction with phospholipid vesicles

Lysozyme is a globular protein which is known to bind to negatively charged phospholipid vesicles. In order to study the relationship between charge state of the protein and its interaction with negatively charged phospholipid membranes chemical modifications of the proteins were carried out. Succinylation and carbodiimide modification was used to shift the isoelectric point of lysozyme to lower and higher pH values, respectively. The binding of the modified lysozyme to phospholipid vesicles prepared from phosphatidic acid (PA) was determined using microelectrophoresis and ultracentrifugation. At acidic pH of the solution all lysozyme species reduced the surface charges of PA vesicles. Succinylated lysozyme (succ lysozyme) reduced the electrophoretic mobility (EPM) to nearly zero, whereas native lysozyme and carboxylated lysozyme (carbo lysozyme) changed the surface charge to positive values. At neutral pH, the reduction of surface charges was less for carbo lysozyme and unmodified lysozyme. Succ lysozyme did not change the EPM. Unmodified and carbo lysozyme decreased the magnitude of EPM, but the whole complex was still negatively charged. The bound fraction of all modified lysozyme to PA vesicles at high lysozyme/PA ratios was nearly constant at acidic pH. At low lysozyme/PA ratios the extent of bound lysozyme is changed in the order carbo>unmodified>succ lysozyme. Increasing the pH, the extent of bound lysozyme to PA large unilamellar vesicles (LUV) is reduced, at pH 9.0 only 35% of carbo lysozyme, 23% of unmodified lysozyme is bound, whereas succ lysozyme does not bind at pH 7.4 and 9.0. At low pH, addition of all lysozyme species resulted in a massive aggregation of PA liposomes, at neutral pH aggregation occurs at much higher lysozyme/PA ratios. Lysozyme binding to PA vesicles is accompanied by the penetration of lysozyme into the phospholipid membrane as measured by monolayer techniques. The penetration of lysozyme into the monolayer was modulated by pH and ionic strengths. The interaction of lysozyme with negatively charged vesicles leads to a decrease of the phospholipid vesicle surface hydration as measured by the shift of the maximum of the fluorescence signal of a headgroup labeled phospholipid. The binding of bis-ANS as an additional indicator for the change of surface hydrophobicity is increased at low pH after addition of lysozyme to the vesicles. More hydrophobic patches of the lysozyme-PA complex are exposed at low pH. At low pH the binding process of lysozyme to PA vesicles is followed by an extensive intermixing of phospholipids between the aggregated vesicles, accompanied by a massive leakage of the vesicle aqueous content. The extent of lysozyme interaction with PA LUV at neutral and acidic pH is in the order carbo lysozyme>lysozyme>succ lysozyme.     

Identification of Folding Intermediates of Streblin,The Most Stable Serine Protease: Biophysical Analysis

Streblin, a serine proteinase from plant Streblus asper, has been used to investigate the conformational changes induced by pH, temperature, and chaotropes. The near/far UV circular dichroism activities under fluorescence emission spectroscopy and 8-aniline-1-naphthalene sulfonate (ANS) binding have been carried out to understand the unfolding of the protein in the presence of denaturants. Spectroscopic studies reveal that streblin belongs to the α+β class of proteins and exhibits stability towards chemical denaturants, guanidine hydrochloride (GuHCl). The pH-induced transition of this protein is noncooperative for transition phases between pH 0.5 and 2.5 (midpoint, 1.5) and pH 2.5 and 10.0 (midpoint, 6.5). At pH 1.0 or lower, the protein unfolds to form acid-unfolded state, and for pH 7.5 and above, protein turns into an alkaline denatured state characterized by the absence of ANS binding. At pH 2.0 (1 M GuHCl), streblin exists in a partially unfolded state with characteristics of a molten globule state. The protein is found to exhibit strong and predominant ANS binding. In total, six different intermediate states has been identified to show protein folding pathways.     

