Divalent Metal-Ion Complexes with Dipeptide Ligands Having Phe

Article pubs.acs.org/JPCA

Divalent Metal-Ion Complexes with Dipeptide Ligands Having Phe and His Side-Chain Anchors: Effects of Sequence, Metal Ion, and Anchor Robert C. Dunbar,*,† Giel Berden,‡ Jonathan K. Martens,‡ and Jos Oomens*,‡,§ †

Chemistry Department, Case Western Reserve University, Cleveland, Ohio 44106, United States Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands § University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands Downloaded by UNIV OF NEW SOUTH WALES on September 11, 2015 | http://pubs.acs.org Publication Date (Web): September 11, 2015 | doi: 10.1021/acs.jpca.5b06315

‡

S Supporting Information *

ABSTRACT: Conformational preferences have been surveyed for divalent metal cation complexes with the dipeptide ligands AlaPhe, PheAla, GlyHis, and HisGly. Density functional theory results for a full set of complexes are presented, and previous experimental infrared spectra, supplemented by a number of newly recorded spectra obtained with infrared multiple photon dissociation spectroscopy, provide experimental verification of the preferred conformations in most cases. The overall structural features of these complexes are shown, and attention is given to comparisons involving peptide sequence, nature of the metal ion, and nature of the side-chain anchor. A regular progression is observed as a function of binding strength, whereby the weakly binding metal ions (Ba2+ to Ca2+) transition from carboxylate zwitterion (ZW) binding to charge-solvated (CS) binding, while the stronger binding metal ions (Ca2+ to Mg2+ to Ni2+) transition from CS binding to metal-ion-backbone binding (Iminol) by direct metal−nitrogen bonds to the deprotonated amide nitrogens. Two new sequence-dependent reversals are found between ZW and CS binding modes, such that Ba2+ and Ca2+ prefer ZW binding in the GlyHis case but prefer CS binding in the HisGly case. The overall binding strength for a given metal ion is not strongly dependent on the sequence, but the histidine peptides are significantly more strongly bound (by 50−100 kJ mol−1) than the phenylalanine peptides.

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Chart 1. Three Binding Motifs for HisGly with Metal Ionsa

INTRODUCTION The side chains of histidine and phenylalanine (or, similarly, tyrosine) often play an important role in the binding of metal ions by peptides and proteins. The characterization of metal-ion complexes in the gas phase can contribute useful perspectives on such interactions, and the recent emergence of capabilities for the spectroscopic characterization of small peptide complexes in the gas phase has opened new possibilities along these lines.1 Here we have set out to study and compare the interactions across a representative series of metal ions with simple peptide pairs, HisGly versus GlyHis and AlaPhe versus PheAla. (The Gly and Ala residues are so similar in their contributions to metal-ion binding by these peptides that our choice of which one to use in each case has been governed by questions of experimental expediency.) Three alternative binding motifs have been found to describe the ground-state conformations of the metal ion−peptide complexes that have been observed or predicted in the gas phase for peptides not having complications due to active side chains (Chart 1). For the weakly binding metal ions, the normal choice is chelation by the amide carbonyl oxygens, known as charge-solvation (CS) binding.2−5 Also, by analogy with the complexes of simple amino acids, there is the possible © XXXX American Chemical Society

a

Green lines are metal-ion interactions with Lewis-basic chelation sites; red dashed lines are probable hydrogen-bonding interactions.

formation and binding to the carboxylate zwitterion (ZW), although this seems to be less favorable in general for peptides than for simple amino acid complexes. (See refs 6−13 for a few examples of the extensive study of this competition in the gas Received: July 1, 2015 Revised: August 31, 2015

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DOI: 10.1021/acs.jpca.5b06315 J. Phys. Chem. A XXXX, XXX, XXX−XXX

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Downloaded by UNIV OF NEW SOUTH WALES on September 11, 2015 | http://pubs.acs.org Publication Date (Web): September 11, 2015 | doi: 10.1021/acs.jpca.5b06315

The Journal of Physical Chemistry A

condensed phase17,19 is reflected when comparing these two different side chains in the corresponding gas-phase complexation. Characteristics of dipeptides having both Phe3,31−33 and His30 residues have been reported in previous infraredspectroscopic studies using the free electron laser for infrared experiments (FELIX) laser and infrared multiple photon dissociation (IRMPD) spectroscopy. In addition to quantum chemical calculations, we have recorded a number of IRMPD spectra which will be presented here to provide new insights on the questions outlined above. New spectra of metal-ion complexes of AlaPhe and PheAla in the hydrogen-stretching region in the vicinity of 3500 cm−1 resolve some important ambiguities left open by the previous mid-IR spectra (1000− 1800 cm−1). New spectra of complexes of GlyHis in the mid-IR region provide comparisons with the previous series of spectra of the HisGly complexes.30

