Protonated Arginine and Protonated Lysine: Hydration and Its Effect on the Stability of Salt-Bridge Structures

Ion Spectroscopy Reveals Structural Difference for Proteins Microhydrated by Retention and Condensation of Water

Protein ubiquitin in its +7 charge state microhydrated by 5 and 10 water molecules has been interrogated in the gas phase by cold ion UV/IR spectroscopy. The complexes were formed either by condensing water onto the unfolded bare proteins in a temperature-controlled ion trap or by incomplete dehydration of the folded proteins. In the case of cryogenic condensation, the UV spectra of the complexes exhibit a resolved vibrational structure, which looks similar to the spectrum of bare unfolded ubiquitin. The spectra become, however, broad-band with no structure when complexes of the same size are produced by incomplete dehydration under soft conditions of electrospray ionization. We attribute this spectroscopic dissimilarity to the structural difference of the protein: condensing a few water molecules cannot refold the gas-phase structure of the bare ubiquitin, while the retained water preserves its solution-like folded motif through evaporative cooling. This assessment is firmly confirmed by IR spectroscopy, which reveals the presence of free NH and carboxylic OH stretching vibrations only in the complexes with condensed water.

Biological importance of arginine: A comprehensive review of the roles in structure, disorder, and functionality of peptides and proteins

Arginine shows Jekyll and Hyde behavior in several respects. It participates in protein folding via ionic and H-bonds and cation-pi interactions; the charge and hydrophobicity of its side chain make it a disorder-promoting amino acid. Its methylation in histones; RNA binding proteins; chaperones regulates several cellular processes. The arginine-centric modifications are important in oncogenesis and as biomarkers in several cardiovascular diseases. The cross-links involving arginine in collagen and cornea are involved in pathogenesis of tissues but have also been useful in tissue engineering and wound-dressing materials. Arginine is a part of active site of several enzymes such as GTPases, peroxidases, and sulfotransferases. Its metabolic importance is obvious as it is involved in production of urea, NO, ornithine and citrulline. It can form unusual functional structures such as molecular tweezers in vitro and sprockets which engage DNA chains as part of histones in vivo. It has been used in design of cell-penetrating peptides as drugs. Arginine has been used as an excipient in both solid and injectable drug formulations; its role in suppressing opalescence due to liquid-liquid phase separation is particularly very promising. It has been known as a suppressor of protein aggregation during protein refolding. It has proved its usefulness in protein bioseparation processes like ion-exchange, hydrophobic and affinity chromatographies. Arginine is an amino acid, whose importance in biological sciences and biotechnology continues to grow in diverse ways.

Hydrophobicity of arginine leads to reentrant liquid-liquid phase separation behaviors of arginine-rich proteins

Intrinsically disordered proteins rich in cationic amino acid groups can undergo Liquid-Liquid Phase Separation (LLPS) in the presence of charge-balancing anionic counterparts. Arginine and Lysine are the two most prevalent cationic amino acids in proteins that undergo LLPS, with arginine-rich proteins observed to undergo LLPS more readily than lysine-rich proteins, a feature commonly attributed to arginine's ability to form stronger cation-π interactions with aromatic groups. Here, we show that arginine's ability to promote LLPS is independent of the presence of aromatic partners, and that arginine-rich peptides, but not lysine-rich peptides, display re-entrant phase behavior at high salt concentrations. We further demonstrate that the hydrophobicity of arginine is the determining factor giving rise to the reentrant phase behavior and tunable viscoelastic properties of the dense LLPS phase. Controlling arginine-induced reentrant LLPS behavior using temperature and salt concentration opens avenues for the bioengineering of stress-triggered biological phenomena and drug delivery systems.

