Ion-peptide interactions between alkali metal ions and a termini-protected dipeptide: modeling a portion of the selectivity filter in K+ channels

Similarity scores of vibrational spectra reveal the atomistic structure of pentapeptides in multiple basins

Vibrational spectroscopy combined with theoretical calculations is a powerful tool for analyzing the interaction and conformation of peptides at the atomistic level. Nonetheless, identifying the structure becomes increasingly difficult as the peptide size grows large. One example is acetyl-SIVSF-N-methylamide, a capped pentapeptide, whose atomistic structure has remained unknown since its first observation [T. Sekiguchi, M. Tamura, H. Oba, P. Çarçarbal, R. R. Lozada-Garcia, A. Zehnacker-Rentien, G. Grégoire, S. Ishiuchi and M. Fujii, Angew. Chem., Int. Ed., 2018, 57, 5626-5629]. Here, we propose a novel conformational search method, which exploits the structure-spectrum correlation using a similarity score that measures the agreement of theoretical and experimental spectra. Surprisingly, the two conformers have distinctly different energy and geometry. The second conformer is 25 kJ mol-1 higher in energy than the other, lowest-energy conformer. The result implies that there are multiple pathways in the early stage of the folding process: one to the global minimum and the other to a different basin. Once such a structure is established, the second conformer is unlikely to overcome the barrier to produce the most stable structure due to a vastly different hydrogen bond network of the backbone. Our proposed method can characterize the lowest-energy conformer and kinetically trapped, high-energy conformers of complex biomolecules.

Stepwise hydration of [CH3COOMg]+ studied by cold ion trap infrared spectroscopy: insights into interactions in the magnesium channel selection filters

The magnesium channel controls Mg2+ concentration in the cell and plays an indispensable role in biological functions. The crystal structure of the Magnesium Transport E channel suggested that Mg2+ hydrated by 6 water molecules is transported through a selection filter consisting of COO- groups on two Asp residues. This Mg2+ motion implies successive pairing with -OOC-R and dissociation mediated by water molecules. For another divalent ion, however, it is known that RCOO-⋯Ca2+ cannot be separated even with 12 water molecules. From this discrepancy, we probe the structure of Mg2+(CH3COO-)(H2O)4-17 clusters by measuring the infrared spectra and monitoring the vibrational frequencies of COO- with the help of quantum chemistry calculations. The hydration by (H2O)6 is not enough to induce ion separation, and partially-separated or separated pairs are formed from 10 water molecules at least. These results suggest that the ion separation between Mg2+ and carboxylate ions in the selection-filter of the MgtE channel not only results from water molecules in their first hydration shell, but also from additional factors including water molecules and protein groups in the second solvation shell of Mg2+.

Can Ag+ Permeate through a Potassium Ion Channel? A Bottom-Up Approach by Infrared Spectroscopy of the Ag+ Complex with the Partial Peptide of a Selectivity Filter

Silver and silver ions have a long history of antimicrobial activity and medical applications. Nevertheless, the activity of Ag⁺ against bacteria, how it enters a cell, has not yet been established. The K⁺ channel, a membrane protein, is a possible route. The addition of a channel inhibitor (4-aminopyridine) to modulate the Ag⁺ uptake could support this view. However, the inhibitor enhances the uptake of Ag⁺, the opposite result. We have applied cold ion trap infrared laser spectroscopy to complexes of Ag⁺ and Ac-Tyr-NHMe (a model for GYG) which is a portion of the selectivity filter in the K⁺ channel to consider the question of permeation. With support from quantum chemical calculations, we have determined the stable conformations of the complex. The conformations strongly suggest that Ag⁺ would not readily permeate the K⁺ channel. The mechanism of the unexpected enhancement by the inhibitor is discussed.

Na+ Selective Binding by Beauvericin and Its Mechanism Studied by Mass-Coupled Cold Ion Trap Infrared Spectroscopy

Beauvericin (Bv) is a cyclic hexadepsipeptide mycotoxin that selectively transports ions across cell membranes. Characterization of its intrinsic ion affinity has been complicated by different previous results in condensed phases and biological membranes. We report the marked specificity between alkali metal ions by Bv using experimental and computational methods. Mass spectrometry shows Bv readily binds all five alkali ions; however, the complex with Na⁺ is the most abundant species, indicating a strong binding preference. Gas phase infrared spectroscopy and theoretical calculations show that Li⁺, K⁺, Rb⁺, and Cs⁺ are coordinated by three amide carbonyl oxygens on the N-methylamino-l-phenylalanyl face. Selectivity for Na⁺ is achieved as Bv sequesters Na⁺ in the center of its cavity formed by three amide carbonyl and three ester carbonyl groups, a configuration unique among alkali metal ions. This finding provides insight into the correlation between selectivity and conformation of Bv, essential for development of this mycotoxin.

