Alanyl Side Chain Research Articles

Biochemistry of plants N-heterocyclic non-protein amino acids.

Plants catalyze the biosynthesis of a large number of non-protein amino acids, which are usually toxic for other organisms. In this review, the chemistry and metabolism of N-heterocyclic non-protein amino acids from plants are described. These N-heterocyclic non-protein amino acids are composed of β-substituted alanines and include mimosine, β-pyrazol-1-yl-L-alanine, willardiine, isowillardiine, and lathyrine. These β-substituted alanines consisted of an N-heterocyclic moiety and an alanyl side chain. This review explains how these individual moieties are derived from their precursors and how they are used as the substrate for biosynthesizing the respective N-heterocyclic non-protein amino acids. In addition, known catabolism and possible role of these non-protein amino acids in the actual host is explained.

Ab initio study of the electronic singlet excited-state properties of tryptophan in the gas phase: The role of alanyl side-chain conformations

The complex electronic structure of gas phase tryptophan is investigated by ab initio methods and time-dependent density functional theory (TD-DFT), as a function of the conformations of the alanyl side chain. Energies, oscillator strengths, and dipole moments of the four lowest lying excited states are determined from multi-configurational (CASSCF/MS-CASPT2) calculations using a rather large basis set. While the second excited state always carries the largest oscillator strength for all conformers investigated in the present work, we find that the permanent dipole moment is strongly conformer dependent. TD-DFT results are barely useful for the proper characterization of the excited states.

Alanyl Side Chain Folding in Phenylalanine: Conformational Assignments through Ultraviolet Rotational Band Contour Analysis

Partially resolved ultraviolet rotational band contours associated with the S1 ← S0 origin bands of the six most populated conformers of jet-cooled phenylalanine have been recorded via resonant two-photon ionization. The strong dependence of their transition moment orientation on the conformation of the alanyl side chain has facilitated their structural assignment through simulations based upon ab initio computation. The S1 lifetimes of all six conformers, measured through pump−probe delayed ionization, reveal an efficient nonradiative decay pathway in the most stable conformer, which is stabilized through a chain of intramolecular hydrogen bonds linking the side chain to the benzene ring.

Synthesis of Amino Acids with Unnatural Nucleobases or Chromophores Suitable for Use in Model Electron‐Transfer Studies

AbstractWe describe the syntheses of Boc‐protected amino acids bearing the chromophores pyromellitic diimide, naphthalene diimide, and pyrene in their side chains, as well as nucleo amino acids with the artificial purines 7‐carbaguanine, 7‐carbaadenine, isoadenine, and 7‐carbaisoadenine covalently linked to the alanyl side chain. These amino acids incorporating chromophores are suitable building blocks for incorporation into alanyl‐PNA for future investigations of the mechanism of nucleobase‐mediated electron transfer. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)

Thermodynamics of protein model compounds: apparent molar volumes and isobaric heat capacities of selected cyclic dipeptides and their transfer properties from water to aqueous urea solutions at T = 298.15 K

The effects of added protein denaturant (urea) on the volumetric and thermochemical properties of several protein model compounds (cyclic dipeptides) have been investigated at T = 298.15 K and p = 0.1 MPa. Relative densities and specific heat capacities are reported for the cyclic dipeptides cyclo-glycylglycine, cyclo-alanylalanine and cyclo-sarcosylsarcosine in aqueous urea solutions in the concentration range 1 ≤ m(urea)/mol kg−1 ≤ 11. The measurements were performed using a Sodev O2D vibrating tube densimeter and a Picker dynamic microcalorimeter. Apparent molar volumes and heat capacities have been calculated and their concentration dependences have been modeled to give partial molar properties at infinite dilution. The partial molar properties have been used to calculate thermodynamic parameters describing the transfer of the cyclic dipeptides from water to aqueous urea solutions. Estimates of transfer properties for the glycyl group and the alanyl side chain have been obtained using the principles of group additivity. The interaction of urea with the investigated protein model compounds is discussed in terms of the role of urea as a protein denaturant.

Conformational landscapes of aromatic amino acids in the gas phase: Infrared and ultraviolet ion dip spectroscopy of tryptophan

The conformational structures of tryptophan, isolated in the gas phase, have been assigned by combining the results of ultraviolet hole-burning and infrared ion dip spectroscopy with the predictions of ab initio calculations conducted at the MP2/6-311 + G(d,p)//B3LYP/6-31 + G(d) levels of theory. As in phenylalanine, the most strongly populated, and lowest energy conformer presents a folded alanyl side chain that is stabilised by a ‘daisy chain’ of hydrogen-bonded interactions. These link the acidic proton, the amino group and the indole ring. There is a further interaction between the carbonyl oxygen and the neighbouring CH group on the pyrrole ring. A quantitative evaluation of the dipole–dipole interactions between the alanyl side chain and the indole ring in the 1La and 1Lb electronic states does not support the suggestion of electronic state mixing. In particular it casts doubt on the assignment of the fluorescence of the most stable, ‘special’ conformer to emission from the 1La state.

