Comparison of biophysical and biologic properties of alpha-helical enantiomeric antimicrobial peptides

In our previous study (Chen et al. J Biol Chem 2005, 280:12316-12329), we utilized an alpha-helical antimicrobial peptide V(681) as the framework to study the effects of peptide hydrophobicity, amphipathicity, and helicity on biologic activities where we obtained several V(681) analogs with dramatic improvement in peptide therapeutic indices against gram-negative and gram-positive bacteria. In the present study, the D-enantiomers of three peptides--V(681), V13A(D) and V13K(L) were synthesized to compare biophysical and biologic properties with their enantiomeric isomers. Each D-enantiomer was shown by circular dichroism spectroscopy to be a mirror image of the corresponding L-isomer in benign conditions and in the presence of 50% trifluoroethanol. L- and D-enantiomers exhibited equivalent antimicrobial activities against a diverse group of Pseudomonas aeruginosa clinical isolates, various gram-negative and gram-positive bacteria and a fungus. In addition, L- and D-enantiomeric peptides were equally active in their ability to lyse human red blood cells. The similar activity of L- and D-enantiomeric peptides on prokaryotic or eukaryotic cell membranes suggests that there are no chiral receptors and the cell membrane is the sole target for these peptides. Peptide D-V13K(D) showed significant improvements in the therapeutic indices compared with the parent peptide V(681) by 53-fold against P. aeruginosa strains, 80-fold against gram-negative bacteria, 69-fold against gram-positive bacteria, and 33-fold against Candida albicans. The excellent stability of D-enantiomers to trypsin digestion (no proteolysis by trypsin) compared with the rapid breakdown of the L-enantiomers highlights the advantage of the D-enantiomers and their potential as clinical therapeutics.

Determination of intrinsic hydrophilicity/hydrophobicity of amino acid side chains in peptides in the absence of nearest-neighbor or conformational effects

Understanding the hydrophilicity/hydrophobicity of amino acid side chains in peptides/proteins is one the most important aspects of biology. Though many hydrophilicity/hydrophobicity scales have been generated, an "intrinsic" scale has yet to be achieved. "Intrinsic" implies the maximum possible hydrophilicity/hydrophobicity of side chains in the absence of nearest-neighbor or conformational effects that would decrease the full expression of the side-chain hydrophilicity/hydrophobicity when the side chain is in a polypeptide chain. Such a scale is the fundamental starting point for determining the parameters that affect side-chain hydrophobicity and for quantifying such effects in peptides and proteins. A 10-residue peptide sequence, Ac-X-G-A-K-G-A-G-V-G-L-amide, was designed to enable the determination of the intrinsic values, where position X was substituted by all 20 naturally occurring amino acids and norvaline, norleucine, and ornithine. The coefficients were determined by reversed-phase high-performance liquid chromatography using six different mobile phase conditions involving different pH values (2, 5, and 7), ion-pairing reagents, and the presence and absence of different salts. The results show that the intrinsic hydrophilicity/hydrophobicity of amino acid side chains in peptides (proteins) is independent of pH, buffer conditions, or whether C(8) or C(18) reversed-phase columns were used for 17 side chains (Gly, Ala, Cys, Pro, Val, nVal, Leu, nLeu, Ile, Met, Tyr, Phe, Trp, Ser, Thr, Asn, and Gln) and dependent on pH and buffer conditions, including the type of salt or ion-pairing reagent for potentially charged side chains (Orn, Lys, His, Arg, Asp, and Glu).

Ion-interaction-capillary zone electrophoresis of cationic proteomic peptide standards

We have employed a novel capillary electrophoresis (CE) approach recently developed in our laboratory, termed ion-interaction-capillary zone electrophoresis (II-CZE), to the resolution of a mixture of 27 synthetic cationic proteomic peptide standards. These peptides were comprised of three groups of nine peptides (with net charges of +1, +2 and +3 for all nine peptides within a group), the hydrophobicity of the nine peptides within a group varying only subtly between adjacent peptides. This bidimensional CE approach achieved excellent resolution of the peptides with high peak capacity by combining the powerful CZE mechanism located in the background electrolyte (BGE) with an hydrophobicity-based mechanism also located in the BGE, the latter consisting of high concentrations (up to 0.4M) of aqueous perfluorinated acids (trifluoroacetic acid, pentafluoropropionic acid and heptafluorobutyric acid). Thus, concomitant with a CZE separation of the three differently charged groups of peptides, there is an hydrophobically-mediated separation of the peptides within these groups effected through interaction of the hydrophobic anions of the perfluorinated acids with hydrophobic amino acid side-chains in the peptides. This methodology is dramatically different from other CE methods that have used complexing agents such as micelles or cyclodextrins in MEKC. Overall, the results presented here demonstrate the value of CE as a peptide separative tool in its own right, including its use for proteomic applications, and not merely as a complementary technique to reversed-phase high-performance liquid chromatography (RP-HPLC).

