Ab initio and DFT conformational study of proline dipeptide

Analytic Gradients for the Electrostatic Embedding QM/MM Model in Periodic Boundary Conditions Using Particle-Mesh Ewald Sums and Electrostatic Potential Fitted Charge Operators

Long-range electrostatic effects are fundamental for describing chemical reactivity in the condensed phase. Here, we present the methodology of an efficient quantum mechanical/molecular mechanical (QM/MM) model in periodic boundary conditions (PBC) compatible with QM/MM boundaries at chemical bonds. The method combines electrostatic potential fitted charge operators and electrostatic potentials derived from the smooth particle-mesh Ewald (PME) sum approach. The total energy and its analytic first derivatives with respect to QM, MM, and lattice vectors allow QM/MM molecular dynamics (MD) in the most common thermodynamic ensembles. We demonstrate the robustness of the method by performing a QM/MM MD equilibration of methanol in water. We simulate the cis/trans isomerization free-energy profiles in water of proline amino acid and a proline-containing oligopeptide, showing a correct description of the reaction barrier. Our PBC-compatible QM/MM model can efficiently be used to study the chemical reactivity in the condensed phase and enzymatic catalysis.

Deducing the conformational space for an octa-proline helix

A molecular dyad, PY-P8-PER, comprising a proline octamer sandwiched between pyrene and perylene terminals has been synthesized in order to address the dynamics of electronic energy transfer (EET) along the oligo-proline chain. A simple pyrene-based control compound equipped with a bis-proline attachment serves as a reference for spectroscopic studies. The N-H NMR signal at the terminal pyrene allows distinction between cis and trans amides and, although the crystal structure for the control has the trans conformation, temperature-dependent NMR studies provide clear evidence for trans/cis isomerisation in D6-DMSO. Polar solvents tend to stabilise the trans structure for the pyrene amide group, even for longer oligo-proline units. Circular dichroism shows that the proline spacer for PY-P8-PER exists mainly in the all-trans geometry in methanol. Preferential excitation of the pyrene chromophore is possible at wavelengths in the 320-350 nm range and, for the dyad, is followed by efficacious EET to the perylene emitter. The probability for intramolecular EET, obtained from analysis of steady-state spectroscopic data, is ca. 80-90% in solvents of disparate polarity. Comparison with the Förster critical distance suggests the terminals are ca. 18 Å apart. Time-resolved fluorescence spectroscopy, in conjunction with DFT calculations, indicates the dyad exists as a handful of conformers displaying a narrow range of EET rates. Optimisation of a distributive model allows accurate simulation of the EET dynamics in terms of reasonable structures based on isomerisation of certain amide groups.

Solvation Induced Ring Puckering Effect in Fluorinated Prolines and Its Inclusion in Classical Force Fields

Strategic incorporation of fluorinated prolines can accelerate folding and increase thermal stability of proteins. It has been suggested that this behavior emerges from puckering effects induced by fluorination of the proline ring. We use electronic structure calculations to characterize the potential energy surface (PES) along puckering coordinates for a simple dipeptide model of proline and its fluorinated derivatives. Significant shifts in puckering trends between gas phase and implicit solvent calculations shed light on the effect of solvation on electronic structure and conformational preferences of the ring. This solvation induced puckering effect is previously unknown in the context of prolines. The PES based on implicit solvent is then utilized to construct a correction for a classical force field. The corrected force field accurately captures the experimental conformational equilibrium including the coupling between ring puckering and cis-trans isomerism in fluorinated prolines. This method can be extended to other rings and substituents besides fluorine.

Which DFT levels of theory are appropriate in predicting the prolyl cis–trans isomerization in solution?

DFTs were assessed for the conformational preferences of the peptides containing Pro and its derivatives in chloroform and water.

