Formation of Protein Charge Ladders by Acylation of Amino Groups on Proteins

Charge Regulation in a Rieske Proton Pump Pinpoints Zero, One, and Two Proton-Coupled Electron Transfer

The degree to which redox-driven proton pumps regulate net charge during electron transfer (ΔZET) remains undetermined due to difficulties in measuring the net charge of solvated proteins. Values of ΔZET can reflect reorganization energies or redox potentials associated with ET and can be used to distinguish ET from proton(s)-coupled electron transfer (PCET). Here, we synthesized protein "charge ladders" of a Rieske [2Fe-2S] subunit from Thermus thermophilus (truncTtRp) and made 120 electrostatic measurements of ΔZET across pH. Across pH 5-10, truncTtRp is suspected of transitioning from ET to PCET, and then to two proton-coupled ET (2PCET). Upon reduction, we found that truncTtRp became more negative at pH 6.0 by one unit (ΔZET = -1.01 ± 0.14), consistent with single ET; was isoelectric at pH 8.8 (ΔZET = -0.01 ± 0.45), consistent with PCET; and became more positive at pH 10.6 (ΔZET = +1.37 ± 0.60), consistent with 2PCET. These ΔZET values are attributed to protonation of H154 and H134. Across pH, redox potentials of TtRp (measured previously) correlated with protonation energies of H154 and H134 and ΔZET for truncTtRp, supporting a discrete proton pumping mechanism for Rieske proteins at the Fe-coordinating histidines.

A method for quantifying how the activity of an enzyme is affected by the net charge of its nearest crowded neighbor

The electrostatic effects of protein crowding have not been systematically explored. Rather, protein crowding is generally studied with co‐solvents or crowders that are electrostatically neutral, with no methods to measure how the net charge (Z) of a crowder affects protein function. For example, can the activity of an enzyme be affected electrostatically by the net charge of its neighbor in crowded milieu? This paper reports a method for crowding proteins of different net charge to an enzyme via semi‐random chemical crosslinking. As a proof of concept, RNase A was crowded (at distances ≤ the Debye length) via crosslinking to different heme proteins with Z = +8.50 ± 0.04, Z = +6.39 ± 0.12, or Z = −10.30 ± 1.32. Crosslinking did not disrupt the structure of proteins, according to amide H/D exchange, and did not inhibit RNase A activity. For RNase A, we found that the electrostatic environment of each crowded neighbor had significant effects on rates of RNA hydrolysis. Crowding with cationic cytochrome c led to increases in activity, while crowding with anionic “supercharged” cytochrome c or myoglobin diminished activity. Surprisingly, electrostatic crowding effects were amplified at high ionic strength (I = 0.201 M) and attenuated at low ionic strength (I = 0.011 M). This salt dependence might be caused by a unique set of electric double layers at the dimer interspace (maximum distance of 8 Å, which cannot accommodate four layers). This new method of crowding via crosslinking can be used to search for electrostatic effects in protein crowding.

Low Fouling Polysulfobetaines with Variable Hydrophobic Content

Amphiphilic polymer coatings combining hydrophilic elements, in particular zwitterionic groups, and hydrophobic elements comprise a promising strategy to decrease biofouling. However, the influence of the content of the hydrophobic component in zwitterionic coatings on the interfacial molecular reorganization dynamics and the anti-fouling performance is not well understood. Therefore, coatings of amphiphilic copolymers of sulfobetaine methacrylate 3-[N-2'-(methacryloyloxy)ethyl-N,N-dimethyl]-ammonio propane-1-sulfonate (SPE) are prepared which contain increasing amounts of hydrophobic n-butyl methacrylate (BMA). Their fouling resistance is compared to that of their homopolymers PSPE and PBMA. The photo-crosslinked coatings form hydrogel films with a hydrophilic surface. Fouling by the proteins fibrinogen and lysozyme as well as by the diatom Navicula perminuta and the green algae Ulva linza is assessed in laboratory assays. While biofouling is strongly reduced by all zwitterionic coatings, the best fouling resistance is obtained for the amphiphilic copolymers. Also in preliminary field tests, the anti-fouling performance of the amphiphilic copolymer films is superior to that of both homopolymers. When the coatings are exposed to a marine environment, the reduced susceptibility to silt incorporation, in particular compared to the most hydrophilic polyzwitterion PSPE, likely contributes to the improved fouling resistance.

Measuring how two proteins affect each other's net charge in a crowded environment

Theory predicts that the net charge (Z) of a protein can be altered by the net charge of a neighboring protein as the two approach one another below the Debye length. This type of charge regulation suggests that a protein's charge and perhaps function might be affected by neighboring proteins without direct binding. Charge regulation during protein crowding has never been directly measured due to analytical challenges. Here, we show that lysine specific protein crosslinkers (NHS ester-Staudinger pairs) can be used to mimic crowding by linking two non-interacting proteins at a maximal distance of ~7.9 Å. The net charge of the regioisomeric dimers and preceding monomers can then be determined with lysine-acyl "protein charge ladders" and capillary electrophoresis. As a proof of concept, we covalently linked myoglobin (Z_monomer  = -0.43 ± 0.01) and α-lactalbumin (Z_monomer  = -4.63 ± 0.05). Amide hydrogen/deuterium exchange and circular dichroism spectroscopy demonstrated that crosslinking did not significantly alter the structure of either protein or result in direct binding (thus mimicking crowding). Ultimately, capillary electrophoretic analysis of the dimeric charge ladder detected a change in charge of ΔZ = -0.04 ± 0.09 upon crowding by this pair (Z_dimer  = -5.10 ± 0.07). These small values of ΔZ are not necessarily general to protein crowding (qualitatively or quantitatively) but will vary per protein size, charge, and solvent conditions.