Optimum concentration of trifluoroacetic acid for reversed-phase liquid chromatography of peptides revisited

Trifluoroacetic acid (TFA) remains the dominant mobile phase additive for reversed-phase high-performance liquid chromatography (RP-HPLC) of peptides after more than two decades since its introduction to this field. Generally, TFA has been employed in a concentration range of 0.05-0.1% (6.5-13 mM) for the majority of peptide separations. In order to revisit the question as to whether such a concentration range is optimum for separations of peptide mixtures containing peptides of varying net positive charge, the present study examined the effect of varying TFA concentration on RP-HPLC at 25 and 70 degrees C of three groups of synthetic 10-residue synthetic peptides containing either one (+1) or multiple (+3, +5) positively charged groups. The results show that the traditional range of TFA concentrations employed for peptide studies is not optimum for many, perhaps the majority, of peptide applications. For efficient resolution of peptide mixtures, particularly those containing peptides with multiple positive charges, our results show that 0.2-0.25% TFA in the mobile phase will achieve optimum resolution. In addition, the use of high temperature as a complement to such TFA concentration levels is also effective in maximizing peptide resolution.

Rational design of alpha-helical antimicrobial peptides with enhanced activities and specificity/therapeutic index

In the present study, the 26-residue peptide sequence Ac-KWKSFLKTFKSAVKTVLHTALKAISS-amide (V681) was utilized as the framework to study the effects of peptide hydrophobicity/hydrophilicity, amphipathicity, and helicity (induced by single amino acid substitutions in the center of the polar and nonpolar faces of the amphipathic helix) on biological activities. The peptide analogs were also studied by temperature profiling in reversed-phase high performance liquid chromatography, from 5 to 80 degrees C, to evaluate the self-associating ability of the molecules in solution, another important parameter in understanding peptide antimicrobial and hemolytic activities. A higher ability to self-associate in solution was correlated with weaker antimicrobial activity and stronger hemolytic activity of the peptides. Biological studies showed that strong hemolytic activity of the peptides generally correlated with high hydrophobicity, high amphipathicity, and high helicity. In most cases, the D-amino acid substituted peptides possessed an enhanced average antimicrobial activity compared with L-diastereomers. The therapeutic index of V681 was improved 90- and 23-fold against Gram-negative and Gram-positive bacteria, respectively. By simply replacing the central hydrophobic or hydrophilic amino acid residue on the nonpolar or the polar face of these amphipathic derivatives of V681 with a series of selected D-/L-amino acids, we demonstrated that this method has excellent potential for the rational design of antimicrobial peptides with enhanced activities.

Monitoring the hydrophilicity/hydrophobicity of amino acid side-chains in the non-polar and polar faces of amphipathic alpha-helices by reversed-phase and hydrophilic interaction/cation-exchange chromatography

The ability to monitor precisely the hydrophobicity/hydrophilicity effects of amino acid substitutions in both the non-polar and polar faces of amphipathic alpha-helical peptides is critical in such areas as the rational de novo design of more effective antimicrobial peptides. The present study reports our initial results of employing the complementary separation modes of reversed-phase high-performance liquid chromatography (RP-HPLC) and hydrophilic interaction/cation-exchange chromatography (HILIC/CEX) to monitor the effect on apparent peptide hydrophilicity/hydrophobicity and amphipathicity of substituting single L- or D-amino acids into the centre of the non-polar or polar faces of a 26-residue biologically active amphipathic alpha-helical peptide, V681. Our results clearly show that RP-HPLC and HILIC/CEX are best suited for resolving amphipathic peptides where substitutions are made in the non-polar and polar faces, respectively. Further, RP-HPLC and HILIC/CEX were demonstrated to be excellent monitors of hydrophilicity/hydrophobicity variations where amino acid substitutions were made in these respective faces. We believe these complementary high-performance modes offer excellent potential for rational design of novel amphipathic alpha-helical biologically active peptides.

