Isoelectric points of proteins: theoretical determination

What drives amyloid molecules to assemble into oligomers and fibrils?

We develop a theory for three states of equilibrium of amyloid peptides: the monomer, oligomer, and fibril. We assume that the oligomeric state is a disordered micellelike collection of a few peptide chains held together loosely by hydrophobic interactions into a spherical hydrophobic core. We assume that fibrillar amyloid chains are aligned and further stabilized by steric zipper interactions-hydrogen bonding, steric packing, and specific hydrophobic side-chain contacts. The model makes a broad set of predictions that are consistent with experimental results: 1), Similar to surfactant micellization, amyloid oligomerization should increase with peptide concentration in solution. 2), The onset of fibrillization limits the concentration of oligomers in the solution. 3), The extent of Aβ fibrillization increases with peptide concentration. 4), The predicted average fibril length versus monomer concentration agrees with data on α-synuclein. 5), Full fibril length distributions agree with data on α-synuclein. 6), Denaturants should melt out fibrils. And finally, 7), added salt should stabilize fibrils by reducing repulsions between amyloid peptide chains. It is of interest that small changes in solvent conditions can tip the equilibrium balance between oligomer and fibril and cause large changes in rates through effects on the transition-state barrier. This model may provide useful insights into the physical processes underlying amyloid diseases.

Calibrative approaches to protein solubility modeling of a mutant series using physicochemical descriptors

A set of physicochemical properties describing a protein of known structure is employed for a calibrative approach to protein solubility. Common hydrodynamic and electrophoretic properties routinely measured in the bio-analytical laboratory such as zeta potential, dipole moment, the second osmotic virial coefficient are first estimated in silico as a function a pH and solution ionic strength starting with the protein crystal structure. The utility of these descriptors in understanding the solubility of a series of ribonuclease Sa mutants is investigated. A simple two parameter model was trained using solubility data of the wild type protein measured at a restricted number of solution pHs. Solubility estimates of the mutants demonstrate that zeta potential and dipole moment may be used to rationalize solubility trends over a wide pH range. Additionally a calibrative model based on the protein's second osmotic virial coefficient, B₂₂ was developed. A modified DVLO type potential along with a simplified representation of the protein allowed for efficient computation of the second viral coefficient. The standard error of prediction for both models was on the order of 0.3 log S units. These results are very encouraging and demonstrate that these models may be trained with a small number of samples and employed extrapolatively for estimating mutant solubilities.

Isoelectric point, electric charge, and nomenclature of the acid-base residues of proteins

The main object of this work is to present the pedagogical usefulness of the theoretical methods, developed in this laboratory, for the determination of the isoelectric point (pI) and the net electric charge of proteins together with some comments on the naming of the acid-base residues of proteins.

The stabilities of protein crystals

We describe a model for protein crystallization equilibria. The model includes four terms, (1) protein translational entropy opposes crystallization, (2) proteins are attracted to each other by a nonelectrostatic contact free energy favoring crystallization, (3) proteins in the crystal repel each other but, to a greater extent, attract counterions sequestered in the crystal, which favors crystallization, and (4) the translational entropy of the counterions opposes their sequestration into the crystal, opposing crystallization. We treat the electrostatics using the nonlinear Poisson-Boltzmann equation, and we use unit cell information from native protein crystals to determine the boundary conditions. This model predicts the stabilities of protein crystals as functions of temperature, pH, and salt concentrations, in good agreement with the data of Pusey et al. on tetragonal and orthorhombic crystal forms of lysozyme. The experiments show a weak dependence of crystal solubility on pH. According to the model, this is because the entropic cost to neutralize the crystal is compensated by favorable protein-salt interactions. Experiments also show that adding salt stabilizes the crystal. Cohn's empirical law predicts that the logarithm of solubility should be a linear function of salt. The present theory predicts nonlinearity, in better agreement with the experiments. The model shows that the salting out phenomena is not due to more counterion shielding but to lowered counterion translational entropy. Models of this type may help guide faster and better ways to crystallize proteins.

Calculation of the isoelectric point of tryptic peptides in the pH 3.5-4.5 range based on adjacent amino acid effects

Current algorithms for the calculation of peptide or protein pI, based on the charge associated with individual amino acids, can calculate pI values to within +/-0.2 pI units. Here, we present a new pI calculation algorithm that takes into account the effect of adjacent amino acids on the pI value. The algorithm accounts for the effect of adjacent amino acids+/-3 residues away from a charged aspartic or glutamic acid, as well as effects on the free C terminus, and applies a correction term to the corresponding pK values. The correction increments are derived from a 5000-peptide training set using a genetic optimization approach. The accuracy of the new pI values obtained with this method approaches the error associated with the manufacture of the IPG strip (<+/-0.03 pI units). The approach is demonstrated for cytosolic cell extracts derived from the breast-cancer cell line DU4475, and from membrane preparations from human lung-tissue samples. One potential application of a more highly accurate pI calculation is data filtering of MS/MS outputs that will allow for more complex database searches including gene finding, and validation, and detection of coding single-nucleotide polymorphisms in their expressed form.

Proteomics based on peptide fractionation by SDS-free PAGE

Here we demonstrate the usefulness of peptide fractionation by SDS-free polyacrylamide gel electrophoresis and its applicability to proteomics studies. In the absence of SDS, the driving force for the electrophoretic migration toward the anode is supplied by negatively charged acidic amino acid residues and other residues as phosphate, sulfate and sialic acid, while the resulting mobility depends on both the charge and the molecular mass of the peptides. A straightforward method was achieved for SDS-PAGE of proteins, enzyme digestion, peptide transfer and fractionation by SDS-free PAGE, which was named dual-fractionation polyacrylamide gel electrophoresis (DF-PAGE). This method increases the number of identified proteins 2.5-fold with respect to the proteins identified after direct analysis, and more than 80% of assigned peptides were found in unique SDS-free gel slices. A vast majority of identified peptides (93%) have p I values below 7.0, and 7% have p I values between 7.0 and 7.35. Peptide digests that were derived from complex protein mixtures were in consequence simplified as peptides that are positively charged are not recovered in the present conditions. The analysis of a membrane protein extract from Neisseria meningitidis by this approach allowed the identification of 97 proteins, including low-abundance components.