Sulfobetaine Methacrylate Polymers of Unconventional Polyzwitterion Architecture and Their Antifouling Properties

Combining high hydrophilicity with charge neutrality, polyzwitterions are intensely explored for their high biocompatibility and low-fouling properties. Recent reports indicated that in addition to charge neutrality, the zwitterion's segmental dipole orientation is an important factor for interacting with the environment. Accordingly, a series of polysulfobetaines with a novel architecture was designed, in which the cationic and anionic groups of the zwitterionic moiety are placed at equal distances from the backbone. They were investigated by in vitro biofouling assays, covering proteins of different charges and model marine organisms. All polyzwitterion coatings reduced the fouling effectively compared to model polymer surfaces of poly(butyl methacrylate), with a nearly equally good performance as the reference polybetaine poly(3-(N-(2-(methacryloyloxy)ethyl)-N,N-dimethylammonio)propanesulfonate). The specific fouling resistance depended on the detailed chemical structure of the polyzwitterions. Still, while clearly affecting the performance, the precise dipole orientation of the sulfobetaine group in the polyzwitterions seems overall to be only of secondary importance for their antifouling behavior.

Effect of Dipole Orientation in Mixed, Charge-Equilibrated Self-assembled Monolayers on Protein Adsorption and Marine Biofouling

While zwitterionic interfaces are known for their excellent low-fouling properties, the underlying molecular principles are still under debate. In particular, the role of the zwitterion orientation at the interface has been discussed recently. For elucidation of the effect of this parameter, self-assembled monolayers (SAMs) on gold were prepared from stoichiometric mixtures of oppositely charged alkyl thiols bearing either a quaternary ammonium or a carboxylate moiety. The alkyl chain length of the cationic component (11-mercaptoundecyl)-N,N,N-trimethylammonium, which controls the distance of the positively charged end group from the substrate's surface, was kept constant. In contrast, the anionic component and, correspondingly, the distance of the negatively charged carboxylate groups from the surface was varied by changing the alkyl chain length in the thiol molecules from 7 (8-mercaptooctanoic acid) to 11 (12-mercaptododecanoic acid) to 15 (16-mercaptohexadecanoic acid). In this way, the charge neutrality of the coating was maintained, but the charged groups exposed at the interface to water were varied, and thus, the orientation of the dipoles in the SAMs was altered. In model biofouling studies, protein adsorption, diatom accumulation, and the settlement of zoospores were all affected by the altered charge distribution. This demonstrates the importance of the dipole orientation in mixed-charged SAMs for their inertness to nonspecific protein adsorption and the accumulation of marine organisms. Overall, biofouling was lowest when both the anionic and the cationic groups were placed at the same distance from the substrate's surface.

Complete Charge Regulation by a Redox Enzyme Upon Single Electron Transfer

The degree by which metalloproteins partially regulate net charge (Z) upon electron transfer (ET) was recently measured for the first time using "protein charge ladders" of azurin, cytochrome c, and myoglobin [Angew. Chem. Int. Ed. 2018, 57(19), 5364-5368; Angew. Chem. 2018, 130, 5462-5466]. Here, we show that Cu, Zn superoxide dismutase (SOD1) is unique among proteins in its ability to resist changes in net charge upon single ET (e.g., ΔZ_ET(SOD1) =0.05±0.08 per electron, compared to ΔZ_ET(Cyt-c) =1.19±0.02). This total regulation of net charge by SOD1 is attributed to the protonation of the bridging histidine upon copper reduction, yielding redox centers that are isoelectric at both copper oxidation states. Charge regulation by SOD1 would prevent long range coulombic perturbations to residue pK_a 's upon ET at copper, allowing SOD1's "electrostatic loop" to attract superoxide with equal affinity (at both redox states of copper) during diffusion-limited reduction and oxidation of superoxide.

What Are We Missing by Not Measuring the Net Charge of Proteins?

The net electrostatic charge (Z) of a folded protein in solution represents a bird's eye view of its surface potentials-including contributions from tightly bound metal, solvent, buffer, and cosolvent ions-and remains one of its most enigmatic properties. Few tools are available to the average biochemist to rapidly and accurately measure Z at pH≠pI. Tools that have been developed more recently seem to go unnoticed. Most scientists are content with this void and estimate the net charge of a protein from its amino acid sequence, using textbook values of pK_a . Thus, Z remains unmeasured for nearly all folded proteins at pH≠pI. When marveling at all that has been learned from accurately measuring the other fundamental property of a protein-its mass-one wonders: what are we missing by not measuring the net charge of folded, solvated proteins? A few big questions immediately emerge in bioinorganic chemistry. When a single electron is transferred to a metalloprotein, does the net charge of the protein change by approximately one elementary unit of charge or does charge regulation dominate, that is, do the pK_a values of most ionizable residues (or just a few residues) adjust in response to (or in concert with) electron transfer? Would the free energy of charge regulation (ΔΔG_z ) account for most of the outer sphere reorganization energy associated with electron transfer? Or would ΔΔG_z contribute more to the redox potential? And what about metal binding itself? When an apo-metalloprotein, bearing minimal net negative charge (e.g., Z=-2.0) binds one or more metal cations, is the net charge abolished or inverted to positive? Or do metalloproteins regulate net charge when coordinating metal ions? The author's group has recently dusted off a relatively obscure tool-the "protein charge ladder"-and used it to begin to answer these basic questions.

Low-Fouling Thin Hydrogel Coatings Made of Photo-Cross-Linked Polyzwitterions

Although zwitterionic chemistries are among the most promising materials for producing nonfouling surfaces, their structural diversity has been low until now. Here, we compare the in vitro fouling behavior of a set of four systematically varied sulfa-/sulfobetaine-containing zwitterionic hydrogel coatings against a series of proteins and nonmotile as well as motile marine organisms as model foulers. The coatings are prepared by simultaneous photoinduced cross-linking and surface anchoring to elucidate the effect of the molecular structure of the zwitterionic moieties on their antifouling activity. Analogously prepared coatings of poly(butyl methacrylate) and poly(oligoethylene glycol methacrylate) serve as references. Photoreactive polymers are synthesized by the statistical copolymerization of sulfobetaine or sulfabetaine methacrylates and methacrylamides with a benzophenone derivative of 2-hydroxyethyl methacrylate and are applied as a thin film coating. While keeping the density of the zwitterionic and cross-linker groups constant, the molecular structure of the zwitterionic side chains is varied systematically, as is the arrangement of the ion pairs in the side chain by changing the classical linear geometry to a novel Y-shaped geometry. All of the polyzwitterions strongly reduce fouling compared to poly(butyl methacrylate). Overall, the sulfabetaine polyzwitterion coatings studied matches the high antifouling effectiveness of oligo(ethylene glycol)-based ones used as a control. Nevertheless, performances varied individually for a given pair of polymer and fouler. The case of the polysulfobetaines exemplifies that minor chemical changes in the polymer structure affect the antifouling performance markedly. Accordingly, the antifouling performance of such polymers cannot be correlated simply to the type of zwitterion used (which could be generally ranked as better performing or poorer performing) but is a result of the polymer's precise chemical structure. Our findings underline the need to enlarge the existing structural diversity of polyzwitterions for antifouling purposes to optimize the potential of their chemical structure.

