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.     

Stabilizing interactions between aromatic and basic side chains in alpha-helical peptides and proteins. Tyrosine effects on helix circular dichroism

Here we investigate the structures and energetics of interactions between aromatic (Phe or Tyr) and basic (Lys or Arg) amino acids in alpha-helices. Side chain interaction energies are measured using helical peptides, by quantifying their helicities with circular dichroism at 222 nm and interpreting the results with Lifson-Roig-based helix/coil theory. A difficulty in working with Tyr is that the aromatic ring perturbs the CD spectrum, giving an incorrect helicity. We calculated the effect of Tyr on the CD at 222 nm by deriving the intensities of the bands directly from the electronic and magnetic transition dipole moments through the rotational strengths corresponding to each excited state of the polypeptide. This gives an improved value of the helix preference of Tyr (from 0.48 to 0.35) and a correction to the helicity for the peptides containing Tyr. We find that Phe-Lys, Lys-Phe, Phe-Arg, Arg-Phe, and Tyr-Lys are all stabilizing by -0.10 to -0.18 kcal.mol-1 when placed i, i + 4 on the surface of a helix in aqueous solution, despite the great difference in polarity between these residues. Interactions between these side chains have previously been attributed to cation-pi bonds. A survey of protein structures shows that they are in fact predominantly hydrophobic interactions between the CH2 groups of Lys or Arg and the aromatic rings.     

Metal ligand aromatic cation-pi interactions in metalloproteins: ligands coordinated to metal interact with aromatic residues

Cation-pi interactions between aromatic residues and cationic amino groups in side chains and have been recognized as noncovalent bonding interactions relevant for molecular recognition and for stabilization and definition of the native structure of proteins. We propose a novel type of cation-pi interaction in metalloproteins; namely interaction between ligands coordinated to a metal cation--which gain positive charge from the metal--and aromatic groups in amino acid side chains. Investigation of crystal structures of metalloproteins in the Protein Data Bank (PDB) has revealed that there exist quite a number of metalloproteins in which aromatic rings of phenylalanine, tyrosine, and tryptophan are situated close to a metal center interacting with coordinated ligands. Among these ligands are amino acids such as asparagine, aspartate, glutamate, histidine, and threonine, but also water and substrates like ethanol. These interactions play a role in the stability and conformation of metalloproteins, and in some cases may also be directly involved in the mechanism of enzymatic reactions, which occur at the metal center. For the enzyme superoxide dismutase, we used quantum chemical computation to calculate that Trp163 has an interaction energy of 10.09 kcal mol(-1) with the ligands coordinated to iron.     

Rigid rod polymers with flexible side chains. X. Thermotropic mesophases from aromatic stiff-chain polyamides bearing n-alkoxy side chains

The synthesis of stiff-chain poly(1,4-phenylene terephthalamide)s substituted by two as well as by four flexible side chains per repeating unit is described. The solubility of the materials bearing only two side chains is still very low. Appending of four side chains leads to polyamides which dissolve in common organic solvents. All polyamides reported herein form layered structures in the solid state as well as in the mesophase. Polyamides with two side chains have a very weak tendency for crystallization and do not exhibit a transition to the isotropic state even for the longest side chains. Polyamides with four side chains show three reversible thermal transitions: a disordering transition of the side chains, a transition to a layered, smectic-like mesophase, and finally the transition to an isotropic melt. It is shown that the phase behavior of these materials is mainly governed by the strong segregation of main- and side-chains which can be compared best to the microphase separation in block copolymers. © 1993 John Wiley & Sons, Inc.     

Rigid-rod polymers with polysiloxane side chains. 2. Synthesis and characterization of aromatic polybenzobisoxazoles with polysiloxane side chains and composite formation with polysiloxane matrices

Aromatic polybenzobisoxazoles, having polydimethylsiloxane side chains (SCPBOs), were prepared using terephthaloyl chloride-terminated polydimethylsiloxane macromonomers and 3,3′-bis(trimethylsiloxy)-4,4′-bis(trimethylsilylamino)biphenyl for the purpose of dispersing rigid-rod molecules in silicone matrices for molecular reinforcement. The degree of polymerization of the side chain was varied from 7.8 to 45.4, and a small amount of (3-butenyloxy)terephthaloyl chloride was copolymerized to give the polymers a functionality that can be linked to the matrices. For all the SCPBOs, the WAXD pattern showed only diffuse reflections, suggesting limited structural regularity, although the polymers were optically anisotropic. No melting transition was observed below the side chain decomposition temperature, 350°C. A polydimethylsiloxane/polybenzobisoxazole composite elastomer was obtained first curing the polysiloxane matrix containing the prepolymer of the SCPBO, followed by in situ thermal ring closure of the prepolymer. Some reinforcement was observed, but the presence of plasticizing effect by the unbound SCPBO was suggested at the same time. © 1995 John Wiley & Sons, Inc.     