Quantum mechanical investigations on the role of C-terminal residue in influencing the structural features of dipeptides containing N-terminal proline

This study investigates the influence of the side chain moiety of C-terminal residue on the structural and molecular properties of seven dipeptides having proline at their N-terminal positions. The C-terminal component of the dipeptides is varied with seven different combinations viz. Ala, Leu, Asp, Thr, Asn, Arg and Sec. The calculations are carried out using B3LYP/6-311++G(d,p) level of theory in gas and implicit aqueous phase. Effects of explicit aqueous environment on the dipeptide structures are also investigated for two systems. The results furnished by this DFT study provide valuable information regarding the role of the side chain groups of C-terminal residues in determining the structural features of the amide planes, values of the ψ and ф dihedrals, geometry about the α-carbon atoms, theoretical IR spectra as well as the number and type of intramolecular H-bond interactions existing in the dipeptides, and extend a fine corroboration to the earlier theoretical and experimental observations. In aqueous phase the dipeptide geometries exhibit larger values of total dipole moments, greater HOMO-LUMO energy gaps and enhanced thermodynamic stability than those in gas phase. The explicit water molecules are found to modify the geometrical parameters related to the amide planes and vibrational spectra of the dipeptides.

Conformational preference and cis-trans isomerization of 4-methylproline residues

Conformational preferences and prolyl cis-trans isomerizations of the (2S,4S)-4-methylproline (4S-MePro) and (2S,4R)-4-methylproline (4R-MePro) residues are explored at the M06-2X/cc-pVTZ//M06-2X/6-31+G(d) level of theory in the gas phase and in water, where solvation free energies were calculated using the implicit SMD model. In the gas phase, the down-puckered γ-turn structure with the trans prolyl peptide bond is most preferred for both Ac-4S-MePro-NHMe and Ac-4R-MePro-NHMe, in which the C(7) hydrogen bond between two terminal groups seems to play a role, as found for Ac-Pro-NHMe. Because of the C(7) hydrogen bonds weakened by the favorable direct interactions between the backbone C==O and H--N groups and water molecules, the 4S-MePro residue has a strong preference of the up-puckered polyproline II (PP(II)) structure over the down-puckered PP(II) structure in water, whereas the latter somewhat prevails over the former for the 4R-MePro residue. However, these two structures are nearly equally populated for Ac-Pro-NHMe. The calculated populations for the backbone structures of Ac-4S-MePro-NHMe and Ac-4R-MePro-NHMe in water are reasonably consistent with CD and NMR experiments. In particular, our calculated results on the puckering preference of the 4S-MePro and 4R-MePro residues with the PP(II) structures are in accord with the observed results for the stability of the (X-Y-Gly)(7) triple helix with X = 4R-MePro or Pro and Y = 4S-MePro or Pro. The calculated rotational barriers indicate that the cis-trans isomerization may in common proceed through the anticlockwise rotation for Ac-4S-MePro-NHMe, Ac-4R-MePro-NHMe, and Ac-Pro-NHMe in water. The lowest rotational barriers become higher by 0.24-1.43 kcal/mol for Ac-4S-MePro-NHMe and Ac-4R-MePro-NHMe than those for Ac-Pro-NHMe in water.

DFT and MP2 investigations of L-proline and its hydrated complexes

A theoretical study of L-proline-nH(2)O (n = 1-3) has been performed using the hybrid DFT-B3LYP and MP2 methods together with the 6-311++G(d,p) basis set. The results show that the P2 conformer is energetically favorable when forming a hydrated structure, and the hydration of the carboxyl group leads to the greatest stability. For hydrated complexes, the adiabatic and vertical singlet-triplet excitation energies tend to decrease with the addition of water molecules. The hydration energy indicates that in the hydrated complexes the order of stability is: binding site 2 > binding site 1 > binding site 3, and binding site 12 > binding site 23 > binding site 13. As water molecules are added, the stabilities of these hydrated structures gradually increase. In addition, an infrared frequency analysis indicated that there are some differences in the low-frequency range, which are mainly dominated by the O-H stretching or bending vibrations of different water molecules. All of these results should aid our understanding of molecular behavior and provide reference data for further studies of biological systems.

