Anna Tempczyk

Exploration of the conformational space of oxytocin and arginine-vasopressin using the electrostatically driven Monte Carlo and molecular dynamics methods

Conformational analysis of the neurohypophyseal hormones oxytocin (OT) and arginine-vasopressin (AVP) has been carried out using two different computational approaches and three force fields, namely by the Electrostatically Driven Monte Carlo (EDMC) method, with the Empirical Conformational Energy Program for Peptides (ECEPP/3) force field or with the ECEPP/3 force field plus a hydration-shell model, and by simulated-annealing molecular dynamics with the Consistent Valence Force Field (CVFF). The low-energy conformations obtained for both hormones were classified using the minimal-tree clustering algorithm and characterized according to the locations of beta-turns in the cyclic moieties. Calculations with the CVFF force field located conformations with a beta-turn at residues 3 and 4 as the lowest energy ones both for OT and for AVP. In the ECEPP/3 force field the lowest energy conformation of OT contained a beta-turn at residues 2 and 3, conformations with this location of the turn being higher in energy for AVP. The latter difference can be attributed to the difference in the size of the side chain in position 3 of the sequences: the bulkier phenylalanine residue of AVP in combination with the bulky Tyr2 residue hinders the formation of a turn at residues 2 and 3. Conformations of OT and AVP with a turn at residues 3,4 were in the best agreement with the x-ray structures of deaminooxytocin and pressinoic acid (the cyclic moiety of vasopressin), respectively, and with the nmr-derived distance constraints. Generally, the low-energy conformations obtained with the hydration-shell model were in a better agreement with the experimental data than the conformations calculated in vacuo. It was found, however, that the obtained low-energy conformations do not satisfy all of the nmr-derived distance constraints and the nuclear Overhauser effect pattern observed in nmr studies can be fully explained only by assuming a dynamic equilibrium between conformations with beta-turns at residues 2,3, 3,4, and 4,5. The low-energy structures of OT with a beta-turn at residues 2,3 have the disulfide ring conformations close to the model proposed recently for a potent bicyclic antagonist of OT [M. D. Shenderovich et al. (1994) Polish Journal of Chemistry, Vol. 25, pp. 921-927], although the native hormone differs from the bicyclic analogue by the conformation of the C-terminal tripeptide. This finding confirms the hypothesis of different receptor-bound conformations of agonists and antagonists of OT.

Comparative conformational analysis of cholesterol and ergosterol by molecular mechanics

A comparative conformational analysis of cholesterol and ergosterol has been carried out using molecular mechanics methods. These studies are aimed at giving a better understanding of the molecular nature of the interaction of these sterols with polyene macrolide antibiotics. Structures of cholesterol and ergosterol determined by X-ray methods have been used as initial geometries of these molecules for force field calculations. The calculation of steric energy has also been made for conformations which do not appear in the crystal. The latter conformers have different conformations of the side chain as well as different conformations of rings A and D. The rotational barriers around bonds C17–C20 and C20–C22 have also been calculated. The results obtained on differences and similarities in the conformations of cholesterol and ergosterol allow us to postulate a mechanism for differential interaction with the antibiotics. The relatively rigid side chain of ergosterol (stretched molecule) in comparison with the flexible side chain of cholesterol (bent molecule), allows better intermolecular contact of the first sterol molecule with a polyene macrolide and in consequence facilitates complex formation involving Van der Waals forces.

Application of mass spectrometry to the study of prototropic equilibria in 5-substituted tetrazoles in the gas phase; experimental evidence and theoretical considerations

The tautomerism of tetrazole, 5-methyltetrazole, and its isotopically substituted derivatives is discussed on the basis of their fragmentation patterns, and of quantum chemical calculations by the LCAO MO method in the CNDO/2 approximation. The equilibrium of these compounds in the gas phase is displaced towards the 2H-tautomer. Analysis of the mass spectra of 5-methyl[2H3]tetrazole revealed randomization of hydrogen between the methyl and the NH groups.

Molecular mechanics calculations on deaminooxytocin and on deamino-arginine-vasopressin and its analogues