Capillary zone electrophoresis of α-helical diastereomeric peptide pairs with anionic ion-pairing reagents

The present study uses an unique capillary electrophoresis (CE) approach, that we have termed ion-interaction capillary zone electrophoresis (II-CZE), for the separation of diastereomeric peptide pairs where a single site in the centre of the non-polar face of an 18-residue amphipathic alpha-helical peptide is substituted by the 19 L- or D-amino acids. Through the addition of perfluorinated acids at very high concentrations (up to 400 mM), such concentration levels not having been used previously in chromatography or CE, to the background electrolyte (pH 2.0), we have been able to achieve baseline resolution of all 19 diastereomeric peptide pairs with an uncoated capillary. Since each diastereomeric peptide pair has the same sequence, identical mass-to-charge ratio and identical intrinsic hydrophobicity, such a separation by CZE has previously been considered theoretically impossible. Excellent resolution was achieved due to maximum advantage being taken of even subtle disruption of peptide structure/conformation (due to the presence of D-amino acids) of the non-polar face of the amphipathic alpha-helix and its interaction with the hydrophobic anionic ion-pairing reagents. In addition, due to the excellent resolution of diastereomeric peptide pairs by this novel CZE approach, we have also been able to separate a mixture of these closely-related alpha-helical peptides.

Selectivity differences in the separation of amphipathic α-helical peptides during reversed-phase liquid chromatography at pHs 2.0 and 7.0

In an ongoing effort to understand the effect of varying reversed-phase high-performance liquid chromatography (RP-HPLC) parameters on the retention behaviour of peptides, necessary for the rational development of separation/optimization protocols, we believe it is important to delineate the contribution of alpha-helical structure to the selectivity of peptide separations. The present study reports the effects of varying column packing, mobile phase conditions and temperature on RP-HPLC retention behaviour at pHs 2.0 and 7.0 of peptides based on the amphipathic peptide sequence Ac-EAEKAAKEXEKAAKEAEK-amide (with position X in the centre of the hydrophobic face of the alpha-helix), where position X is substituted by L- or D-amino acids. At pH 2.0, an increase in trifluoroacetic acid concentration or the addition of sodium perchlorate to a phosphoric acid-based mobile phase had the similar effect of improving peak shape as well as increasing peptide retention time due to ion-pairing effects with the positively-charged peptides; in contrast, at pH 7.0, the addition of salt had little effect save an improvement in peak shape. Temperature was shown to have a complex influence on peptide selectivity due to varying effects on peptide conformation. In addition, subtle effects on peptide selectivity were also noted based on the column packings employed at pHs 2.0 and 7.0.

Capillary electrophoresis of cationic random coil peptide standards: Effect of anionic ion-pairing reagents and comparison with reversed-phase chromatography

The present study compares a charge/hydrophobicity capillary electrophoresis (CE) approach to reversed-phase high-performance liquid chromatography (RP-HPLC) for the separation of three series of four synthetic, random coil peptide standards. Each series has peptides of the same positive charge (+1, +2 and +3 series) and length but differing in hydrophobicity. Complete resolution of the 12 peptides was achieved via a novel CE approach: a capillary zone electrophoresis (CZE) mode effected a separation of identically charged peptides; within each charged group of peptides, the addition of perfluorinated acid anionic ion-pairing reagents allowed resolution of the peptides through a mechanism based on peptide hydrophobicity which we have termed ioninteraction (II)-CZE. The peak capacity and peptide resolution of this CE approach was superior to that of RP-HPLC and stresses an important role for CE for peptide/proteomic applications.

