Influences of peptide side chains on the metal ion binding site in metal ion-cationized peptides: Participation of aromatic rings in metal chelation

Aromatic side chains on amino acids influence the fragmentations of cationic complexes of doubly charged metal ions and singly deprotonated peptides. The metal ion interacts with an aromatic side chain and binds to adjacent amide nitrogens. When fragmentation occurs, this bonding leads to the formation of abundant metal-containing a-type ions by reactions that occur at the sites of amino acids that contain the aromatic side chain. Furthermore, formation of metal-containing immonium ions of the amino acids that contain the aromatic side chain also are formed. The abundant a-type ions may be useful in interpretation strategies in which it is necessary to locate in a peptide the position of an amino acid that bears an aromatic side chain.     

Aromatic interactions in unusual backbone nitrogen-coordinated zinc peptide complexes: a crystallographic and spectroscopic study

A series of zinc complexes with dipeptide ligands of the type Dpg-Xaa was synthesized, where Dpg is dipicolylglycine and Xaa is phenylalanine (Phe), tyrosine (Tyr), tryptophan (Trp), 2-naphthylalanine (Nal), or glycine (Gly). It was shown that aromatic interactions promote the unusual coordination of an anionic peptide backbone nitrogen atom to zinc. This binding mode was, for the first time, characterized by X-ray structure analyses of the electrically neutral complexes [(Dpg-Phe)(-H)Zn], [(Dpg-Tyr)(-H)Zn], [(Dpg-Trp)(-H)Zn], and [(Dpg-Nal)(-H)Zn]. The pKa values for amide nitrogen deprotonation were determined by 1H NMR titrations {[(Dpg-Phe)Zn], 7.17; [(Dpg-Tyr)Zn], 6.85; [(Dpg-Trp)Zn], 6.85; [(Dpg-Nal)Zn], 6.64; [(Dpg-Gly)Zn], 8.54}. It was calculated that aromatic interactions contribute ca. -8 to -11 kJ/mol of stabilizing free enthalpy changes in the derivatives with aromatic amino acid side chains. These are the first quantitative data obtained for crystallographically characterized metal complexes. A comparison with the literature shows that it is difficult to distinguish between pi-cation attraction and pi-pi stacking. However, it is evident that modification of small peptides with synthetic pyridine ligands enhances their ability to stabilize secondary structures by noncovalent interactions. This is an important consideration for the design of biomimetic metallopeptides.     

The role of cation-pi interactions in biomolecular association. Design of peptides favoring interactions between cationic and aromatic amino acid side chains.