Conformations and vibrational spectra of a model tripeptide: change of secondary structure upon micro-solvation

Mid-infrared (IR) hole burning spectra of the model tripeptide Z-Aib-Pro-NHMe (Z = benzyloxycarbonyl) in gas phase and its micro-clusters with one and two methanol molecules are presented. To establish a relation between experimental spectra and the underlying conformations, calculations at the DFT [B3LYP/6-311++G(d,p)] level of theory are performed. In particular, the intra-peptide and the peptide-methanol hydrogen bonds can be identified from spectral shifts in the amide I, II, and III regions. While the unsolvated tripeptide as well as its one-methanol cluster prefer a gamma-turn structure, a beta-turn structure is found for the two-methanol cluster, in agreement with previous condensed phase studies. Comparison of measured and simulated spectra reveals that the favorable methanol binding sites are at the head and tail parts of the tripeptide. The interconversions between gamma-turn and beta-turn structures are governed by potential barriers below 10 kJ mol(-1) inside one of the low energy basins of the potential energy surface.

Conformational preferences and cis-trans isomerization of L-3,4-dehydroproline residue

The conformational study of N-acetyl-N'-methylamide of L-3,4-dehydroproline (Ac-Dhp-NHMe, the Dhp dipeptide) is carried out using hybrid density functional methods with the self-consistent reaction field method in the gas phase and in solution (chloroform and water). The incorporation of a double bond between C(beta) and C(gamma) into the prolyl ring results in the puckering, backbone population, and barriers to prolyl cis-trans isomerization different from those of the Pro dipeptide. For local minima of the Dhp dipeptide in the gas phase and in water, the C(beta)-C(gamma) bonds become shorter by approximately 0.2 A and the bond angles C(alpha)-C(beta)-C(gamma) and C(beta)-C(gamma)-C(delta) are widened by approximately 8 degrees than those of the Pro dipeptide, and the puckering amplitude is computed to be 0.01-0.07 A, indicating that the 3,4-dehydroprolyl ring is quite less puckered. However, polyproline-like conformations become preferred and the relative stability of the conformation tC with a C(7) intramolecular hydrogen bond decreases as the solvent polarity increases, as found for the Pro dipeptide. The barriers to cis-trans isomerization of the Ac-Dhp peptide bond increase with the increase of solvent polarity and the isomerization is likely to proceed through the clockwise rotation in water, as found for the prolyl peptide bond. The hydrogen bond between the prolyl nitrogen and the following amide N-H group seems to contribute in stabilizing the transition state structures.

Trans-cis switching mechanisms in proline analogues and their relevance for the gating of the 5-HT3 receptor

Trans-cis isomerization of a proline peptide bond is a potential mechanism to open the channel of the 5-HT(3) receptor. Here, we have used the metadynamics method to theoretically explore such a mechanism. We have determined the free energy surfaces in aqueous solution of a series of dipeptides of proline analogues and evaluated the free energy difference between the cis and trans isomers. These theoretical results were then compared with data from mutagenesis experiments, in which the response of the 5-HT(3) receptor was measured when the proline at the apex of the M2-M3 transmembrane domain loop was mutated. The strong correlation between the experimental and the theoretical data supports the existence of a trans-cis proline switch for opening the 5-HT(3) receptor ion channel.