Temperature profiling of polypeptides in reversed-phase liquid chromatography. II. Monitoring of folding and stability of two-stranded alpha-helical coiled-coils

The present study extends the utility of reversed-phase high-performance liquid chromatography (RP-HPLC) to monitor folding and stability of de novo designed synthetic two-stranded alpha-helical coiled-coils. Thus, we have compared the effect of temperature on the RP-HPLC retention behaviour of both oxidized (two identical five-heptad alpha-helical peptides linked by a disulfide bridge) and reduced coiled-coil analogues with various amino acids substituted into the hydrophobic core of the coiled-coil. We were able to correlate the RP-HPLC retention behaviour of the oxidized analogues over the temperature range of 10 to 80 degrees C with the stability of the analogues as determined by conventional thermal and chemical denaturation approaches. In addition, the contribution of a disulfide bridge to coiled-coil stability was highlighted by comparing the elution behaviour of the oxidized and reduced analogues. Overall, we demonstrate the excellent potential of "temperature profiling" by RP-HPLC to monitor differences in oligomerization state and protein stability.

Capillary electrophoresis of amphipathicα-helical peptide diastereomers

We have made a rigorous assessment of the ability of capillary electrophoresis to resolve peptide diastereomers through its application to the separation of a series of synthetic 18-residue, amphipathic alpha-helical monomeric peptide analogues, where a single site in the centre of the hydrophobic face of the alpha-helix is substituted by 19 L- or D-amino acids. Such L- and D-peptide pairs have the same mass-to-charge ratio, amino acid sequence and intrinsic hydrophobicity, varying only in the stereochemistry of one residue. CE approaches assessed in their ability to separate diastereomeric peptide pairs included capillary zone electrophoresis (uncoated capillary), micellar electrokinetic chromatography (uncoated capillary in the presence of 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate, CHAPS), open-tubular capillary electrochromatography (C(8)-coated capillary in the presence of 25% 2,2,2-trifluoroethanol (TFE) or 25% ethanol). Overall, the OT-CEC methods were the most effective at separating the most peptide pairs, particularly for those containing hydrophilic side chains. However, the MEKC approach proved most effective for separation of peptide pairs containing hydrophobic or aromatic side chains.

Capillary electrophoresis of synthetic peptide standards varying in charge and hydrophobicity

A mixture of eight structurally closely related synthetic peptides as capillary electrophoretic (CE) standards is introduced. The almost identical mass-to-charge ratio of the standards, coupled with their random-coil (i.e., no secondary structure) nature, offer a potent analytical test for CE to separate peptides varying only subtly in hydrophobicity. Parameters varied to effect a separation included background electrolyte concentration, temperature, applied voltage in capillary zone electrophoresis (CZE in uncoated capillaries), as well as the introduction of hydrophobic mechanisms to the separation either through the use of micelles or C8-coated capillaries. Our step-by-step approach culminated in an optimized combination of a CZE mechanism for separation of differently charged peptide groups (based on common mass-to-charge ratio) and an ion-pairing mechanism (effecting a separation within each group of identically charged peptides), which we have termed ion-interaction CZE or II-CZE. The study clearly shows how the peptide standards allow an excellent assessment of the resolving power of CE.

Comparison of reversed-phase liquid chromatography and hydrophilic interaction/cation-exchange chromatography for the separation of amphipathic α-helical peptides with l- and d-amino acid substitutions in the hydrophilic face

Mixed-mode hydrophilic interaction/cation-exchange chromatography (HILIC/CEX) is a novel high-performance technique which has excellent potential for peptide separations. Separations by HILIX/CEX are carried out by subjecting peptides to linear increasing salt gradients in the presence of high levels of acetonitrile, which promotes hydrophilic interactions overlaid on ionic interactions with the cation-exchange matrix. In the present study, HILIC/CEX has been compared to reversed-phase liquid chromatography (RP-HPLC) for separation of mixtures of diastereomeric amphipathic alpha-helical peptide analogues, where L- and D-amino acid substitutions were made in the centre of the hydrophilic face of the amphipathic alpha-helix. Unlike RP-HPLC, temperature had a substantial effect on HILIC/CEX of the peptides, with a rise in temperature from 25 to 65 degrees C increasing the retention times of the peptides as well as improving resolution. Our results again highlight the potential of HILIC/CEX as a peptide separation mode in its own right as well as an excellent complement to RP-HPLC.