Cation-pi interactions between amino acid side chains are increasingly being recognized as important structural and functional features of proteins and other biomolecules. Although these interactions have been found in static protein structures, they have not yet been detected in dynamic biomolecular systems. We determined, by (1)H NMR spectroscopic titrations, the energies of cation-pi interactions of the amino acid derivative AcLysOMe (1) with AcPheOEt (2) and with AcTyrOEt (3) in aqueous and three organic solvents. The interaction energy is substantial; it ranges from -2.1 to -3.4 kcal/mol and depends only slightly on the dielectric constant of the solvent. To assess the effects of auxiliary interactions and structural preorganization on formation of cation-pi interactions, we studied these interactions in the association of pentapeptides. Upon binding of the positively-charged peptide AcLysLysLysLysLysNH(2) (5) to the negatively-charged partner AcAspAspXAspAspNH(2) (6), in which X is Leu (6a), Tyr (6b), and Phe (6c), multiple interactions occur. Association of the two pentapeptides is dynamic. Free peptides and their complex are in fast exchange on the NMR time-scale, and 2D (1)H ROESY spectra of the complex of the two pentapeptides do not show intermolecular ROESY peaks. Perturbations of the chemical shifts indicated that the aromatic groups in peptides 6b and 6c were affected by the association with 5. The association constants K(A) for 5 with 6a and with 6b are nearly equal, (4.0 +/- 0.7) x 10(3) and (5.0 +/- 1.0) x 10(3) M(-)(1), respectively, while K(A) for 5 with 6c is larger, (8.3 +/- 1.3) x 10(3) M(-)(1). Molecular-dynamics (MD) simulations of the pentapeptide pairs confirmed that their association is dynamic and showed that cation-pi contacts between the two peptides are stereochemically possible. A transient complex between 5 and 6 with a prominent cation-pi interaction, obtained from MD simulations, was used as a template to design cyclic peptides C(X) featuring persistent cation-pi interactions. The cyclic peptide C(X) had a sequence in which X is Tyr, Phe, and Leu. The first two peptides do, but the third does not, contain the aromatic residue capable of interacting with a cationic Lys residue. This covalent construct offered conformational stability over the noncovalent complexes and allowed thorough studies by 2D NMR spectroscopy. Multiple conformations of the cyclic peptides C(Tyr) and C(Phe) are in slow exchange on the NMR time-scale. In one of these conformations, cation-pi interaction between Lys3 and Tyr9/Phe9 is clearly evident. Multiple NOEs between the side chains of residues 3 and 9 are observed; chemical-shift changes are consistent with the placement of the side chain of Lys3 over the aromatic ring. In contrast, the cyclic peptide C(Leu) showed no evidence for close approach of the side chains of Lys3 and Leu9. The cation-pi interaction persists in both DMSO and aqueous solvents. When the disulfide bond in the cyclic peptide C(Phe) was removed, the cation-pi interaction in the acyclic peptide AC(Phe) remained. To test the reliability of the pK(a) criterion for the existence of cation-pi interactions, we determined residue-specific pK(a) values of all four Lys side chains in all three cyclic peptides C(X). While NOE cross-peaks and perturbations of the chemical shifts clearly show the existence of the cation-pi interaction, pK(a) values of Lys3 in C(Tyr) and in C(Phe) differ only marginally from those values of other lysines in these dynamic peptides. Our experimental results with dynamic peptide systems highlight the role of cation-pi interactions in both intermolecular recognition at the protein-protein interface and intramolecular processes such as protein folding.     

Immobilized metal ion affinity chromatography. Effect of solute structure, ligand density and salt concentration on the retention of peptides

The adsorption characteristics of a variety of synthetic peptide hormones and di-, tri- and tetrapeptides on Cu(II) immobilized on two commercially available high-performance chelating gels run under various experimental conditions are described. Methods for determining the concentration of immobilized Cu(II) in situ are also described. The Cu(II)-charged columns exhibit a net negative charge as judged from the significantly higher retention of some basic peptides in the absence of NaCl in the equilibration and elution buffers. At higher NaCl concentrations (2-4 M), aromatic interactions seem to be superimposed on the metal ion affinity characteristics of the peptides. The relationship between resolution of peptides and the concentration of immobilized Cu(II) ions has also been established for the Chelating Superose gel where 40 mumol Cu(II) ml-1 gel apparently gives the optimum resolution. The nature of the gel matrix also plays a role in the resolution of some peptides, the extent of which is difficult to predict. The results obtained also suggest that peptides containing aromatic and hydroxy amino acids are retarded more than those which lack them. Moreover, these same amino acids apparently strengthen the existing strong binding of peptides containing His, Trp or Cys to a Chelating Superose-Cu(II) column. Dipeptides with C-terminal His (i.e., X-His) are neither bound nor retarded on a column of Chelating Superose-Cu(II) whereas those having the structure His-X are strongly bound. Some tri- and tetrapeptides containing His were also found not to bind to the column. The underlying cause of this anomalous adsorption behaviour is discussed and is ascribed to "metal ion transfer" arising from the relatively higher affinity of such peptides towards immobilized Cu(II) ions than the chelator groups (iminodiacetate) which are covalently bound to the gel matrix.     

Equilibrium Studies of Binary and Mixed-Ligand Complexes of Zinc(II) Involving 2-(Aminomethyl)-Benzimidazole and Some Bio-Relevant Ligands