phase by various approaches.) Finally, for stronger-binding metal ions, deprotonation of amide nitrogens (by tautomerization) becomes favorable, leading to chelation by direct metal− nitrogen bonds in the “Iminol” (Im) binding motif.14 The CS motif is characteristic of alkali metal ions and Ca2+ ions, whereas the Im motif is characteristic of transition metal ions like Co2+, Ni2+, Cu2+, Zn2+, Pd2+, and Cd2+. Consistently, Mg2+ and Mn2+ have been found to lie near the transition from CS to Im. References 3, 14, and 15 show some examples of our group’s study of the competition between CS and Im. Peptideand protein-related condensed-phase analogues of the CS motif are common, for example, in calcium transporter proteins like calmodulin.16 Solution-phase examples of the binding to deprotonated amide nitrogens (analogous to the gas-phase Im binding pattern) have been known since the early days of peptide organometallic chemistry.17−22 The imidazole side chain of histidine often provides an anchor ligand site for this binding mode, which gives impetus to the present study of histidine-containing dipeptide complexes. Our future plans for studying larger ligands will include comparisons with the frequently studied protein domain sometimes referred to as the ATCUN (amino terminal Cu(II) and Ni(II)) structural pattern,18,19,23,24 which is characteristically anchored by His in third position. A few other widely noted examples of the nitrogen backbone binding motif include the binding of metal ions in oxytocin24,25 and the binding of Cu(II) in a similar pattern in the prion protein.26,27 Finally, in analogy to the gas-phase ZW pattern, it is not unusual to find carboxylate chelation in the condensed phase, especially with Asp and Glu side chains involved in the binding of metal ions in proteins.28 In condensed-phase peptides, deprotonation of the backbone amide nitrogen can be accompanied by removal of the proton into the solvent environment (forming net anionic species, as can be modeled by proton-loss processes in gas-phase ion formation29) or onto remote locations in a larger structure (forming zwitterionic species). In small isolated systems like the present examples, however, attachment of the metal cation to an amide nitrogen (without changing the net charge) must accommodate the proton locally, and our work has focused on the iminol tautomerization as the mechanism to achieve this result.3,14,15,30 Several themes of interest are taken up in the work described here. The overall theme is elucidating the factors that determine the preferred binding mode for a given complex. Within this framework we will address four specific questions: (1) Considering the choice between ZW and CS, these modes are competitive for the weak-binding metals, and we will be looking at the transition between these two binding modes as we go from Ba2+ to Ca2+ complexes. (2) Considering the choice between CS and Im, it is found that the weakest-binding metal Ba2+ never prefers Im, while strongest-binding metals like Ni2+ and Cu2+ often prefer Im. Here, our attention will be on the transitional region covering the intermediate metals Ca2+ and Mg2+. (3) As we refine the characterization of the foregoing two transitional regions, we will address the effect of reversal of the position of the side chain (C-terminal versus N-terminal). (4) Finally, we will be concerned with how the observations regarding these questions are similar or different for the phenylalanine dipeptides versus the histidine peptides. It is of interest to see whether the exceptional status of histidine as an anchor for deprotonated nitrogen binding of peptides in the

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METHODS Structure Notation. A descriptive structure notation is used (for example, Im [NONR]). The binding type is indicated (charge solvated (CS), iminol (Im), or carboxylate zwitterion (ZW)). Following in brackets is the set of metal-bound chelation points. Deprotonated amide Nitrogens are given first (N), then carbonyl oxygens (O), then N-terminal amino nitrogen (N), and finally ring (R) (either imidazole nitrogen or π-complexed phenyl). At the levels of computation used, a proton which participates in a hydrogen bond between O and N frequently yields two distinct potential energy minima, which will be distinguished when necessary by an appended _OH or _NH symbol indicating the shorter bond. Sometimes a prime will be used, as in [OO′], to indicate monodentate coordination by one carboxyl or carboxylate oxygen along with complexation by the amide oxygen, distinguished from [OO] which will indicate bidentate complexation by both oxygens of the carboxylate. Computational Methods. All calculations were carried out using the Gaussian09 quantum chemical package.34 The default computational level was B3LYP/6-31+G(d,p). For Ba2+ complexes, the SDD basis set with a relativistic effective core potential was used on the metal ion, with the normal 631+G(d,p) (or 6-311++G(d,p)) basis functions on the H, C, O, and N atoms. Previous density functional theory (DFT) studies cited from our group and others have commonly used this or similar relativistic effective core potentials on large atoms like Ba. The principal reason for this is the known importance of such effects for such large atoms, and the SDD pseudopotential is a straightforward and proven way to take them into account. A secondary advantage is to reduce the size of the calculation without affecting accuracy compared with a simple all-electron approach. For complexes of all other metals, all-electron calculations were done using the chosen 6-31+G(d,p) or 6311++G(d,p) basis. The two different basis sets usually agreed within a few kJ mol−1 and seldom disagreed by as much as 5 kJ mol−1, allowing us to consider the smaller basis set to be large enough for reliable energy comparisons (to the extent of the validity of the B3LYP functional) within the present set of complexes. In citing relative energy values, the larger-basis-set values have been reported, when available and without comment. Some small effects are well-known to give minor adjustments to binding energies, including basis set superposition error, thermal corrections from 0 K, and vibrational zero-point energies. It was assumed that these effects would be B


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Binding energies were calculated by a straightforward subtraction of the energy of the separate metal ion plus neutral ligand from the energy of the most stable conformation found for the complex. The conformation of the neutral ligand was the one with lowest energy coming from modest Amber structure searches combined with DFT refinement. We would not guarantee to have located the true most stable conformations of the neutral ligands, and given the modest computational level and the noninclusion of vibrational and basis set superposition corrections, these binding energy values should be taken as useful numbers for comparison, but not as the most precise values that can be computed by current methods. IRMPD Experiments. IR spectra of the gaseous metal-ion complexes were recorded employing a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) coupled to the FELIX laser and to a benchtop optical parametric oscillator/amplifier (OPO/OPA) system, as has been detailed elsewhere.32,40−42 Metal-ion peptide complexes were generated by electrospray ionization (ESI, Waters Z-Spray) from a solution containing the peptide and metal salt in acetonitrile/ H2O (∼4:1). Target ions were trapped and mass-selected in the FT-ICR cell and were irradiated with the wavelength-tunable infrared light from FELIX (in the range of 1000−1850 cm−1) or the OPO/OPA system (3000−3800 cm−1). When the sum of all dissociation channels ratioed to the total ion count as a function of laser frequency was plotted, an infrared action spectrum was generated and interpreted as a surrogate IR spectrum of the complex. DFT-computed linear IR spectra of candidate ion structures were compared with the observed spectra, with the calculated relative energetics providing additional guidance, to assign conformational and tautomeric isomers.