Thermodynamics of protein model compounds: An investigation of the apparent and partial molar heat capacities and volumes of aqueous solutions of alanyl and seryl side-chain containing cyclic dipeptides

This study reports relative densities and heat capacity ratios for the cyclic dipeptides cyclo-glycylserine, cyclo-alanylglycine, cyclo-alanylserine and cyclo-serylserine in water over the temperature range 288.15 to 328.15 K. These values are used to calculate apparent molar volumes, V2,ϕ, and heat capacities, Cp2, ϕ, which have been modelled to give partial molar volumes and heat capacities at infinite dilution. The partial molar properties at infinite dilution have been used to calculate the thermodynamic parameters for the amino acid side-chains of alanine and serine, which have been compared to values previously reported in the literature.

Structure-fluorescence correlations in a single tryptophan mutant of carp parvalbumin: solution structure, backbone and side-chain dynamics

Heterogeneous fluorescence intensity decays of tryptophan in proteins are often rationalized using a model which proposes that different rotameric states of the indole alanyl side-chain are responsible for the observed fluorescence lifetime heterogeneity. We present here the study of a mutant of carp parvalbumin bearing a single tryptophan residue at position 102 (F102W) whose fluorescence intensity decay is heterogeneous and assess the applicability of a rotamer model to describe the fluorescence decay data. We have determined the solution structure of F102W in the calcium ligated state using multi-dimensional nuclear magnetic resonance (NMR) and have used the minimum perturbation mapping technique to explore the possible existence of multiple conformations of the indole moiety of Trp102 of F102W and, for comparison, Trp48 of holo-azurin. The maps for parvalbumin suggest two potential conformations of the indole side-chain. The high energy barrier for rotational isomerization between these conformers implies that interwell rotation would occur on time-scales of milliseconds or greater and suggests a rotamer basis for the heterogeneous fluorescence. However, the absence of alternate Trp102 conformers in the NMR data (to within 3 % of the dominant species) suggests that the heterogeneous fluorescence of Trp102 may arise from mechanisms independent of rotameric states of the Trp side-chain. The map for holo-azurin has only one conformation, and suggests a rotamer model may not be required to explain its heterogeneous fluorescence intensity decay. The backbone and Trp102 side-chain dynamics at 30 °C of F102W has been characterized based on an analysis of 15N NMR relaxation data which we have interpreted using the Lipari-Szabo formalism. High order parameter ( S 2) values were obtained for both the helical and loop regions. Additionally, the S 2 values imply that the calcium binding CD and EF loops are not strictly equivalent. The S 2 value for the indole side-chain of Trp102 obtained from the fluorescence, NMR relaxation and minimum perturbation data are consistent with a Trp moiety whose motion is restricted.

Cyclotheonamides E2 and E3, new potent serine protease inhibitors from the marine sponge of the genus Theonella.

Two new potent serine protease inhibitors, cyclotheonamides E2 (3) and E3 (4), have been isolated from a marine sponge of the genus Theonella. Their structures were determined by interpretation of spectral data and chemical degradation studies. They are closely related to the previously reported cyclotheonamide E, from which they differ in the N-acyl group of the alanyl side chain. Cyclotheonamides E, E2, and E3 were more active against thrombin than against trypsin.

Ab initio calculations on blocked Pro-Ala dipeptides

The effect of the chirality of the amino acid at position i + 2 on a β-turn was investigated by a grid scan ab initio calculation on the Ac- l -Pro- l -Ala-NH 2 and Ac- l -Pro- d -Ala-NH 2 blocked dipeptides. Th6–31G basis set was used to estimate the effect of the alanyl side chain on the conformation of the peptide backbone in a blocked dipeptide as a simple, but complete model for a reverse turn. This study provides a quantum mechanical evaluation of the ability of the NH at the i + 3 residue to form the Hbond that closes the 10 membered ring which stabilizes the turn. The lowest energy of all 64 probed conformations of the D -Ala containing peptide corresponded to a good type II β-turn with a hydrogen bond distance between the acetyl oxygen and the amide terminal hydrogen of 2.21 Å. A comparison with the nonblocked dipeptide ab initio study indicates that the presence of the end blocks enhances the propensity of the d -Ala-containing dipeptide for a type II β-turn, but does not seem to enhance the propensity of the l -Ala-containing dipeptide for a type I β-turn. The energies and geometric parameters for the lowest four optimized conformations identified by the grid scan search for each molecule have been calculated.