Conformational preferences of beta- and gamma-aminated proline analogues

Quantum mechanical calculations have been used to investigate how the incorporation of an amino group to the Cbeta- or Cgamma-positions of the pyrrolidine ring affects the intrinsic conformational properties of the proline. Specifically, a conformational study of the N-acetyl-N'-methylamide derivatives of four isomers of aminoproline, which differ not only in the beta- or gamma-position of the substituent but also in its cis or trans relative disposition, has been performed. To further understand the role of the intramolecular hydrogen bonds between the backbone carbonyl groups and the amino side group, a conformational study was also performed on the corresponding four analogues of (dimethylamino)proline. In addition, the effects of solvation on aminoproline and (dimethylamino)proline dipeptides have been evaluated using a self-consistent reaction field model, and considering four different solvents (carbon tetrachloride, chloroform, methanol and water). Results indicate that the incorporation of the amino substituent into the pyrrolidine ring affects the conformational properties, with backbone...side chain intramolecular hydrogen bonds detected when it is incorporated in a cis relative disposition. In general, the incorporation of the amino side group tends to stabilize those structures where the peptide bond involving the pyrrolidine nitrogen is arranged in cis. The aminoproline isomer with the substituent attached to the Cgamma-position with a cis relative disposition is the most stable in the gas phase and in chloroform, methanol and water solutions. Replacement of the amino side group by the dimethylamino substituent produces significant changes in the potential energy surfaces of the four investigated (dimethylamino)proline-containing dipeptides. Thus, these changes affect not only the number of minima, which increases considerably, but also the backbone and pseudorotational preferences. In spite of these effects, comparison of the conformational preferences, i.e., the more favored conformers, calculated for different isomers of aminoproline and (dimethylamino)proline dipeptides showed a high degree of consistency for the two families of compounds.

Estimating the "steric clash" at cis peptide bonds

To account for the scarcity of cis peptide bonds in proteins, especially in nonproline (or secondary amide) cases, a steric-clash argument is often put forward, in a scheme where the R lateral chains are facing parallel one another, and the backbone is kept in an "all- trans"-like arrangement. Although such a steric conflict can be partly relieved through proper adjustment of the backbone dihedral angles, one can try to estimate its associated energy cost. To this end, quantum-chemistry approaches using a differential-torsion protocol and bond-separation-energy analyses are applied to N-ethyl propionamide CH3-CH2-CO-NH-CH2-CH3, regarded as a model capable of exhibiting C beta...C beta interaction as in alanine succession. The calculations provide an increment of 9 kcal/mol, quite close to that obtained in the nearly isostere (gsg) rotamer of n-hexane (10 kcal/mol), suggesting the local effects induced by methyl-methyl contact are similar in both cases. Analogous treatments on larger radicals as encountered in leucine or phenylalanine dimers do not change this increment much, which therefore defines the basic reference per-plaque quota to be overcome along all- cis chains. Explicit modeling indicated it can be reduced by up to a factor of 4.

Conformations of proline analogues having double bonds in the ring

The intrinsic conformational preferences of proline analogues having double bonds between carbon atoms in their rings have been investigated using quantum mechanical calculations at the B3LYP/6-31+G(d,p) level. For this purpose, the potential energy surface of the N-acety-N'-methylamide derivatives of three dehydroprolines (proline analogues unsaturated at alpha,beta; beta,gamma; and gamma,delta) and pyrrole (proline analogue with unsaturations at both alpha,beta and gamma,delta) have been explored, and the results are compared with those obtained for the derivative of the nonmodified proline. We found that the double bonds affect the ring puckering and the geometric internal parameters, even though the backbone conformation was influenced the most. Results indicate that the formation of double bonds between carbon atoms in the pyrrolidine ring should be considered as an effective procedure to restrict the conformational flexibility of prolines. Interestingly, we also found that the N-acetyl-N'-methylamide derivative of pyrrole shows a high probability of having a cis peptide bond preceding the proline analogue.