Biophysical analysis of partially folded state of α-lactalbumin in the presence of cationic and anionic surfactants

The role of different types of interactions and their contribution in the stabilization of bovine α-lactalbumin (α-LA) molten globule in presence of cationic surfactant, hexadecyl trimethyl ammonium bromide (HTAB) and anionic surfactant, sodium dodecyl sulphate (SDS) have been examined using a combination of spectroscopic, light scattering and calorimetric techniques. The results correlated well with each other and were used to characterize the partially folded states of the protein both qualitatively and quantitatively. At lower concentration of the surfactants, the thermodynamic parameters obtained from UV-visible spectroscopy suggested an increased exposure of non-polar groups in HTAB while a possible restructuring of non-polar groups were indicated in SDS. The fluorescence and circular dichroism spectroscopy showed the formation of an intermediate state at various concentrations of HTAB and SDS while the lifetime measurements supported the assumption of protein-surfactant complex stability in HTAB as compared to SDS. The hydrodynamic diameter and the ζ-potential were analyzed by dynamic light scattering (DLS) which also implicated the combined influence of electrostatic and hydrophobic interactions in protein unfolding in HTAB and only hydrophobic interactions in SDS. The binding parameters for ANS obtained from isothermal titration calorimetric (ITC) measurements suggested a high stability of α-LA molten globule and the role of enthalpic and entropic contribution in the binding of ANS in HTAB. It also indicated the fragility of α-LA molten globule in SDS. The possible binding sites as well as the interactions of ANS with the partially folded protein were also studied from the thermodynamic parameters obtained from the ITC.     

Monitoring the Tanford transition in β‐lactoglobulin by 8‐anilino‐1‐naphthalene sulfonate and mass spectrometry

The fluorescent dye 8‐anilino‐1‐naphthalene sulfonate (ANS) is known to interact with proteins by conformation‐specific hydrophobic interactions and rather nonspecific electrostatic interactions. To which category the complexes detectable by mass spectrometry (MS) belong is still the subject of debate. Here, the Tanford transition in β‐lactoglobulin (BLG) is exploited as an experimental device to expose hydrophobic binding sites by an increase in pH, rather than, as usually done, by lowering the pH. Complex formation is monitored by electrospray ionization (ESI)‐MS and fluorescence spectroscopy. Both techniques reveal stronger ANS binding to BLG at pH 7.9 than at pH 5.9, suggesting that dye binding inside the calyx, which is known to be hydrophobically driven in solution, can contribute to the complexes detected by ESI‐MS. Electrostatic interactions between the protein and the ANS sulfonate group can only be weaker at pH 7.9 than at pH 5.9, supporting the interpretation of the results by the protein conformational change. Lysozyme is used as a negative control, which shows no variation in the interaction with ANS in the same range of pH, in the absence of conformational changes. However, comparison of MS and fluorescence data at variable pH for BLG and myoglobin (Mb) suggests that conformation‐specific ANS binding to proteins is detectable by ESI‐MS only inside well‐structured cavities of folded structures, like the BLG calyx and apoMb heme pocket. Indeed, ANS interactions with highly dynamic structures or molten globules, although detectable in solution, are easily lost in the gas phase. Copyright © 2008 John Wiley & Sons, Ltd.     

Probing the effect of temperature on the backbone dynamics of the human alpha-lactalbumin molten globule

Molten globules are compact, partially folded proteins postulated to be general intermediates in protein folding. Human alpha-lactalbumin (alpha-LA) is a two-domain Ca(2+)-binding protein that partially unfolds at low pH to form a molten globule. NMR spectra of molten globules are characterized by broadened resonances due to conformational fluctuations on microsecond to millisecond time scales. These species are often studied at high temperature where NMR resonances are observed to sharpen. The effect of higher temperatures on fast time-scale backbone dynamics of molten globules has not been investigated previously. Here, 1D (15)N direct-detection and 2D indirect-detection (1)H-(15)N heteronuclear NOE experiments have been used to probe fast time-scale dynamics at low and high temperatures for three disulfide-bond variants of human alpha-LA that form molten globules. Disulfide bonds are found to have a significant effect on backbone dynamics within the beta-domain of the molten globule; within the alpha-domain, dynamics are not significantly influenced by these bonds. At 20 degrees C, backbone mobility is significantly decreased in both domains of the molten globule compared to the mobility at 40-50 degrees C. Heteronuclear NOE values determined at 20 degrees C for the alpha-domain are closely similar to those observed for native alpha-LA, indicating that the alpha-LA molten globule has even more native-like character than suggested by studies conducted at higher temperature. Our results highlight the importance of considering the temperature dependence of the molten globule ensemble when making comparisons between experimental data obtained under different conditions.     