The isoelectric point, a key to understanding a variety of biochemical problems: a minireview

We address the importance of the isoelectric point (IEP) of proteins and membrane components such as phospholipids for our understanding and interpretation of isoforms and opposite charge interactions in the formation of complexes. Five examples drawn from the literature are newly approached from the IEP point of view to clarify general principles.

Improved application of the oscillating method for the isoelectric point determination of protein: Potential connection with protein data banks

The oscillating method (OM) for the theoretical determination of the pI values, one by one, of proteins and other macromolecules has been previously published [Sillero and Maldonado, Comput. Biol. Med 36 (2006) 157-166]. An improved application of the method, here named as improved oscillating method (IOM), allows the pI determination of group of proteins. This characteristic may be useful to explore the pI value and electric charge of family of enzymes. As an example the pI values of 1630 enzymes collected in a Swiss-Prot data bank (www.expasy.org), as belonging to the enzymes ligases (EC 6. 2. 1. *) is presented. The method also permits the determination of the pI value of any group of proteins stored in data banks provided that they can be supplied to the program in a FASTA format. Free access to IOM can be reached at http://www.bq.uam.es/otros/pical3.zip.

Protein pI shifts due to posttranslational modifications in the separation and characterization of proteins

Proteins from breast cancer cell lines are characterized using a 2-D liquid separation technique in which protein pI is used as the first-dimension separation parameter. To effect this protein pI separation, chromatofocusing(CF) is employed whereby a pH gradient is generated on-column using a weak anion exchange medium with the intact proteins fractionated and collected every 0.2 pH unit. It is demonstrated that the pI for expressed intact proteins as generated by CF is an important parameter for identification and characterization of the actual protein modifications occurring in the cancer cell. For most proteins, the experimentally determined pI is very close to that predicted by the databases. In other cases, however, where the pI is observed to be shifted from the expected value, it is shown that this shift is often correlated to protein modifications. The modifications that cause such shifts include truncations and deletions often observed in cancer cells or phosphorylations that can shift the pI by several pH units. It is also shown that the effects of phosphorylation on the observed shift can vary depending upon the protein and the amount of phosphorylation. Moreover, large changes in the pI are often observed for proteins with a pI above 7.0 upon phosphorylation, whereas little change is observed for proteins with a pI of approximately 5.0. The expressed protein's pI value thus becomes an important parameter together with the intact MW value, peptide map, and MS/MS results for identification of the presence and type of posttranslational modifications occurring in the cancer cell.

Zwitterionic stationary phase with covalently bonded phosphorylcholine type polymer grafts and its applicability to separation of peptides in the hydrophilic interaction liquid chromatography mode

A novel phosphorylcholine type zwitterionic stationary phase was synthesized by graft polymerization of 2-methacryloyloxyethyl phosphorylcholine onto the surface of porous silica particles. The resulting material possesses both negatively charged phosphoric acid and positively charged quaternary ammonium groups, which renders it a low net charge over a wide pH range. The composition of the surface grafts were determined by elemental analysis and solid state NMR, and the surface charge (zeta-potential) in different buffer solutions were measured using photon correlation spectroscopy. Separation of several peptides was investigated on packed columns in the hydrophilic interaction liquid chromatography (HILIC) separation mode. It was shown that small peptides can be separated based on hydrophilic interaction and ionic interaction between the stationary phase and analyte. The organic solvent composition, the pH and the salt concentration of the eluent have strong effects on the retention time. Compared to native silica before grafting, the newly synthesized zwitterionic material gave more stable retention times for basic peptides over pH range 3-7 due to elimination of the dissociation of silanol groups.

Evaluation of the electrophoretic behaviour of opioid peptides

A general equation established in a previous study was used to model the electrophoretic mobility of a series of opioid peptides as a function of pH of the separation electrolyte. The concordance between the predicted and the experimental electrophoretic mobilities was excellent and the optimum pH for the separation of the modelled compounds could be predicted from a limited amount of experimental data. The equations were also useful for the accurate determination of the ionization constants of the polyprotic analytes. It was also demonstrated that if ionization constant values are known, the CE separations of the studied peptides can easily be predicted taking into account the classical semiempirical relationships between electrophoretic mobility and charge-to-mass ratio (m(e) versus q/M(alpha)). The separations simulated considering the accurate charge-to-mass ratios of each peptide at a certain pH value were in good agreement with the experimental results. Once an optimum separation pH value and a running buffer compatible with electrospray mass spectrometry (ESI) detection were selected, a method for the separation and characterization of this series of analytes by capillary electrophoresis-electrospray ionization mass spectrometry (CE-ESI-MS) was established using a commercial sheath-flow interface. Method validation was performed in order to prove the suitability of the proposed method for quantitative analysis. Thus, quality parameters, such as repeatability, reproducibility, limits of detection and linearity were determined.

