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

Dissecting the stability determinants of a challenging de novo protein fold using massively parallel design and experimentation

Designing entirely new protein structures remains challenging because we do not fully understand the biophysical determinants of folding stability. Yet, some protein folds are easier to design than others. Previous work identified the 43-residue ɑββɑ fold as especially challenging: The best designs had only a 2% success rate, compared to 39 to 87% success for other simple folds [G. J. Rocklin et al., Science 357, 168-175 (2017)]. This suggested the ɑββɑ fold would be a useful model system for gaining a deeper understanding of folding stability determinants and for testing new protein design methods. Here, we designed over 10,000 new ɑββɑ proteins and found over 3,000 of them to fold into stable structures using a high-throughput protease-based assay. NMR, hydrogen-deuterium exchange, circular dichroism, deep mutational scanning, and scrambled sequence control experiments indicated that our stable designs fold into their designed ɑββɑ structures with exceptional stability for their small size. Our large dataset enabled us to quantify the influence of universal stability determinants including nonpolar burial, helix capping, and buried unsatisfied polar atoms, as well as stability determinants unique to the ɑββɑ topology. Our work demonstrates how large-scale design and test cycles can solve challenging design problems while illuminating the biophysical determinants of folding.

Modeling charge separation in charged nanochannels for single-molecule electrometry

We model the transport of electrically charged solute molecules by a laminar flow within a nanoslit microfluidic channel with electrostatic surface potential. We derive the governing convection–diffusion equation, solve it numerically, and compare it with a Taylor–Aris-like approximation, which gives excellent results for small Péclet numbers. We discuss our results in light of designing an assay that can measure simultaneously the hydrodynamic size and electric charge of single molecules by tracking their motion in such nanoslit channels with electrostatic surface potential.

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).

Utilization of lysozyme charge ladders to examine the effects of protein surface charge distribution on binding affinity in ion exchange systems

A lysozyme library was employed to study the effects of protein surface modification on protein retention and to elucidate preferred protein binding orientations for cation exchange chromatography. Acetic anhydride was used as an acetylating agent to modify protein surface lysine residues. Partial acetylation of lysozyme resulted in the formation of a homologous set of modified proteins with varying charge densities and distribution. The resulting protein charge ladder was separated on a cation exchange column, and eluent fractions were subsequently analyzed using capillary zone electrophoresis and direct infusion electrospray ionization mass spectrometry. The ion exchange separation showed a significant degree of variation in the retention time of the different variants. Several fractions contained coelution of variants, some with differing net charge. In addition, several cases were observed where variants with more positive surface charge eluted from the column prior to variants with less positive charge. Enzymatic digest followed by mass spectrometry was performed to determine the sites of acetylation on the surface of the variants eluting in various fractions. Electrostatic potential maps of these variants were then generated to provide further insight into the elution order of the variants.

Global Model for Optimizing Crossflow Microfiltration and Ultrafiltration Processes: A New Predictive and Design Tool

A global model and algorithm that predicts the performance of crossflow MF and UF process individually or in combination in the laminar flow regime is presented and successfully tested. The model accounts for solute polydispersity, ionic environment, electrostatics, membrane properties and operating conditions. Computer programs were written in Fortran 77 for different versions of the model algorithm that can optimize MF/UF processes rapidly in terms of yield, purity, selectivity, or processing time. The model is validated successfully with three test cases: separation of bovine serum albumin (BSA) from hemoglobin (Hb), capture of immunoglobulin (IgG) from transgenic goat milk by MF, and separation of BSA from IgG by UF. These comparisons demonstrate the capability of the global model to conduct realistic in silico simulations of MF and UF processes. This model and algorithm should prove to be an invaluable technique to rapidly design new or optimize existing MF and UF processes separately or in combination in both pressure-dependent and pressure-independent regimes.