Ferrocenoyl peptides with sulfur-containing side chains: synthesis, solid state and solution structures

The synthesis and full characterization of a number of amino acid and dipeptide derivatives with sulfur-containing side chains derived from ferrocene carboxylic acid and ferrocene-1,1′-dicarboxylic acid is presented. In particular, compounds Fc-CO-(Aaa)_n-OMe (4) and Fe[C₅H₄-CO-(Aaa)_n-OMe]₂ (3) with (Aaa)_n = Cys(Bzl) (a), Cys(Bzl)-Cys(Bzl) (b), Cys(p-OMe-Bzl) (c), Cys(p-OMe-Bzl)-Cys(p-OMe-Bzl) (d), Met (e), and Met-Met (f) were prepared. Also, the free acid derivatives Fe[C₅H₄-CO-Met-OH]₂ (6e) and Fc-CO-Met-OH (7e) were prepared and characterized. The solid state structures of 3a, 4b, and 4e were determined by single crystal X-ray diffraction. Compound 3a shows a 1,3′ substitution pattern on the Cp rings in the solid state. Structures in solution were determined by NMR, IR and CD spectroscopy, with particular emphasis on the question of hydrogen bonding and helical chirality of the metallocene. As an example, the full assignment for the Cp signals in the disubstituted derivative 3a was achieved by simulation of the ¹H NMR signals from the cyclopentadienyl ring in combination with 2D-NOESY spectra. In solution, 3a has the known 1,2′ substitution pattern, which is stabilized by intramolecular hydrogen bonds.     

Peptoid oligomers with alpha-chiral, aromatic side chains: effects of chain length on secondary structure.

Oligomeric N-substituted glycines or "peptoids" with alpha-chiral, aromatic side chains can adopt stable helices in organic or aqueous solution, despite their lack of backbone chirality and their inability to form intrachain hydrogen bonds. Helical ordering appears to be stabilized by avoidance of steric clash as well as by electrostatic repulsion between backbone carbonyls and pi clouds of aromatic rings in the side chains. Interestingly, these peptoid helices exhibit intense circular dichroism (CD) spectra that closely resemble those of peptide alpha-helices. Here, we have utilized CD to systematically study the effects of oligomer length, concentration, and temperature on the chiral secondary structure of organosoluble peptoid homooligomers ranging from 3 to 20 (R)-N-(1-phenylethyl)glycine (Nrpe) monomers in length. We find that a striking evolution in CD spectral features occurs for Nrpe oligomers between 4 and 12 residues in length, which we attribute to a chain length-dependent population of alternate structured conformers having cis versus trans amide bonds. No significant changes are observed in CD spectra of oligomers between 13 and 20 monomers in length, suggesting a minimal chain length of about 13 residues for the formation of stable poly(Nrpe) helices. Moreover, no dependence of circular dichroism on concentration is observed for an Nrpe hexamer, providing evidence that these helices remain monomeric in solution. In light of these new data, we discuss chain length-related factors that stabilize organosoluble peptoid helices of this class, which are important for the design of helical, biomimetic peptoids sharing this structural motif.     

Optically active hydrocarbon polymers with aromatic side chains. II. Poly-(S)-p-sec-butylstyrene

The synthesis of optically active p-sec-butylstyrene (I) has been carried out starting with (S)-2-phenylbutane (II) having optical purity 88–91%. The optical purity of I thus obtained was found to be 73–75%. The polymerization of I with stereospecific coordinated anionic catalysts gave amorphous polymers, as in the case of many other p-substituted styrene derivatives. The fractions obtained from these polymers have very similar rotatory power at 589 nm which is practically equal to that of polymer of I obtained by nonstereospecific radical initiator and of low molecular weight structural models. Accordingly the ¹L_b electronic transition of the aromatic chromophore shows a very low rotatory strength in all samples examined. This result is related to the lack in solution of conformations with a predominant single chirality of the main chain of the macromolecules derived from I.     