Binary and mixed-ligand complexes of zinc(II) involving 2-(aminomethyl)-benzimidazole (AMBI) and amino acids, peptides (HL) or DNA constituents have been investigated. Ternary complexes of amino acids or peptides are formed simultaneously. Amino acids form the complex Zn(AMBI)L, whereas amides form two complex species Zn(AMBI)L and Zn(AMBI)(LH_?1). The ternary complexes of zinc(II) with AMBI and DNA are formed in a stepwise process, whereby binding of zinc(II) to AMBI is followed by ligation of the DNA constituents. The stability of ternary complexes is quantitatively compared with their corresponding binary complexes in terms of the parameters ??log₁₀ K, log₁₀ ??_stat and log₁₀ X. The effect of the side chains of amino acid ligands (??_R) on complex formation is discussed. The values of ??log₁₀ K indicated that the ternary complexes containing aromatic amino acids are significantly more stable than the complexes containing alkyl- and hydroxyalkyl-substituted amino acids. This may be taken as evidence for a stacking interaction between the aromatic moiety of AMBI and the aromatic side chains of the bio-active ligands. The concentration distributions of various species formed in solution were also evaluated as a function of the pH.     

C18柱串联冠醚手性柱高效分离3种芳香族氨基酸对映体

将C18柱与手性冠醚柱串联,建立了一种反相高效液相色谱法用于3种芳香族氨基酸对映体同时拆分的方法.考察了反相色谱流动相的组成、pH值、柱温、流速对对映体拆分的影响.实验结果表明,当流动相为HClO4-乙睛溶液(86:14,V/V,pH 2.0)、柱温20℃、流速0.4 mL/min时,3种氨基酸对映体可获得基线分离.进一步对比了C18柱、冠醚手性柱和串联顺序不同的4种分离模式,结果表明,C18柱不能拆分氨基酸对映体,仅能分离不同种类氨基酸;冠醚手性柱可分离氨基酸映体,但不同种类氨基酸色谱峰出现重叠;串联模式能实现3种氨基酸对映体的基线分离,实现双柱优势互补,而串联顺序对分离影响不大,仅影响色谱峰的峰形.     

Supramolecular Recognition of Amino Acids by Twisted Cucurbit[14]uril

Binding interactions between twisted cucurbit[14]uril (tQ[14]) and twenty standard amino acids (AAs) have been investigated by NMR spectroscopy and isothermal titration calorimetry (ITC) in aqueous HCl solutions and in DMSO. The results showed that tQ[14] displays clear binding affinity for AAs with a positively charged side chain or containing an aromatic ring, but weaker binding affinity for AAs with hydrophobic or polar side chains, with the binding mode depending on the type of side chain present in the AAs.     

Investigation of the retention mechanism of naphthol and benzenediol on calix[4]arene stationary phase based on quantum chemistry calculations

Calixarenes are macrocyclic oligomers having the shape of a conical vase. Their inner cavity can accommodate various guest molecules, i. e. form supramolecules. Thus, calixarenes can be employed to manipulate selectivity in separation sciences. The essential step of separation is the interaction between calixarene and analytes. Therefore, in the present work, the retention mechanisms of benzenediol and naphthol positional isomers on a calix[4]arene column were investigated. The optimized supramolecular structures showed that there exist hydrogen bonding and pi-pi interactions for benzenediol, and for naphthol the pi-pi interactions dominate. Thermodynamic results from quantum chemistry calculations using DFT-B3LYP/STO-3G** basis set were consistent with the retention behaviors of benzenediol and naphthol positional isomers on the calix[4]arene column. This work will provide theoretical support for the design of new calixarene stationary phases.     

HPLC retention behaviors of pi-electron rich compounds on Ni2+- and Cu2+-phthalocyanine derivatives bound to silica gels in polar eluents.

The effect of the central metal of columns packed with silica gels binding Ni(2+)- and Cu(2+)-phthalocyanine derivatives (Ni-and Cu-PCS(D)s) on the retention behavior of poly-aromatic-hydrocarbons (PAHs) thereof in a polar eluent was examined. The retention factors of PAHs on the Ni- and Cu-PCS(D)s in 80% methanol showed a good linear correlation. The Cu-PCS(D) column exhibited the pi-pi interactions for PAHs, while the Ni-PCS(D) column exhibited the pi-d interactions for PAHs in addition to the pi-pi interaction for PAHs. Further, an investigation of the retention behavior of anthracene derivatives having different substituents revealed that the Ni- and Cu-PCS(D) columns could recognize the differences of substituents only in a polar eluent.     