Retinoic acid induces p27Kip1 nuclear accumulation by modulating its phosphorylation

All-trans-retinoic acid (ATRA), the most biologically active metabolite of vitamin A, controls cell proliferation, apoptosis, and differentiation depending on the cellular context. These activities point to ATRA as a candidate for cancer therapy. A pivotal effect of the molecule is the modulation of p27Kip1, a cyclin-dependent kinase (CDK) inhibitor (CDKI). Here, we investigate the mechanisms by which ATRA regulates p27Kip1 level in LAN-5, a neuroblastoma cell line. When added to the cells, ATRA causes a rapid nuclear increase of p27Kip1, which clearly precedes growth arrest. The early buildup is not due to impairment of the CDKI degradation, in contrast to previous observations. Particularly, we did not detect the down-regulation of Skp2 and Cks1, two proteins involved in the nuclear ubiquitin-dependent p27Kip1 removal. Moreover, the morphogen does not impair the CDKI nuclear export and does not cause CDK2 relocalization. The characterization of CDKI isoforms by two-dimensional PAGE/immunoblotting showed that ATRA induces an early nuclear up-regulation of monophosphorylated p27Kip1. Immunologic studies established that this isoform corresponds to p27Kip1 phosphorylated on S10. The buildup of phospho(S10)p27Kip1 precedes the CDKI accumulation and increases its half-life. Finally, ATRA-treated nuclear LAN-5 extracts showed an enhanced capability of phosphorylating p27Kip1 on S10, thus explaining the nuclear up-regulation of the isoform. In conclusion, our data suggest a novel mechanism of ATRA antiproliferative activity, in which the morphogen rapidly up-regulates a nuclear kinase activity that phosphorylates p27Kip1 on S10. In turn, this event causes the stabilization of p27Kip1 and its accumulation in the nuclear compartment.

Modelling migration behavior of peptide hormones in capillary electrophoresis-electrospray mass spectrometry

The applicability in capillary electrophoresis-electrospray mass spectrometry (CE-ESI-MS) of the classical semiempirical relationships between electrophoretic mobility and charge-to-mass ratio (me versus q/Malpha) has been investigated in order to describe the migration behavior of a series of bioactive peptide hormones. The influence upon the models of the separation electrolyte pH and the accuracy of the pK values of these compounds were studied first by capillary electrophoresis with ultraviolet detection (CE-UV). The classical polymer model, alpha = 1/2, resulted in slightly better correlations at any of the studied pH. Furthermore, a general linear equation can be adjusted combining all the experimental data pairs, which suggests that correlation in the whole pH range is independent of the ionic form of the studied peptide hormones. The plots of q/M1/2 against separation electrolyte pH were used to predict their electrophoretic separations, using the accurate pK values obtained in a previous work by CE-UV for charge calculations. A volatile separation electrolyte containing 50 mM of acetic acid and 50 mM of formic acid at pH 2.85 was selected for optimum CE-UV and CE-ESI-MS analysis of the peptide mixture. At this pH and taking into account the specific features of the coupling, the correlation using the classical polymer law was excellent and its parameters were similar to the ones of the general linear equation previously obtained by CE-UV. This confirmed the applicability in CE-ESI-MS of the semiempirical relationship originally established by CE-UV.

Alteration of protein subcellular location and domain formation by alternative translational initiation

Alternative translation is an important cellular mechanism contributing to the generation of proteins and the diversity of protein functions. Instead of studying individual cases, we systematically analyzed the alteration of protein subcellular location and domain formation by alternative translational initiation in eukaryotes. The results revealed that 85.7% of alternative translation events generated biological diversity, attributed to different subcellular localizations and distinct domain contents in alternative isoforms. Analysis of isoelectric point values revealed that most N-terminal truncated isoforms significantly lowered their isoelectric point values targeted at different subcellular localizations, whereas they had conserved domain contents the same as the full-length isoforms. Furthermore, Fisher's exact test indicated that the two ways-targeting at different cellular compartments and changing domain contents-were negatively associated. The N-term truncated isoforms should have only one way to diversify their functions distinct from the full-length ones. The peculiar consequence of subcellular relocation as well as change of domain contents reflected the very high level of biological complexity as alternative usage of initiation codons.

Expression, purification, and characterization of Clostridium botulinum type B light chain

A full-length synthetic gene encoding the light chain of botulinum neurotoxin serotype B, approximately 50 kDa (BoNT/B LC), has been cloned into a bacterial expression vector pET24a+. BoNT/B LC was expressed in Escherichia coli BL21.DE3.pLysS and isolated from the soluble fraction. The resultant protein was purified to homogeneity by cation chromatography and was determined to be >98% pure as assessed by SDS-polyacrylamide gel stained with SilverXpress and analyzed by densitometry. Mass spectroscopic analysis indicated the protein to be 50.8 kDa, which equaled the theoretically expected mass. N-terminal sequencing of the purified protein showed the sequence corresponded to the known reported sequence. The recombinant BoNT/B light chain was found to be highly stable, catalytically active, and has been used to prepare antisera that neutralizes against BoNT/B challenge. Characterization of the protein including pH, temperature, and the stability of the protein in the presence or absence of zinc is described within. The influence of pH differences, buffer, and added zinc on secondary and tertiary structure of BoNT/B light chain was analyzed by circular dichroism and tryptophan fluorescence measurements. Optimal conditions for obtaining maximum metalloprotease activity and stabilizing the protein for long term storage were determined. We further analyzed the thermal denaturation of BoNT/B LC as a function of temperature to probe the pH and added zinc effects on light chain stability. The synthetic BoNT/B LC has been found to be highly active on its substrate (vesicle associated membrane protein-2) and, therefore, can serve as a useful reagent for BoNT/B research.

Isoelectric point determination of proteins and other macromolecules: oscillating method

A program written in Visual Basic has been developed to calculate the isoelectric point of proteins and other macromolecules bearing acid-basic residues. The pI value can be theoretically calculated with the precision required. The computer automatically supplies a representation of the charge of the protein versus pH values. The corresponding values can also be obtained, on command, in the form of table.