Mellitate: A multivalent anion with extreme charge density causes rapid aggregation and misfolding of wild type lysozyme at neutral pH

Due to its symmetric structure and abundance of carboxyl groups, mellitic acid (MA–benzenehexacarboxylic acid) has an uncommon capacity to form highly ordered molecular networks. Dissolved in water, MA dissociates to yield various mellitate anions with pronounced tendencies to form complexes with cations including protonated amines. Deprotonation of MA at physiological pH produces anions with high charge densities (MA^5- and MA^6-) whose influence on co-dissolved proteins has not been thoroughly studied. As electrostatic attraction between highly symmetric MA^6- anions and positively charged low-symmetry globular proteins could lead to interesting self-assembly patterns we have chosen hen egg white lysozyme (HEWL), a basic stably folded globular protein as a cationic partner for mellitate anions to form such hypothetical nanostructures. Indeed, mixing of neutral HEWL and MA solutions does result in precipitation of electrostatic complexes with the stoichiometry dependent on pH. We have studied the self-assembly of HEWL-MA structures using vibrational spectroscopy (infrared absorption and Raman scattering), circular dichroism (CD), atomic force microscopy (AFM). Possible HEWL-MA^6- molecular docking scenarios were analyzed using computational tools. Our results indicate that even at equimolar ratios (in respect to HEWL), MA^5- and MA^6- anions are capable of inducing misfolding and aggregation of the protein upon mild heating which results in non-native intermolecular beta-sheet appearing in the amide I’ region of the corresponding infrared spectra. The association process leads to aggregates with compacted morphologies entrapping mellitate anions. The capacity of extremely diluted mellitate anions (i.e. at sub-millimolar concentration range) to trigger aggregation of proteins is discussed in the context of mechanisms of misfolding.

Molecular Engineering and Design of Semiconducting Polymer Dots with Narrow-Band, Near-Infrared Emission for in Vivo Biological Imaging

This article describes the design and synthesis of donor-bridge-acceptor-based semiconducting polymer dots (Pdots) that exhibit narrow-band emissions, ultrahigh brightness, and large Stokes shifts in the near-infrared (NIR) region. We systematically investigated the effect of π-bridges on the fluorescence quantum yields of the donor-bridge-acceptor-based Pdots. The Pdots could be excited by a 488 or 532 nm laser and have a high fluorescence quantum yield of 33% with a Stokes shift of more than 200 nm. The emission full width at half-maximum of the Pdots can be as narrow as 29 nm, about 2.5 times narrower than that of inorganic quantum dots at the same emission wavelength region. The average per-particle brightness of the Pdots is at least 3 times larger than that of the commercially available quantum dots. The excellent biocompatibility of these Pdots was demonstrated in vivo, and their specific cellular labeling capability was also approved by different cell lines. By taking advantage of the durable brightness and remarkable stability of these NIR fluorescent Pdots, we performed in vivo microangiography imaging on living zebrafish embryos and long-term tumor monitoring on mice. We anticipate these donor-bridge-acceptor-based NIR-fluorescent Pdots with narrow-band emissions to find broad use in a variety of multiplexed biological applications.

Motion of nanoprobes in complex liquids within the framework of the length-scale dependent viscosity model

This paper deals with the recent phenomenological model of the motion of nanoscopic objects (colloidal particles, proteins, nanoparticles, molecules) in complex liquids. We analysed motion in polymer, micellar, colloidal and protein solutions and the cytoplasm of living cells using the length-scale dependent viscosity model. Viscosity monotonically approaches macroscopic viscosity as the size of the object increases and thus gives a single, coherent picture of motion at the nano and macro scale. The model includes interparticle interactions (solvent-solute), temperature and the internal structure of a complex liquid. The depletion layer ubiquitously occurring in complex liquids is also incorporated into the model. We also discuss the biological aspects of crowding in terms of the length-scale dependent viscosity model.

A New Type of Electron Relay Station in Proteins: Three-Piece S:Π∴S↔S∴Π:S Resonance Structure

A type of relay station for electron transfer in proteins, three-piece five-electron bonding, is introduced in this paper, which is also first proposed here. The ab initio calculations predict the formation of S:Π∴S↔S∴Π:S resonance binding with an aromatic ring located in the middle of two sulfur-containing groups, which may participate in electron-hole transport in proteins. These special structures can lower the local ionization energies to capture electron holes efficiently and may be easily formed and broken because of their proper binding energies. In addition, the UV-vis spectra provide evidence of the formations of the three-piece five-electron binding. The cooperation of three adjacent pieces may be advantage to promote electron transfer a longer distance.

Protein charge ladders reveal that the net charge of ALS-linked superoxide dismutase can be different in sign and magnitude from predicted values

This article utilized "protein charge ladders"-chemical derivatives of proteins with similar structure, but systematically altered net charge-to quantify how missense mutations that cause amyotrophic lateral sclerosis (ALS) affect the net negative charge (Z) of superoxide dismutase-1 (SOD1) as a function of subcellular pH and Zn(2+) stoichiometry. Capillary electrophoresis revealed that the net charge of ALS-variant SOD1 can be different in sign and in magnitude-by up to 7.4 units per dimer at lysosomal pH-than values predicted from standard pKa values of amino acids and formal oxidation states of metal ions. At pH 7.4, the G85R, D90A, and G93R substitutions diminished the net negative charge of dimeric SOD1 by up to +2.29 units more than predicted; E100K lowered net charge by less than predicted. The binding of a single Zn(2+) to mutant SOD1 lowered its net charge by an additional +2.33 ± 0.01 to +3.18 ± 0.02 units, however, each protein regulated net charge when binding a second, third, or fourth Zn(2+) (ΔZ < 0.44 ± 0.07 per additional Zn(2+) ). Both metalated and apo-SOD1 regulated net charge across subcellular pH, without inverting from negative to positive at the theoretical pI. Differential scanning calorimetry, hydrogen-deuterium exchange, and inductively coupled plasma mass spectrometry confirmed that the structure, stability, and metal content of mutant proteins were not significantly affected by lysine acetylation. Measured values of net charge should be used when correlating the biophysical properties of a specific ALS-variant SOD1 protein with its observed aggregation propensity or clinical phenotype.