sufficiently small and similar for all systems so that they can be ignored. In other reported studies of weakly bound neutral− neutral complexes there has been concern about the adequacy of the B3LYP functional to calculate the contribution of dispersion to binding,35 but for ion−neutral complexes, like the present systems, the binding is so strong compared with dispersion forces that such concerns were assumed to be insignificant. For comparison of computed DFT spectra with observed IRMPD spectra, the computed frequencies in the 1000−1900 cm−1 range were scaled by a factor of 0.975 (or 0.98 for the larger basis set), which our experience suggests to be appropriate at these levels of theory. In the 3000−3800 cm−1 range, vibrations have been scaled by 0.955, consistent with previously reported scaling factors for this spectral range using similar levels of theory.36−40 Computed spectra were convoluted with a 20 cm−1 fwhm Gaussian line shape function for comparison to experimental IR spectra. A comprehensive search of configuration space was not practicable, particularly for the transition metals, at a level of computation sufficiently high to give reliable energies. The conformations to be studied were developed by a combination of molecular mechanics searching of Mg2+ or Ca2+ structures using HyperChem and the Amber force field, along with manual inclusion of structures known from prior studies to be chemically reasonable. Searching was done for CS structures and carboxylate zwitterions. Iminol searching by molecular mechanics was not attempted because the metal−nitrogen bonds were not well-parametrized in the force fields used. Iminol structures are generally highly constrained in such small systems, so manual assignment of likely structures was considered quite satisfactory. Promising conformations were further refined at the B3LYP/3-21G level prior to final selection and calculation with a more adequate basis set. For most complexes, the calculated vibrational spectra were insensitive to the basis set choice. More than 20 comparisons were made between spectra calculated with both the 631+g(d,p) and 6-311++g(d,p) basis sets, and the agreement was almost always very good, with peak-position deviations of as much as 10 cm−1 being rare. Relative peak heights were not always as reproducible between basis sets, with occasional deviations of the order of a factor of 2 or more. This lack of consistency of peak heights was not considered to be a problem because IRMPD relative peak heights are commonly accepted as being somewhat uncertain, with little emphasis being placed on interpretations based on precise peak heights. Consistent with previous work,30 most AlaPhe and PheAla spectrum plots are presented at the small-basis level below, and the GlyHis calculations at the large-basis level. However, the small basis calculation of Ni2+FA [NONR] gave energy and spectrum results that were clearly unreasonable and inconsistent with other systems. Taking this as a possible indication that this basis set was too small for reliable all-electron calculations for Ni2+ complexes, it was considered more reliable for this metal ion to present both energies and spectra using the large-basis calculations, as will be seen in Figure 8 below. For the nickel complexes, the triplet spin state was found to be substantially more stable than the corresponding singlet in most cases where singlet state trials were made. In our ongoing studies of Ni(II) iminol complexes of peptides larger than the present subjects, some singlet ground states have been identified, but singlet spin is apparently not preferable for the dipeptides studied here.

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RESULTS AND DISCUSSION Comprehensive computational results will be surveyed in order to achieve a full predicted description of the conformational trends for each of these ligands. The new spectroscopic results will be described for both sets of ligands. Following that, in a final section, conclusions will be drawn about the questions posed above. Thermochemistry. Histidine Dipeptides. Figure 1 displays the metal-ion dependence of the calculated relative energies of the principal structures for each of the two peptide isomers. The metals are ordered along the horizontal axis in order of increasing binding energy (see the discussion of binding energies below and, for example, ref 15). The energies of the various conformations are also noted along with structure diagrams in the Supporting Information (Table S1). In large measure, the plots for the two isomers are similar. As expected, ZW and CS conformations dominate for weak-binding metals and CS for intermediate binding; Im becomes dominant for strong-binders. One observable CS-binding effect of the sidechain position is that in the HG case, folding to give fourcoordinate CS [OONR] is relatively favorable, while for the GH case it is more favorable to open up to give threecoordinate CS [OOR]. Carboxylate Zwitterions. The lowest-energy zwitterion-type complexes were found to relocate the carboxyl proton to the imidazole nitrogen in preference to the amino nitrogen. This is as expected because primary amines are less basic than imidazoles,43 and in addition histidine itself is preferentially protonated on the imidazole44 (although the energy difference C


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possible for Ba2+, but is closer to being competitive for Ca2+. For both of the present ligand isomers, iminol binding appears to be somewhat unfavorable at Ca2+, but not by amounts that are decisively beyond computational uncertainty or slightly disequilibrated ion populations. For Mg2+ and stronger metal ions, iminol binding is favored over CS. At this level of theory Ca2+ is predicted to favor the zwitterion complex for GH, and the CS complex for HG. In almost all cases where iminol binding is favored, it is the iminol conformation Im [NONR] with the imidazole bound to the metal that is favored. The Im [NON] conformation, with the imidazole remote from the metal and strongly hydrogenbonded to the iminol OH, becomes gradually more favorable as the metal ion binding becomes stronger (compare Im [NONR] and Im [NON]) but is indicated as the ground state only for Cu2+ with GH. In the Im [NON] conformation, the hydrogenbonding proton lies quite strongly on the side of the imidazole nitrogen, effectively creating a zwitterion form of the ligand. Moving the proton back to the oxygen side of this unsymmetrical hydrogen bond to form the iminol conformation is calculated to cost about 50 kJ mol−1. Phenylalanine Dipeptides. Figure 2 shows the computed relative energies of the low-lying conformations of the PheAla

Figure 1. Calculated energies of HisGly and GlyHis complexes. (See Table S1 for structure drawings.) For each metal−ligand combination, the energies are given relative to the most stable conformation for the given peptide−metal combination.