Partial purification and characterization of a non-cyanobacterial cyanophycin synthetase from Acinetobacter calcoaceticus strain ADP1 with regard to substrate specificity, substrate affinity and binding to cyanophycin

This study reports, for the first time, purification and biochemical characterization of a cyanophycin synthetase from a non-cyanobacterial strain. Cyanophycin synthetase of Acinetobacter calcoaceticus strain ADP1 was purified 69-fold from recombinant Escherichia coli by two chromatographic steps and one novel affinity step utilizing the Mg(2+)-dependent binding of the enzyme to cyanophycin. Unlike cyanobacterial cyanophycin synthetases characterized so far, the purified enzyme from A. calcoaceticus strain ADP1 did not accept lysine as an alternative substrate to arginine. The apparent K(m)-values for arginine (47 microM) and aspartic acid (240 microM) were similar to those of known cyanophycin synthetases from cyanobacteria, but this enzyme had a slightly higher affinity for aspartic acid. In addition, the two different ATP-binding sites of the enzyme were characterized independently of each other with respect to K(m) values for ATP. The ATP-binding site responsible for the addition of arginine was found to have a much higher affinity for ATP (38 microM) than that responsible for the addition of aspartate (210 mM). Furthermore, the binding of the enzyme to the two possible forms of cyanophycin granule polypeptide (CGP), CGP-Asp and CGP-Arg, was studied. While both forms bound around 30-40 % of the enzyme activity present under the assay conditions, binding was Mg(2+)-dependent in the case of CGP-Asp. Two-dimensional gel electrophoresis revealed that both forms of cyanophycin were equally abundant in cyanophycin-accumulating cells of A. calcoaceticus ADP1.

ProMoST (Protein Modification Screening Tool): a web-based tool for mapping protein modifications on two-dimensional gels

ProMoST is a flexible web tool that calculates the effect of single or multiple posttranslational modifications (PTMs) on protein isoelectric point (pI) and molecular weight and displays the calculated patterns as two-dimensional (2D) gel images. PTMs of proteins control many biological regulatory and signaling mechanisms and 2D gel electrophoresis is able to resolve many PTM-induced isoforms, such as those due to phosphorylation, acetylation, deamination, alkylation, cysteine oxidation or tyrosine nitration. These modifications cause changes in the pI of the protein by adding, removing or changing titratable groups. Proteins differ widely in buffering capacity and pI and therefore the same PTMs may give rise to quite different patterns of pI shifts in different proteins. It is impossible by visual inspection of a pattern of spots on a gel to determine which modifications are most likely to be present. The patterns of PTM shifts for different proteins can be calculated and are often quite distinctive. The theoretical gel images produced by ProMoST can be compared to the experimental 2D gel results to implicate probable PTMs and focus efforts on more detailed study of modified proteins. ProMoST has been implemented as cgi script in Perl available on a WWW server at http://proteomics.mcw.edu/promost.

Phosphorylations of cyclin-dependent kinase 2 revisited using two-dimensional gel electrophoresis

To control the G1/S transition and the progression through the S phase, the activation of the cyclin-dependent kinase (CDK) 2 involves the binding of cyclin E then cyclin A, the activating Thr-160 phosphorylation within the T-loop by CDK-activating kinase (CAK), inhibitory phosphorylations within the ATP binding region at Tyr-15 and Thr-14, dephosphorylation of these sites by cdc25A, and release from Cip/Kip family (p27kip1 and p21cip1) CDK inhibitors. To re-assess the precise relationship between the different phosphorylations of CDK2, and the influence of cyclins and CDK inhibitors upon them, we introduce here the use of the high resolution power of two-dimensional gel electrophoresis, combined to Tyr-15- or Thr-160-phosphospecific antibodies. The relative proportions of the potentially active forms of CDK2 (phosphorylated at Thr-160 but not Tyr-15) and inactive forms (non-phosphorylated, phosphorylated only at Tyr-15, or at both Tyr-15 and Thr-160), and their respective association with cyclin E, cyclin A, p21, and p27, were demonstrated during the mitogenic stimulation of normal human fibroblasts. Novel observations modify the current model of the sequential CDK2 activation process: (i) Tyr-15 phosphorylation induced by serum was not restricted to cyclin-bound CDK2; (ii) Thr-160 phosphorylation engaged the entirety of Tyr-15-phosphorylated CDK2 associated not only with a cyclin but also with p27 and p21, suggesting that Cip/Kip proteins do not prevent CDK2 activity by impairing its phosphorylation by CAK; (iii) the potentially active CDK2 phosphorylated at Thr-160 but not Tyr-15 represented a tiny fraction of total CDK2 and a minor fraction of cyclin A-bound CDK2, underscoring the rate-limiting role of Tyr-15 dephosphorylation by cdc25A.

A proteomic study reveals novel insights into the diversity of aquaporin forms expressed in the plasma membrane of plant roots

Aquaporins are channel proteins that facilitate the diffusion of water across cell membranes. The genome of Arabidopsis thaliana encodes 35 full-length aquaporin homologues. Thirteen of them belong to the plasma membrane intrinsic protein (PIP) subfamily and predominantly sit at the plasma membrane (PM). In the present work we combine separations of membrane proteins (by one- and two-dimensional gel electrophoresis) with identification by MS (matrix-assisted laser-desorption ionization-time-of-flight and electrospray-ionization tandem MS) to take an inventory of aquaporin isoforms expressed in the PM of Arabidopsis thaliana roots. Our analysis provides direct evidence for the expression of five PIPs (PIP1;1, PIP1;5, PIP2;1, PIP2;2 and PIP2;7) in the root PM and suggests the presence of at least three other PIP isoforms. In addition, we show that the same PIP isoform can be present under several forms with distinct isoelectric points. More specifically, we identify phosphorylated aquaporins in the PIP1 and PIP2 subgroups and suggest the existence of other post-translational modifications. Their identification should provide clues to reveal novel molecular mechanisms for aquaporin regulation.