Effect of surfactant hydrophobicity on the pathway for unfolding of ubiquitin

This paper describes the interaction between ubiquitin (UBI) and three sodium n-alkyl sulfates (SC(n)S) that have the same charge (Z = -1) but different hydrophobicity (n = 10, 12, or 14). Increasing the hydrophobicity of the n-alkyl sulfate resulted in (i) an increase in the number of distinct intermediates (that is, complexes of UBI and surfactant) that form along the pathway of unfolding, (ii) a decrease in the minimum concentrations of surfactant at which intermediates begin to form (i.e., a more negative ΔG(binding) of surfactant for UBI), and (iii) an increase in the number of surfactant molecules bound to UBI in each intermediate or complex. These results demonstrate that small changes in the hydrophobicity of a surfactant can significantly alter the binding interactions with a folded or unfolded cytosolic protein.

Capillary zone electrophoresis as a tool to monitor the last stages of the degradation of water-sensitive polymers

In order to monitor the formation of the water-soluble by-products from chain-scission of degradable polymers used in the biomedical field, four capillary electrophoresis methods are discussed with the aim of giving the limits and performance for each. Three of them (electroosmotic flow reversal by dynamic adsorption of a polycation, multilayer polyelectrolyte coatings and physical binding of polyethylene oxide) are based on the use of dynamic coatings onto the inner surface of a fused silica capillary, a simple means to adapt performance to specific separations via modification and control of the electroosmotic flow of fused capillary. Using oligomers of lactic acid considered as standards the methods are compared. Other examples of ester-containing macromolecules (poly(hydroxybutyrate)), as well as degradable polyanions are described, namely N-acetylneuraminate polymer and poly(beta-malic acid).

Complexes of native ubiquitin and dodecyl sulfate illustrate the nature of hydrophobic and electrostatic interactions in the binding of proteins and surfactants

A previous study, using capillary electrophoresis (CE) [J. Am. Chem. Soc. 2008, 130, 17384-17393], reported that six discrete complexes of ubiquitin (UBI) and sodium dodecyl sulfate (SDS) form at different concentrations of SDS along the pathway to unfolding of UBI in solutions of SDS. One complex (which formed between 0.8 and 1.8 mM SDS) consisted of native UBI associated with approximately 11 molecules of SDS. The current study used CE and (15)N/(13)C-(1)H heteronuclear single quantum coherence (HSQC) NMR spectroscopy to identify residues in folded UBI that associate specifically with SDS at 0.8-1.8 mM SDS, and to correlate these associations with established biophysical and structural properties of this well-characterized protein. The ability of the surface charge and hydrophobicity of folded UBI to affect the association with SDS (at concentrations below the CMC) was studied, using CE, by converting lys-ε-NH(3)(+) to lys-ε-NHCOCH(3) groups. According to CE, the acetylation of lysine residues inhibited the binding of 11 SDS ([SDS] < 2 mM) and decreased the number of complexes of composition UBI-(NHAc)(8)·SDS(n) that formed on the pathway of unfolding of UBI-(NHAc)(8) in SDS. A comparison of (15)N-(1)H HSQC spectra at 0 mM and 1 mM SDS with calculated electrostatic surface potentials of folded UBI (e.g., solutions to the nonlinear Poisson-Boltzmann (PB) equation) suggested, however, that SDS binds preferentially to native UBI at hydrophobic residues that are formally neutral (i.e., Leu and Ile), but that have positive electrostatic surface potential (as predicted from solutions to nonlinear PB equations); SDS did not uniformly interact with residues that have formal positive charge (e.g., Lys or Arg). Cationic functional groups, therefore, promote the binding of SDS to folded UBI because these groups exert long-range effects on the positive electrostatic surface potential (which extend beyond their own van der Waals radii, as predicted from PB theory), and not because cationic groups are necessarily the site of ionic interactions with sulfate groups. Moreover, SDS associated with residues in native UBI without regard to their location in α-helix or β-sheet structure (although residues in hydrogen-bonded loops did not bind SDS). No correlation was observed between the association of an amino acid with SDS and the solvent accessibility of the residue or its rate of amide H/D exchange. This study establishes a few (of perhaps several) factors that control the simultaneous molecular recognition of multiple anionic amphiphiles by a folded cytosolic protein.

Interfacial biocatalysis on charged and immobilized substrates: the roles of enzyme and substrate surface charge

An enzyme charge ladder was used to examine the role of electrostatic interactions involved in biocatalysis at the solid-liquid interface. The reactive substrate consisted of an immobilized bovine serum albumin (BSA) multilayer prepared using a layer-by-layer technique. The zeta potential of the BSA substrate and each enzyme variant was measured to determine the absolute charge in solution. Enzyme adsorption and the rate of substrate surface hydrolysis were monitored for the enzyme charge ladder series to provide information regarding the strength of the enzyme-substrate interaction and the rate of interfacial biocatalysis. First, each variant of the charge ladder was examined at pH 8 for various solution ionic strengths. We found that for positively charged variants the adsorption increased with the magnitude of the charge until the surface became saturated. For higher ionic strength solutions, a greater positive enzyme charge was required to induce adsorption. Interestingly, the maximum catalytic rate was not achieved at enzyme saturation but at an invariable intermediate level of adsorption for each ionic strength value. Furthermore, the maximum achievable reaction rate for the charge ladder was larger for higher ionic strength values. We propose that diffusion plays an important role in interfacial biocatalysis, and for strong enzyme-substrate interaction, the rate of diffusion is reduced, leading to a decrease in the overall reaction rate. We investigated the effect of substrate charge by varying the solution pH from 6.1 to 8.7 and by examining multiple ionic strength values for each pH. The same intermediate level of adsorption was found to maximize the overall reaction rate. However, the ionic strength response of the maximum achievable rate was clearly dependent on the pH of the experiment. We propose that this observation is not a direct effect of pH but is caused by the change in substrate surface charge induced by changing the pH. To prove this hypothesis, BSA substrates were chemically modified to reduce the magnitude of the negative charge at pH 8. Chemical modification was accomplished by the amidation of aspartic and glutamic acids to asparagine and glutamine. The ionic strength response of the chemically modified substrate was considerably different than that for the native BSA substrate at an identical pH, consistent with the trend based on substrate surface charge. Consequently, for substrates with a low net surface charge, the maximum achievable catalytic rate of the charge ladder was relatively independent of the solution ionic strength over the range examined; however, at high net substrate surface charge, the maximum rate showed a considerable ionic strength dependence.