Interfacial property modulation of thermoresponsive polymer brush surfaces and their interaction with biomolecules

Dense poly(N-isopropylacrylamide) (PIPAAm) brushes were created on silica bead surfaces by surface-initiated atom transfer radical polymerization (ATRP). Interfacial properties of PIPAAm brushes were characterized by thermoresponisve interaction with biomolecules. The grafted amounts of PIPAAm on silica bead surfaces exceeded that from previously reported polymer-hydrogel-modified silica beads prepared by conventional radical polymerization by nearly 1 order of magnitude. Temperature-dependent chromatographic interactions with soluble analytes were modulated by changing the grafted PIPAAm chain lengths. Short PIPAAm-grafted silica beads produce insufficient dehydration and chain aggregation to separate steroids using weak hydrophobic interactions. In contrast, broad unresolved peaks were observed on silica beads column grafted with long PIPAAm chains due to steroid partitioning into thick, densely grafted PIPAAm brush layers. Thus, silica beads column grafted with PIPAAm chains of proper length can demonstrate baseline separation of steroids with relatively high resolution among the tested columns. Relatively longer retention times for steroid analytes were observed on all columns compared to those previously reported for other PIPAAm-grafted silica beads. This indicates that densely PIPAAm-grafted chains enable control of strong hydrophobic interactions with steroids by changing the column temperature. Densely grafted PIPAAm columns were also successful in separating two peptides into two peaks as the column temperature was increased to 40 degrees C. This provides an effective separation alternative for peptides using substantial hydrophobicity without modification of hydrophobic surfaces and/or low mobile phase pH. In conclusion, densely PIPAAm-grafted surfaces exhibit strong, reversible temperature-modulated hydrophobic interactions, facilitating baseline separations of steroids and peptides in aqueous milieu without changes in the mobile phase pH and high ionic strength.     

A comparative molecular similarity index analysis (CoMSIA) study identifies an HLA-A2 binding supermotif

The 3D-QSAR CoMSIA technique was applied to a set of 458 peptides binding to the five most widespread HLA-A2-like alleles: A^*0201, A^*0202, A^*0203, A^*0206 and A^*6802. Models comprising the main physicochemical properties (steric bulk, electron density, hydrophobicity and hydrogen-bond formation abilities) were obtained with acceptable predictivity (q ² ranged from 0.385 to 0.683). The use of coefficient contour maps allowed an A2-supermotif to be identified based on common favoured and disfavoured areas. The CoMSIA definition for the best HLA-A2 binder is as follows: hydrophobic aromatic amino acid at position 1; hydrophobic bulky side chains at positions 2, 6 and 9; non-hydrogen-bond-forming amino acids at position 3; small aliphatic hydrogen-bond donors at position 4; aliphatic amino acids at position 5; small aliphatic side chains at position 7; and small aliphatic hydrophilic and hydrogen-bond forming amino acids at position 8.     

Impact of methanol and acetonitrile on separations based on pi-pi interactions with a reversed-phase phenyl column

Studies were performed to investigate the roles of methanol and acetonitrile on the retention mechanism of an active pharmaceutical ingredient (API) and related compounds with a reversed phase phenyl column. Different retention orders were observed depending upon whether acetonitrile or methanol was used as the organic modifier. We propose that acetonitrile impedes the selective pi-pi interactions between the analyte molecules and the phenyl groups in the stationary phase. Further study with 1-naphthoic acid and 1-naphthol as test compounds in the HPLC separation provides additional support for the influence of acetonitrile on pi-pi interactions between analyte molecules and a phenyl stationary phase. This study suggests that methanol be used as the preferred organic modifier with phenyl columns to achieve selectivity based upon pi-pi interactions.     

Molecular-length and chiral discriminations by beta-structural poly(L-alanine) on silica

Poly(L-alanine)-grafted porous silica (Sil-Ala22) was prepared by polymerization of N-carboxyanhydride of L-alanine initiated by 3-aminopropylated silica. Its selective interaction with aromatic guest molecules was evaluated by the retention time in liquid chromatography using the column packed with Sil-Ala22. Sil-Ala22 showed a specific selective retention with discriminating molecular shapes, such as molecular length, linearity and planarity. This selectivity can be explained by a multiple pi-pi interaction with the carbonyl groups one dimensionally-aligned on the rigid beta-form structure in the peptide main chain. Chiral separation with Sil-Ala22 was also described.     