Do Stereochemical Effects Overcome a Charge-Induced Perturbation in Isolated Protonated Cyclo(Tyr-Tyr)?

Two diastereomers of the protonated diketopiperazine (DKP) dipeptide cyclo(Tyr-Tyr), namely, cyclo(LTyr-LTyr)H⁺ and cyclo(LTyr-DTyr)H⁺, are studied in a cryogenic ion trap by means of IR photodissociation spectroscopy combined with quantum chemical calculations. The two diastereomers have similar structures in which one of the rings is folded over the DKP ring and the other one is extended in a trans geometry, allowing a strong OH⁺···π interaction to take place. This contrasts to the observation of a stacked geometry for neutral cyclo(LTyr-LTyr) only under supersonic expansion conditions that do not exist for cyclo(LTyr-DTyr). In the protonated form, the strength of the OH⁺···π interaction is different for the two diastereomers, resulting in a ∼110 cm^-1 difference in the ν(OH⁺) frequency and a smaller but clearly identifiable difference in the protonated amide ν(NH) frequency. Stereochemical effects are therefore still evidenced despite the strong perturbation due to the excess charge.

A bottom-up approach to the ion recognition mechanism of K+ channels from laser spectroscopy of hydrated partial peptide-alkali metal ion complexes

K⁺ channels allow selective permeation of K⁺, but not physiologically abundant Na⁺, at almost diffusion limit rates. The conduction mechanism of K⁺ channels is still controversial, with experimental and computation studies supporting two distinct conduction mechanisms: either with or without water inside the channel. Here, we employ a bottom-up approach on hydrated alkali metal complexes of a model peptide of K⁺ channels, Ac-Tyr-NHMe, to characterize metal-peptide, metal-water, and water-peptide interactions that govern the selectivity of K⁺ channels at a molecular level. Both the extension to the series of alkali metal ions and to temperature-dependent studies (approaching physiological values) have revealed the clear difference between permeable and non-permeable ions in the spectral features of the ion complexes. Furthermore, the impact of hydration is discussed in relation to the K⁺ channels by comparisons of the non-hydrated and hydrated complexes.

Excited state dynamics of protonated dopamine: hydration and conformation effects

Electronic and vibrational spectroscopy in a cryogenic ion trap has been applied to protonated dopamine water clusters and assigned with the help of quantum chemistry calculations performed in the ground and electronic excited states. A dramatic hydration effect is observed when dopamine is solvated by three water molecules. The broad electronic spectra recorded for the bare and small water clusters containing protonated dopamine turn to sharp, well-resolved vibronic transitions in the 1-3 complex. This reflects the change induced by hydration in the photodynamics of protonated dopamine which is initially controlled by an excited state proton transfer (ESPT) reaction from the ammonium group toward the catechol ring. Interestingly, conformer selectivity is revealed in the 1-3 complex which shows two low lying energy conformers for which the ESPT reaction is prevented or not depending on the H-bond network formed between the dopamine and water molecules.

Conformation and Metal Cation Binding of Zwitterionic Alanine Tripeptide in Saline Solutions by Infrared Vibrational Spectroscopy and Molecular Dynamics Simulations

In this work, linear infrared (IR) spectroscopy and molecular dynamics (MD) simulations were used to examine the interaction of different metal cations (Na⁺, Ca²⁺, Mg²⁺, and Zn²⁺) with backbone (amide C═O) and C-terminal carboxylate (COO^-) groups in zwitterionic alanine tripeptide (Ala3) in aqueous solutions with varying saline concentrations. Circular dichroism spectra and MD results suggest that Ala3 is predominantly in polyproline-II (PP_II) conformation, whose amide-I and asymmetric carboxylate stretching IR vibration signatures are also supported by quantum-chemistry calculations. The zwitterionic form of Ala3 separates the two amide-I modes in frequency, which are weakly coupled modes, as revealed by two-dimensional IR measurement, and can be used to probe backbone-cation interactions at different scenarios (near charged or neutral chemical groups respectively). Cation concentration-dependent IR frequency red shifts in the amide-I mode are seen for both amide-I modes, whereas blue shifts are also seen in the amide-I mode far from the NH₃⁺ group. The observed spectral changes are discussed from the perspective of the salting-in and salting-out abilities of the cations. In addition, all the metal cations studied here (except Zn²⁺) can specifically coordinate to the COO^- group in bidentate and pseudo-bridging forms simultaneously. For Zn²⁺, only the pseudo-bridging form exists. Our results shed light on the macroscopic protein salting-in and salting-out phenomena from the perspective of key chemical bonds in peptides.