Temperature selectivity effects in reversed-phase liquid chromatography due to conformation differences between helical and non-helical peptides

In order to characterize the effect of temperature on the retention behaviour and selectivity of separation of polypeptides and proteins in reversed-phase high-performance liquid chromatography (RP-HPLC), the chromatographic properties of four series of peptides, with different peptide conformations, have been studied as a function of temperature (5-80 degrees C). The secondary structure of model peptides was based on either the amphipathic alpha-helical peptide sequence Ac-EAEKAAKEX(D/L)EKAAKEAEK-amide, (position X being in the centre of the hydrophobic face of the alpha-helix), or the random coil peptide sequence Ac-X(D/L)LGAKGAGVG-amide, where position X is substituted by the 19 L- or D-amino acids and glycine. We have shown that the helical peptide analogues exhibited a greater effect of varying temperature on elution behaviour compared to the random coil peptide analogues, due to the unfolding of alpha-helical structure with the increase of temperature during RP-HPLC. In addition, temperature generally produced different effects on the separations of peptides with different L- or D-amino acid substitutions within the groups of helical or non-helical peptides. The results demonstrate that variations in temperature can be used to effect significant changes in selectivity among the peptide analogues despite their very high degree of sequence homology. Our results also suggest that a temperature-based approach to RP-HPLC can be used to distinguish varying amino acid substitutions at the same site of the peptide sequence. We believe that the peptide mixtures presented here provide a good model for studying temperature effects on selectivity due to conformational differences of peptides, both for the rational development of peptide separation optimization protocols and a probe to distinguish between peptide conformations.

Temperature profiling of polypeptides in reversed-phase liquid chromatography

The present study sets out to extend the utility of reversed-phase liquid chromatography (RP-HPLC) by demonstrating its ability to monitor dimerization and unfolding of de novo designed synthetic amphipathic alpha-helical peptides on stationary phases of varying hydrophobicity. Thus, we have compared the effect of temperature (5-80 degrees C) on the RP-HPLC (C8 or cyano columns) elution behaviour of mixtures of peptides encompassing amphipathic alpha-helical structure, amphipathic alpha-helical structure with L- or D-substitutions or non-amphipathic alpha-helical structure. By comparing the retention behaviour of the helical peptides to a peptide of negligible secondary structure (a random coil), we rationalize that "temperature profiling" by RP-HPLC can monitor association of peptide molecules, either through oligomerization or aggregation, or monitor unfolding of alpha-helical peptides with increasing temperature. We believe that the conformation-dependent response of peptides to RP-HPLC under changing temperature has implications both for general analysis and purification of peptides but also for the de novo design of peptides and proteins.

A novel method to measure self-association of small amphipathic molecules: temperature profiling in reversed-phase chromatography

Biophysical techniques such as size-exclusion chromatography, sedimentation equilibrium analytical ultracentrifugation, and non-denaturing gel electrophoresis are the classical methods for determining the self-association of molecules into dimers, trimers, or other higher order species. However, these techniques usually require high (mg/ml) loading concentrations to detect self-association and also possess a lower size limit that is dependent on the ability of the technique to resolve monomeric from higher order species. Here we describe a novel, sensitive method with no upper or lower molecular size limits that indicates self-association of molecules driven together by the hydrophobic effect under aqueous conditions. "Temperature profiling in reversed-phase chromatography" analyzes the retention behavior of a sample over the temperature range of 5-80 degrees C during gradient elution reversed-phase high-performance liquid chromatography. Because this technique greatly increases the effective concentration of analyte upon adsorption to the column, it is extremely sensitive, requiring very small sample quantities (microgram or less). In contrast, the classical techniques mentioned above decrease the effective analyte concentration during analysis, decreasing sensitivity by requiring larger amounts of analyte to detect molecular self-association. We demonstrate the utility of this technique with 14-residue cyclic and linear cationic peptides (<2000 Da) based on the sequence of the de novo-designed cytolytic peptide, GS14. The only requirements for the analyte molecule when using this technique are its ability to be retained on the reversed-phase column and to be subsequently removed from the column during gradient elution.