Composition and properties of the soluble organic matrix of the otolith of a marine fish: Gadus morhua Linne, 1758 (Teleostei, Gadidae)

The soluble matrix of the sagittal otolith of the cod Gadus morhua was analyzed using UV and IR spectroscopy, liquid chromatography and electrophoresis. This matrix is a complex mixture of proteins and glycoproteins, with a large range of molecular weights. High weights (>1000 kDa) are shown for the first time in water-soluble matrix of otolith. However, the 2D denaturing electrophoresis and large range of sorting used in high performance liquid chromatography columns do not separate the soluble matrix to well-defined molecular weights. The IR data indicate that several conformations are present and the main part of the sugars is not sulfated. Additionally, electrophoresis data show that the acidity of the sugar components is higher than that of the proteins. Despite the relative scarcity of literature data, our study of G. morhua suggests that the chemical composition of otolith soluble organic matrix may differ among species.

Semi-empirical relationships between effective mobility, charge, and molecular weight of pharmaceuticals by pressure-assisted capillary electrophoresis: applications in drug discovery

Relationships between effective mobility (m(eff)), calculated charge (Z(c)), and molecular weight (MW) are semi-empirically derived for pharmaceuticals using pressure-assisted capillary electrophoresis (PACE). We determined the m(eff) at 12 different pH points (2.0-11.4) of 66 pharmaceutical-like compounds ranging in MW from 79 to 825 g/mol. Plots of the observed m(eff) values versus Z(c)/MW(x ) (where x is a fractional coefficient) gave linear relationships. For anions, it was found that the best correlation (R(2) = 0.9666) exists when the fractional coefficient is equal to 0.4920, resulting in the equation m(eff) = 0.1853 (Z(c)/MW (0.4920)). For cations, the best linear relationship (R(2) = 0.9861) gave the equation m(eff) = 0.3888 (Z(c)/MW (0.6330)). The m(eff), Z(c)/MW(x) relationships were then applied to: (i) developing a technique for selecting an appropriate pH to achieve optimal separation of pharmaceuticals and (ii) determining the maximum charge of a molecule in the pH range of determination of negative log of the dissociation constants (pK(a)) by PACE, thus enabling the correct choice of model equation to be automated without structure analysis.

Liquid chromatography-mass spectrometry and capillary electrophoresis combined approach for separation and characterization of multicomponent peptide mixtures. Application to crude products of leuprolide synthesis

A sequential combination of reversed-phase liquid chromatography-mass spectrometry (LC-MS) and capillary electrophoresis (CE) has been explored in order to perform separation and characterization of a multicomponent peptide mixture from the synthesis of leuprolide. The mixture was first analyzed and fractionated by LC-MS, and the collected fractions were subsequently separated by CE. Unambiguous identification of the electrophoretic peaks was achieved by injecting the collected fractions separately and spiking the leuprolide crude mixture. Furthermore, structural information about the components of the mixture provided by several semi-empirical migration models has been used to check the accuracy of the structures previously proposed by LC-MS. Combination of the two orthogonal techniques results in an enhancement of their individual selectivity characteristics.

The effect of net charge on the solubility, activity, and stability of ribonuclease Sa

The net charge and isoelectric pH (pI) of a protein depend on the content of ionizable groups and their pK values. Ribonuclease Sa (RNase Sa) is an acidic protein with a pI = 3.5 that contains no Lys residues. By replacing Asp and Glu residues on the surface of RNase Sa with Lys residues, we have created a 3K variant (D1K, D17K, E41K) with a pI = 6.4 and a 5K variant (3K + D25K, E74K) with a pI = 10.2. We show that pI values estimated using pK values based on model compound data can be in error by >1 pH unit, and suggest how the estimation can be improved. For RNase Sa and the 3K and 5K variants, the solubility, activity, and stability have been measured as a function of pH. We find that the pH of minimum solubility varies with the pI of the protein, but that the pH of maximum activity and the pH of maximum stability do not.

Whole Proteome pI Values Correlate with Subcellular Localizations of Proteins for Organisms within the Three Domains of Life

Isoelectric point (pI) values have long been a standard measure for distinguishing between proteins. This article analyzes distributions of pI values estimated computationally for all predicted ORFs in a selection of fully sequenced genomes. Histograms of pI values confirm the bimodality that has been observed previously for bacterial and archaeal genomes (Van Bogelen et al. 1999) and reveal a trimodality in eukaryotic genomes. A similar analysis on subsets of a nonredundant protein sequence database generated from the full database by selecting on subcellular localization shows that sequences annotated as corresponding to cytosolic and integral membrane proteins have pI distributions that appear to correspond with the two observed modes of bacteria and archaea. Furthermore, nuclear proteins have a broader distribution that may account for the third mode observed in eukaryotes. On the basis of this association between pI and subcellular localization, we conclude that the bimodal character of whole proteome pI values in bacteria and archaea and the trimodal character in eukaryotes are likely to be general properties of proteomes and are associated with the need for different pI values depending on subcellular localization. Our analyses also suggest that the proportions of proteomes consisting of membrane-associated proteins may be currently underestimated.