Probing Gas-Phase-Clustering Thermodynamics with Ion Mobility-Mass Spectrometry: Association Energies of Phenylalanine Ions with Gas-Phase Alcohols

Vapor assisted mobility shift measurements were made with atmospheric pressure drift-tube ion mobility-mass spectrometry (IM-MS) to determine the thermodynamic properties of weakly bound ion-molecule clusters formed from protonated phenylalanine and neutral vapor molecules with hydroxyl functional groups. Relative binding energies and gas-phase association energies of amino acid ions clustered with small organic molecules have been established previously using high-pressure mass spectrometry. However, the issue of volatility largely prohibits the use of high-pressure mass spectrometry for the determination of gas-phase associations of amino acid ions clustered with neutral vapor molecules in many instances. In contrast, ion mobility measurements can be made at atmospheric pressure with volatile vapor additives near and above their boiling points, providing access to clustering equilibria not possible using high-vacuum techniques. In this study, we report the gas-phase association energies, enthalpies, and entropies for a protonated phenylalanine ion clustered with three neutral vapor molecules: 2-propanol, 1-butanol, and 2-pentanol based upon measurements at temperatures ranging from 120 to 180 °C. The gas-phase enthalpy and entropy changes ranged between -4 to -7 kcal/mol and -3 to 6 cal/(mol K), respectively. We found enthalpically favored ion-neutral cluster reactions for phenylalanine with entropic barriers for the formation of phenylalanine-1-butanol and phenylalanine-2-pentanol cluster ions, while phenylalanine-2-propanol cluster ion formation is both enthalpically and (weakly) entropically favorable. Under the measurement conditions examined, phenylalanine-vapor modifier cluster ion formation is clearly observed via shifts in the drift time for the three test vapor molecules. In comparison, negligible shifts in mobility are observed for protonated arginine exposed to the same vapor modifiers.

Pulsed Nano-ESI: Application in Ion Mobility-MS and Insights into Spray Dynamics

We have previously shown that pulsed nano-ESI offers direct ion introduction into an AP-IM cell in the absence of conventional gates and desolvation. Here, we further characterize this ion injection method and utilize it to gain insights into nano-ESI pulsed spray dynamics. We demonstrate that a pulsed nano-ESI operated at 20 Hz with ion generation pulses of 170-510 μs offers reproducible ion arrival times (0.09-0.21% RSD). Arrival times are then translated to effective collision cross sections (CCSs) using tetraalkylammonium ions as CCS internal standards. For ions with low solvent affinity, effective CCS values match those reported for fully desolvated ions. For amino acids and a series of alkylamine homologues, the effective CCS values are higher than those for fully desolvated ions and correlate with solvent affinity, suggesting that ions with high hydration affinities traverse the mobility cell as hydrated ions. Notably, hydrates are not observed in the MS spectra due to ion activation during the transport into vacuum. Using these observations as a framework to interpret effective CCS values, we investigate the impact of nano-ESI pulse duration on ion properties. We observe that longer pulse durations lead to the enhancement of ion abundance for low-ionization-efficiency analytes and a reduction in clustering. However, effective CCSs are not significantly altered by spray pulse duration, implying that similar ion structures emerge rapidly at all investigated pulse durations. Ion abundance results suggest a temporal evolution of droplets in pulsed nano-ESI where droplets emitted later in the spray formation appear to be smaller, providing enhanced ionization.

Infrared multiple photon dissociation action spectroscopy of protonated glycine, histidine, lysine, and arginine complexed with 18-crown-6 ether

Complexes of 18-crown-6 ether (18C6) with four protonated amino acids (AAs) are examined using infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light generated by the infrared free electron laser at the Centre Laser Infrarouge d'Orsay (CLIO). The AAs examined in this work include glycine (Gly) and the three basic AAs: histidine (His), lysine (Lys), and arginine (Arg). To identify the (AA)H⁺(18C6) conformations present in the experimental studies, the measured IRMPD spectra are compared to spectra calculated at the B3LYP/6-311+G(d,p) level of theory. Relative energies of various conformers and isomers are provided by single point energy calculations carried out at the B3LYP, B3P86, M06, and MP2(full) levels using the 6-311+G(2p,2d) basis set. The comparisons between the IRMPD and theoretical IR spectra indicate that 18C6 binds to Gly and His via the protonated backbone amino group, whereas protonated Lys prefers binding via the protonated side-chain amino group. Results for Arg are less definitive with strong evidence for binding to the protonated guanidino side chain (the calculated ground conformer at most levels of theory), but contributions from backbone binding to a zwitterionic structure are likely.