is not large). There is a marked difference in zwitterion favorability depending on the side-chain position. For HG binding to the weak Ba2+ ion, the two-coordinate zwitterion ZW [OO] is preferred, with the imidazole ring remote from the metal ion and hydrogen-bonded to the amide oxygen. For calcium, this binding mode is sharply higher in energy, making the HG zwitterion highly unfavorable for calcium and more strongly binding metals. For GH, a three-coordinate zwitterion, ZW [OOO], becomes possible. This zwitterion is much more favorable (by 50 kJ mol−1) than the corresponding HG zwitterion, and is predicted to be the ground state for both Ba2+ and Ca2+ complexes of GH. It is apparently highly stabilized by a favorable salt-bridge Coulomb interaction, analogous to the salt-bridge structures of simple amino acid complexes (as for Ba2+His (ref 13)). However, the energy of GH ZW [OOO] rises sharply for Mg and stronger binding metals, and zwitterion conformations are not competitive with other binding modes for these metal ions. CS Binding. Looking at CS [OOR] and CS [OONR], we see that the plots for these two structures are reasonably parallel over the span of metal ions. This suggests that even for the smallest metal ions, there is no added steric crowding resisting bringing the additional amino nitrogen anchor into coordination with the metal. For HG compared with GH, the play of steric factors makes it consistently more favorable (by about 20 or 30 kJ mol−1) to fold the amino nitrogen into coordination with the metal (CS [OONR] rather than CS [OOR]). Iminol Binding. The competition between CS and Iminol binding reverses at Ca2+. Iminol binding is nowhere near

Figure 2. Calculated energies of PheAla and AlaPhe complexes with M2+. (See Table S2 for structure drawings.) For each metal−ligand combination, the energies are given relative to the most stable conformation for the given metal−ligand combination.

and AlaPhe complexes. Structures and complete energy results are displayed in the Table S2. Features similar to the histidine dipeptides include the following: (i) ZW is competitive only for the weakest-binding metal ions, and is much more stable (relatively) for C−terminal AlaPhe than for N-terminal PheAla. (ii) The transition from CS to Im preference occurs between Ca and Mg. (iii) Four-coordinate Im [NONR] is more D


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favorable than the three-coordinate conformations Im [NOR] or Im [NON]. In fact, Im [NON] is very unfavorable in these cases because no strong hydrogen bond is available to the iminol OH to stabilize the free aromatic ring. However, at least for the PheAla case, Im [NOR] is not unreasonably high in energy and cannot be discounted as a possible ground state for the strong-binding metals. Spectroscopy. Spectra and Structures of Histidine Dipeptides. Mid-IR spectra have been obtained for the Ba2+ and Ca2+ complexes with GlyHis and are shown in Figures 3

Figure 4. IRMPD spectrum of Ca2+GlyHis, along with computed spectra (large basis) of possible structures of low relative energy. The most likely interpretation is a mixture of comparable amounts of CS [OOR] and ZW [OOO]. The spectrum of Ca2+HisGly (ref 30) is also shown for comparison (light gray spectrum), showing a prominent peak just below 1700 cm−1 that was interpreted as indicating a substantial fraction of CS structures in that population.

Spectra and Structures of Phenylalanine Dipeptides. A fair amount of progress has already been described in previous work on the spectroscopic analysis of complexes of phenylalanine-containing small peptides, including the metal(II) complexes of interest here. However, some questions have remained open where convincing agreement was not achieved between the observed results and computational predictions, or because the spectra, restricted for the most part to the mid-IR, were not sufficiently informative. The previously discussed structure preferences correlating the dipeptide ligand series FA, AF, and FF as a function of sidechain placement3,14,15,32,33 are revisited here with the help of the new spectroscopic results. The recent OPO laser capabilities at the FELIX laboratory have opened new possibilities in the 3000−4000 cm−1 wavelength range, and useful new insights have emerged. OPO spectra of the PheAla complexes are displayed below, or in the Ba2+ case, in the Supporting Information. Spectroscopic evidence is particularly interesting for the Ca2+ and Mg2+ complexes because this is the region of ligand binding strength which encompasses the crossover from CS to Iminol structures for the PheAla and AlaPhe ligands. The Ca2+AlaPhe spectrum in the OPO region (Figure 5) very clearly rules out the Im [NONR] possibility, which would show its presence by a pattern of two similar-sized OH stretching bands in this wavelength region, due to the COOH and iminol OH stretch modes. This complex is hence confidently assigned as CS. Looking at the reverse residue sequence (Ca2+PheAla), it was previously noted3 that the mid-IR spectrum did not give an unambiguous assignment for that complex. However, the new OPO spectrum (Figure 6) definitively rules out a predominant contribution from Im [NONR] by the same argument as for Ca2+AlaPhe, although the smaller features in the spectrum suggest a possible admixture of a small fraction of Iminol in a predominantly CS population. This spectroscopic evidence firmly confirms Ca2+ as preferring CS binding for both PheAla and AlaPhe.