Free energy surfaces for the interaction of D-glucose with planar aromatic groups in aqueous solution

Multidimensional potentials of mean force for the interactions in aqueous solution of both anomers of D-glucopyranose with two planar aromatic molecules, indole and para-methyl-phenol, have been calculated using molecular dynamics simulations with umbrella sampling and were subsequently used to estimate binding free energies. Indole and para-methyl-phenol serve as models for the side chains of the amino acids tryptophan and tyrosine, respectively. In all cases, a weak affinity between the glucose molecules and the flat aromatic surfaces was found. The global minimum for these interactions was found to be for the case when the pseudoplanar face of β-D-glucopyranose is stacked against the planar surfaces of the aromatic residues. The calculated binding free energies are in good agreement with both experiment and previous simulations. The multidimensional free energy maps suggest a mechanism that could lend kinetic stability to the complexes formed by sugars bound to sugar-binding proteins.     

The organization of aromatic side groups in an amyloid fibril probed by solid-state 2H and 19F NMR spectroscopy

Some 25 diseases are associated with proteins and peptides that assemble into amyloid fibrils composed of beta-strands connected by hydrogen bonds oriented parallel to the fiber long axis. There is mounting evidence that amyloid formation involves specific interactions between amino acid side groups, which bring together beta-sheets to form layers with buried and exposed faces. This work demonstrates how a combination of solid-state 2H and 19F NMR experiments can provide constraints on fibril architecture by probing the environment and spatial organisation of aromatic side groups. It is shown that phenylalanine rings within fibrils formed by a decapeptide fragment of the islet amyloid polypeptide, amylin, are highly motionally restrained and are situated within 6.5 A of one another. Taken together with existing structural constraints for this peptide, these results are consistent with a fibril architecture that comprises layers of two or more beta-sheets, with the aromatic residues facing into the inter-sheet space and possibly engaged in pi-pi interactions. The methods presented will be of general utility in exploring the architecture of fibrils of larger, full-length peptides and proteins, including amylin itself.     

Preparation of anhydrochymotrypsin diol silica as selective adsorbent for affinity chromatography of peptides with aromatic amino acids at C-termini

Summary Anhydrochymotrypsin (AHC), a catalytically inert derivative of chymotrypsin in which the serine-residue active site has been converted chemically to a dehydroalanine residue, was immobilized on diol silica by activation with trifluoroethanesulfonyl chloride. A AHC-diol-silica column was used for high-performance affinity chromatographic separation of peptides with aromatic amino acids at their C-termini from other peptides. Faster separations were achieved.     

Laterally attached liquid-crystalline polymers as stationary phases. Effect of temperature in RP HPLC and comparison with a commercial C18 stationary phase

Summary Specific side-on-fixed liquid-crystalline polymers (SOLCP) have been synthesized for use in silica-modified stationary phases in high-performance liquid chromatography (HPLC). The mesogenic side group of the SOLCP is composed of three benzoate-type phenyl rings with terminal alkoxy chains and is laterally linked to a polysiloxane backbone via an alkyl ester spacer arm. The dependence of the logarithm of the retention factor on the reciprocal temperature showed that the liquid-crystalline anisotropic order was conserved in the small pores (200 ? diameter) of the silica gel. The first-order nematic-isotropic transition is lost and probably becomes second-order. Adsorption enthalpies for the liquid-crystalline stationary phases have been measurement for three polycyclic aromatic hydrocarbon isomers (ortho-terphenyl, triphenylene, and chrysene) and compared with those for a commercial C₁₈ phase. The adsorption enthalpies never exceeded 30 kJ mol⁻¹, i.e. ten times the thermal agitation energy,RT. They were always less on the SOLCP stationary phase than on the C₁₈ column, emphasizing the more rigid structure of the liquid crystalline phase and its mechanism based upon adsorption. Better separation of steroids, pesticides and amino acids were obtained with the LCP-coated silica than the commercial bonded C₁₈ column. Four small peptides were successfully separated by using pure water as mobile phase.     