Interaction of 1-anilinonaphthalene-8-sulphonate with cross-linked poly (N-vinyl-2-pyrrolidone)

The interaction of 1-anilinonaphthalene-8-sulphonate (ANS) with cross-linked poly(N-vinyl-2-pyrrolidone) (CPVP) was studied by the adsorption technique at different temperatures and at two different pH values. Analysis by the Scatchard method and the study made in the presence of urea showed that the iceberg structure of water affects the sorption of ANS to CPVP, leading to cooperativity. The observed Giles sorption isotherms at both the pH values were of theL-type which indicated the interaction of ANS in flat configuration with the binding site in CPVP. The sorption of ANS to CPVP was enhanced considerably at acidic pH due to some structural factors which also resulted in multilayer sorption at this pH. Comparison of binding of ANS to CPVP and to linear poly(N-vinyl-2-pyrrolidone) demonstrated the greater contribution of hydrophobic interaction in CPVP than in the linear polymer.     

FAMBE-pH: a fast and accurate method to compute the total solvation free energies of proteins

A fast and accurate method to compute the total solvation free energies of proteins as a function of pH is presented. The method makes use of a combination of approaches, some of which have already appeared in the literature; (i) the Poisson equation is solved with an optimized fast adaptive multigrid boundary element (FAMBE) method; (ii) the electrostatic free energies of the ionizable sites are calculated for their neutral and charged states by using a detailed model of atomic charges; (iii) a set of optimal atomic radii is used to define a precise dielectric surface interface; (iv) a multilevel adaptive tessellation of this dielectric surface interface is achieved by using multisized boundary elements; and (v) 1:1 salt effects are included. The equilibrium proton binding/release is calculated with the Tanford-Schellman integral if the proteins contain more than approximately 20-25 ionizable groups; for a smaller number of ionizable groups, the ionization partition function is calculated directly. The FAMBE method is tested as a function of pH (FAMBE-pH) with three proteins, namely, bovine pancreatic trypsin inhibitor (BPTI), hen egg white lysozyme (HEWL), and bovine pancreatic ribonuclease A (RNaseA). The results are (a) the FAMBE-pH method reproduces the observed pK a's of the ionizable groups of these proteins within an average absolute value of 0.4 p K units and a maximum error of 1.2 p K units and (b) comparison of the calculated total pH-dependent solvation free energy for BPTI, between the exact calculation of the ionization partition function and the Tanford-Schellman integral method, shows agreement within 1.2 kcal/mol. These results indicate that calculation of total solvation free energies with the FAMBE-pH method can provide an accurate prediction of protein conformational stability at a given fixed pH and, if coupled with molecular mechanics or molecular dynamics methods, can also be used for more realistic studies of protein folding, unfolding, and dynamics, as a function of pH.     

Study of metal ion labeling of the conformational and charge states of lysozyme by ion mobility mass spectrometry

The efficiency of Zn(2+), Cu(2+), Ni(2+), Co(2+), Fe(2+) or Mn(2+) labeling of the conformational and charge states of lysozyme was studied in H(2)O solvent at pH 2.5-6.8. Labeling of lysozyme was conducted with 50 M, 100 M and 500 M excess of the metal ion, resulting in the number of metal ions attached to lysozyme increasing two-fold over this range. At pH 6.2-6.8, Zn(2+), Cu(2+), Ni(2+), Co(2+) and Mn(2+) labeled the highly folded 7+ conformer and the 8+ and 9+ partially unfolded conformers of lysozyme with the same number of metal ion tags, with only Fe(2+) exhibiting no labeling. Lysozyme conserved its charge after metal ion labeling which shows at each charge state the divalent metal ion is replacing two protons. As the pH is lowered to 4.7-5.0 and 2.5-2.9, the labeling of lysozyme by Zn(2+), Cu(2+), Ni(2+), Co(2+) or Mn(2+) decreased in efficiency due to increased competition from protons for the aspartate and glutamate binding sites. The metal ions preferentially labeled the highly folded 7+ and partially unfolded 8+ conformers, but labeling decreased as the charge of lysozyme increased. In contrast to the other metal ions, Fe(2+) exhibited labeling of lysozyme only at the lowest pH of 2.8. At higher pH, the oxidation of Fe(2+) and formation of hydroxy-bridged complexes probably make the Fe(2+) unreactive towards lysozyme.     