Hydration of Guanidinium Ions: An Experimental Search for Like-Charged Ion Pairs

Guanidinium ions (GdmH⁺) are reported to form stable complexes (GdmH⁺/GdmH⁺) in aqueous solution despite strong repulsive interactions between the like-charged centers. These complexes are thought to play important roles in protein folding, membrane penetration, and formation of protein dimers. Although GdmH⁺ ions are weakly hydrated, semiempirical calculations provide evidence that these like-charged complexes are stabilized by water molecules, which serve important structural and energetic roles. Specifically, water molecules bridge between the GdmH⁺ ions of GdmH⁺/GdmH⁺ complexes as well as complexes involving the guanidinium side chains of arginine. Potential biological significances of like-charged complexes have been largely confirmed by ab initio molecular dynamics simulations and indirect experimental evidence. We report cryo-ion mobility-mass spectrometry results for the GdmH⁺/GdmH⁺ ion pair confined in a nanodroplet- the first direct experimental observation of this like-charged complex. A second like-charged complex, described as a water-mediated complex involving GdmH⁺ and H₃O⁺, was also observed.

Charge and Peptide Concentration as Determinants of the Hydrogel Internal Aqueous Environment

Self-assembling peptides are a promising class of biomaterials with desirable biocompatibility and versatility. In particular, the oligopeptide (RADA)₄, consisting of arginine (R), alanine (A), and aspartic acid (D), self-assembles into nanofibers that develop into a three-dimensional hydrogel of up to 99.5% (w/v) water; yet, the organization of water within the hydrogel matrix is poorly understood. Importantly, peptide concentration and polarity are hypothesized to control the internal water structure. Using variable temperature deuterium solid-state nuclear magnetic resonance (²H NMR) spectroscopy, we measured the amount of bound water in (RADA)₄-based hydrogels, quantified as the non-frozen water content. To investigate how peptide polarity affects water structure, five lysine (K) moieties were appended to (RADA)₄ to generate (RADA)₄K₅. Hydrogels at 1 and 5% total peptide concentration were prepared from a 75:25 (w/w) blend of (RADA)₄:(RADA)₄K₅ and similarly analyzed by ²H NMR. Interestingly, at 5% peptide concentration, there was lower mobile water content in the lysinated versus the pristine (RADA)₄ hydrogel. Regardless of the presence of lysine, the 5% peptide concentration had higher non-frozen water content at temperatures as low as 217 ± 1.0 K, suggesting that bound water increases with peptide concentration. The bound water, though non-frozen, may be strongly bound to the charged lysine moiety to appear as immobilized water. Further understanding of the factors controlling water structure within hydrogels is important for tuning the transport properties of bioactive solutes in the hydrogel matrix when designing for biomedical applications.

Matrix Isolation Spectroscopy: Aqueous p-Toluenesulfonic Acid Solvation

Interaction between p-toluenesulfonic acid (pTSA) and water is studied at -20 °C in a CCl₄ matrix. In CCl₄ water exists as monomers with restricted rotational motion about its symmetry axis. Additionally, CCl₄ is transparent in the hydrogen-bonded region; CCl₄ thus constitutes an excellent ambient thermal energy matrix isolation medium for diagnosing interactions with water. Introducing pTSA-nH₂O gives rise to two narrow resonances at 3642 cm^-1 and at 2835 cm^-1 plus a broad 3000-3550 cm^-1 absorption. In addition, negative monomer symmetric and asymmetric stretch features relative to nominally dry CCl₄ indicate that fewer water monomers exist in the cooled (-20 °C) acid solution than in room-temperature anhydrous CCl₄. The negative peaks along with the broad absorption band indicate that water monomers are incorporated into clusters. The 3642 cm^-1 resonance is assigned to the OH-π interaction with a cluster containing many water molecules per acid molecule. The 2835 cm^-1 resonance is assigned to the (S-)O-H stretch of pTSA-dihydrate. The coexistence of these two species provides insights into interactions in this acid-water CCl₄ system.

