Aromatic Ring Of Phe Research Articles

Probing assembly/disassembly of ordered molecular hydrogels.

Supramolecular hydrogels have a wide range of applications in the biomedical field, acting as scaffolds for cell culture, matrices for tissue engineering and vehicles for drug delivery. L-Phenylalanine (Phe) is a natural amino acid that plays a significant role in several physiological and pathophysiological processes (phenylketonuria and assembly of fibrils linked to tissue damage). Since Myerson et al. [Chem. Eng. Commun., 2002, 189(8), 1079-1090] reported that Phe forms a fibrous network in vitro, Phe's self-assembly processes in water have been thoroughly investigated. We have reported structural control over gelation by introduction of a halogen atom in the aromatic ring of Phe, driving changes in the packing motifs, and therefore, dictating gelation functionality. The additional level of control gained over supramolecular gelation via the preparation of multi-component gel systems offers significant advantages in tuning functional properties of such materials. Gaining molecular-level information on the distribution of gelators between the inherent structural and dynamic heterogeneities of these materials remains a considerable challenge. Using multicomponent gels based on Phe and amino-L-phenylalanine (NH2-Phe), we will explore the patterns of ordered/disordered domains in the gel fibres and will attempt to come up with general trends of interactions in the gel fibres and at the fibre/solution interfaces. Phe and NH2-Phe were found to self-assemble in water into crystalline hydrogels. The determined faster dynamics of exchange between the gel and solution states of NH2-Phe in comparison with Phe were correlated with weaker intermolecular interactions, highlighting the role of head groups in dictating the strength of intermolecular interactions. In the mixed Phe/NH2-Phe systems, at a low concentration of NH2-Phe, disruption of the network was promoted by interference of the aliphatics of NH2-Phe with the electrostatic interactions between Phe molecules. At high concentrations of NH2-Phe, multiple-gelator hydrogels were formed with crystal habits different from those of the pure gel fibres. NMR crystallography approaches combining the strengths of solid- and solution-state NMR proved particularly suitable to obtain structural and dynamic insights into the "ordered" fibres, solution phase and fibre/solution interfaces in these gels. These findings are supported by a plethora of experimental (diffraction, rheology, microscopy and thermal analysis) and computational methods.

Cost-effective selective deuteration of aromatic amino acid residues produces long-lived solution 1H NMR magnetization in proteins

Solution NMR studies of large proteins are hampered by rapid signal decay due to short-range dipolar 1H–1H and 1H–13C interactions. These are attenuated by rapid rotation in methyl groups and by deuteration (2H), so selective 1H,13C-isotope labelling of methyl groups in otherwise perdeuterated proteins, combined with methyl transverse relaxation optimized spectroscopy (methyl-TROSY), is now standard for solution NMR of large protein systems > 25 kDa. For non-methyl positions, long-lived magnetization can be introduced as isolated 1H–12C groups. We have developed a cost-effective chemical synthesis for producing selectively deuterated phenylpyruvate and hydroxyphenylpyruvate. Feeding these amino acid precursors to E. coli in D2O, along with selectively deuterated anthranilate and unlabeled histidine, results in isolated and long-lived 1H magnetization in the aromatic rings of Phe (HD, HZ), Tyr (HD), Trp (HH2, HE3) and His (HD2 and HE1). We are additionally able to obtain stereoselective deuteration of Asp, Asn, and Lys amino acid residues using unlabeled glucose and fumarate as carbon sources and oxalate and malonate as metabolic inhibitors. Combining these approaches produces isolated 1H–12C groups in Phe, Tyr, Trp, His, Asp, Asn, and Lys in a perdeuterated background, which is compatible with standard 1H–13C labeling of methyl groups in Ala, Ile, Leu, Val, Thr, Met. We show that isotope labeling of Ala is improved using the transaminase inhibitor L-cycloserine, and labeling of Thr is improved through addition of Cys and Met, which are known inhibitors of homoserine dehydrogenase. We demonstrate the creation of long-lived 1H NMR signals in most amino acid residues using our model system, the WW domain of human Pin1, as well as the bacterial outer membrane protein PagP.

Synthesis and pharmacology of halogenated δ-opioid-selective [d-Ala(2)]deltorphin II peptide analogues.