Neutralizing positive charges at the surface of a protein lowers its rate of amide hydrogen exchange without altering its structure or increasing its thermostability

This paper combines two techniques--mass spectrometry and protein charge ladders--to examine the relationship between the surface charge and hydrophobicity of a representative globular protein (bovine carbonic anhydrase II; BCA II) and its rate of amide hydrogen-deuterium (H/D) exchange. Mass spectrometric analysis indicated that the sequential acetylation of surface lysine-ε-NH3(+) groups--a type of modification that increases the net negative charge and hydrophobicity of the surface of BCA II without affecting its secondary or tertiary structure--resulted in a linear decrease in the aggregate rate of amide H/D exchange at pD 7.4, 15 °C. According to analysis with MS, the acetylation of each additional lysine generated between 1.4 and 0.9 additional hydrogens that are protected from H/D exchange during the 2 h exchange experiment at 15 °C, pD 7.4. NMR spectroscopy demonstrated that none of the hydrogen atoms which became protected upon acetylation were located on the side chain of the acetylated lysine residues (i.e., lys-ε-NHCOCH3) but were instead located on amide NHCO moieties in the backbone. The decrease in rate of exchange associated with acetylation paralleled a decrease in thermostability: the most slowly exchanging rungs of the charge ladder were the least thermostable (as measured by differential scanning calorimetry). This observation--that faster rates of exchange are associated with slower rates of denaturation--is contrary to the usual assumptions in protein chemistry. The fact that the rates of H/D exchange were similar for perbutyrated BCA II (e.g., [lys-ε-NHCO(CH2)2CH3]18) and peracetylated BCA II (e.g., [lys-ε-NHCOCH3]18) suggests that the electrostatic charge is more important than the hydrophobicity of surface groups in determining the rate of H/D exchange. These electrostatic effects on the kinetics of H/D exchange could complicate (or aid) the interpretation of experiments in which H/D exchange methods are used to probe the structural effects of non-isoelectric perturbations to proteins (i.e., phosphorylation, acetylation, or the binding of the protein to an oligonucleotide or to another charged ligand or protein).

Molecular signatures of enzyme-solid interactions: thermodynamics of protein binding to alpha-Zr(IV) phosphate nanoplates

Isothermal titration calorimetry (ITC) was used to determine the thermodynamics of protein binding to the nanoplates of alpha-Zr(HPO4)2.H2O (alpha-ZrP). The binding constants (K(b)) and DeltaG, DeltaH, and DeltaS have been evaluated for a small set of proteins, and K(b) values are in the range of 2-760 x 10(5) M(-1). The binding of positively charged proteins to the negatively charged alpha-ZrP was endothermic, while the binding of negatively charged proteins was exothermic, and these are contrary to expectations based on a simple electrostatic model. The binding enthalpies of the proteins varied over a range of -24 to +25 kcal/mol, and these correlated roughly with the net charge on the protein (R2 = 0.964) but not with other properties such as the number of basic residues, polar residues, isoelectric point, surface area, or molecular mass. Linear fits to the enthalpy plots indicated that each charge on the protein contributes 1.18 kcal/mol toward the binding enthalpy. Binding entropies of positively charged proteins were favorable (>0) while the binding entropies of negatively charged proteins were unfavorable (<0). The DeltaS values varied over a range of -51 to +98 cal/mol x K, and these correlated very well with the net charge on the protein (R2 = 0.999), but DeltaS is in the opposite direction of DeltaH. The binding or release of cations to/from the protein-solid interface can account for these observations. There was no correlation between the binding free energy (DeltaG(obs)) and any specific molecular properties, but it is likely to be a sum of several opposing interactions of large magnitudes. For the first time, the binding enthalpies and entropies are connected to specific molecular properties. The model suggests that the thermodynamic parameters can be controlled by choosing appropriate cations or by adjusting the net charge on the protein. We hope that physical insights such as these will be useful in understanding the complex behavior of proteins at biological interfaces.

Separation of Protein Charge Variants by Ultrafiltration

The removal of product variants that form during downstream processing remains a challenge in the purification of recombinant therapeutic proteins. We examined the feasibility of separating variants with slightly different net charge using high-performance membrane ultrafiltration. A myoglobin variant was formed by reaction of the lysine epsilon-amino group with succinic anhydride. Sieving data were obtained over a range of solution conditions using commercial polyethersulfone ultrafiltration membranes. Maximum selectivity of about 7-fold was obtained at very low conductivity due to the strong electrostatic repulsion of the more negatively charged variant. Protein separations were performed by diafiltration. A two-stage process generated solutions of the normal myoglobin (in the permeate) and the charge variant (in the retentate), both at greater than 9-fold purification and 90% yield. These results provide the first demonstration that membrane systems can be used to separate proteins that differ by only a single charged amino acid residue.

PEGMA/MMA copolymer graftings: generation, protein resistance, and a hydrophobic domain

We synthesized various graft copolymer films of poly(ethylene glycol) methacrylate (PEGMA) and methyl methacrylate (MMA) on silicon to examine the dependency of protein-surface interactions on grafting composition. We optimized atom transfer radical polymerizations to achieve film thicknesses from 25 to 100 nm depending on the monomer mole fractions, and analyzed the resulting surfaces by X-ray photoelectron spectroscopy (XPS), ellipsometry, contact angle measurements, and atomic force microscopy (AFM). As determined by XPS, the stoichiometric ratios of copolymer graftings correlated with the concentrations of provided monomer solutions. However, we found an unexpected and pronounced hydrophobic domain on copolymer films with a molar amount of 10-40% PEGMA, as indicated by advancing contact angles of up to 90 degrees . Nevertheless, a breakdown of the protein-repelling character was only observed for a fraction of 15% PEGMA and lower, far in the hydrophobic domain. Investigation of the structural basis of this exceptional wettability by high-resolution AFM demonstrated the independence of this property from morphological features.