Soluble FasR ligand-binding domain: high-yield production of active fusion and non-fusion recombinant proteins using the baculovirus/insect cell system

We used the recombinant baculovirus/insect cell system to express two soluble forms of the mouse Fas receptor (mFasR) extracellular domain (ECD): a monomer comprising the entire ligand-binding portion of mFasR followed by a carboxy-terminal hexa-histidine extension aiding purification by immobilized metal affinity chromatography and an immunoadhesin in which the same 148 residues were fused to the Fc portion of a truncated human IgG1 immunoglobulin heavy chain. Both constructs harboured a 24 base pairs insertion placed upstream of the initiating ATG [Peakman, Charles, Sydenham, Gewert, Page, and Makoff (1992) Nucleic Acids Res. 20, 6111-6112]. Despite its hexa-histidine extension, the monovalent recombinant protein from crude culture media failed to bind immobilized Ni2+ unless proteins were first precipitated twice by ammonium sulphate. The overall procedure then yielded approximately 10mg/l of protein which could be purified to near homogeneity using two additional chromatographic steps. The glycosylated polypeptide migrated as a band of Mr=(21-31) x 10(3) in SDS/PAGE and was monomeric in physiological buffers. Under non-reducing conditions, denaturation in 6 M guanidinium chloride was reversible after slow removal of the denaturing agent. The mFasR immunoadhesin was secreted (approximately 5-10 mg/l) as a disulphide-linked homodimer, and endowed with ligand-binding activity since it could bind FasL on the surface of D11S, FasL-expressing cells. When tested for their ability to inhibit FasR-dependent cell lysis, the soluble dimeric immunoadhesin markedly inhibited FasL-mediated cytotoxicity (IC50 approximately 30 nM), and was approximately 6 times as effective as its monomeric counterpart.

Behavior of peptides in capillary electrophoresis: effect of peptide charge, mass and structure

In the last decade the large potential of capillary electrophoresis as a technique for separation and characterization of peptides has been demonstrated extensively. In this field, a large number of chemical structures has to be taken into consideration, for which very often no data or even standards are available. As a result, there has been a strong desire to relate electrophoretic behavior to molecular properties and structure of the compounds. The activities in that direction, in the area of capillary zone electrophoresis, are critically reviewed. Special attention is paid to peptide charge, mass, hydrophobicity and structure, and their influence on the selectivity of the separation. Also, some complexation phenomena are discussed.

Rules relating electrophoretic mobility, charge and molecular size of peptides and proteins

The absence of supporting media in free solution high-performance capillary electrophoresis (HPCE) makes it an ideal system for the study of the relationship between electrophoretic mobility (mu(em)) and the molecular size and charge of proteins and peptides. In this review, the theory of electrophoresis, developed for rigid, insulating, spherical particles, is modified to develop models for the electrophoretic behaviour of proteins and peptides. For a given set of experimental conditions, mu(em) of a protein/peptide is proportional to its charge (q) and is inversely proportional to its Stoke's radius (r). Furthermore, mu(em) is most sensitive to changes in q and, as a consequence, the reliability of equations relating mu(em) to protein/peptide q and r is dependent upon the accurate calculation or determination of q. For convenience, q and r of proteins and peptides are generally expressed in terms of calculated valence (Zc) and molecular mass (M), respectively, both of which can be determined from the amino acid sequence of the protein/peptide. However, the calculation of q using Zc is made more complex by the effects of electrostatic charge suppression, such that Zc is an overestimation of actual charge. Charge suppression becomes increasingly significant as the protein/peptide charge increases, such that, for peptides, the relationship between q and Zc can be approximated by a logarithmic function. The mu(em) for peptides, therefore, can be approximated by the equation: mu(em) = ln(Zc + 1)/K Ms where s varies between 1/3 and 2/3, and K is a constant that is valid for a particular set of experimental conditions. The rather simplistic compensation for charge suppression in this equation is inadequate for proteins where the magnitude of charge suppression is greater and the mechanisms are more complex. For proteins, the relationship suggested for the prediction of mu(em) from Zc and M is: mu(em) = Zc/KFzMs where s again varies between 1/3 and 2/3 and Fz is a pH-independent proportionality factor defined as the quotient, Zc/Za, with Za being actual protein valence. The factor Fz can be determined empirically, however, it is valid only for the particular set of experimental conditions under which it is determined. For peptides, the mass exponent, s, approaches 1/3 when the peptides have high charge densities and open structures. However, s approaches 1/2 for peptides with lower charge densities that are capable of more randomized motion during electrophoresis. Finally, s approaches 2/3 for proteins, suggesting that the frictional forces acting on a protein undergoing electrophoretic motion are proportional to the surface area of these larger, more rigid, structures. In conclusion, the development of relationships between mu(em), M and Zc for peptides and proteins offers a powerful tool, not only for predicting electrophoretic mobility, but also for optimising HPCE separations, studying structural modifications (e.g. phosphorylation, glycosylation, deamidation, etc.), and for the investigation of surface charge characteristics and conformation.

Isoelectric properties of the soluble matrices in relation to the chemical composition of some Scleractinian skeletons

Soluble matrices of four Scleractinian skeletons (Madrepora, Favia, Leptastrea and Fungia), were extracted and studied by isoelectric focusing (IEF). The main part of the extracted matrices is acidic. IEF gels are poorly stained or unstained by Coomassie Blue and silver. The positive Alcian Blue staining is indicative of a sulfated and acidic nature of the glycoproteins. Chemical analysis shows high S contents in Scleractinian skeletons. These results are supported by the comparison with IEF and chemical contents of Molluscan shells.