Folding and stability of the isolated Greek key domains of the long-lived human lens proteins gammaD-crystallin and gammaS-crystallin

The transparency of the eye lens depends on the high solubility and stability of the lens crystallin proteins. The monomeric gamma-crystallins and oligomeric beta-crystallins have paired homologous double Greek key domains, presumably evolved through gene duplication and fusion. Prior investigation of the refolding of human gammaD-crystallin revealed that the C-terminal domain folds first and nucleates the folding of the N-terminal domain. This result suggested that the human N-terminal domain might not be able to fold on its own. We constructed and expressed polypeptide chains corresponding to the isolated N- and C-terminal domains of human gammaD-crystallin, as well as the isolated domains of human gammaS-crystallin. Both circular dichroism and fluorescence spectroscopy indicated that the isolated domains purified from Escherichia coli were folded into native-like monomers. After denaturation, the isolated domains refolded efficiently at pH 7 and 37 degrees C into native-like structures. The in vitro refolding of all four domains revealed two kinetic phases, identifying partially folded intermediates for the Greek key motifs. When subjected to thermal denaturation, the isolated N-terminal domains were less stable than the full-length proteins and less stable than the C-terminal domains, and this was confirmed in equilibrium unfolding/refolding experiments. The decrease in stability of the N-terminal domain of human gammaD-crystallin with respect to the complete protein indicated that the interdomain interface contributes of 4.2 kcal/mol to the overall stability of this very long-lived protein.

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.

On the application of CZE to the study of protein denaturation

Experimental mobilities obtained from CZE are used to study protein denaturation through a model based on known physicochemical theories. This model is able to provide additional information concerning the folded and unfolded protein states from mobility data. Its use comprises first the evaluation of relevant parameters of the protein microstates like the electrostatic free energy, apart from the classical conformational free energy, and second the expression of raw experimental data concerning the folding-unfolding transition into more specific physicochemical parameters like protein hydrodynamic radius, net charge number, and hydration. Spurious effects that are intrinsic to the experimental evaluation of the mobility of protein states, like BGE viscosity, pH, and ionic strength variations accompanying the changes of the denaturant agent intensity are eliminated. In order to illustrate the proposal of this work, two case studies are considered here. The first one concerns thermal and urea denaturations of horse heart ferricytochrome c and the second one involves thermal denaturation of hen egg-white lysozyme. Thus, relevant theoretical thermodynamic considerations of the folded-unfolded protein transition are presented, where the electrostatic free energy is included explicitly in the effective free energy. It is found that this transition involves sharp increases of hydrodynamic radius and protein hydration.

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.

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.

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.

Eliminating positively charged lysine epsilon-NH3+ groups on the surface of carbonic anhydrase has no significant influence on its folding from sodium dodecyl sulfate

This study compares the folding of two polypeptides--bovine carbonic anhydrase (BCA) and peracetylated BCA (BCA-Ac(18))--having the same sequence of amino acids but differing by 18 formal units of charge, from a solution containing denaturing concentrations of sodium dodecyl sulfate (SDS). Acetylation of BCA with acetic anhydride converts all 18 lysine-epsilon-NH(3)(+) groups to lysine-epsilon-NHCOCH(3) groups and generates BCA-Ac(18). Both BCA and BCA-Ac(18) are catalytically active, and circular dichroism spectroscopy (CD) suggests that they have similar secondary and tertiary structures. SDS at concentrations above approximately 10 mM denatured both proteins. When the SDS was removed by dialysis, both proteins were regenerated in native form. This study suggests that large differences in the net charge of the polypeptide have no significant influence on the structure, the ability to refold, or the rate of refolding of this protein from solutions containing SDS. This study reinforces the idea that charged residues on the surface of BCA do not guide protein folding and raises the broader question of why proteins have charged residues on their surface, outside of the region of the active site.