Reversed-phase liquid chromatography as a tool in the determination of the hydrophilicity/hydrophobicity of amino acid side-chains at a ligand-receptor interface in the presence of different aqueous environments. II. Effect of varying peptide ligand hydrophobicity

The present study represents a continuation of our development of a chromatographic model for studying the hydrophobic interactions which characterize the way a ligand binds to its receptor. We have designed 18-residue amphipathic alpha-helical peptides (representing the hydrophobic binding domain of a ligand), where the non-polar face interacts with the non-polar face of a reversed-phase stationary phase (representing a receptor protein with a hydrophobic binding pocket). Two series of amphipathic alpha-helical peptides were subjected to reversed-phase liquid chromatography at pH 2.0, where the "native" Ala-face peptide contains seven Ala residues in its non-polar face and the "native" Leu-face series contains seven Leu residues in its non-polar face. Mutants of the two series were then prepared by replacing one residue in the centre of the non-polar face in both series of peptides, resulting in amino acid side-chains being exposed to a moderately non-polar environment (Ala series) or a very hydrophobic environment (Leu series) surrounding the substitution site. With this model, we have demonstrated that an increase in non-polarity of the ligand enhances hydrophilicity (decreases hydrophobicity) of all amino acids at the ligand-receptor interface, this effect being dependent on the intrinsic hydrophilicity/hydrophobicity of the side-chain. The addition of salt to the aqueous environment surrounding the binding site of the ligand and receptor was also shown to affect the hydrophilicity/hydrophobicity of amino acids in the binding interface. For the Ala-face mutants, the majority of the non-polar side-chains and the three positively charged residues (Arg, His, Lys) showed significant enhancement of hydrophobicity in the presence of salt; in contrast, in the much more hydrophobic environment of the Leu-face mutants, there was a trend of lesser hydrophobicity enhancement and/or significantly more hydrophilicity enhancement in the presence of salt. Our results should have major implications for the understanding of the hydrophilicity/ hydrophobicity of side-chains in varying hydrophobic and aqueous environments.

Preparative reversed-phase liquid chromatography of proteins from rabbit skeletal troponin, a multi-protein complex

A reversed-phase high-performance liquid chromatography protocol for purification of all proteins in a multi-protein (TnI, TnC, TnT, tropomyosin) complex from rabbit skeletal muscle has been developed, enabling efficient purification of sample amounts ranging from 43 mg of protein complex on a standard analytical column, to 1400 mg on a column of 21.2 mm I.D. and finally, to 5700 mg on a column of 50 mm I.D. Due to problems associated with scale-up procedures for these proteins (e.g. aggregation and/or solubility issues), an initial sample fractionation was devised whereby 50% of the TnC component was precipitated with acetonitrile prior to sample introduction on the RPLC column. By subsequently taking advantage of sample overload conditions to enhance the displacement effect between sample components, coupled with very slow gradient conditions (0.1% acetonitrile/min), we were able to achieve excellent protein separations at high yields of purified proteins.

Reversed-phase liquid chromatography as a tool in the determination of the hydrophilicity/hydrophobicity of amino acid side-chains at a ligand-receptor interface in the presence of different aqueous environments. I. Effect of varying receptor hydrophobicity

We have developed further a chromatographic model for studying the hydrophobic interactions which characterize the way a ligand binds to its receptor. This model is based on observing the retention behaviour of de novo designed model 18-residue amphipathic alpha-helical peptides (representing the hydrophobic binding domain of a ligand) on reversed-phase packings by varying hydrophobicity (representing a receptor protein with a hydrophobic binding pocket). Mutants of the "native" peptide ligand (which contains seven Leu residues in its non-polar face) were designed by replacing one residue in the center of the extremely non-polar face of the amphipathic alpha-helix. Through reversed-phase liquid chromatography of these peptides at pH 2.0 on cyano and C18 columns, we have demonstrated how an increase in receptor hydrophobicity (represented by an increase in column stationary phase hydrophobicity; cyano --> C18) significantly enhances hydrophilicity of polar amino acid side-chains at the ligand-receptor interface while moderately enhancing the hydrophobicity of non-polar side-chains. The addition of salt (100 mM sodium perchlorate) to the aqueous environment surrounding the binding site of receptor and ligand was also shown to have a profound effect on side-chain hydrophilicity/hydrophobicity in the binding interface. This effect was particularly dramatic for the positively charged side-chains Arg, Lys and His, whose significant enhancement of hydrophobicity in the presence of the cyano column contrasted with their increase in hydrophilicity in the presence of the considerably more hydrophobic C18 stationary phase. Our results have major implications to understanding the influence of hydrophobic and aqueous environment on hydrophilicity/hydrophobicity of amino acid side-chains and the role side-chains play in the folding and stability of proteins.