Lysine acetylation can generate highly charged enzymes with increased resistance toward irreversible inactivation

This paper reports that the acetylation of lysine epsilon-NH3(+) groups of alpha-amylase--one of the most important hydrolytic enzymes used in industry--produces highly negatively charged variants that are enzymatically active, thermostable, and more resistant than the wild-type enzyme to irreversible inactivation on exposure to denaturing conditions (e.g., 1 h at 90 degrees C in solutions containing 100-mM sodium dodecyl sulfate). Acetylation also protected the enzyme against irreversible inactivation by the neutral surfactant TRITON X-100 (polyethylene glycol p-(1,1,3,3-tetramethylbutyl)phenyl ether), but not by the cationic surfactant, dodecyltrimethylammonium bromide (DTAB). The increased resistance of acetylated alpha-amylase toward inactivation is attributed to the increased net negative charge of alpha-amylase that resulted from the acetylation of lysine ammonium groups (lysine epsilon-NH3(+) --> epsilon-NHCOCH3). Increases in the net negative charge of proteins can decrease the rate of unfolding by anionic surfactants, and can also decrease the rate of protein aggregation. The acetylation of lysine represents a simple, inexpensive method for stabilizing bacterial alpha-amylase against irreversible inactivation in the presence of the anionic and neutral surfactants that are commonly used in industrial applications.

Microfluidic separation and capture of analytes for single-molecule spectroscopy

A complex mixture of fluorescently labeled biological molecules is separated electrophoretically on a chip and the constituent molecules are confined in a sub-nanolitre microchamber, which allows analysis by various single-molecule techniques.

Why are proteins charged? Networks of charge-charge interactions in proteins measured by charge ladders and capillary electrophoresis

Almost all proteins contain charged amino acids. While the function in catalysis or binding of individual charges in the active site can often be identified, it is less clear how to assign function to charges beyond this region. Are they necessary for solubility? For reasons other than solubility? Can manipulating these charges change the properties of proteins? A combination of capillary electrophoresis (CE) and protein charge ladders makes it possible to study the roles of charged residues on the surface of proteins outside the active site. This method involves chemical modification of those residues to generate a large number of derivatives of the protein that differ in charge. CE separates those derivatives into groups with the same number of modified charged groups. By studying the influence of charge on the properties of proteins using charge ladders, it is possible to estimate the net charge and hydrodynamic radius and to infer the role of charged residues in ligand binding and protein folding.

Quantitative description of the relation between protein net charge and protein adsorption to air-water interfaces

In this study a set of chemically engineered variants of ovalbumin was produced to study the effects of electrostatic charge on the adsorption kinetics and resulting surface pressure at the air-water interface. The modification itself was based on the coupling of succinic anhydride to lysine residues on the protein surface. After purification of the modified proteins, five homogeneous batches were obtained with increasing degrees of modification and zeta-potentials ranging from -19 to -26 mV (-17 mV for native ovalbumin). These batches showed no changes in secondary, tertiary, or quaternary structure compared to the native protein. However, the rate of adsorption as measured with ellipsometry was found to decrease with increasing net charge, even at the initial stages of adsorption. This indicates an energy barrier to adsorption. With the use of a model based on the random sequential adsorption model, the energy barrier for adsorption was calculated and found to increase from 4.7 kT to 6.1 kT when the protein net charge was increased from -12 to -26. A second effect was that the increased electrostatic repulsion resulted in a larger apparent size of the adsorbed proteins, which went from 19 to 31 nm2 (native and highest modification, respectively), corresponding to similar interaction energies at saturation. The interaction energy was found to determine not only the saturation surface load but also the surface pressure as a function of the surface load. This work shows that, in order to describe the functionality of proteins at interfaces, they can be described as hard colloidal particles. Further, it is shown that the build-up of protein surface layers can be described by the coulombic interactions, exposed protein hydrophobicity, and size.

Net charge and electrophoretic mobility of lysozyme charge ladders in solutions of nonionic surfactant

We report on the electrophoretic mobility and on the thermal diffusion of lysozyme proteins dissolved in aqueous solutions of a nonionic surfactant (C12E6) at a wide range of concentrations of the surfactant (0-20% by weight). We want to estimate the influence of a dense network of elongated micelles of C12E6 on the effective charge of the proteins as observed in the capillary electrophoresis experiments. The possible mechanism leading to the change in the effective charge of protein could involve the deformation of the cloud of counterions around the protein when it squeezes through the narrow (of the order of a protein diameter) aqueous channels formed in the solution of elongated micelles. The combination of independent measurements of the electrophoretic mobility of a family of modified proteins (lysozyme charge ladder [Colton et al. J. Am. Chem. Soc. 1997, 119, 12701]), of the microviscosity of the solutions of surfactant (obtained via fluorescence correlation spectroscopy), and of the hydrodynamic radius of the proteins (photon correlation spectroscopy) allow us to conclude that the effective charge of the proteins is not affected by the presence of surfactant, even at high concentrations.

Stability of proteins in the presence of carbohydrates; experiments and modeling using scaled particle theory

The effects of sucrose and fructose on the free energy of unfolding, DeltaG(N-->D), and on the change in hydrodynamic radius, R(H), upon unfolding were measured for RNase A and alpha-lactalbumin. Recently we analyzed the results for RNase A and showed that the effects of the carbohydrates on the protein's thermal stability can be accurately accounted for by scaled particle theory (SPT), and are thus largely entropic in nature. In this paper we extend this analysis to alpha-lactalbumin and demonstrate the generality of this finding. We also investigate the relationship between SPT and the thermodynamic formalism of preferential interactions. The preferential binding parameters calculated using SPT are in excellent agreement with experimentally measured values available in the literature. This agreement is expected to hold as long as enthalpic interactions between the cosolute and the protein are not important, as appears to be the case here. Finally we use the experimental data and SPT to calculate the change in the number of sugar molecules excluded from the protein surface during unfolding from knowledge of the preferential binding parameter for the native and denatured state of the protein.