Conformational Preferences and cis−trans Isomerization of Azaproline Residue

The conformational study of N-acetyl-N'-methylamide of azaproline (Ac-azPro-NHMe, the azPro dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore the effects of the replacement of the backbone CHalpha group by the nitrogen atom on the conformational preferences and prolyl cis-trans isomerization in the gas phase and in solution (chloroform and water). The incorporation of the Nalpha atom into the prolyl ring results in the different puckering, backbone population, and barriers to prolyl cis-trans isomerization from those of Ac-Pro-NHMe (the Pro dipeptide). In particular, the azPro dipeptide has a dominant backbone conformation D (beta2) with the cis peptide bond preceding the azPro residue in both the gas phase and solution. This may be ascribed to the favorable electrostatic interaction or intramolecular hydrogen bond between the prolyl nitrogen and the amide hydrogen following the azPro residue and to the absence of the unfavorable interactions between electron lone pairs of the acetyl carbonyl oxygen and the prolyl Nalpha. This calculated higher population of the cis peptide bond is consistent with the results from X-ray and NMR experiments. As the solvent polarity increases, the conformations B and B* with the trans peptide bond become more populated and the cis population decreases more, which is opposite to the results for the Pro dipeptide. The conformation B lies between conformations D and A (alpha) and conformation B* is a mirror image of the conformation B on the phi-psi map. The barriers to prolyl cis-trans isomerization for the azPro dipeptide increase with the increase of solvent polarity, and the cis-trans isomerization proceeds through only the clockwise rotation with omega' approximately +120 degrees about the prolyl peptide bond for the azPro dipeptide in the gas phase and in solution, as seen for the Pro dipeptide. The pertinent distance d(N...H-NNHMe) and the pyramidality of imide nitrogen can describe the role of this hydrogen bond in stabilizing the transition state structure and the lower rotational barriers for the azPro dipeptide than those for the Pro dipeptide in the gas phase and in solution.

Conformational Preferences of Proline Analogues with Different Ring Size

The conformational study on L-azetidine-2-carboxylic acid (Ac-Aze-NHMe, the Aze dipeptide) and (S)-piperidine-2-carboxylic acid (Ac-Pip-NHMe, the Pip dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore the differences in conformational preferences and cis-trans isomerization for proline residue and its analogues with different ring size in the gas phase and in solution (chloroform and water). The change of ring size by deleting a CH2 group from or adding a CH2 group to the prolyl ring results the remarkable changes in backbone and ring structures compared with those of the Pro dipeptide, especially in the C'-N imide bond length and the bond angles around the N-C(alpha) bond. The four-membered azetidine ring can have either puckered structure depending on the backbone structure because of the less puckered structure. The six-membered piperidine ring can adopt chair and boat conformations, but the chair conformation is more preferred than the boat conformation. These calculated preferences for puckering are consistent with experimental results from analysis of X-ray structures of Aze- and Pip-containing peptides. On going from Pro to Aze to Pip, the axiality (i.e., a tendency to adopt the axial orientation) of the NHMe group becomes stronger, which can be ascribed to reduce the steric hindrances between 1,2-substituted Ac and NHMe groups. As the solvent polarity increases, the polyproline II-like conformation becomes more populated and the relative stability of conformation tC with a C7 hydrogen bond between C'=O of the amino group and N-H of the carboxyl group decreases for both the Aze and Pip dipeptides, as seen for the Pro dipeptide. The cis population and rotational barriers for the imide bond increase with the increase of solvent polarity for both the Aze and Pip dipeptides, as seen for the Pro dipeptide. In particular, the cis-trans isomerization proceeds in common through only the clockwise rotation with omega' approximately +120 degrees about azetyl and piperidyl peptide bonds in the gas phase and in solution, as seen for alanyl and prolyl peptide bonds. The pertinent distance d(N...H-N(NHMe)) and the pyramidality of imide nitrogen can describe the role of this hydrogen bond in stabilizing the transition state structure, but the lower rotational barriers for the Aze and Pip dipeptides than those for the Pro dipeptide, which is observed from experiments, cannot be rationalized.