Assessing Physicochemical Properties of Drug Molecules via Microsolvation Measurements with Differential Mobility Spectrometry

The microsolvated state of a molecule, represented by its interactions with only a small number of solvent molecules, can play a key role in determining the observable bulk properties of the molecule. This is especially true in cases where strong local hydrogen bonding exists between the molecule and the solvent. One method that can probe the microsolvated states of charged molecules is differential mobility spectrometry (DMS), which rapidly interrogates an ion's transitions between a solvated and desolvated state in the gas phase (i.e., few solvent molecules present). However, can the results of DMS analyses of a class of molecules reveal information about the bulk physicochemical properties of those species? Our findings presented here show that DMS behaviors correlate strongly with the measured solution phase pK_a and pK_b values, and cell permeabilities of a set of structurally related drug molecules, even yielding high-resolution discrimination between isomeric forms of these drugs. This is due to DMS's ability to separate species based upon only subtle (yet predictable) changes in structure: the same subtle changes that can influence isomers' different bulk properties. Using 2-methylquinolin-8-ol as the core structure, we demonstrate how DMS shows promise for rapidly and sensitively probing the physicochemical properties of molecules, with particular attention paid to drug candidates at the early stage of drug development. This study serves as a foundation upon which future drug molecules of different structural classes could be examined.

Arginine-containing ligands enhance H₂ oxidation catalyst performance

Hydrogenase enzymes use Ni and Fe to oxidize H2 at high turnover frequencies (TOF) (up to 10,000 s(-1)) and low overpotentials (<100 mV). In comparison, the fastest reported synthetic electrocatalyst, [Ni(II)(P(Cy)2N(tBu)2)2](2+), oxidizes H2 at 60 s(-1) in MeCN under 1 atm H2 with an unoptimized overpotential of ca. 500 mV using triethylamine as a base. Here we show that a structured outer coordination sphere in a Ni electrocatalyst enhances H2 oxidation activity: [Ni(II)(P(Cy)2N(Arg)2)2](8+) (Arg=arginine) has a TOF of 210 s(-1) in water with high energy efficiency (180 mV overpotential) under 1 atm H2 , and 144,000 s(-1) (460 mV overpotential) under 133 atm H2. The complex is active from pH 0-14 and is faster at low pH, the most relevant condition for fuel cells. The arginine substituents increase TOF and may engage in an intramolecular guanidinium interaction that assists in H2 activation, while the COOH groups facilitate rapid proton movement. These results emphasize the critical role of features beyond the active site in achieving fast, efficient catalysis.

Locating protonated amines in clathrates

The structures and inherent stabilities of hydrated, protonated ammonia, select protonated primary, secondary, and tertiary amines as well as tetramethylammonium with 19-21 water molecules were investigated using infrared photodissociation (IRPD) spectroscopy and blackbody infrared radiative dissociation (BIRD) at 133 K. Magic number clusters (MNCs) with 20 water molecules were observed for all ions except tetramethylammonium, and the BIRD results indicate that these clusters have stable structures, which are relatively unaffected by addition of one water molecule but are disrupted in clusters with one less water molecule. IRPD spectra in the water free O-H stretch region are consistent with clathrate structures for the MNCs with 20 water molecules, whereas nonclathrate structures are indicated for tetramethylammonium as well as ions at the other cluster sizes. The locations of protonated ammonia and the protonated primary amines either in the interior or at the surface of a clathrate were determined by comparing IRPD spectra of these ions to those of reference ions; Rb(+) and protonated tert-butylammonia with 20 water molecules were used as references for an ion in the interior and at the surface of a clathrate, respectively. These results indicate that protonated ammonia is in the interior of the clathrate, whereas protonated methyl- and n-heptylamine are at the surface. Calculations suggest that the number of hydrogen bonds in these clusters does not directly correlate with structural stability, indicating that both the number and orientation of the hydrogen bonds are important. These experimental results should serve as benchmarks for computational studies aimed at elucidating ion effects on the hydrogen-bonding network of water molecules and the surface activity of ions.

Interactions of oligomers of organic polyethers with histidine amino acid

RATIONALE

Knowledge on noncovalent intermolecular interactions of organic polyethers with amino acids is essential to gain a better understanding on how polymers assemble in organic nanoparticles which are promising for drug delivery and cryoprotection. The main objective of the present study was to determine how polyethers assemble around ionizable amino acids such as histidine.

METHODS

Electrospray mass spectrometry was applied to probe the interactions in model systems consisting of polyethylene glycol PEG-400 or oxyethylated glycerol OEG-5 and amino acid histidine hydrochloride. Molecular dynamics simulation was utilized to visualize the structure of complexes of polyether oligomers with histidine in different charge states.