Anticancer alpha-helical peptides and structure/function relationships underpinning their interactions with tumour cell membranes

Cancer is a major cause of premature death and there is an urgent need for new anticancer agents with novel mechanisms of action. Here we review recent studies on a group of peptides that show much promise in this regard, exemplified by arthropod cecropins and amphibian magainins and aureins. These molecules are alpha-helical defence peptides, which show potent anticancer activity (alpha-ACPs) in addition to their established roles as antimicrobial factors and modulators of innate immune systems. Generally, alpha-ACPs exhibit selectivity for cancer and microbial cells primarily due to their elevated levels of negative membrane surface charge as compared to non-cancerous eukaryotic cells. The anticancer activity of alpha-ACPs normally occurs at micromolar levels but is not accompanied by significant levels of haemolysis or toxicity to other mammalian cells. Structure/function studies have established that architectural features of alpha-ACPs such as amphiphilicty levels and hydrophobic arc size are of major importance to the ability of these peptides to invade cancer cell membranes. In the vast majority of cases the mechanisms underlying such killing involves disruption of mitochondrial membrane integrity and/or that of the plasma membrane of the target tumour cells. Moreover, these mechanisms do not appear to proceed via receptor-mediated routes but are thought to be effected in most cases by the carpet/toroidal pore model and variants. Usually, these membrane interactions lead to loss of membrane integrity and cell death utilising apoptic and necrotic pathways. It is concluded that that alpha-ACPs are major contenders in the search for new anticancer drugs, underlined by the fact that a number of these peptides have been patented in this capacity.     

Preferred spatial arrangement of the aromatic side chains in linear oligopeptides containing tyrosine.

¹H-NMR. studies of the protected linear tetrapeptides CF₃CO-Gly-Gly-L -Tyr-L -Ala-OCH₃, CF₃CO-Gly-L -Ala-L -Tyr-L -Ala-OCH₃ and CF₃CO-Gly-L -Ala-L -Tyr-Gly-OCH₃ showed that the side chain of the tyrosyl residue was in all three peptides preferentially oriented towards the amino terminus of the peptide chain. This preferred spatial arrangement of the aromatic side chain was manifested in the chemical shifts of the amino acid residue preceding tyrosine and in the vicinal spin-spin coupling constants ³J_HCαCβH of tyrosine.     

Mercury binding by ferrocenoyl peptides with sulfur-containing side chains: Electrochemical, spectroscopic and structural studies

Ferrocenoyl peptides incorporating amino acids derived from either l-methionine, l-cysteine or dl-homocysteine have been synthesised and investigated as agents for heavy metal binding and detection. Heavy metal-peptide interactions have been characterised using cyclic voltammetry to follow changes in the potential of the Fe(II)/Fe(III) redox couple, revealing that these systems interact with mercury(II) ions more strongly than with other thiophilic heavy metals such as cadmium(II), silver(I) and lead(II). Proton NMR experiments have demonstrated 1:1 peptide:mercury binding and enabled quantitative characterisation of this binding interaction. Crystal structures for two of these ferrocenoyl peptide derivatives have been elucidated, revealing that these compounds adopt a P-1,3′ open solid state conformation in the absence of mercury; this arrangement precludes intramolecular hydrogen bonding between chains, while extensive intermolecular hydrogen bonding is evident. The particular affinity of these systems for mercury(II) opens the possibility of incorporating them in new, biologically inspired sensors for detecting this toxic pollutant.     

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.     

Cyclic sulfonium salts with S ... O interactions 2. Molecular structures with six-membered rings

1-[2-(N-methylcarbamoyl)phenyl]-3H-2,1-naphto-(1,8-d,e)-oxathiin-1-ium chloride (2), 1-[2-(N-methylcarbamoyl)-phenyl]-2-methyl-3-oxo-3H-1, 2-naphto-(1,8-d,e)-thiazin-1-ium chloride (3), 1-[8-(N-methylcarbamoyl)naphtyl]-2-methyl-3-oxo-3H-1, 2-naphto-(1,8-d,e)-thiazin-1-ium chloride (4) and 1-(8-carboxylatonaphtyl)-2-methyl-3-oxo-3H-1,2-naphto-(1,8-d,e)-thiazin-1-ium dipolar ion (5) cyclic sulfonium salts were prepared and their chemical properties investigated (spirosulfurane-formation, hydrolysis). The molecular structures obtained from x-ray diffraction can be described with a considerably distorted trigonal bipyramidal arrangement of the ligands about the sulfonium center, with O/N—S ... O=apical angles of 173.9, 164.9, 156.6, and 159.0°, as well as with S—O/N apical bond lengths of 1.648, 1.671, 1.664, and 1.682 Å. The structures exhibit relatively short S ... O close contacts with interatomic distances of 2.253, 2.448, 2.795, and 2.619 Å.     