SummaryThe backbone conformations of the cyclic moieties of 1-[β-mercaptopropionic acid]-oxytocin ([Mpa1]-OT), [1-β-mercaptopropionic acid]-arginine-vasopressin ([Mpa1]-AVP), [1-(β′-mercapto-β,β-cyclopentamethylene)propionic acid]-arginine-vasopressin ([Cpp1]-AVP), and [1-thiosalicylic acid]-arginine-vasopressin ([Ths1]-AVP) have been analyzed by means of molecular mechanics. In these calculations, the side chains were simulated by pseudoatoms. For the three last compounds, the calculations were also performed on the whole molecules, in order to shed light on the differences in their biological activity. Their starting conformations were obtained by attaching the acyclic tail and side chains to the lowest energy conformations of the cyclic parts. In the case of [Ths1]-AVP, however, other starting conformations were also examined, which were obtained by attaching the planar benzene ring to the lowest energy conformations of [Mpa1]-AVP. In the calculations, all the degrees of freedom were relaxed and Weiners force field was used, the parameters required for the benzene parts of [Ths1]-AVP being determined from the experimental data available, as well as from the results of molecular dynamics calculations on the model compounds. The lowest energy conformations of [Mpa1]-AVP and [Cpp1]-AVP are similar, while [Ths1]-AVP differs from them near the disulphide region, due to the presence of a planar benzene ring. Interactions involving the charged guanidine group of arginine make, in each case, an important contribution to the conformational energy. A model description of the shapes of the oxytocin and vasopressin ring has been proposed, which is based on the cyclohexane geometry. This description is in good correlation with the energetics of the conformations corresponding to different shapes.

Theoretical and experimental studies on the UV spectra of pyridine N-oxide perchlorates

Abstract The UV-spectra of pyridine N-oxide /PyO/, pyridinium N-oxide perchlorate /PyOHClO 4 /, and pyridinium N-oxide semiperchlorate //PyO/2HClO 4 / in acetonitrile have been discussed in details. In the series PyO - PyOHClO 4 - /PyO/ 2 HClO 4 the blue shift of the longest intensive band is observed. CNDO/S-CI calculations have been carried out to explain this. In the case of PyO the first intensive band /276 nm/ involves the charge-transfer from oxygen to the pyridine ring, while the second one /216 nm/ corresponds to 1L b transition of pyridine. For PyOHClO 4 and /PyO/ 2 HClO 4 we have found the opposite sequence. The variation of the positions of the above bands can be explained in terms of the charge-transfer during the transition.

A molecular mechanics study of the effect of substitution in position 1 on the conformational space of the oxytocin/vasopressin ring

SummaryThe effect of the substitution in position 1 on the low-energy conformations of the oxytocin/vasopressin 20-membered ring was investigated by means of molecular mechanics. Three representative substitutions were considered: β′-mercapto-β,β-dimethyl)propionic acid (Dmp), (β′-mercapto-β,β-cyclopentamethylene)propionic acid (Cpp), both forming strong antagonists, and (α,α-dimethyl-β-mercapto)propionic acid (α-Dmp), forming analogs of strongly reduced biological activity, with the β-mercaptopropionic (Mpa) residue taken as reference. Both ECEPP/2 (rigid valence geometry) and AMBER (flexible valence geometry) force fields were employed in the calculations. Three basic types of backbone conformations were taken into account which are distinguished by the type of β-turn at residues 3 and 4: β1/βIII, βII, and βI′/βIII′, all types containing one or two intra-annular hydrogen bonds. The allowed (ring-closed) disulfide-bridge conformations were searched by an algorithm formulated in terms of scanning the disulfide-bridge torsional angle Cβ-S-S-Cβ. The ECEPP/2 and AMBER energies of the obtained conformations were found to be in reasonable agreement. Two of the low-energy conformers of the [Mpa1]-compound agreed very well with the cyclic part of the two conformers found in the crystal structure of [Mpa1]-oxytocin. An analysis of the effect of β-substitution on relative energies showed that the conformations with the N-C′-CH2-CH2 (ψ′1) and C′-CH2-CH2-S (ϰ′1) angles of the first residue around (−100°, 60°) and (100°, −60°) are not affected; this in most cases implies a left-handed disulfide bridge. In the case of α-substitution the allowed values of ψ′1 are close to ± 60°. This requirement, being in contradiction to the one concerning β-substitution, could explain the very low biological activity of the α-substituted analogs. The conformational preferences of substituted compounds can largely be explained by the analysis of local interactions within the first residue. Based on the selection of the conformations which are low in energy for both the reference and β-substituted compounds, two distinct types of possible binding conformations were proposed, the first one being similar to the crystal conformer with a left-handed disulfide bridge, the second one having a right-handed bridge, but a geometry different from that of the crystal conformer with the right-handed bridge. The first type of disulfide-bridge arrangement is equally favorable for both βI/βIII and βII types of backbone structure, while the second one is allowed only for the βII type of backbone. No conformation of the βI′/βIII′ type has a low enough energy to be considered as a possible binding conformation for all of the active compounds studied in this work.

Gas phase prototropic equilibrium studies of 2,4-dihydroxyquinoline by cndo/2 calculations, mass spectrometry and derivatization

Abstract The tautomerism of 2,4-dihydroxyquinoline in the gas phase is discussed in terms of its electron impact fragmentation pattern and of quantum chemical calculations by the LCAO-MO method in the CNDO/2 approximation. Dihydroxyquinoline methylated at position 4 can only exist in two tautomeric forms. Thus, comparison of mass spectrometric data of this compound with dihydroxyquinoline provided additional evidence for the gas phase equilibrium of the latter. The equilibria of these compounds in the gas phase were found to be displaced towards the hydroxyl tautomers.