Double Ion Trap Laser Spectroscopy of Alkali Metal Ion Complexes with a Partial Peptide of the Selectivity Filter in K+ Channels─Temperature Effect and Barrier for Conformational Conversions

Potassium ion channels selectively permeate K⁺, as well as Rb⁺ and Cs⁺ to some degree, while excluding Na⁺ and Li⁺. Conformations of alkali metal complexes of Ac-Tyr-NHMe, a model peptide of the selectivity filter in a K⁺ channel, were previously found to correlate with the permeability of alkali metal ions to a K⁺ channel by cold ion trap infrared spectroscopy. With an additional temperature-controlled ion trap, we examined the conformations of the alkali metal complexes, allowing the ions to collide with a He buffer gas at different temperatures, prior to spectroscopic investigation. The conformational distribution of the K⁺-peptide complex shows the most significant variation with temperature, which suggests that this complex has more flexibility when complexed with K⁺ and suggests lower barrier heights than other metal-peptide complexes. The variability of the conformational distribution with temperature for the ions follows the same order of ion permeability of a K⁺ channel. This work demonstrates that the additional temperature-controlled ion trap is a powerful tool to explore the conformational landscape of flexible molecular systems.

Some opinions on MD-based vibrational spectroscopy of gas phase molecules and their assembly: An overview of what has been achieved and where to go

We hereby review molecular dynamics simulations for anharmonic gas phase spectroscopy and provide some of our opinions of where the field is heading. With these new directions, the theoretical IR/Raman spectroscopy of large (bio)-molecular systems will be more easily achievable over longer time-scale MD trajectories for an increase in accuracy of the MD-IR and MD-Raman calculated spectra. With the new directions presented here, the high throughput 'decoding' of experimental IR/Raman spectra into 3D-structures should thus be possible, hence advancing e.g. the field of MS-IR for structural characterization by spectroscopy. We also review the assignment of vibrational spectra in terms of anharmonic molecular modes from the MD trajectories, and especially introduce our recent developments based on Graph Theory algorithms. Graph Theory algorithmic is also introduced in this review for the identification of the molecular 3D-structures sampled over MD trajectories.

Ion Selectivity in the ENaC/DEG Family: A Systematic Review with Supporting Analysis

The Epithelial Sodium Channel/Degenerin (ENaC/DEG) family is a superfamily of sodium-selective channels that play diverse and important physiological roles in a wide variety of animal species. Despite their differences, they share a high homology in the pore region in which the ion discrimination takes place. Although ion selectivity has been studied for decades, the mechanisms underlying this selectivity for trimeric channels, and particularly for the ENaC/DEG family, are still poorly understood. This systematic review follows PRISMA guidelines and aims to determine the main components that govern ion selectivity in the ENaC/DEG family. In total, 27 papers from three online databases were included according to specific exclusion and inclusion criteria. It was found that the G/SxS selectivity filter (glycine/serine, non-conserved residue, serine) and other well conserved residues play a crucial role in ion selectivity. Depending on the ion type, residues with different properties are involved in ion permeability. For lithium against sodium, aromatic residues upstream of the selectivity filter seem to be important, whereas for sodium against potassium, negatively charged residues downstream of the selectivity filter seem to be important. This review provides new perspectives for further studies to unravel the mechanisms of ion selectivity.