Deltorphins are naturally occurring peptides produced by the skin of the giant monkey frog (Phyllomedusa bicolor). They are δ-opioid receptor-selective agonists. Herein, we report the design and synthesis of a peptide, Tyr-d-Ala-(pI)Phe-Glu-Ile-Ile-Gly-NH2 3 (GATE3-8), based on the [d-Ala(2)]deltorphin II template, which is δ-selective in in vitro radioligand binding assays over the μ- and κ-opioid receptors. It is a full agonist in [(35)S]GTPγS functional assays and analgesic when administered supraspinally to mice. Analgesia of 3 (GATE3-8) is blocked by the selective δ receptor antagonist naltrindole, indicating that the analgesic action of 3 is mediated by the δ-opioid receptor. We have established a radioligand in which (125)I is incorporated into 3 (GATE3-8). The radioligand has a KD of 0.1 nM in Chinese hamster ovary (CHO) cells expressing the δ receptor. Additionally, a series of peptides based on 3 (GATE3-8) was synthesized by incorporating various halogens in the para position on the aromatic ring of Phe(3). The peptides were characterized for binding affinity at the μ-, δ-, and κ-opioid receptors, which showed a linear correlation between binding affinity and the size of the halogen substituent. These peptides may be interesting tools for probing δ-opioid receptor pharmacology.

Cargo surface hydrophobicity is sufficient to overcome the nuclear pore complex selectivity barrier

To fulfil their function, nuclear pore complexes (NPCs) must discriminate between inert proteins and nuclear transport receptors (NTRs), admitting only the latter. This specific permeation is thought to depend on interactions between hydrophobic patches on NTRs and phenylalanine-glycine (FG) or related repeats that line the NPC. Here, we tested this premise directly by conjugating different hydrophobic amino-acid analogues to the surface of an inert protein and examining its ability to cross NPCs unassisted by NTRs. Conjugation of as few as four hydrophobic moieties was sufficient to enable passage of the protein through NPCs. Transport of the modified protein proceeded with rates comparable to those measured for the innate protein when bound to an NTR and was relatively insensitive both to the nature and density of the amino acids used to confer hydrophobicity. The latter observation suggests a non-specific, small, and plant interaction network between cargo and FG repeats.

Alkali Metal Complexes of the Dipeptides PheAla and AlaPhe: IRMPD Spectroscopy

Complexes of PheAla and AlaPhe with alkali metal ions Na(+) and K(+) are generated by electrospray ionization, isolated in the Fourier-transform ion cyclotron resonance (FT-ICR) ion trapping mass spectrometer, and investigated by infrared multiple-photon dissociation (IRMPD) using light from the FELIX free electron laser over the mid-infrared range from 500 to 1900 cm(-1). Insight into structural features of the complexes is gained by comparing the obtained spectra with predicted spectra and relative free energies obtained from DFT calculations for candidate conformers. Combining spectroscopic and energetic results establishes that the metal ion is always chelated by the amide carbonyl oxygen, whilst the C-terminal hydroxyl does not complex the metal ion and is in the endo conformation. It is also likely that the aromatic ring of Phe always chelates the metal ion in a cation-pi binding configuration. Along with the amide CO and ring chelation sites, a third Lewis-basic group almost certainly chelates the metal ion, giving a threefold chelation geometry. This third site may be either the C-terminal carbonyl oxygen, or the N-terminal amino nitrogen. From the spectroscopic and computational evidence, a slight preference is given to the carbonyl group, in an RO(a)O(t) chelation pattern, but coordination by the amino group is almost equally likely (particularly for K(+)PheAla) in an RO(a)N(t) chelation pattern, and either of these conformations, or a mixture of them, would be consistent with the present evidence. (R represents the pi ring site, O(a) the amide oxygen, O(t) the terminal carbonyl oxygen, and N(t) the terminal nitrogen.) The spectroscopic findings are in better agreement with the MPW1PW91 DFT functional calculations of the thermochemistry compared with the B3LYP functional, which seems to underestimate the importance of the cation-pi interaction.