Influence of excitation and solvation on the shift of tautomeric equilibrium. A quantum-mechanical study

Abstract Two quantum-mechanical models are proposed to described a shift of tautomeric equilibrium as a result of electronic excitation and change of environment. According to the first n PD MEP model which is used to estimate the relative solvation effect on the stability of tautomers in an excited state, the calculation of the interaction energy between a solvent (simulated by a set of n point dipoles, n PD) and an excited solute molecule is based on the molecular electrostatic potential (MEP) of the corresponding excited state. In the second n PDQ model, a solvent represented by a set of n point dipoles and quadrupoles ( n PDQ) modifies the solutes hamiltonian via an electrostatic interaction contribution. Comparing the results of the calculation for isolated and solvated tautomers, the n PDQ model is used to estimate the influence of electronic excitation on the change of relative stability of tautomers existing in a solution. An application of both models to 2- and 4-oxopyridine predicts a shift of the tautomeric equilibria in their excited states in accordance with experimental evidence.

Theoretical studies of the mechanism of the action of the neurohypophyseal hormones. I. Molecular electrostatic potential (MEP) and molecular electrostatic field (MEF) maps of some vasopressin analogues.

SummaryContinuing our theoretical studies of the oxytocin and vasopressin analogues, we have analysed the molecular electrostatic potential (MEP) and the norm of the molecular electrostatic field (MEF) of [1-β-mercaptopropionic acid]-arginine-vasopressin ([Mpa1]-AVP), [1-(β-mercapto-β,β-cyclopentamethylene)propionic acid]-arginine-vasopressin ([Cpp′]-AVP), and [1-thiosalicylic acid]-arginine-vasopressin ([Ths′]-AVP) whose low-energy conformations were calculated in our previous work. These compounds are known from experiment to exhibit different biological activity. The scalar fields mentioned determine the energy of interaction with either charged (MEP) or polar (MEF) species, the energy being in the second case either optimal or Boltzmann-averaged over all the possible orientations of the dipole moment versus the electrostatic field. The electrostatic interactions slowly vanish with distance and can therefore be considered to be the factor determining the molecular shape at greater distances, which can help in both predicting the interactions with the receptor at the stage of remote recognition and in finding the preferred directions of solvation by a polar solvent. In the analysis of the fields three techniques have been used: (i) the construction of maps in certain planes; (ii) the construction of maps on spheres centered in the charge center of the molecule under study and of poles chosen according to the main axes of the quadrupole moment; and (iii) the construction of surfaces corresponding to a given value of potential. The results obtained show that the shapes of both MEP and MEF are similar in the case of [Mpa1]-AVP and [Cpp1-AVP (biologically active), while some differences emerge when comparing these compounds with [Ths1]-AVP (inactive). It has also been found that both MEP and MEF depend even more strongly on conformation.

A theoretical study of protonation and tautomerization of N-substituted aminoazobenzenes

Semiempirical AM1 and ab initio SCF STO-3G calculations with full geometry optimization were performed on aminoazobenzene (AAB) and its N-methyl (MAAB), N,N-dimethyl (DMAAB), and N-phenyl (PhAAB) derivatives, as well as their azonium and ammonium conjugated acids. AM1 calculations were also performed on hydrated cationic acids, in order to estimate the effect of amphiprotic solvents on tautomerization. In all the cases studied but DMAAB the AM1 and STO-3G proton affinity of the azo nitrogen was definitely higher than that of the amino nitrogen. For the amino nitrogen the calculated proton affinity was found to increase in the series AAB < MAAB < PhAAB < DMAAB. The calculated proton affinity of the azo nitrogen increased in the same order with the exception of the STO-3G results of PhAAB. The tautomerization energy/enthalpy (i.e. difference of the gas-phase proton affinity of the azo and the amino nitrogen) was found to increase in the series DMAAB < MAAB < AAB, the position of PhAAB in the series depending on whether the AM1 or STO-3G method was used. These results contradict the experimental data regarding aminoazobenzene protonation and tautomerization constants determined in various solvents, which indicates a strong effect of solvation on the protonation and tautomerization equilibria of aminoazobenzenes. AM1 calculations on hydrated cationic acids showed that solvation effects can be satisfactorily accounted for by enthalpy contributions in the case of tautomerization, because the order of tautomerization constants determined in methanol and dioxane–water mixture generally conforms with the order of tautomerization enthalpies with hydration included. However, the estimated proton affinities in water are still ranked in the same order as in vacuo which may indicate that entropy contributions play a much greater role in the case of protonation than in the case of tautomerization phenomena.