Preparative reversed-phase liquid chromatography of peptides. Isocratic two-step elution system for high loads on analytical columns

We have developed further our novel sample displacement chromatography (SDC) methodology to carry out preparative separations on analytical equipment and 15-cm analytical columns for sample loads < or = 200 mg. Thus, a two-step isocratic SDC protocol was developed and applied to the purification of important biologically active peptides, i.e. bradykinin antagonists of 10 and 11 residues. Following sample loading in 100% aqueous solvent at a concentration of approximately 7-10 mg/ml (with sample loads varying from 67 to 200 mg) onto a small C18 column (150 x 4.6 mm I.D., made up of three 50-mm columns attached in series), we applied isocratic elution with aqueous acetonitrile at two concentrations, the first (lower concentration) to displace hydrophilic impurities off the column and the second (higher concentration) to displace pure product from the column; hydrophobic impurities remain trapped on the column. This modified SDC approach promises to allow great flexibility in purifying peptides, at high yield of pure product (> 99% purity), and encompassing a range of sample hydrophobicities as well as sample loads (< or = 200 mg) varying by as much as a factor of three.

Importance of secondary structural specificity determinants in protein folding: insertion of a native beta-sheet sequence into an alpha-helical coiled-coil

To examine how a short secondary structural element derived from a native protein folds when in a different protein environment, we inserted an 11-residue beta-sheet segment (cassette) from human immunoglobulin fold, Fab new, into an alpha-helical coiled-coil host protein (cassette holder). This de novo design protein model, the structural cassette mutagenesis (SCM) model, allows us to study protein folding principles involving both short- and long-range interactions that affect secondary structure stability and conformation. In this study, we address whether the insertion of this beta-sheet cassette into the alpha-helical coiled-coil protein would result in conformational change nucleated by the long-range tertiary stabilization of the coiled-coil, therefore overriding the local propensity of the cassette to form beta-sheet, observed in its native immunoglobulin fold. The results showed that not only did the nucleating helices of the coiled-coil on either end of the cassette fail to nucleate the beta-sheet cassette to fold with an alpha-helical conformation, but also the entire chimeric protein became a random coil. We identified two determinants in this cassette that prevented coiled-coil formation: (1) a tandem dipeptide NN motif at the N-terminal of the beta-sheet cassette, and (2) the hydrophilic Ser residue, which would be buried in the hydrophobic core if the coiled-coil structure were to fold. By amino acid substitution of these helix disruptive residues, that is, either the replacement of the NN motif with high helical propensity Ala residues or the substitution of Ser with Leu to enhance hydrophobicity, we were able to convert the random coil chimeric protein into a fully folded alpha-helical coiled-coil. We hypothesized that this NN motif is a "secondary structural specificity determinant" which is very selective for one type of secondary structure and may prevent neighboring residues from adopting an alternate protein fold. These sequences with secondary structural specificity determinants have very strong local propensity to fold into a specific secondary structure and may affect overall protein folding by acting as a folding initiation site.

The role of unstructured highly charged regions on the stability and specificity of dimerization of two-stranded alpha-helical coiled-coils: analysis of the neck-hinge region of the kinesin-like motor protein Kif3A

We investigated the folding, stability, and specificity of dimerization of the neck-hinge region (residues 356-416) of the kinesin-like protein Kif3A. We showed that the predicted coiled-coil on its own (residues 356-377) will fold autonomously in solution. We then explored the ability of oppositely charged regions to specify heterodimer formation in coiled-coils by synthesizing analogs of the neck coiled-coil region with and without various negatively and positively charged extensions to the C-terminus of the neck coiled-coil and characterizing these analogs by circular dichroism spectroscopy. The charged region alone (residues 378-416) adopted a random-coil structure and this region remained unfolded in the presence of the coiled-coil. Redox experiments demonstrated that oppositely charged regions specified the formation of a hetero-two-stranded coiled-coil. Denaturation studies with urea demonstrated a decrease in coiled-coil stability with the addition of negatively charged residues in the homostranded coiled-coil; conversely, the addition of the positively charged region (residues 403-416) of Kif3A C-terminally to the neck coiled-coil did not affect coiled-coil stability. Overall, our results suggest that electrostatic attractions drive the specificity of heterodimerization of the coiled-coil, not the removal of positive or negative charge-charge repulsions, while maintaining the stability of the heterodimer compared to that of the stablest homodimer.