Diffusion and Viscosity in a Crowded Environment: from Nano- to Macroscale

Although water is the chief component of living cells, food, and personal care products, the supramolecular components make their viscosity larger than that of water by several orders of magnitude. Using fluorescence correlation spectroscopy (FCS), photon correlation spectroscopy (PCS), NMR, and rheology data, we show how the viscosity changes from the value for water at the molecular scale to the large macroviscosity. We determined the viscosity experienced by nanoprobes (of sizes from 0.28 to 190 nm) in aqueous micellar solution of hexaethylene-glycol-monododecyl-ether (in a range of concentration from 0.1% w/w to 35% w/w) and identified a clear crossover at the length scale of 17 +/- 2 nm (slightly larger than persistence length of micelles) at which viscosity acquires its macroscopic value. The sharp dependence of the viscosity coefficients on the size of the probe in the nanoregime has important consequences for diffusion-limited reactions in crowded environments (e.g., living cells).

Effects of Surface Charge on Denaturation of Bovine Carbonic Anhydrase

This work compares the denaturation of two proteins-bovine carbonic anhydrase II (BCA) and its derivative with all lysine groups acetylated (BCA-Ac(18))-by urea, guanidinium chloride (GuHCl), heat, and sodium dodecyl sulfate (SDS). It demonstrates that increasing the net negative charge of the protein by acetylation of lysines reduces its stability to urea, GuHCl, and heat, but increases its kinetic stability (its thermodynamic stability cannot be measured) towards denaturation by SDS. Increasing the ionic strength of the buffer improves the stability of BCA-Ac(18) to urea and heat, but still leaves it less stable than unacetylated BCA to those denaturants. In urea, the large change in electrostatic interactions not only modifies the free energy of denaturation, but also introduces a stable intermediate into the unfolding pathway. This work shows that modifications of charges on the surfaces of proteins can have a large effect--positive or negative, depending on the denaturant--on the stability of the proteins despite the exposure of these charges to high dielectric solvent and buffer ions.

A novel glass slide-based peptide array support with high functionality resisting non-specific protein adsorption

Glass slides have been modified with a multifunctional poly(ethylene glycol) (PEG)-based polymer with respect to array applications in the growing field of proteome research. We systematically investigated the stepwise synthesis of the PEG films starting from self-assembled alkyl silane monolayers via monolayer peroxidation and subsequent graft polymerization of PEG methacrylate (PEGMA). Chemical composition was examined by X-ray photoelectron spectroscopy (XPS); infrared spectroscopy provided information about order and composition of the films as well; film thickness was determined by ellipsometry; using fluorescence microscopy and again XPS, the amount of proteins adsorbed on the slides was investigated. The novel support material allows a versatile modification of the amino group surface density up to 40 nmol/cm(2) for the linkage of probe molecules. Further on, we carried out standard peptide synthesis based on the well-established 9-fluorenylmethoxycarbonyl (Fmoc) chemistry, which was monitored by UV/Vis quantification of the Fmoc deblocking and mass spectrometry. The polymer coating is stable with respect to a wide range of chemical and thermal conditions, and prevents the glass surface from unspecific protein adsorption. Finally, we applied our modified glass slides in immunoassays and thus examined specific interactions of monoclonal antibodies with appropriate peptide epitopes.

Increasing the net charge and decreasing the hydrophobicity of bovine carbonic anhydrase decreases the rate of denaturation with sodium dodecyl sulfate

This study compares the rate of denaturation with sodium dodecyl sulfate (SDS) of the individual rungs of protein charge ladders generated by acylation of the lysine epsilon-NH3+ groups of bovine carbonic anhydrase II (BCA). Each acylation decreases the number of positively charged groups, increases the net negative charge, and increases the hydrophobic surface area of BCA. This study reports the kinetics of denaturation in solutions containing SDS of the protein charge ladders generated with acetic and hexanoic anhydrides; plotting these rates of denaturation as a function of the number of modifications yields a U-shaped curve. The proteins with an intermediate number of modifications are the most stable to denaturation by SDS. There are four competing interactions-two resulting from the change in electrostatics and two resulting from the change in exposed hydrophobic surface area-that determine how a modification affects the stability of a rung of a charge ladder of BCA to denaturation with SDS. A model based on assumptions about how these interactions affect the folded and transition states has been developed and fits the experimental results. Modeling indicates that for each additional acylation, the magnitude of the change in the activation energy of denaturation (DeltaDeltaG(double dagger)) due to changes in the electrostatics is much larger than the change in DeltaDeltaG(double dagger) due to changes in the hydrophobicity, but the intermolecular and intramolecular electrostatic effects are opposite in sign. At the high numbers of acylations, hydrophobic interactions cause the hexanoyl-modified BCA to denature nearly three orders of magnitude more rapidly than the acetyl-modified BCA.

Intrinsic charge ladders of a monoclonal antibody in hydroxypropylcellulose-coated capillaries

Capillary zone electrophoresis (CZE) has been used to resolve the charge heterogeneity of an intact ( approximately 150 kDa) monoclonal IgG antibody (mAb). Although this microheterogeneity can also be observed by isoelectric focusing, CZE allows the net charge of each variant to be measured as a function of pH and other solution conditions. Separation was achieved in both borate and Tris run buffers using capillaries that had been statically coated with hydroxypropylcellulose (HPC). The HPC coating makes inadvertent chromatographic retention of the mAb undetectably small and decreases electroosmotic flow (EOF) to approximately 10(-5) cm(2) V(-1) s(-1), with reasonable stability over dozens of runs under the conditions tested (pH 8.5 and 9.0 for each buffer). We also describe a novel means of measuring small, positive EOF coefficients and larger, negative net mobilities in the same run. This allows determination of accurate electrophoretic mobilities despite variations in EOF. The resolved mAb charge variants (which most likely result from deamidation or partial truncation) constitute what we call an "intrinsic" charge ladder. As with conventional charge ladders formed by deliberate modification of a homogeneous protein, net charge is obtained by extrapolating a plot of electrophoretic mobility versus (assumed) incremental charge difference. At a given pH, the mAb is more negatively charged in borate than in Tris, reflecting specific binding of the B(OH)(4)(-) anion. We also report hydrodynamic radii calculated from the slopes of these plots.