Recombinant hirustasin: production in yeast, crystallization, and interaction with serine proteases

A synthetic gene coding for the 55-amino acid protein hirustasin, a novel tissue kallikrein inhibitor from the leech Hirudo medicinalis, was generated by polymerase chain reaction using overlapping oligonucleotides, fused to the yeast alpha-factor leader sequence and expressed in Saccharomyces cerevisiae. Recombinant hirustasin was secreted mainly as incompletely processed fusion protein, but could be processed in vitro using a soluble variant of the yeast yscF protease. The processed hirustasin was purified to better than 97% purity. N-terminal sequence analysis and electrospray ionization mass spectrometry confirmed a correctly processed N-terminus and the expected amino acid sequence and molecular mass. The biological activity of recombinant hirustasin was identical to that of the authentic leech protein. Crystallized hirustasin alone and in complex with tissue kallikrein diffracted beyond 1.4 A and 2.4 A, respectively. In order to define the reactive site of the inhibitor, the interaction of hirustasin with kallikrein, chymotrypsin, and trypsin was investigated by monitoring complex formation in solution as well as proteolytic cleavage of the inhibitor. During incubation with high, nearly equimolar concentration of tissue kallikrein, hirustasin was cleaved mainly at the peptide bond between Arg 30 and Ile 31, the putative reactive site, to yield a modified inhibitor. In the corresponding complex with chymotrypsin, mainly uncleaved hirustasin was found and cleaved hirustasin species accumulated only slowly. Incubation with trypsin led to several proteolytic cleavages in hirustasin with the primary scissile peptide bond located between Arg 30 and Ile 31. Hirustasin appears to fall into the class of protease inhibitors displaying temporary inhibition.

Purification, characterization and biological evaluation of recombinant leech-derived tryptase inhibitor (rLDTI) expressed at high level in the yeast Saccharomyces cerevisiae

An efficient expression/purification procedure has been developed which allows the production of pure, biologically active recombinant leech-derived tryptase inhibitor (rLDTI), originally found in the leech Hirudo medicinalis. The gene for LDTI was generated synthetically from three overlapping oligonucleotides by PCR synthesis. LDTI was expressed in the yeast Saccharomyces cerevisiae under the control of the copper-inducible CUP1 promoter and fused to the invertase signal sequence (SUC2). The entire expression cassette was inserted into the yeast high-copy vector pDP34. Appropriate host strains transformed with the expression plasmid secreted rLDTI into the medium upon copper addition. Proteinchemical analysis of the secreted rLDTI revealed exclusively inhibitor with the correct N-terminal sequence. Up to 60% of the rLDTI, however, appeared to be modified by glycosylation and the unglycosylated material showed heterogeneity at the C-terminus. Besides full-length rLDTI, truncated rLDTI species lacking either the terminal Asn46 or in addition the penultimate Leu45 were isolated. The C-terminally truncated variants were eliminated using a S. cerevisiae host strain disrupted in the structural genes of carboxypeptidases yscY and ysca, thus identifying these proteases as being responsible for the degradation of rLDTI. Mature rLDTI was purified in high yields from the culture supernatant of the carboxypeptidase-deficient yeast strain by cation-exchange chromatography and reverse-phase HPLC. The recombinant protein is at least 98% pure, based on HPLC and capillary electrophoresis, and is fully biologically active. Structural identity with the authentic leech protein was confirmed by sequence analysis and molecular-mass determination. The purified protein was tested for its ability to inhibit tryptase and trypsin in vitro and to interfere with the tryptase-induced proliferation of human fibroblasts and keratinocytes. Recombinant LDTI appears to be as potent as the authentic leech protein, exhibiting Ki-values of approximately 1.5 nM and approximately 1.6 nM against human tryptase and bovine trypsin, respectively. The tryptase-induced proliferation of human fibroblasts and keratinocytes was inhibited with half-maximum values of approximately 0.1 nM and approximately 1 nM, respectively. The availability of the recombinant material will allow evaluation of the concept of tryptase inhibition in various disease models and to test the therapeutic potential of LDTI in mast-cell-related disorders.

Identification of different galectins by immunoblotting after two-dimensional polyacrylamide get electrophoresis with immobilized pH gradients

Vertebrate soluble beta-galactoside-binding lectins form a growing protein family that recently have been named galectins. Seven different galectins have been sequenced and characterized in mammals, and there is compelling evidence for the existence of other members of this lectin family. Three among six galectins are homodimers with (i) an identical subunit of a relative molecular mass of about 14500, and (ii) amino acid sequence homologies giving rise to possible immunochemical cross-reactivities. They are indistinguishable from each other by conventional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), even when followed by immunoblotting. However, their different isoelectric points allow their identification using isoelectric focusing and two-dimensional (2-D) polyacrylamide gel electrophoresis. A strategy was developed to identify these galectins in crude extracts from cells and tissues, based on the two-dimensional electrophoresis with immobilized pH gradient (IPG-Dalt) analysis of the specific spots of purified galectins and of the spots of crude extracts, after silver staining. In addition, 2-D immunoblotting using anti-galectin 1 (Gal-1) and anti carbohydrate-binding protein 15 (CPB15) antibodies were performed on brain and leukemia cells (HL60) allowing an identification of related polypeptides. Our results indicate that the use of IPG-Dalt provides a suitable reproducibility and allows the detection of galectins or other galactoside-binding proteins even at basic pIs.

Variation of the pH of the background electrolyte due to electrode reactions in capillary electrophoresis: theoretical approach and in situ measurement

Electrode reactions during the electrophoretic process may change the pH of the buffer and subsequently the migration behavior of solutes with resultant loss of reproducibility. A theoretical treatment of pH variations due to electrolytic processes is presented. The choice of buffer appears to have a dramatic influence on the pH variations observed, even if substantial buffer action is expected at the pH chosen. The experimental evaluation of the separation of 4-hydroxy-3-methoxycinnamic acid and 3-hydroxybenzoic acid reveals that the quality of the separation decreases continuously from a baseline separation observed in the first experiment to a comigration of the two solutes (resolution = 0) in the ninth experiment. A pH decrease of about 0.05 pH units accounts for the observed changes in mobility. A novel in situ pH measurement approach is presented, in which the mobility, peak area, and peak height of an indicator dye are related to the pH in the capillary. This enables the identification and quantitation of pH variations during electrophoretic runs: the pH decreases at the anodic side already after the first experiment and pH variations as small as 0.02 pH units can be measured. The variations in peak height appear to be less suited. The calculated pH variations are in close agreement with the ones obtained experimentally.