Ab initio calculations on blocked Pro-Ala dipeptides

The effect of the chirality of the amino acid at position i + 2 on a β-turn was investigated by a grid scan ab initio calculation on the Ac- l-Pro- l-Ala-NH 2 and Ac- l-Pro- d-Ala-NH 2 blocked dipeptides. Th6–31G basis set was used to estimate the effect of the alanyl side chain on the conformation of the peptide backbone in a blocked dipeptide as a simple, but complete model for a reverse turn. This study provides a quantum mechanical evaluation of the ability of the NH at the i + 3 residue to form the Hbond that closes the 10 membered ring which stabilizes the turn. The lowest energy of all 64 probed conformations of the D-Ala containing peptide corresponded to a good type II β-turn with a hydrogen bond distance between the acetyl oxygen and the amide terminal hydrogen of 2.21 Å. A comparison with the nonblocked dipeptide ab initio study indicates that the presence of the end blocks enhances the propensity of the d-Ala-containing dipeptide for a type II β-turn, but does not seem to enhance the propensity of the l-Ala-containing dipeptide for a type I β-turn. The energies and geometric parameters for the lowest four optimized conformations identified by the grid scan search for each molecule have been calculated.

Conformational dynamics of thyroid hormones by variable temperature nuclear magnetic resonance: the role of side chain rotations and cisoid/transoid interconversions.

1H NMR spectra of the thyroid hormone thyroxine recorded at low temperature and high field show splitting into two peaks of the resonance due to the H2,6 protons of the inner (tyrosyl) ring. A single resonance is observed in 600 MHz spectra at temperatures above 185 K. An analysis of the line shape as a function of temperature shows that the coalescence phenomenon is due to an exchange process with a barrier of 37 kJ mol-1. This is identical to the barrier for coalescence of the H2',6' protons of the outer (phenolic) ring reported previously for the thyroid hormones and their analogues. It is proposed that the separate peaks at low temperature are due to resonances for H2,6 in cisoid and transoid conformers which are populated in approximately equal populations. These two peaks are averaged resonances for the individual H2 and H6 protons. Conversion of cisoid to transoid forms can occur via rotation of either the alanyl side chain or the outer ring, from one face of the inner ring to the other. It is proposed that the latter process is the one responsible for the observed coalescence phenomenon. The barrier to rotation of the alanyl side chain is > or = 37 kJ mol-1, which is significantly larger than has previously been reported for Csp2-Csp3 bonds in other Ph-CH2-X systems. The recent crystal structure of a hormone agonist bound to the ligand-binding domain of the rat thyroid hormone receptor (Wagner et al. Nature 1995, 378, 690-697) shows the transoid form to be the bound conformation. The significant energy barrier to cisoid/transoid interconversion determined in the current study combined with the tight fit of the hormone to its receptor suggests that interconversion between the forms cannot occur at the receptor site but that selection for the preferred bound form occurs from the 50% population of the transoid form in solution.

Ab initio calculations on Pro-Ala and Pro-Gly dipeptides

The geometries of the dipeptides l-Pro- l-Ala, l-Pro- d-Ala and l-Pro-Gly were investigated by a grid scan ab initio calculation. The 6-31G basis set was used to estimate the effect of the alanyl side-chain on the conformation of the peptide backbone and to provide a computational basis for the interpretation of known physical-chemical properties of larger peptides that contain these dipeptides. These calculations furnish a direct quantum mechanical assessment of the energetic consequences of a methyl side-chain in the i + 2 position of a turn. The results of the calculation support the current view that the presence of a d-Ala residue in the i + 2 position favors a type II β-turn over a type I β-turn conformation, while l-Ala has the opposite effect. Total and relative energies for all the optimized conformations identified by the grid search are given and geometric parameters (bond lengths, bond angles and dihedral angles) and net atomic charges have been calculated.

Partial molar isentropic pressure coefficients of some N-acetyl amino acid and peptide amides at infinite dilution in aqueous solutions at the temperature 298.15 K

The partial molar isentropic pressure coefficients at infinite dilution k ∞ S,2 = −(∂ V∞/∂ p) S , where V ∞ 2is the partial molar volume at infinite dilution, have been determined for six N-acetyl amino acid and peptide amides in aqueous solution at the temperature 298.15 K. The results obtained have been rationalized in terms of the likely solute — water interactions. The contribution of an alanyl side-chain to the value of k ∞ S,2 of a peptide has been derived. The result obtained is almost in agreement with that reported in previous work.