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.

Hydrodynamic radius ladders of proteins

We introduce hydrodynamic radius ladders of proteins as a new tool to isolate and measure the role of hydrodynamic size on transport properties of proteins. Radius ladders are collections of derivatives of a protein that differ incrementally in number of polyethylene glycol (PEG) chains grafted to their surface. The addition of these chains causes the hydrodynamic size of the protein to increase. Capillary electrophoresis (CE) separates these derivatives into individual peaks or "rungs" of a ladder composed of proteins that have the same number of PEG chains, and provides a way to measure the values of hydrodynamic radius of proteins that constitute the rungs of the ladder. We demonstrate the utility of this approach by measuring the partitioning of radius ladders into polymer hydrogels. The combination of radius ladders and CE produces a large amount of internally consistent data on hydrodynamic size. This technique will have applicability to the study of the role of hydrodynamic size on transport.

Benzoyl Derivatization as a Method To Improve Retention of Hydrophilic Peptides in Tryptic Peptide Mapping

This study exploits the increase in chromatographic retention that accrues from benzoyl derivatization of primary amines as a tool to increase sequence coverage in tryptic peptide mapping. N-hydroxysuccinamide sulfonyl benzoate quantitatively derivatizes primary amines of peptides. Introduction of the hydrophobic benzoyl moiety into peptides increased retention of peptides during reversed-phase chromatography (RPC), particularly in the case of smaller hydrophilic peptides. Short chain (1-6 amino acids) tryptic fragments of model proteins lysozyme, myoglobin, and cytochrome c derivatized with N-hydroxysuccinamide sulfonyl benzoate eluted in the linear acetonitrile gradient. Application of benzoyl derivatization was further extended to achieve complete sequence coverage of a therapeutic protein, recombinant human growth hormone, and in detection of single amino acid polymorphism.

Biochips beyond DNA: technologies and applications

Technological advances in miniaturization have found a niche in biology and signal the beginning of a new revolution. Most of the attention and advances have been made with DNA chips yet a lot of progress is being made in the use of other biomolecules and cells. A variety of reviews have covered only different aspects and technologies but leading to the shared terminology of "biochips." This review provides a basic introduction and an in-depth survey of the different technologies and applications involving the use of non-DNA molecules such as proteins and cells. The review focuses on microarrays and microfluidics, but also describes some cellular systems (studies involving patterning and sensor chips) and nanotechnology. The principles of each technology including parameters involved in biochip design and operation are outlined. A discussion of the different biological and biomedical applications illustrates the significance of biochips in biotechnology.

Analysis by capillary electrophoresis of the kinetics of charge ladder formation for bovine carbonic anhydrase

A series of charge ladders of bovine carbonic anhydrase II were synthesized and the relative abundances of the rungs analyzed by capillary electrophoresis as a function of the quantity of acylating agent used. A simulation that models the kinetics of formation of the members of the charge ladders is described. The observed rate constants decreased as the extent of acylation increased. These rate constants correlated adequately with theoretical rate constants calculated using Debye-Hückel theory. The data are compatible with, but do not demand, a model for the formation of this charge ladder in which all unacetylated amino groups in each rung have indistinguishable reactivity and in which the reactivity of the amines in each rung decreases as the net charge on the protein increases; in this model, decreased reactivity is due to increased extent of protonation. This agreement between experiment and model suggests that the charge shielding that results from an ionic strength of 130 mM is not sufficient to suppress the influence of the increasingly negative charge of the protein with acetylation on the extent of protonation of Lys epsilon-NH2 groups.

Measurement of electrostatic interactions in protein folding with the use of protein charge ladders

This paper describes a new method for the measurement of the role of interactions between charged groups on the energetics of protein folding. This method uses capillary electrophoresis (CE) and protein charge ladders (mixtures of protein derivatives that differ incrementally in number of charged groups) to measure, in a single set of electrophoresis experiments, the free energy of unfolding (DeltaG(D-N)) of alpha-lactalbumin (alpha-LA) as a function of net charge. These same data also yield the hydrodynamic radius, R(H), and net charge measured by CE, Z(CE), of the folded and denatured proteins. Alpha-LA unfolds to a compact denatured state under mildly alkaline conditions; a small increase in R(H) (11%, 2 A) coincides with a large increase in Z(CE) (71%, -4 charge units), relative to the folded state. The increase in Z(CE), in turn, predicts a large pH dependence of free energy of unfolding (-22 kJ/mol per unit increase in pH), due to differences in proton binding in the folded and denatured states. The free energy of unfolding correlates with the square of net charge of the members of the charge ladder. The differential dependence of DeltaG(D-N) on net charge for holo-alpha-LA, (partial differential) DeltaG(D-N)/(partial differential)Z = -0.14Z kJ/mol per unit of charge. This dependence of DeltaG(D-N) on net charge is a result of a net electrostatic repulsion among charge groups on the protein. These results, together with data from pH titrations, show that both the effects of electrostatic repulsion and differences in proton binding in the folded and denatured states can play an important role in the pH dependence of this protein; the relative magnitude of these effects varies with pH. The combination of charge ladders and CE is a rapid and efficient tool that measures the contributions of electrostatics to the energetics of protein folding, and the size and charge of proteins as they unfold. All this information is obtained from a single set of electrophoresis experiments.

Basicity of the amino groups of the aminoglycoside amikacin using capillary electrophoresis and coupled CE-MS-MS techniques

This paper describes the use of capillary electrophoresis (CE), and coupled CE and mass spectrometric techniques, to measure the values of the pKa of the amino groups of the aminoglycoside antibiotic amikacin and of its acetylated derivatives. These values of pKa (8.4, 6.7, 9.7, 8.4) were determined by measuring the electrophoretic mobilities of the molecules as a function of pH; they are within 0.7 unit of certain values reported in the literature (by 13C and 15N NMR spectroscopies) but resolved ambiguities left by these earlier studies. The range of values of pKa of amino groups also indicates the complex dependence of the acidity of a functional group (and thus the extent of ionization at a specified value of pH) on the molecular environment of that group.