Influence of matrix solution conditions on the MALDI-MS analysis of peptides and proteins

Sample-matrix preparation procedures are shown to greatly influence the quality of the matrix-assisted laser desorption/ionization (MALDI) mass spectra of peptides and proteins. In particular, dramatic mass discrimination effects are observed when the matrix 4-hydroxy-alpha-cyanocinnamic acid is used for analyzing complex mixtures of peptides and proteins. The discrimination effects are found to be strongly dependent on the sample-matrix solution composition, pH, and the rates at which the sample-matrix cocrystals are grown. These findings demonstrate the need to exercise great care in performing and interpreting the MALDI analysis of biological samples. The results also indicate that there is a reverse-phase chromatographic-like dimension in the sample-matrix preparation procedures that can be exploited to optimize the analysis. The present work describes the conditions under which the majority of components of a complex mixture of peptides and proteins can be successfully measured.

Calculation of the isoelectric points of native proteins with spreading of pKa values

The isoelectric points (pI) of native proteins are important in several separation techniques. For estimating pI values the net charge of several proteins was calculated versus pH by use of the Henderson-Hasselbalch equation. Amino acid composition, pKa values for amino acid side chains and for the N- and C-terminal groups, and the presence of other charged groups were taken into account. A set of pKa values was chosen for amino acid residues with ionizable side chains. Each particular type of ionizable group was assumed to have pKa values distributed around the chosen value, thereby simulating the situation in proteins and polypeptides. The calculated pI values showed reasonably good agreement with experimental ones for most of 16 native proteins over a wide pH range (3.4-11) when charge contributions of heme groups, sialic acid residues, etc., were taken into account. The calculated pI for the human red cell glucose transporter (Glut1) with one sialic acid residue was decreased from 8.8 to 8.5 by introducing pKa value spreading and became consistent with the experimental pI value of 8.4 +/- 0.05 at 15 degrees C determined in the presence of 6 M urea. The pI of the native Glut1 was lower, 8.0 +/- 0.1, at 22 degrees C. In general, the pI values for native proteins are affected by the three-dimensional structure of the proteins, which causes greater differences between calculated and experimental pI values than in the case of polypeptides for which pI values are determined in the presence of urea.

Purification and partial characterization of a Schizolobium parahyba chymotrypsin inhibitor

Schizolobium parahyba seed chymotrypsin inhibitor (SPC) is a protein with M(r) of 20,000 and four half-cystine residues and no free thiol group. SPC is stable at temperatures up to 75 degrees at pH 7 but gradually loses activity when kept at 95 degrees for 1 hr and total inactivation occurs after 5 hr. Amino acid analysis shows a high content of glycine, aspartate, glutamate and alanine residues. A pI of 4.52 predicted from the amino acid content agrees with experimental results. A stable binary complex with M(r) of 45,000, Ki = 5.85 x 10(-8) M and molar ratio of 1:1 is formed between SPC and chymotrypsin. The determined single N-terminal sequence of SPC shows homology with Kunitz type soybean trypsin inhibitors.

Peptides as standards for denaturing isoelectric focusing

A set of commercially available peptides suitable for use as standards in denaturing isoelectric focusing (IEF) is described. The peptides N-procalcitonin fragment 1-57 (pI 3.98), Gln11-amyloid beta-protein fragment 1-28 (pI 5.76), gastric inhibitory polypeptide (pI 7.14), parathyroid hormone fragment 1-34 (pI 8.64) and human beta-endorphin (pI 9.49) can be focused to their isoelectric point in the presence of 8 M urea and 2% Nonidet P-40, and subsequently fixed and stained in polyacrylamide gels. The peptides give a linear standard curve in close agreement with a slope determined with a surface pH electrode. Under the same conditions some proteins focus to positions significantly at odds with their theoretical isoelectric point. The origins of these discrepancies and the implications for the determination of isoelectric points of unknown proteins by denaturing IEF are discussed.

Simulation and optimization of peptide separation by capillary electrophoresis

The different mobility equations that have appeared in the literature for predicting peptide mobility were compared. A modified equation that relates the mobility of individual proteolytic species of a peptide to its composition has been obtained: mu = 1758 log(1 + 0.297q)/M0.411, where mu is the electrophoretic mobility in 10(-9) m2/s.V, q is the integral value of the charge of the species and M its molecular mass. Also, a rough estimation of the set of pKa values for a peptide was developed. The usefulness of this equation together with a computer program for predicting separations of compounds by capillary zone electrophoresis is demonstrated, employing real electropherograms of peptides from the literature or from experiments.

Chemical characterization of a novel peptide from the neuroendocrine light yellow cells of Lymnaea stagnalis

The neuroendocrine light yellow cells of Lymnaea stagnalis form two clusters of cells in the visceral and right parietal ganglion, respectively. These cells are endogenously bursting neurons whose activities are modified during egg-laying and feeding. Using gel permeation chromatography and reverse phase HPLC we have purified two highly related novel peptides from the light yellow cells. These peptides differ only in length, due to truncation of the amino-terminal aspartic acid residue, which causes a major shift in the charge of the molecule. We conclude that the longer peptide is the immediate precursor of the shorter form. Using whole mount immunocytochemistry, it was confirmed that the light yellow cells produce these peptides.