Figure 3. IRMPD spectrum of Ba2+GlyHis (red spectrum), along with computed spectra (large basis) of the possible structures with low relative energies. The spectrum is a good match to a nearly pure population of ZW [OOO]. The spectrum of Ba2+HisGly (ref 30) is also shown for comparison (light gray spectrum), featuring a prominent peak near 1700 cm−1 that is interpreted as a C-terminal CO stretch vibration, suggesting a substantial fraction of CS structures in that population.

and 4, respectively, along with the calculated spectra of the energetically most likely structures composing the populations. The question to address is the competition between ZW and CS for these two weak-binding metal ions. The Ba2+GH spectrum fits well to the prediction for pure ZW, in agreement with the calculation showing that other structure types are considerably higher in energy. This is a reversal from the previously reported Ba2+HG complex, which was assigned as pure CS.30 The spectrum of this latter Ba2+HG complex is also shown in the figure, and it can be seen that the presence or absence of the very strong peak near 1700 cm−1 (C-terminal CO stretch, diagnostic for CS structures) highlights the contrast between these two isomers. In contrast, the Ca2+GH spectrum (Figure 4) shows a strong peak near 1700 cm−1 which must correspond to CS. The prominent feature at 1620 cm−1 also strongly suggests the presence of ZW, and we assign this population as consisting of comparable abundances of CS and ZW, which is not unreasonable in view of the fairly small difference in the calculated energies of these two conformers: 0 kJ mol−1 for ZW[OOO] and 8 kJ mol−1 for CS[OOR]. This assignment also offers a contrast, although less extreme than in the Ba2+ case, between the GH and HG isomers: In the Ca2+HG case, whose spectrum is also displayed in Figure 4, there is much less indication of a ZW component in the population than in the GH case. E


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Figure 5. IRMPD spectrum of Ca2+AlaPhe. The population is attributed to CS, with no significant contribution of either Im [NONR] or ZW [OOR]. Figure 7. IRMPD spectrum of Mg2+PheAla. The double feature at 3500−3600 cm−1 strongly confirms a population consisting of Im [NONR].

Progressing from Mg2+ to the stronger metal Ni2+ with PheAla, we would confidently expect, like the Mg2+ case, to see the same characteristic double-peak structure between 3500 and 3600 cm−1 corresponding to an Im [NONR] population, so it was a surprise to observe only a single sharp peak in the Ni2+PheAla OPO spectrum (Figure 8). The calculations suggest an explanation for this anomaly, showing that the Im [NONR] conformation may not be best for Ni2+, and that the amino nitrogen can decouple from the metal with little or no energetic cost, forming a hydrogen bond to the iminol OH to give the Im [NOR_OH] conformation. The predicted Im [NOR_OH] spectrum of the Ni2+PheAla complex matches well to the

Figure 6. IRMPD spectrum of Ca2+PheAla. A predominant CS population is indicated.

Mg2+ provides a striking contrast. For the Mg2+PheAla complex, the CS and Iminol conformations are virtually the same in calculated energy. In Figure 7, the OPO region shows the characteristic pattern of two peaks, with the Iminol OH stretch peak at 3570 cm−1 clearly indicating a major contribution of Im [NONR]. A simultaneous contribution from the CS structure is not ruled out by the spectrum in this OPO region, but in the mid-IR region the apparent absence in Figure 7 of the characteristic Amide II peak expected near 1500−1550 cm−1 for the CS structure (as is clearly evident in Figure 6) provides at least some evidence against a major contribution from CS [OOR]. In the Mg2+AlaPhe case, the CS [OOR] and Im [NONR] conformations are calculated as nearly equal in energy (with a small advantage for the Iminol). No spectrum is yet available, so an experimental confirmation is not yet possible for the preference in this case. Taking the computed result for Mg2+AlaPhe as an indication of a mixed CS/Im population, we can tentatively conclude that going from Ca2+ to Mg2+ for this ligand pair gives at least a partial switch from CS to Iminol.

Figure 8. IRMPD spectrum of Ni2+PheAla. The single peak in the 3500 cm−1 region rules out the (lowest-energy) Im [NONR] structure and strongly indicates a preference for the tridentate Im [NOR_OH] coordination, with simultaneous H2N...HO hydrogen bonding between the iminol OH and the N-terminal NH2. F


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reversals between ZW and CS have previously been reported for Ba2+ with Phe-containing dipeptides33 (as is noted in Figure 9), and Li+and Na+ with Arg-containing dipeptides.45 The side chain in the N-terminal position is evidently better able to wrap around and solvate the metal ion because it is always the Nterminal isomer that favors CS. Given the computational predictions of a switch from CS to Im binding between Ca2+ and Mg2+ for both AlaPhe and GlyHis complexes, it would be very desirable to have spectroscopic proof that these Mg2+ complexes do indeed favor Im complexation. Unfortunately, it has not been possible to prepare either of these complexes in the instruments we have used in this study. A mild contrast is observed for Ba2+ and Ca2+ between the present dipeptides versus the simple amino acids that were recently summarized in refs 41 and 1. For the simple amino acids, these metal ions often favor zwitterionic binding, whereas for the dipeptides, growing experience suggests that ZW binding is the exception rather than the rule. Figure 9 illustrates that the choice between zwitterion and charge-solvated is closely dependent on the accidental details of steric constraints and electrostatic stabilization for each individual ligand, but the majority of systems prefer CS to ZW. Table 1 shows computed electronic binding energies for the set of complexes studied here. Of interest is the observation


observed spectrum in both the OPO and the mid-IR regions. Such an opening up to go from a four-coordinate Mg2+ complex to a three-coordinate Ni2+ complex might be rationalized by the slightly smaller size and greater steric crowding of the Ni2+ ion. No experimental evidence is yet available for the Ni2+AlaPhe complex, although the calculations indicate a strong preference for an iminol conformation. Dipeptide Trends Compared. Summarized in Figure 9 is a comprehensive picture of dipeptide conformational prefer-

Table 1. Binding Energies of the Complexes in Their Most Stable Conformations (kJ mol−1)

Figure 9. Predictions and observations of favored conformations. Black bars are carboxylate zwitterions (ZW), red bars charge-solvated complexes (CS), and blue bars iminol complexes (Im). The most stable conformation (the one with lowest calculated energy) for each metal−ligand pair is assigned a stability of zero and has the tallest bar, and the less stable conformation types are displayed with negative energies relative to this one. Conformations which are disfavored by more than 20 kJ mol−1 are plotted at −20 kJ mol−1. Solid bars designate complexes which have been observed and confirmed by the IRMPD spectra. Hollow bars show relative energies for conformations which have only been predicted from the calculations but not yet directly observed. Shaded bars ([Ca FA Im] and [Mg FA CS]) are less-stable conformations with significant calculated abundances whose presence is consistent with, but not actually proven by, the experimental spectra.