Molecular structure study of dimethoxyphenyl‐substituted phosphonodipeptides by infrared, Raman, and surface enhanced Raman spectroscopies

AbstractIn this study, Fourier‐transform Raman (FT‐RS) and infrared (FT‐IR) absorption spectroscopies were employed to characterize the molecular structures of L‐Ala‐(3,4‐dimethoxy)‐L‐Phe‐PO3H2 (A) and L‐Ala‐(3,4‐dimethoxy)‐(des‐CH2)‐L‐Phe‐PO3H2 (B) phosphonodipeptides, where L‐Phe denotes L‐phenylalanine and L‐Ala, L‐alanine. The vibrational band assignments have been proposed. In order to determine the structures of these dimethoxyphenyl‐substituted phosphonodipeptides adsorbed on a colloidal silver surface, surface enhanced Raman spectra (SERS) were measured. The analysis of SERS band intensities showed that these dimethoxyphenyl‐substituted phosphonodipeptides directly interacted with the silver surface through the aromatic ring of Phe that adopted an orientation almost perpendicular to the silver surface. We also showed that intense enhancement of the νas(NH2), δas(PO32−), and ν(PO) modes of L‐Ala‐(3,4‐dimethoxy)‐L‐Phe‐PO3H2 suggested that these groups were mainly involved in the interaction with the silver colloid. Additionally, we proved that in the SERS spectrum of L‐Ala‐(3,4‐dimethoxy)‐(des‐CH2)‐L‐Phe‐PO3H2, several vibrations of the CH3 group were enhanced, indicating a flattened orientation of the peptide backbone on the silver surface. Copyright © 2005 John Wiley & Sons, Ltd.

The geometry and efficacy of cation-pi interactions in a diagonal position of a designed beta-hairpin.

Cation-pi interactions are common in proteins, but their contribution to the stability and specificity of protein structure has not been well established. In this study, we examined the impact of cation-pi interactions in a diagonal position of a beta-hairpin peptide through comparison of the interaction of Phe or Trp with Lys or Arg. The diagonal interactions ranged from -0.20 to -0.48 kcal/mole. Our experimental values for the diagonal cation-pi interactions are similar to those found in alpha-helical studies. Upfield shifting of the Lys and Arg side chains indicates that the geometries of cation-pi interactions adopted in the 12-residue beta-hairpin are comparable to those found in protein structures. The Lys was found to interact through the polarized Cepsilon, and the Arg is stacked against the aromatic ring of Phe or Trp. Folding of these peptides was found to be enthalpically favorable (DeltaH degrees equals approximately -3 kcal/mole) and entropically unfavorable (DeltaS degrees equals approximately -8 cal mole(-1) K(-1)).

Carbonic Anhydrase Inhibitors: X-ray Crystallographic Structure of the Adduct of Human Isozyme II with the Perfluorobenzoyl Analogue of Methazolamide. Implications for the Drug Design of Fluorinated Inhibitors

The X-ray crystal structure for the adduct of human carbonic anhydrase (hCA) II with 4-methyl-5-perfluorophenylcarboximido-δ2-1,3,4-thiadiazoline-2-sulfonamide (PFMZ), a topically acting antiglaucoma sulfonamide, has been resolved at a resolution of 1.8 Å. This compound is almost 10 times more effective as a hCA II inhibitor (KI of 1.5 nM) compared to the lead molecule, methazolamide, a clinically used drug (KI of 14 nM). Its binding to the enzyme active site is similar to that of other sulfonamide inhibitors, considering the interactions of the sulfonamide zinc anchoring group and thiadiazoline ring contacts, but differs considerably when the perfluorobenzoylimino fragment of the molecule is analyzed. Indeed, several unprecedented strong hydrogen bonds involving the imino nitrogen, carbonyl oxygen, a fluorine atom in the ortho position of the inhibitor, and two water molecules, as well as Gln 92 of the enzyme active site were seen. A stacking interaction of the perfluorophenyl ring of the inhibitor and the aromatic ring of Phe 131 was also observed for the first time in a CA–sulfonamide adduct. All these findings prove that more potent CA inhibitors incorporating perfluoroaryl/alkyl tails may be designed, with potentially improved antiglaucoma properties, in view of the new types of interactions seen here between the enzyme and the perfluorobenzoylated analogue of methazolamide.