Determination of stereochemistry stability coefficients of amino acid side-chains in an amphipathic alpha-helix

We describe here a systematic study to determine the effect on secondary structure of d-amino acid substitutions in the nonpolar face of an amphipathic alpha-helical peptide. The helix-destabilizing ability of 19 d-amino acid residues in an amphipathic alpha-helical model peptide was evaluated by reversed-phase HPLC and CD spectroscopy. l-Amino acid and d-amino acid residues show a wide range of helix-destabilizing effects relative to Gly, as evidenced in melting temperatures (DeltaTm) ranging from -8.5 degrees C to 30.5 degrees C for the l-amino acids and -9.5 degrees C to 9.0 degrees C for the d-amino acids. Helix stereochemistry stability coefficients defined as the difference in Tm values for the l- and d-amino acid substitutions [(DeltaTm' = TmL and TmD)] ranging from 1 degrees C to 34.5 degrees C. HPLC retention times [DeltatR(XL-XD)] also had values ranging from -0.52 to 7.31 min at pH 7.0. The helix-destabilizing ability of a specific d-amino acid is highly dependent on its side-chain, with no clear relationship to the helical propensity of its corresponding l-enantiomers. In both CD and reversed-phase HPLC studies, d-amino acids with beta-branched side-chains destabilize alpha-helical structure to the greatest extent. A series of helix stability coefficients was subsequently determined, which should prove valuable both for protein structure-activity studies and de novo design of novel biologically active peptides.

Development of simultaneous purification methodology for multiple synthetic peptides by reversed-phase sample displacement chromatography

We have developed a low-pressure protocol, designed as a rapid, simple and cost-effective procedure for the efficient and parallel purification of multiple peptide mixtures. This was achieved through adaptation of our novel reversed-phase sample displacement chromatography (SDC) method, where the major separation process takes place in the absence of organic modifier, to modular solid-phase extraction (SPE) technology. Thus, crude peptide sample is applied at overload conditions to extraction columns consisting of SPE tubes containing silica-based reversed-phase packing. By applying a vacuum to draw the solution through the packing, product separation from hydrophobic and hydrophilic impurities is accomplished in a two-stage purification unit: a short pre-column functions as a trap for hydrophobic impurities, while a second, longer SPE column is used as a product isolation column. Thus, under ideal SDC conditions, washing with a 100% aqueous solvent will achieve retention of hydrophobic impurities on the trap, with displacement of product and hydrophilic impurities from the trap to the product isolation column; hydrophilic impurities are thus displaced off the product isolation to waste, leaving only product retained on the main column. In this initial evaluation, this purification system has demonstrated excellent separation of product, in good yield, from both hydrophilic and hydrophobic impurities over a wide range of peptide hydrophobicity and crude composition for model synthetic peptide systems representing crude peptide mixtures.

Trapping the monomeric alpha-helical state during unfolding of coiled-coils by reversed-phase liquid chromatography

Reversed-phase liquid chromatography (RPLC) offers a unique opportunity to monitor the transition from the native state (N) to the structural intermediate state (I) for proteins whose secondary structure is comprised entirely of amphipathic helices, such as coiled-coils. During RPLC, the hydrophobicity of the stationary phase and mobile phase results in the unfolding of the tertiary/quaternary structure of coiled-coils but retains alpha-helical secondary structure and thus isolates the I state. A set of five peptides, alphaalpha-36, betabeta-36, alphabeta-36, gammadelta-36 and omegaomega-36, was generated by shuffling guest hydrophobes at equivalent sites in a symmetric host frame. In one of the peptides, omegaomega-36, all the alpha-glutamic residues in the host frame were replaced by gamma-glutamic residues. alphaalpha-36, betabeta-36, alphabeta-36, gammadelta-36 form two-stranded coiled-coils of identical helical content and unfold as a two-state transition during temperature denaturation while the fifth peptide, omegaomega-36, is a random coil and cannot be induced in to an alpha-helical structure even in the presence of a helix inducing solvent, 50% trifluoroethanol. By comparing the stability order of the four coiled-coils in the N-->I transition (measured by RPLC studies) with that in the N-->D (denatured state) transition (measured by calorimetry), it is concluded that there is a direct correlation between the relative stabilities of these peptides in these two unfolding transitions. This result supports a hierarchical folding mechanism for coiled-coils.