that the histidine dipeptides bind more strongly, by about 50− 100 kJ mol−1, than the corresponding phenylalanine complexes, regardless of whether the binding mode is ZW, CS, or Im. There is, however, no obviously strong difference in binding energy between the N-terminal and C-terminal side-chain isomers.

ences determined for the two side-chain-dominated ligand pairs in the present study. The general behavior correlates with the binding strength of the metal ion, in the sense that the assigned preferences of binding motifs make the transitions from zwitterion to charge-solvated to iminol as we go from weakest-binding (Ba2+) to strongest (Ni2+). Ca2+ is the most characteristically transitional metal ion in that it shows meaningful competitions both for ZW versus CS, and also for CS versus Iminol. Ba2+ shows transitional character between ZW and CS, while Mg2+ shows transitional character between CS and Im. Ni2+ always has a strong preference for Im. Out of the present set of complexes, two new examples have emerged where the amino acid sequence governs a direct reversal, spectroscopically verified, of the character of complexation. These are the cases of Ba2+ and Ca2+ complexing to the histidine-containing dipeptides. The complexes with the Nterminal histidine ligand (HisGly) are predominantly or fully charge-solvated, while the complexes with the C-terminal histidine ligand (GlyHis) are predominantly or fully zwitterionic. Such spectroscopically verified sequence-dependent

CONCLUSIONS A full picture, with nearly comprehensive confirmation by experiment, has been laid out for the conformational preferences as summarized in Figure 9. Out of all the 12 metal−peptide pairs having spectroscopic data, only in the Ba2+AlaPhe case does the observed structure (ZW) not match the structure with lowest computed energy (CS) at the present level of theory. The comprehensive agreement between the experimental observations and the computational predictions of the lowest-energy conformations can be considered as support for the assumption that the process of electrospraying and trapping the ions results in reasonable equilibration to the most stable gas-phase distribution of conformations. The new information from IRMPD spectra using the OPO laser in the hydrogen stretching region was found to complement the previous mid-IR spectra, making possible quite detailed discrimination of different conformations. For instance, the series of complexes of PheAla has been shown to progress from pure CS [OOR] for Ba2+, to CS [OOR] with some admixture of Im [NONR] for Ca2+, to pure Im [NONR] for Mg2+, to the three-coordinate Im [NOR_OH] for Ni2+.

PheAla AlaPhe HisGly GlyHis

Ba

Ca

Mg

Ni

537 538 601 628

676 673 756 745

1002 992 1122 1109

1403 1388 1530 1516

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(4) Semrouni, D.; Balaj, O. P.; Calvo, F.; Correia, C. F.; Clavaguera, C.; Ohanessian, G. Structure of Sodiated Octa-Glycine: IRMPD Spectroscopy and Molecular Modeling. J. Am. Soc. Mass Spectrom. 2010, 21, 728−738. (5) Ye, S. J.; Armentrout, P. B. Absolute Thermodynamic Measurements of Alkali Metal Cation Interactions with a Simple Dipeptide and Tripeptide. J. Phys. Chem. A 2008, 112, 3587−3596. (6) Drayss, M. K.; Armentrout, P. B.; Oomens, J.; Schäfer, M. IR Spectroscopy of Cationized Aliphatic Amino Acids: Stability of Charge-Solvated Structure Increases with Metal Cation Size. Int. J. Mass Spectrom. 2010, 297, 18−27. (7) Dunbar, R. C.; Polfer, N. C.; Oomens, J. Gas-Phase Zwitterion Stabilization by a Metal Dication. J. Am. Chem. Soc. 2007, 129, 14562− 14563. (8) Jockusch, R. A.; Lemoff, A. S.; Williams, E. R. Hydration of Valine-Cation Complexes in the Gas Phase: On the Number of Water Molecules Necessary to Form a Zwitterion. J. Phys. Chem. A 2001, 105, 10929−10942. (9) Kapota, C.; Lemaire, J.; Maitre, P.; Ohanessian, G. Vibrational Signature of Charge Solvation vs Salt Bridge Isomers of Sodiated Amino Acids in the Gas Phase. J. Am. Chem. Soc. 2004, 126, 1836− 1842. (10) Moision, R. M.; Armentrout, P. B. Experimental and Theoretical Dissection of Sodium Cation/Glycine Interactions. J. Phys. Chem. A 2002, 106, 10350−10362. (11) Prell, J. S.; Chang, T. M.; Biles, J. A.; Berden, G.; Oomens, J.; Williams, E. R. Isomer Population Analysis of Gaseous Ions From Infrared Multiple Photon Dissociation Kinetics. J. Phys. Chem. A 2011, 115, 2745−2751. (12) Wyttenbach, T.; Witt, M.; Bowers, M. T. On the Stability of Amino Acid Zwitterions in the Gas Phase: The Influence of Derivatization, Proton Affinity, and Alkali Ion Addition. J. Am. Chem. Soc. 2000, 122, 3458−3464. (13) Dunbar, R. C.; Hopkinson, A. C.; Oomens, J.; Siu, C. K.; Siu, K. W. M.; Steill, J. D.; Verkerk, U. H.; Zhao, J. F. Conformation Switching in Gas-Phase Complexes of Histidine with Alkaline Earth Ions. J. Phys. Chem. B 2009, 113, 10403−10408. (14) Dunbar, R. C.; Steill, J. D.; Polfer, N. C.; Berden, G.; Oomens, J. Peptide Bond Tautomerization Induced by Divalent Metal Ions: Characterization of the Iminol Configuration. Angew. Chem., Int. Ed. 2012, 51, 4591−4593. (15) Dunbar, R. C.; Berden, G.; Oomens, J. How Does a Small Peptide Choose How to Bind a Metal Ion? IRMPD and Computational Survey of CS Versus Iminol Binding Preferences. Int. J. Mass Spectrom. 2013, 354, 356−364. (16) Chattopadhyaya, R.; Meador, W. E.; Means, A. R.; Quiocho, F. A. Calmodulin Structure Refined at 1.7 Angstrom Resolution. J. Mol. Biol. 1992, 228, 1177−1192. (17) Kozlowski, H.; Bal, W.; Dyba, M.; Kowalik-Jankowska, T. Specific structure-stability relations in metallopeptides. Coord. Chem. Rev. 1999, 184, 319−346. (18) Martin, R. B. Nickel Ion Binding to Amino Acids and Peptides. In Metal Ions in Biological Systems: Nickel and Its Role in Biology; Sigel, A., Sigel, H., Eds.; Marcel Dekker: New York, 1988; Vol. 23; p 156. (19) Sóvágó, I.; Ő sz, K. Metal Ion Selectivity of Oligopeptides. Dalton Trans. 2006, 3841−3854. (20) Martin, R. B.; Chamberlin, M.; Edsall, J. T. The Association of Nickel(II) Ion with Peptides1. J. Am. Chem. Soc. 1960, 82, 495−498. (21) Sovago, I. Metal Complexes of Peptides and Their Derivatives. In Ellis Horwood Series in Inorganic Chemistry: Biocoordination Chemistry: Coordination Equilibria in Biologically Active Systems; Burger, K., Ed.; Ellis Hornwood: New York, 1990; pp 135−184. (22) Sigel, H.; Martin, R. B. Coordinating Properties of the Amide Bond. Stability and Structure of Metal Ion Complexes of Peptides and Related Ligands. Chem. Rev. 1982, 82, 385−426. (23) Harford, C.; Sarkar, B. Amino Terminal Cu(II)- and Ni(II)Tinding (ATCUN) Motif of Proteins and Peptides: Metal Binding, DNA Cleavage, and Other Properties. Acc. Chem. Res. 1997, 30, 123− 130.