A novel method for the biosynthesis of deuterated proteins with selective protonation at the aromatic rings of Phe, Tyr and Trp.

A novel biosynthetic strategy is described for the preparation of deuterated proteins containing protons at the ring carbons of Phe, Tyr and Trp, using the aromatic amino acid precursor shikimic acid. Specific protonation at aromatic side chains, with complete deuteration at C(alpha/beta) positions was achieved in proteins overexpressed in bacteria grown in shikimate-supplemented D2O medium. Co-expression of a shikimate transporter in prototrophic bacteria resulted in protonation levels of 62-79%, whereas complete labeling was accomplished using shikimate auxotrophic bacteria. Our labeling protocol permits the measurement of important aromatic side chain derived distance restraints in perdeuterated proteins that could be utilized to enhance the accuracy of NMR structures calculated using low densities of NOEs from methyl selectively protonated samples.

Molecular basis of the selectivity of gastrin-releasing peptide receptor for gastrin-releasing peptide.

The mammalian bombesin peptides [gastrin-releasing peptide (GRP) and neuromedin B (NMB)] are important in numerous biological and pathological processes. These effects are mediated by the heptahelical GRP receptor (GRPR) and NMB receptor (NMBR). GRP has high affinity for GRPR and lower affinity for NMBR. Almost nothing is known about the molecular basis for the selectivity of GRP. To address this question, we first studied four loss-of-affinity GRPR chimeric receptors formed by exchanging the four extracellular (EC) domains of GRPR with the corresponding NMBR EC domains. Receptors were transiently expressed, and affinities were determined by binding studies. Only substitution of the third EC domain (EC3) of GRPR markedly decreased GRP affinity. In the reverse study using gain-of-affinity NMBR chimeras, only replacement of EC3 of NMBR markedly increased GRP affinity. Replacing each of the 20 comparable EC3 amino acids that differed in the NMBR in GRPR showed that two separate NMBR substitutions in the GRPR, Ile for Phe(185) or Ile for Ala(198), markedly decreased GRP affinity. Additional point mutants demonstrated that an amino acid with an aromatic ring in position 185 of GRPR and the size of the backbone substitution in position 198 of GRPR were important for GRP selectivity. These results demonstrate that selectivity of GRP for GRPR over NMBR is primarily determined by two amino acid differences in the EC3 domains of the receptor. Our results suggest that an interaction between the aromatic ring of Phe(185) of the GRPR with GRP is the most important for GRP selectivity.

Flavopiridol Inhibits Glycogen Phosphorylase by Binding at the Inhibitor Site

Flavopiridol (L86-8275) ((-)-cis-5, 7-dihydroxy-2-(2-chlorophenyl)-8-[4-(3-hydroxy-1-methyl)-piperidinyl] -4H-benzopyran-4-one), a potential antitumor drug, currently in phase II trials, has been shown to be an inhibitor of muscle glycogen phosphorylase (GP) and to cause glycogen accumulation in A549 non-small cell lung carcinoma cells (Kaiser, A., Nishi, K., Gorin, F.A., Walsh, D.A., Bradbury, E. M., and Schnier, J. B., unpublished data). Kinetic experiments reported here show that flavopiridol inhibits GPb with an IC(50) = 15.5 microm. The inhibition is synergistic with glucose resulting in a reduction of IC(50) for flavopiridol to 2.3 microm and mimics the inhibition of caffeine. In order to elucidate the structural basis of inhibition, we determined the structures of GPb complexed with flavopiridol, GPb complexed with caffeine, and GPa complexed with both glucose and flavopiridol at 1.76-, 2.30-, and 2.23-A resolution, and refined to crystallographic R values of 0.216 (R(free) = 0.247), 0.189 (R(free) = 0.219), and 0.195 (R(free) = 0.252), respectively. The structures provide a rational for flavopiridol potency and synergism with glucose inhibitory action. Flavopiridol binds at the allosteric inhibitor site, situated at the entrance to the catalytic site, the site where caffeine binds. Flavopiridol intercalates between the two aromatic rings of Phe(285) and Tyr(613). Both flavopiridol and glucose promote the less active T-state through localization of the closed position of the 280s loop which blocks access to the catalytic site, thereby explaining their synergistic inhibition. The mode of interactions of flavopiridol with GP is different from that of des-chloro-flavopiridol with CDK2, illustrating how different functional parts of the inhibitor can be used to provide specific and potent binding to two different enzymes.