Simultaneous determination of structural and thermodynamic effects of carbohydrate solutes on the thermal stability of ribonuclease A

This communication describes a new technique for the study of the effects of carbohydrates on the thermal stability of proteins. This approach combines capillary electrophoresis (CE) and protein charge ladders, collections of proteins that differ incrementally in number of chemically modified charged groups, to provide information on both the thermodynamics (i.e., the free energy, DeltaGN-D, of denaturation), and structural changes (i.e., the effective hydrodynamic radius, RH, of proteins in both the native and denatured states) associated with stability. This information, obtained in a single set of electrophoresis experiments, allows a simple microscopic interpretation of the effects of carbohydrate solutes on protein stability. We use this technique to show that the stabilization of ribonuclease A at pH 8.4 by sucrose and fructose can be explained entirely by the contribution these solutes make to the entropy of formation of the protein-solution interface. There is no need, in this case, to refer to quasichemical concepts such as preferential hydration, binding, or exchange of solutes with water at specific sites on the protein to account for the stabilizing effects observed.

Roles of Hydrophobic Interaction in a Volume Phase Transition of Alkylacrylamide Gel Induced by the Hydrogen-Bond-Driving Alkylphenol Binding

It was found that a degree of the binding of alkylphenols to N-alkylacrylamide gel increased transitionally to induce the volume phase transition of gel. Binding isotherms of nonylphenol (n-Ph), propylphenol (p-Ph), ethylphenol (e-Ph), methylphenol (m-Ph), and phenol (Ph) to N-isopropylacrylamide (NIPA), N,N-diethylacrylamide (DEA), N,N-dimethylacrylamide (DMA), and acrylamide (AM) gels were examined. Two types of binding, the site binding at beta < 1 and the multimolecular binding at beta > 1, were observed, where beta was a degree of binding to a monomeric unit of the chain. The former binding was analyzed with the Hill equation applicable to the cooperative binding and the latter binding with the Brunauer-Emmett-Teller (BET) equation applicable to the multilayer adsorption. The binding constant, K, and the Hill coefficient, N, decreased and increased, respectively, in the order of DEA, NIPA, and DMA gels in the case where the binding alkylphenol was the same. The K value increased in the order of Ph, m-Ph, e-Ph, p-Ph, and n-Ph that bound to the same type of gel. The N value was found to change little with the type of binding alkylphenol. The complexes of N-alkylamide with alkylphenol were condensed to form the ordered nanostructures that were observed as broad scattering peaks in small-angle X-ray scattering experiments. The fluorescence excimer emission was observed for the phenol-binding DMA gel, which corresponded to the condensed state of phenol.

Protein unfolding in detergents: effect of micelle structure, ionic strength, pH, and temperature

The 101-residue monomeric protein S6 unfolds in the anionic detergent sodium dodecyl sulfate (SDS) above the critical micelle concentration, with unfolding rates varying according to two different modes. Our group has proposed that spherical micelles lead to saturation kinetics in unfolding (mode 1), while cylindrical micelles prevalent at higher SDS concentrations induce a power-law dependent increase in the unfolding rate (mode 2). Here I investigate in more detail how micellar properties affect protein unfolding. High NaCl concentrations, which induce cylindrical micelles, favor mode 2. This is consistent with our model, though other effects such as electrostatic screening cannot be discounted. Furthermore, unfolding does not occur in mode 2 in the cationic detergent LTAB, which is unable to form cylindrical micelles. A strong retardation of unfolding occurs at higher LTAB concentrations, possibly due to the formation of dead-end protein-detergent complexes. A similar, albeit much weaker, effect is seen in SDS in the absence of salt. Chymotrypsin inhibitor 2 exhibits the same modes of unfolding in SDS as S6, indicating that this type of protein unfolding is not specific for S6. The unfolding process in mode 1 has an activation barrier similar in magnitude to that in water, while the activation barrier in mode 2 is strongly concentration-dependent. The strong pH-dependence of unfolding in SDS and LTAB suggests that the rate of unfolding in anionic detergent is modulated by repulsion between detergent headgroups and anionic side chains, while cationic side chains modulate unfolding rates in cationic detergents.