Qualitative and quantitative characterization of the arsenic‐binding behaviour of sulfur‐containing peptides and proteins by the coupling of reversed phase liquid chromatography to electrospray ionization mass spectrometry

Phenylarsenic‐substituted cysteine‐containing peptides and proteins were completely differentiated from their unbound original forms by the coupling of reversed phase liquid chromatography with electrospray ionization mass spectrometry. The analysis of biomolecules possessing structure‐stabilizing disulfide bridges after reduction provides new insights into requirements concerning the accessibility of cysteine residues for reducing agents as well as for arsenic compounds in a spatial protein structure. Complementary binding studies performed using direct ESI‐MS without chromatographic coupling in different solvent systems demonstrated that more than one binding site were activated for aprotinin and lysozyme in denaturing solvents because of a stronger defolding. From the intensities of the different charge states occurring in the mass spectra as well as from the LC elution behaviour, it can be deduced that the folding state of the arsenic‐bound protein species resembles the native, oxidized conformation. In contrast, although the milk protein α‐lactalbumin has several disulfide bridges, only one phenylarsenic moiety was bound under strongly denaturing conditions. Because of the charge state distribution in the ESI mass spectra, a conformational change to a molten globule structure is assumed. For the second considered milk protein ß‐lactoglobulin, a noncovalent interaction with phenylarsine oxide was detected. In general, smaller apparent binding constants for the condensation reactions of the biomolecules with phenylarsine oxide leading to covalent arsenic–sulfur bindings were determined from direct injection ESI‐MS measurements than from LC‐ESI‐MS coupling. The following order of binding affinities for one phenylarsenic group can be assumed from both ESI‐MS and LC‐ESI‐MS: nonapeptide vasopressin > nonapeptide vasotocin > lysozyme > aprotinin > α‐lactalbumin > thioredoxin. Kinetic investigations by LC‐ESI‐MS yielded a partial reaction order of 2 for vasopressin, Lys and α‐lactalbumin and corresponding half‐lives of 0.93, 2.56 and 123.5 min, respectively. Copyright © 2012 John Wiley & Sons, Ltd.     

Cytochrome c–dimyristoylphosphatidylglycerol interactions studied by asymmetrical flow field-flow fractionation

Lipid membranes are well recognized ligands that bind peripheral and integral proteins in a specific manner and regulate their function. Cytochrome c (cyt c) is one of the partner peripheral protein that binds to the lipid membranes via electrostatic and hydrophobic interactions. In this study, asymmetrical flow field-flow fractionation (AsFlFFF) was used to compare the interactions of cyt c with the acidic phospholipid 1,2-dimyristoyl-sn-glycero-3-phospho-rac-glycerol (DMPG), oleic acid (OA), and sodium dodecyl sulfate (SDS). The influence of pH and the cyt c–lipid molar mass ratios were evaluated by monitoring the diffusion coefficients and particle diameter distributions obtained for the free and lipid-bound protein. The hydrodynamic particle diameter of cyt c (pI 10) was 4.1 nm at pH 11.4 and around 4.2 nm at pH 7.0 and 8.0. Standard molar mass marker proteins were used for calibration to obtain the molar masses of free cyt c and its complexes with lipids. AsFlFFF revealed the binding of cyt c to DMPG and to OA to be mainly electrostatic. In the absence of electrostatic interactions, minor complex formation occurred, possibly due to the extended lipid anchorage involving the hydrophobic cavity of cyt c and the hydrocarbon chains of DMPG or SDS. The possibility of the formation of the molten globule state of cyt c, induced by the interaction between cyt c and lipids, is discussed.Electronic Supplementary Material Supplementary material is available for this article at     

Vapor Treatment of Electrospray Droplets: Evidence for the Folding of Initially Denatured Proteins on the Sub-Millisecond Time-Scale

The exposure of electrospray droplets generated from either highly acidic or highly basic solutions to basic or acidic vapors, respectively, admitted into the counter-current drying gas, has been shown to lead to significant changes in the observed charge state distributions of proteins. In both cases, distributions of charge states changed from relatively high charge states, indicative of largely denatured proteins, to lower charge state distributions that are more consistent with native protein conformations. Ubiquitin, cytochrome c, myoglobin, and carbonic anhydrase were used as model systems. In some cases, bimodal distributions were observed that are not noted under any solution pH conditions. The extent to which changes in charge state distributions occur depends upon the initial solution pH and the pK_a or pK_b of the acidic or basic reagent, respectively. The evolution of charged droplets in the sampling region of the mass spectrometer inlet aperture, where the vapor exposure takes place, occurs within roughly 1 ms. The observed changes in the spectra, therefore, are a function of the magnitude of the pH change as well as the rates at which the proteins can respond to this change. The exposure of electrospray droplets in this fashion may provide means for accessing transient folding states for further characterization by mass spectrometry.     