Conformational Preferences of Non-Prolyl and Prolyl Residues

The conformational study on Ac-Ala-NHMe (the alanine dipeptide) and Ac-Pro-NHMe (the proline dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore the differences in the backbone conformational preference and the cis-trans isomerization for the non-prolyl and prolyl residues in the gas phase and in the solutions (chloroform and water). For the alanine and proline dipeptides, with the increase of solvent polarity, the populations of the conformation tC with an intramolecular C(7) hydrogen bond significantly decrease, and those of the polyproline II-like conformation tF and the alpha-helical conformation tA increase, which is in good agreement with the results from circular dichroism and NMR experiments. For both the dipeptides, as the solvent polarity increases, the relative free energy of the cis conformer to the trans conformer decreases and the rotational barrier to the cis-trans isomerization increases. It is found that the cis-trans isomerization proceeds in common through only the clockwise rotation with omega' approximately +120 degrees about the non-prolyl and prolyl peptide bonds in both the gas phase and the solutions. The pertinent distance d(N...H-N(NHMe)) can successfully describe the increase in the rotational barriers for the non-prolyl and prolyl trans-cis isomerization as the solvent polarity increases and the higher barriers for the non-prolyl residue than for the prolyl residue, as seen in experimental and calculated results. By analysis of the contributions to rotational barriers, the cis-trans isomerization for the non-prolyl and prolyl peptide bonds is proven to be entirely enthalpy driven in the gas phase and in the solutions. The calculated cis populations and rotational barriers to the cis-trans isomerization for both the dipeptides in chloroform and/or water accord with the experimental values.

Conformational Preferences of Proline Oligopeptides

A conformational study on the terminally blocked proline oligopeptides, Ac-(Pro)(n)()-NMe(2) (n = 2-5), is carried out using the ab initio Hartree-Fock level of theory with the self-consistent reaction field method in the gas phase and in solutions (chloroform, 1-propanol, and water) to explore the preference and transition between polyproline II (PPII) and polyproline I (PPI) conformations depending on the chain length, the puckering, and the solvent. The mean differences in the free energy per proline of the up-puckered conformations relative to the down-puckered conformations for both diproline and triproline increases for the PPII-like conformations and decreases for the PPI-like conformations as the solvent polarity increases. These calculated results indicate that the PPII-like structures have preferentially all-down puckerings in solutions, whereas the PPI-like structures have partially mixed puckerings. The free energy difference per proline residue between the PPII- and PPI-like structures decreases as the proline chain becomes longer in the gas phase but increases as the proline chain becomes longer in solutions and the solvent polarity increases. In particular, our calculated results indicate that each of the proline oligopeptides can exist as an ensemble of conformations with the trans and cis peptide bonds in solutions, although the PPII-like structure with all-trans peptide bonds is dominantly preferred, which is reasonably consistent with the previously observed results. In diproline Ac-(Pro)(2)-NMe(2), the rotational barrier to the cis-to-trans isomerization for the first prolyl peptide bond increases as the solvent polarity increases, whereas the rotational barrier for the second prolyl peptide bond does not show the monotonic increase as the solvent polarity increases. When the rotational barriers for these two prolyl peptide bonds were compared, it could be deduced that the conformational transition from PPI with the cis peptide bond to PPII with the trans peptide bond is initiated at the C-terminus and proceeds to the N-terminus in water. This is consistent with the results from NMR experiments on polyproline in D(2)O but opposite to the results from enzymatic hydrolysis kinetics experiments on polyproline.