Structural and energetic effects in the molecular recognition of protonated peptidomimetic bases by 18-crown-6

Absolute 18-crown-6 (18C6) affinities of nine protonated peptidomimetic bases are determined using guided ion beam tandem mass spectrometry techniques. The bases (B) included in this work are mimics for the n-terminal amino group and the side chains of the basic amino acids, i.e., the favorable sites for binding of 18C6 to peptides and proteins. Isopropylamine is chosen as a mimic for the n-terminal amino group, imidazole and 4-methylimidazole are chosen as mimics for the side chain of histidine (His), 1-methylguanidine is chosen as a mimic for the side chain of arginine (Arg), and several primary amines including methylamine, ethylamine, n-propylamine, n-butylamine, and 1,5-diamino pentane as mimics for the side chain of lysine (Lys). Theoretical electronic structure calculations are performed to determine stable geometries and energetics for neutral and protonated 18C6 and the peptidomimetic bases, as well as the proton bound complexes comprised of these species, (B)H(+)(18C6). The measured 18C6 binding affinities of the Lys side chain mimics are larger than the measured binding affinities of the mimics for Arg and His. These results suggest that the Lys side chains should be the preferred binding sites for 18C6 complexation to peptides and proteins. Present results also suggest that competition between Arg or His and Lys for 18C6 is not significant. The mimic for the n-terminal amino group exhibits a measured binding affinity for 18C6 that is similar to or greater than that of the Lys side chain mimics. However, theory suggests that binding to n-terminal amino group mimic is weaker than that to all of the Lys mimics. These results suggest that the n-terminal amino group may compete with the Lys side chains for 18C6 complexation.     

Structure-Lipophilicity and Structure-Polarity relationships of amino acids and peptides

The objectives of this study were to gain insights into the structure-lipophilicity relationships of peptides and to propose an improved model for estimating their lipophilicity. First, existing databases were extended to obtain the distribution coefficients of a total of 208 free or protected peptides (di- to pentapeptides). The polarity parameters (Λ) of 23 free amino acids and 19 protected amino acids (AcNH? CHR? CONH₂) and of their side chains were calculated from experimental distribution coefficients and computed molecular volumes. An analysis of the polarity parameters revealed that the hydrophobicity of the amino-acid side chains is largely reduced due to the polar field of the backbone. The polarity parameters of the peptides were then obtained in a similar manner and shown to be highly correlated with the sum of the polarity parameters of their side chains, i.e., the lipophilicity of peptides can be calculated from their molecular volume and the sum of their side-chain polarities using the regression established for each individual series of peptides (Fig. 1). This last restriction is essential since the polarity and lipophilic increment of a NH? C*H? CO unit were shown to decrease with increasing length of backbone.     

Investigation of mixed-mode monolithic stationary phases for the analysis of charged amino acids and peptides by capillary electrochromatography

The potential of N,N-dimethylacrylamide-piperazine diacrylamide-based monolithic stationary phases bearing sulfonic acid groups for electroosmotic flow generation is investigated for the separation of positively charged amino acids and peptides. The capillary columns were used under electrochromatographic but also under purely chromatographic (nano-HPLC) conditions and the separations interpreted as the result of possible chromatographic and electrophoretic contributions. The stationary phases were found to be mechanically stable up to pressures of 190 bar and chemically stable towards a wide variety of organic and hydro-organic mobile phases. In order to investigate the retention mechanism, the salt concentration and the organic solvent content of the (hydro-)organic mobile phase were varied in a systematic manner, taking three aromatic amino acids (phenylalanine, tryptophan, histidine) as model analytes. The respective contributions of electrostatic and hydrophobic and/or hydrophilic interactions were further investigated by varying the charge density and the hydrophobicity of the standard stationary phase. The former was done by varying the amount of charged monomer (vinylsulfonic acid) added during synthesis, the latter by (partially) replacing the interactive monomer (N,N-dimethylacrylamide) by other more hydrophobic monomers. A mixed mode retention mechanism based primarily on electrostatic interactions modified in addition by "hydrophilic" ones seems most suited to interpret the behavior of the amino acids, which stands in contradistinction to the previously investigated case of the behavior of neutral analytes on similar stationary phases. Finally the separation of small peptides was investigated. While the separation of Gly-Phe and Gly-Val was not possible, the separation of Phe-Gly-Phe-Gly and Gly-Phe but also of the closely related Gly-His and Gly-Gly-His could be achieved.