In most cases the preferred conformational type is the same for the N-terminal and the C-terminal position of the side chain. However, two CS/ZW reversals have been newly characterized (as seen in Figure 9), for the Ba2+ and Ca2+ complexes of the histidine dipeptides, where the preferred conformation switches between ZW and CS depending on sequence. In CS/ZW reversals previously reported33,45as well as the present examples, an N-terminal position of the side chain is more favorable for CS binding than a C-terminal position of the side chain. No obvious reversals were seen for the preferred conformational type in CS versus Im cases as a function of sequence. The phenylalanine peptides generally appeared to favor CS somewhat more over Im as compared with the histidine peptides. Metal-ion binding is significantly stronger for the histidine peptides than for the phenylalanine peptides, regardless of the sequence and regardless of the nature of the preferred conformation. This preference has to reflect a systematically stronger interaction of the metal ions with the imidazole lonepair anchor point in histidine compared with the cation-π anchor point of the aromatic phenyl side chain. Such a preference goes along with the apparently privileged status of histidine as an anchor for metal ions embedded in proteins.17,19

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ASSOCIATED CONTENT

S Supporting Information *

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jpca.5b06315. Complete citation for ref 34; structures and energies of metal-ion complexes of HisGly, GlyHis, PheAla, and AlaPhe; and spectrum of Ba2+PheAla (PDF)

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AUTHOR INFORMATION

Corresponding Authors

*E-mail: [email protected]. *E-mail: [email protected]. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS R.C.D. acknowledges support from the National Science Foundation, Grant PIRE-0730072, and expresses gratitude to the FELIX Laboratory for its continuing welcome. The FELIX staff, and particularly Dr. Lex van der Meer and Dr. Britta Redlich, are gratefully acknowledged for their assistance. Financial support for this project was provided by NWO Chemical Sciences under VICI Project 724.011.002. The authors also thank NWO Physical Sciences (EW) and the SARA Supercomputer Center for providing the computational resources (Grants MP-264-14 and SH-260-14).

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REFERENCES

(1) Dunbar, R. C. Spectroscopy of Metal Complexes with PeptideRelated Ligands. In Gas-Phase IR Spectroscopy and Structure of Biological Molecules; Oomens, J., Rijs, A., Eds.; Springer: Cham, Switzerland, 2015. (2) Balaj, O. P.; Kapota, C.; Lemaire, J.; Ohanessian, G. Vibrational Signatures of Sodiated Oligopeptides (GG-Na+, GGG-Na+, AA-Na+ and AAA-Na+) in the Gas Phase. Int. J. Mass Spectrom. 2008, 269, 196−209. (3) Dunbar, R. C.; Polfer, N. C.; Berden, G.; Oomens, J. Metal Ion Binding to Peptides: Oxygen or Nitrogen Sites? Int. J. Mass Spectrom. 2012, 330−332, 71−77. H