Ab initio conformational study of N-acetyl-L-proline-N',N'-dimethylamide: a model for polyproline

We report here the results on N-acetyl-l-proline-N',N'-dimethylamide (Ac-Pro-NMe2) as a model for polyproline at the HF/6-31+G(d) level with the conductor-like polarizable continuum model of self-consistent reaction field methods to figure out the conformational preference and cis-trans isomerization of polyproline in the gas phase, chloroform, methanol, and water. The second methyl substitution at the carboxyl amide end results in different backbone structures and their populations from those of N-acetyl-L-proline-N-methylamide (Ac-Pro-NHMe). In particular, all conformations with the C7 hydrogen bond between acetyl and amide ends, which is the most probable conformations of Ac-Pro-NHMe in the gas phase and in nonpolar solvents, disappeared for Ac-Pro-NMe2 even in the gas phase due to the lack of amide hydrogen. The dominant conformation for Ac-Pro-NMe2 is the polyproline II structure with the trans prolyl peptide bond in the gas phase and in solutions. In methanol, the population of the polyproline I structure with the cis prolyl peptide bond is calculated to be larger than that in water, which is consistent with experiments. It should be noted that Ac-Pro-NMe2 has higher rotational barriers for the cis-trans isomerization of the Ac-Pro peptide bond than Ac-Pro-NHMe in the gas phase and in solutions, which could be due to the lack of the intramolecular hydrogen bond between prolyl nitrogen and carboxyl N-H group for the transition state of Ac-Pro-NMe2. The rotational barriers for Ac-Pro-NMe2 are increased with the increase of solvent polarity, as seen for Ac-Pro-NHMe.

Conformational Preference and Cis−Trans Isomerization of 4(R)-Substituted Proline Residues

We report here the conformational preference and prolyl cis-trans isomerization of 4(R)-substituted proline dipeptides, N-acetyl-N'-methylamides of 4(R)-hydroxy-L-proline and 4(R)-fluoro-L-proline (Ac-Hyp-NHMe and Ac-Flp-NHMe, respectively), studied at the HF/6-31+G(d), B3LYP/6-31+G(d), and B3LYP/6-311++G(d,p) levels of theory. The 4(R)-substitution by electron-withdrawing groups did not result in significant changes in backbone torsion angles as well as endocyclic torsion angles of the prolyl ring. However, the small changes in backbone torsion angles phi and psi and the decrease of bond lengths r(Cbeta-Cgamma) or r(Cgamma-Cdelta) appear to induce the increase of the relative stability of the trans up-puckered conformation and to alter the relative stabilities of transition states for prolyl cis-trans isomerization. Solvation free energies of local minima and transition states in chloroform and water were calculated using the conductor-like polarizable continuum model at the HF/6-31+G(d) level of theory. The population of trans up-puckered conformations increases in the order Ac-Pro-NHMe < Ac-Hyp-NHMe < Ac-Flp-NHMe in chloroform and water. The increase in population for trans up-puckered conformations in solution is attributed to the increase in population for the polyproline-II-like conformations with up puckering. The barriers DeltaGct++ to prolyl cis-to-trans isomerization for Ac-Hyp-NHMe and Ac-Flp-NHMe increase as the solvent polarity increases, as seen for Ac-Pro-NHMe. In particular, it was identified that the cis-trans isomerization proceeds through the clockwise rotation about the prolyl peptide bond for Ac-Hyp-NHMe and Ac-Flp-NHMe in chloroform and water, as seen for Ac-Pro-NHMe.

A comparative theoretical study of dipeptide solvation in water

Molecular dynamics studies have been performed on the zwitterionic form of the dipeptide glycine-alanine in water, with focus on the solvation and electrostatic properties using a range of theoretical methods, from purely classical force fields, through mixed quantum mechanical/molecular mechanical simulations, to fully quantum mechanical Car-Parrinello calculations. The results of these studies show that the solvation pattern is similar for all methods used for most atoms in the dipeptide, but can differ substantially for some groups; namely the carboxy and aminoterminii, and the backbone amid NH group. This might have implications in other theoretical studies of peptides and proteins with charged -NH(3) (+) and -CO(2) (-) side chains solvated in water. Hybrid quantum mechanical/molecular mechanical simulations successfully reproduce the solvation patterns from the fully quantum mechanical simulations (PACS numbers: 87.14.Ee, 87.15.Aa, 87.15.He, 71.15.Pd).