Minimum structure of diapause hormone required for biological activity.

Diapause hormone is a 24-amino acid peptide amide, and its C-terminal penta-peptide amide structure of FGPRL-NH2 is believed to be essential for biological activity. The penta-peptide amide, the shorter peptide amides, and their derivatives and analogs were prepared to determine the minimal structure for biological activity. The C-terminal amide group of penta-peptide amide was not replaced with the other functional groups, but Gly, the 4th amino acid from the C terminal, could be substituted with an other amino acid while maintaining the biological activity. The shorter peptide amide, PRL-NH2, possessed low but significant activity, indicating the minimum structure of diapause hormone. By modifying its N-terminal, the aromatic ring of Phe is shown to enhance the activity of PRL-NH2.

Sequence-specific recognition of the internalization motif of the Alzheimer's amyloid precursor protein by the X11 PTB domain.

The crystal structure of the phosphotyrosine-binding domain (PTB) of the X11 protein has been determined, in complex with unphosphorylated peptides corresponding to a region of beta-amyloid precursor protein (betaAPP) that is required for receptor internalization. The mode of binding to X11 of the unphosphorylated peptides, which contain an NPxY motif, resembles that of phosphorylated peptides bound to the Shc and IRS-1 PTB domains. Eight peptide residues make specific contacts with the X11 PTB domain, and they collectively achieve high affinity (KD = 0.32 microM) and specificity. These results suggest that, in contrast to the SH2 domains, the PTB domains are primarily peptide-binding domains that have, in some cases, acquired specificity for phosphorylated tyrosines.

Locations of local anesthetic dibucaine in model membranes and the interaction between dibucaine and a Na+ channel inactivation gate peptide as studied by 2H- and 1H-NMR spectroscopies

To study the molecular mechanisms of local anesthesia, locations of local anesthetic dibucaine in model membranes and the interactions of dibucaine with a Na+ channel inactivation gate peptide have been studied by 2H- and 1H-NMR spectroscopies. The 2H-NMR spectra of dibucaine-d9 and dibucaine-d1, which are deuterated at the butoxy group and at the 3 position in its quinoline ring, respectively, have been observed in multilamellar dispersions of the lipid mixture composed of phosphatidylcholine, phosphatidylserine, and phosphatidylethanolamine. 2H-NMR spectra of deuterated palmitic acids incorporated, as a probe, into the lipid mixture containing cholesterol have also been observed. An order parameter, SCD, for each carbon segment was calculated from the observed quadrupole splittings. Combining these results, we concluded that first, the butoxy group of dibucaine is penetrating between the acyl chains of lipids in the model membranes, and second, the quinoline ring of dibucaine is located at the polar region of lipids but not at the hydrophobic acyl chain moiety. These results mean that dibucaine is situated in a favorable position that permits it to interact with a cluster of hydrophobic amino acids (Ile-Phe-Met) within the intracellular linker between domains III and IV of Na+ channel protein, which functions as an inactivation gate. To confirm whether the dibucaine molecule at the surface region of lipids can really interact with the hydrophobic amino acids, we synthesized a model peptide that includes the hydrophobic amino acids (Ac-GGQDIFMTEEQK-OH, MP-1), the amino acid sequence of which corresponds to the linker part of rat brain type IIA Na+ channel, and the one in which Phe has been substituted by Gln (MP-2), and measured 1H-NMR spectra in both phosphate buffer and phosphatidylserine liposomes. It was found that the quinoline ring of dibucaine can interact with the aromatic ring of Phe by stacking of the rings; moreover, the interaction can be reinforced by the presence of lipids. In conclusion, we wish to propose that local anesthesia originates from the pi-stacking interaction between aromatic rings of an anesthetic molecule located at the polar headgroup region of the so-called boundary lipids and of the Phe in the intracellular linker between domains III and IV of the Na+ channel protein, prolonging the inactivated state and consequently making it impossible to proceed to the resting state.