Article


The Journal of Physical Chemistry A (24) Kozlowski, H.; Potocki, S.; Remelli, M.; Rowinska-Zyrek, M.; Valensin, D. Specific Metal Ion Binding Sites in Unstructured Regions of Proteins. Coord. Chem. Rev. 2013, 257, 2625−2638. (25) Wyttenbach, T.; Liu, D.; Bowers, M. T. Interactions of the Hormone Oxytocin with Divalent Metal Ions. J. Am. Chem. Soc. 2008, 130, 5993−6000. (26) Burns, C. S.; Aronoff-Spencer, E.; Dunham, C. M.; Lario, P.; Avdievich, N. I.; Antholine, W. E.; Olmstead, M. M.; Vrielink, A.; Gerfen, G. J.; Peisach, J.; Scott, W. G.; Millhauser, G. L. Molecular Features of the Copper Binding Sites in the Octarepeat Domain of the Prion Protein. Biochemistry 2002, 41, 3991−4001. (27) Guerrieri, F.; Minicozzi, V.; Morante, S.; Rossi, G.; Furlan, S.; La Penna, G. Modeling the Interplay of Glycine Protonation and Multiple Histidine Binding of Copper in the Prion Protein Octarepeat Subdomains. JBIC, J. Biol. Inorg. Chem. 2009, 14, 361−374. (28) Petri, E. T.; Celic, A.; Kennedy, S. D.; Ehrlich, B. E.; Boggon, T. J.; Hodsdon, M. E. Structure of the EF-hand Domain of Polycystin-2 Suggests a Mechanism for Ca2+-dependent Regulation of Polycystin-2 Channel Activity. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 9176−9181. (29) Hu, P.; Gross, M. L. Strong Interactions of Anionic Peptides and Alkaline Earth Metal Ions: Metal-Ion-Bound Peptides in the Gas Phase. J. Am. Chem. Soc. 1992, 114, 9153−9160. (30) Dunbar, R. C.; Oomens, J.; Berden, G.; Lau, J. K. C.; Verkerk, U. H.; Hopkinson, A. C.; Siu, K. W. M. Metal Ion Complexes with HisGly: Comparison with PhePhe and PheGly. J. Phys. Chem. A 2013, 117, 5335−5343. (31) Polfer, N. C.; Oomens, J.; Dunbar, R. C. Alkali Metal Complexes of the Dipeptides PheAla and AlaPhe: IRMPD Spectroscopy. ChemPhysChem 2008, 9, 579−589. (32) Dunbar, R. C.; Steill, J. D.; Oomens, J. Encapsulation of Metal Cations by the PhePhe Ligand: A Cation-π Ion Cage. J. Am. Chem. Soc. 2011, 133, 9376−9386. (33) Dunbar, R. C.; Steill, J.; Polfer, N. C.; Oomens, J. Peptide Length, Steric Effects and Ion Solvation Govern Zwitterion Stabilization in Barium-Chelated Di- and Tripeptides,. J. Phys. Chem. B 2009, 113, 10552−10554. (34) Frisch, M. J. et al. Gaussian 09, revision A.02, Gaussian, Inc.: Pittsburgh, PA, 2009. See Supporting Information for full reference. (35) Grimme, S. Density Functional Theory with London Dispersion Corrections. WIREs Comput. Mol. Sci. 2011, 1, 211−228. (36) Patrick, A. L.; Stedwell, C. N.; Schindler, B.; Compagnon, I.; Berden, G.; Oomens, J.; Polfer, N. C. Insights Into the Fragmentation Pathways of Gas-Phase Protonated Sulfoserine. Int. J. Mass Spectrom. 2015, 379, 26−32. (37) Turecek, F.; Moss, C. L.; Pikalov, I.; Pepin, R.; Gulyuz, K.; Polfer, N. C.; Bush, M. F.; Brown, J.; Williams, J.; Richardson, K. GasPhase Structures of Phosphopeptide Ions: A Difficult Case. Int. J. Mass Spectrom. 2013, 354−355, 249−256. (38) Wang, D.; Gulyuz, K.; Stedwell, C. N.; Yu, L.; Polfer, N. C. Effect of Phenol and Acidic Side Chains on the Protonation Sites of b2 Ions Confirmed by IRMPD Spectroscopy. Int. J. Mass Spectrom. 2012, 330−332, 144−151. (39) Wu, R. R.; Yang, B.; Berden, G.; Oomens, J.; Rodgers, M. T. Gas-Phase Conformations and Energetics of Protonated 2′-Deoxyguanosine and Guanosine: IRMPD Action Spectroscopy and Theoretical Studies. J. Phys. Chem. B 2014, 118, 14774−14784. (40) Almasian, M.; Grzetic, J.; van Maurik, J.; Steill, J. D.; Berden, G.; Ingemann, S.; Buma, W. J.; Oomens, J. Non-Equilibrium Isomer Distribution of the Gas-Phase Photoactive Yellow Protein Chromophore. J. Phys. Chem. Lett. 2012, 3, 2259−2263. (41) Polfer, N. C.; Oomens, J. Vibrational Spectroscopy of Bare and Solvated Ionic Complexes of Biological Relevance. Mass Spectrom. Rev. 2009, 28, 468−494. (42) Martens, J. K.; Grzetic, J.; Berden, G.; Oomens, J. Gas-Phase Conformations of Small Polyprolines and Their Fragment Ions by IRMPD Spectroscopy. Int. J. Mass Spectrom. 2015, 377, 179−187. (43) Hunter, E. P. L.; Lias, S. G. Evaluated Gas Phase Basicities and Proton Affinities of Molecules: An Update. J. Phys. Chem. Ref. Data 1998, 27, 413−656.

(44) Huang, Z.; Lin, Z.; Song, C. Protonation Processes and Electronic Spectra of Histidine and Related Ions. J. Phys. Chem. A 2007, 111, 4340−4352. (45) Prell, J. S.; Demireva, M.; Oomens, J.; Williams, E. R. Role of Sequence in Salt-Bridge Formation for Alkali Metal Cationized GlyArg and ArgGly Investigated with IRMPD Spectroscopy and Theory. J. Am. Chem. Soc. 2009, 131, 1232−1242.

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Divalent Metal-Ion Complexes with Dipeptide Ligands Having Phe

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