Selective generation of charge-cependent/independent ion energy distributions from a heated capillary electrospray source

Retarding grid and Fourier transform ion cyclotron resonance (FTICR) mass spectrometry variable trap potential measurements are performed to determine factors that contribute to the kinetic energy distribution of ions formed in an electrospray source that uses a heated capillary for desolvation. The control of ion kinetic energies is achieved by manipulating the skimmer position in the postcapillary expansion and by varying the potential appEed to the skimmer. The selective generation of either charge-dependent or charge-independent ion energy distributions is demonstrated. Charge-dependent energy distributions of electro-sprayed ions are created by sampling ions near the Mach disk of the supersonic expansion and by using a larger diameter skimmer orifice; the FTICR spectra acquired under these conditions exhibit mass-to-charge ratio-dependent mass discrimination determined by the potential used to trap the ions. Charge-independent energies of electrosprayed ions are created by positioning the capillary adjacent to the skimmer to sample thermal ions and by using a smaller skimmer orifice to reduce expansion cooling; under these conditions ion kinetic energy is determined primarily by the skimmer potential and no mass-to-charge ratio-dependence is observed in the selection of optimum FTICR trapping conditions. The ability to select between proteins of different conformation on the basis of kinetic energy differences is demonstrated. For example, a 0.4 V difference in trap potential is observed in the selective trapping of open and closed forms of the +10 charge state of lysozyme. Finally, it is demonstrated that by operating the source under conditions which deliver a beam of ions with charge-independent energies to the cell, it is possible to obtain precursor and product ion signal magnitudes in FTTCR spectra without charge-dependent mass discrimina-tion.     

Solvation dynamics of a protein in the pre molten globule state

The nature of solvent molecules around proteins in native and different non-native states is crucial for understanding the protein folding problem. We have characterized two compact denatured states of glutaminyl-tRNA synthetase (GlnRS) under equilibrium conditions in the presence of a naturally occurring osmolyte, l-glutamate. The solvation dynamics of the compact denatured states and the fully unfolded state has been studied using a covalently attached probe, acrylodan, near the active site. The solvation dynamics progressively becomes faster as the protein goes from the native to the molten globule to the pre molten globule to the fully unfolded state. Anisotropy decay measurements suggest that the pre-molten-globule intermediate is more flexible than the molten globule although the secondary structure is largely similar. Dynamic light scattering studies reveal that both the compact denatured states are aggregated under the measurement conditions. The implications of solvation dynamics in aggregated compact denatured states have been discussed.     

Interactions between single-walled carbon nanotubes and lysozyme

Dispersions of single-walled and non-associated carbon nanotubes in aqueous lysozyme solution were investigated by analyzing the stabilizing effect of both protein concentration and pH. It was inferred that the medium pH, which significantly modifies the protein net charge and (presumably) conformation, modulates the mutual interactions with carbon nanotubes. At fixed pH, in addition, the formation of protein/nanotube complexes scales with increasing lysozyme concentration. Electrophoretic mobility, dielectric relaxation and circular dichroism were used to determine the above features. According to circular dichroism, lysozyme adsorbed onto nanotubes could essentially retain its native conformation, but the significant amount of free protein does not allow drawing definitive conclusions on this regard. The state of charge and charge distribution around nanotubes was inferred by combining electrophoretic mobility and dielectric relaxation methods. The former gives information on changes in the surface charge density of the complexes, the latter on modifications in the electrical double layer thickness around them. Such results are complementary each other and univocally indicate that some LYS molecules take part to binding. Above a critical protein/nanotube mass ratio, depletion phenomena were observed. They counteract the stabilization mechanism, with subsequent nanotube/nanotube aggregation and phase separation. Protein-based depletion phenomena are similar to formerly reported effects, observed in aqueous surfactant systems containing carbon nanotubes.