Rotamer interconversion and its influence on the fluorescence decay of tyrosine: A molecular dynamics study

To test the hypothesis of charge-transfer quenching between an electrophile in the alanyl sidechain (carbonyl carbon or protonated amino group) and the excited aromatic phenol-subunit, which leads to a bi-exponential fluorescence decay of tyrosine in acidic aqueous solution, we investigated the dynamics of this amino acid and of the peptide Gly—Tyr—Gly in vacuo and in water with classical molecular dynamics (MD) and with stochastic dynamics (SD) computer simulation. The proposed low-frequency of interconversions between sidechain rotamers on a fluorescence timescale could not be confirmed. Instead, frequent transitions for both, χ 1 and χ 2, dihedrals were observed. Simulating a low pH situation (protonated carboxylate group) did not significantly affect the transition frequency. Rotamer interconversions in the peptide Gly—Tyr—Gly, though significantly less, were also observed although the fluorescence decay of this compound could be described by a uni-modal lifetime distribution centered at 0.8 ns. The results obtained from simulations in vacuo and in solution were critically compared with those of stochastic simulations. We found the stochastic simulation in a better agreement to full MD (water explicitly included), which is highly time consuming, whereas the in vacuo simulations clearly deviated from both. We conclude from our results that, since the rotamers do frequently interconvert within the fluorescence lifetime of tyrosine, their contribution to the non-exponential fluorescence decay should be negligible.

Fluorescence of a rotationally constrained tryptophan derivative, 3-carboxy-1,2,3,4-tetrahydro-2-carboline

Despite a plethora of work on tryptophan photophysics, the origin of the complex fluorescence decay kinetics is still unknown. A question remains whether the two fluorescence lifetimes of the tryptophan zwitterion are due to ground-state and therefore excited-state heterogeneity resulting from rotameric forms. To test the conformer model, we synthesized a tryptophan derivative, 3-carboxyl-1,2,3,4-tetrahydro-2-carbolin, which restricts rotation of the alanyl side chain. The constraint limits the number of conformations available to the molecule without greatly affecting the electronic properties. The absorption and emission spectra and the pK of the amino group are similar to those of tryptophan

ChemInform Abstract: Productive Conformation in the Bound State and Hydrolytic Behavior of Thiopeptide Analogues of Angiotensin‐Converting Enzyme Substrates.

AbstractIn contrast to (Ia) and the oxygen analogues (IIa) and (IIb), the thiopeptide (Ib) is not hydrolyzed in the presence of the title enzyme, due to the combined presence of the alanyl side chain methyl group and the neighboring sulfur atom.

The eosin-sensitized photooxidation of substituted phenylalanines and tyrosines.

Abstract— The eosin‐sensitized photooxidation of tyrosine and a number of compounds related to tyrosine (substituted phenylalanines) was studied by steady‐state kinetic and flash photolysis techniques. In particular, the role of the phenolic group and the amino and carboxyl groups of the alanyl side chain in the photooxidation mechanism was investigated in detail. Several relationships between substrate structure and susceptibility to photooxidation as well as effects of substrate structure on photooxidation mechanisms were found.For example, phenylalanine is not photooxidizable, hut substitution of electron‐donating (activating) groups such as‐OH (as in tyrosine) or‐NH2 (as in p‐aminophenylalanine) results in rapidly photooxidized derivatives. However, substituting deactivating groups such as—C1 (as in p‐chlorophenylalanine) or weakly activating groups such as ‐ OCH3 (as in 4‐methoxyphenylalanine) result in non‐photooxidiz‐able derivatives. Substitution of additional activating groups to the ring of hydroxy‐substituted phenylalanines results in increased rates of photooxidation, whereas additional deactivating groups result in decreased photooxidation rates.The rate‐determining step in the photooxidation mechanism is shown to be dependent on the presence and position of an electron‐donating substituent on the benzenoid ring. Only minor involvement of the side chain amino and carboxyl groups was found. Both singlet oxygen and hydrogen abstraction mechanisms are involved in the eosin‐sensitized photooxidation of hydroxy‐substituted phenylalanines (e.g. tyrosine). The hydrogen abstraction mechanism probably predominates at both pH 8 and 11.

Biosynthesis of mimosine: Incorporation of serine and of α-aminoadipic acid

Serine serves as a precursor of the alanyl side-chain of mimosine. Activity from α-aminoadipic acid is incorporated into the γ-pyridone nucleus. Pipecolic acid and 5-hydroxypipecolic acid occur in Mimosa pudica.