Peptoid oligomers with alpha-chiral, aromatic side chains: sequence requirements for the formation of stable peptoid helices.

The achiral backbone of oligo-N-substituted glycines or "peptoids" lacks hydrogen-bond donors, effectively preventing formation of the regular, intrachain hydrogen bonds that stabilize peptide alpha-helical structures. Yet, when peptoids are N-substituted with alpha-chiral, aromatic side chains, oligomers with as few as five residues form stable, chiral, polyproline-like helices in either organic or aqueous solution. The adoption of chiral secondary structure in peptoid oligomers is primarily driven by the steric influence of these bulky, chiral side chains. Interestingly, peptoid helices of this class exhibit intense circular dichroism (CD) spectra that closely resemble those of peptide alpha-helices. Here, we have taken advantage of this distinctive spectroscopic signature to investigate sequence-related factors that favor and disfavor stable formation of peptoid helices of this class, through a comparison of more than 30 different heterooligomers with mixed chiral and achiral side chains. For this family of peptoids, we observe that a composition of at least 50% alpha-chiral, aromatic residues is necessary for the formation of stable helical structure in hexameric sequences. Moreover, both CD and 1H-13C HSQC NMR studies reveal that these short peptoid helices are stabilized by the placement of an alpha-chiral, aromatic residue on the carboxy terminus. Additional stabilization can be provided by the presence of an "aromatic face" on the helix, which can be patterned by positioning aromatic residues with three-fold periodicity in the sequence. Extending heterooligomer chain length beyond 12-15 residues minimizes the impact of the placement, but not the percentage, of alpha-chiral aromatic side chains on overall helical stability. In light of these new data, we discuss implications for the design of helical, biomimetic peptoids based on this structural motif.     

Mimicking trimeric interactions in the aromatic side chains of the proteins: a gas phase study of indole...(pyrrole)2 heterotrimer

Aromatic trimeric interactions are extremely significant in the stabilization of the specific structures of the proteins as well as protein-protein, and protein-ligand interactions. Here we have reported a direct evidence of the observation of a cyclic asymmetric structure of indole...(pyrrole)(2) trimer bound by three N-H...π hydrogen bonding interactions in a supersonic jet. The experiment has been performed by using resonant two-photon ionization (R2PI), IR-UV, and UV-UV double resonance spectroscopic techniques. Density functional theory (DFT) calculations nicely corroborate the experimental results showing one weakly allowed IR-active band due to symmetric stretch of the N-H bonds and two strongly allowed IR-active bands due to two types of asymmetric stretches of the N-H bonds in the trimer. The present spectroscopic investigation demonstrates that the strength of the three N-H...π bound intermolecular interactions in the cyclic asymmetric trimer is quite different unlike the corresponding interactions of similar strength in a cyclic symmetric trimer.     

Reversible anion exchange and sensing in large porous materials built from 4,4'-bipyridine via pi...pi and H-bonding interactions

Two unusual d10 compounds, [Zn2(bipy)3(H2O)8(ClO4)2(paba)2].2(bipy).4H2O (1) and [Cd2(bipy)4(H2O)6(ClO4)2(paba)2].(bipy).5H2O (2) (bipy = 4,4'-bipyridine, paba = p-aminobenzoate), were obtained from reaction of the metal salts, bipy and paba in an EtOH/H2O mixture. The bipy ligands in the two compounds exhibit two new modes of coordinating to transition metal ions, resulting in the formation of large porous frameworks. Immersion of single crystals of 1 in an aqueous solution of NH4PF6 results in the formation of its hexafluorophosphate derivative 3 as shown by single crystal diffraction. Immersion of crystals of 3 in NaClO4 regenerates 1. Furthermore, compound 1 also shows interesting anion sensing properties in an EtOH/H2O mixture.