Potassium and sodium ion complexes with a partial peptide of the selectivity filter in K+ channels studied by cold ion trap infrared spectroscopy: the effect of hydration

Potassium channels allow K+ to rapidly diffuse, while the selectivity filter (SF) actively blocks Na+. The presence of water in the SF during ion translocation remains under debate due to the experimental and computational challenges in characterizing the interactions between water, ions, and the SF. Our bottom-up approach has been applied to a system composed of a partial peptide of the SF (Ac-tyrosine-NHMe) with a metal ion and a single water molecule to probe these interactions. The IR photodissociation spectra of M+Ac-tyrosine-NHMe(H2O) (M = Na, K) combined with quantum chemical calculations revealed that the water molecule binding sites are ion-dependent. In addition, the ion-peptide distances are elongated significantly for the K+ complex in comparison to the Na+ complex by the addition of a single water molecule. This striking structural difference with the water molecule is discussed in relation to ion selectivity and translocation within the K+ channel.

Rethinking Ion Transport by Ionophores: Experimental and Computational Investigation of Single Water Hydration in Valinomycin-K+ Complexes

Valinomycin is a macrocyclic ionophore that transports K⁺ across hydrophobic membranes. Its function depends on selectivity, capture, transport, and release of the ion. While thermodynamics clearly indicate that valinomycin binds K⁺ preferentially over all other alkali ions, characterizing the capture/transport/release of K⁺ by valinomycin at the molecular level remains a challenge. The bracelet-like structure of valinomycin-K⁺ (K⁺VM) has the ion completely enveloped, facilitating transport through the cell membrane. We report that hydration by a single water molecule, (K⁺VM)(H₂O), produces three different conformers, identified by infrared spectroscopy and supporting computational studies. For two minor conformers, the water prevents the ionophore from closing, a conformation that would inhibit diffusion through the membrane. However, the dominant conformer encloses both the ion and the water, replicating the bracelet-like K⁺VM and arguably enhancing diffusion through the membrane. This potential for active participation of water in transport through the hydrophobic cellular membrane has never been previously considered.

Chiral discrimination between tyrosine and β-cyclodextrin revealed by cryogenic ion trap infrared spectroscopy

Complexes of permethylated β-cyclodextrin (β-MCD) with the two enantiomers of protonated tyrosine (l- and d-TyrH⁺) are studied by cryogenic ion trap infrared photo-dissociation spectroscopy. The vibrational spectra in the OH/NH stretch and fingerprint regions are assigned based on density functional theory calculations. The spectrum of both l- and d-TyrH⁺ complexes contains features characteristic of a first structure with ammonium and acid groups of the amino acid simultaneously interacting with the β-MCD, the phenolic OH remaining free. A second structure involving additional interaction between the phenolic OH and the β-MCD is observed only for the complex with d-TyrH⁺. The larger abundance of the d-TyrH⁺ complex in the mass spectrum is tentatively explained in terms of (1) better insertion of d-TyrH⁺ within the cavity with the hydrophobic aromatic moiety less exposed to hydrophilic solvent molecules and (2) a stiff structure involving three interaction points, namely the ammonium, the phenolic OH and the carboxylic acid OH, which is not possible for the complex with l-TyrH⁺. The recognition process does not occur through size effects that induce complementarity to the host molecule but specific interactions. These results provide a comprehensive understanding of how the cyclodextrin recognises a chiral biomolecule.

Gas-Phase Infrared Spectroscopy of Neutral Peptides: Insights from the Far-IR and THz Domain

Gas-phase, double resonance IR spectroscopy has proven to be an excellent approach to obtain structural information on peptides ranging from single amino acids to large peptides and peptide clusters. In this review, we discuss the state-of-the-art of infrared action spectroscopy of peptides in the far-IR and THz regime. An introduction to the field of far-IR spectroscopy is given, thereby highlighting the opportunities that are provided for gas-phase research on neutral peptides. Current experimental methods, including spectroscopic schemes, have been reviewed. Structural information from the experimental far-IR spectra can be obtained with the help of suitable theoretical approaches such as dynamical DFT techniques and the recently developed Graph Theory. The aim of this review is to underline how the synergy between far-IR spectroscopy and theory can provide an unprecedented picture of the structure of neutral biomolecules in the gas phase. The far-IR signatures of the discussed studies are summarized in a far-IR map, in order to gain insight into the origin of the far-IR localized and delocalized motions present in peptides and where they can be found in the electromagnetic spectrum.

Conformational assignment of gas phase peptides and their H-bonded complexes using far-IR/THz: IR-UV ion dip experiment, DFT-MD spectroscopy, and graph theory for mode assignment

Graph theory based vibrational modes as new entities for vibrational THz spectroscopy.