Gas-phase models of γ turns: Effect of side-chain/backbone interactions investigated by IR/UV spectroscopy and quantum chemistry

The conformations of laser-desorbed jet-cooled short peptide chains Ac-Phe-Xxx-NH2 (Xxx=Gly, Ala, Val, and Pro) have been investigated by IR/UV double resonance spectroscopy and density-functional-theory (DFT) quantum chemistry calculations. Singly gamma-folded backbone conformations (betaL-gamma) are systematically observed as the most stable conformers, showing that in these two-residue peptide chains, the local conformational preference of each residue is retained (betaL for Phe and gamma turn for Xxx). Besides, beta turns are also spontaneously formed but appear as minor conformers. The theoretical analysis suggests negligible inter-residue interactions of the main conformers, which enables us to consider these species as good models of gamma turns. In the case of valine, two similar types of gamma turns, differing by the strength of their hydrogen bond, have been found both experimentally and theoretically. This observation provides evidence for a strong flexibility of the peptide chain, whose minimum-energy structures are controlled by side-chain/backbone interactions. The qualitative conformational difference between the present species and the reversed sequence Ac-Xxx-Phe-NH2 is also discussed.

First Principle Computational Study on the Full Conformational Space of l-Proline Diamides

Ab initio molecular orbital computations were carried out at three levels of theory: RHF/3-21G, RHF/6-31G(d), and B3LYP/6-31G(d), on four model systems of the amino acid proline, HCO-Pro-NH2 [I], HCO-Pro-NH-Me [II], MeCO-Pro-NH2 [III], and MeCO-Pro-NH-Me [IV], representing a systematic variation in the protecting N- and C-terminal groups. Three previously located backbone conformations, gammaL, epsilonL, and alphaL, were characterized together with two ring-puckered forms syn (gauche+ = g+) or "DOWN" and anti (gauche- = g-) or "UP", as well as trans-trans, trans-cis, cis-trans, and cis-cis peptide bond isomers. The topologies of the conformational potential energy cross-sections (PECS) of the potential energy hypersurfaces (PEHS) for compounds [I]-[IV] were explored and analyzed in terms of potential energy curves (PEC), and HCO-Pro-NH2 [I] was also analyzed in terms of potential energy surfaces (PESs). Thermodynamic functions were also calculated for HCO-Pro-NH2 [I] at the CBS-4M and G3MP2 levels of theory. The study confirms that the use of the simplest model, compound [I] with P(N) = P(C) = H, along with the RHF/3-21G level of theory, is an acceptable practice for the analysis of peptide models because only minor differences in geometry and stability are observed.

Cis–trans isomerization and puckering of proline residue

We report here the results on N-acetyl-L-proline-N'-methylamide (Ac-Pro-NHMe) calculated at the HF/6-31+G(d) level with the conductor-like polarizable continuum model (CPCM) of self-consistent reaction field methods to investigate the changes of backbone and prolyl ring along the cis-trans isomerization of the prolyl peptide bond. From the potential energy surface, the barrier to ring flip from the down-puckered conformation to the up-puckered one is estimated to be 2.5 and 3.2 kcal/mol for trans and cis conformers of Ac-Pro-NHMe, respectively. In particular, the ring flip seems to be inaccessible in the intermediate regions between trans and cis conformations, because of higher barriers (approximately 13-19 kcal/mol) to rotation of the prolyl peptide bond. The torsion angles for backbone and prolyl ring vary largely around the transition states at omega' approximately 120 degrees and -70 degrees for the prolyl peptide bond. Three kinds of puckering amplitudes show the same trend of puckering along the cis-trans isomerization although their absolute values are different. In particular, trans and cis conformations have the almost same degree of puckering. The cis populations and barriers to rotation of the prolyl peptide bond for Ac-Pro-NHMe are increased with the increase of solvent polarity, which is mainly ascribed to the decreases of relative free energies for cis conformations and the increase of relative free energies for transition states.