RESULTS

Stable gas-phase clusters composed of polyether oligomers (PEG(n), OEG(n)) with protonated histidine--PEG(n)•His•H(+), OEG(n)•His•H(+), OEG(n)•OEG(m)•His•H(+) and chlorine counterion--PEG(n)•Cl(-), OEG(n)•Cl(-), were observed under electrospray conditions. Molecular dynamics simulation of representative polyether-histidine complexes revealed the stabilization of oligomers by multiple hydrogen and coordination bonds whereby charged groups are wrapped by the polymeric chains.

CONCLUSIONS

The self-organization of polyether chains around the protonated imidazole group of histidine was revealed. This finding should be considered when modelling a pegylated protein structure and polyether-based organic nanoparticles.

Aldehyde complexes with protonated peptides in the gas phase

This Article presents a study of aldehyde complexes with peptide ions formed by bimolecular collisions in the gas phase. Desolvated ions generated by electrospray ionization are stored within a radio frequency (RF) ion trap and exposed to aldehyde vapor. Mass spectrometry measurements were performed on the resulting aldehyde complexes formed with single amino acids (LysH(+), HisH(+), and ArgH(+)) and polypeptides [Pro(n)-Lys+2H](2+) and [(Gly-Ser)(m)-Lys+2H](2+). These data identify several interesting and unexpected aspects of the aldehyde complex kinetics. It is observed that the formation of stable complexes requires the presence of water vapor. The formation kinetics of aldehyde-peptide complexes exhibits multiexponential time dependence that is modeled by interactions in the presence of structural heterogeneity. Aldehyde binding appears to involve a competition between conformers with unhindered access to protonation sites and conformers with intramolecular solvation of these sites. Proton transfer to the aldehyde ligand is responsible for the loss of the complexes. This is supported by proton affinity calculations and identified by reaction products exhibiting loss of protonation by the parent ion accompanied by the appearance of aldehyde cations.

Enhancements in travelling wave ion mobility resolution

The use of ion mobility separation to determine the collision cross-section of a gas-phase ion can provide valuable structural information. The introduction of travelling-wave ion mobility within a quadrupole/time-of-flight mass spectrometer has afforded routine collision cross-section measurements to be performed on a range of ionic species differing in gas-phase size/structure and molecular weight at physiologically relevant concentrations. Herein we discuss the technical advances in the second-generation travelling-wave ion mobility separator, which result in up to a four-fold increase in mobility resolution. This improvement is demonstrated using two reverse peptides (mw 490 Da), small ruthenium-containing anticancer drugs (mw 427 Da), a cisplatin-modified protein (mw 8776 Da) and the noncovalent tetradecameric chaperone complex GroEL (mw 802 kDa). What is also shown are that the collision cross-sections determined using the second-generation mobility separator correlate well with the previous generation and theoretically derived values.

Hydration isomers of protonated phenylalanine and derivatives: relative stabilities from infrared photodissociation

The binding sites of water molecules to protonated Phe and its derivatives are investigated using infrared photodissociation (IRPD) spectroscopy and kinetics as well as by computational chemistry. Calculated relative energies for hydration of PheH(+) at various sites on the N- and C-termini depend on the type of theory and basis set used, and no one hydration site was consistently calculated to be most favorable. Infrared photodissociation (IRPD) spectra between approximately 2650 and 3850 cm(-1) are reported for PheH(+)(H(2)O)(1-4) at 133 K and compared to calculated absorption spectra of low-energy hydration isomers, which do not resemble the IRPD spectra closely enough to unambiguously assign spectral bands. The IRPD spectra of PheH(+)(H(2)O)(1-4) are instead compared to those of N,N-Me(2)PheH(+)(H(2)O)(1,2), N-MePheH(+)(H(2)O)(1-3), and PheOMeH(+)(H(2)O)(1-3) at 133 K, which makes possible systematic band assignments. A unique band associated with a binding site not previously reported for PheH(+)(H(2)O), in which the water molecule accepts a hydrogen bond from the N-terminus of PheH(+) and donates a weak hydrogen bond to the pi-system of the side chain, is identified in the IRPD spectra. IRPD kinetics at laser frequencies resonant with specific hydration isomers are found to be biexponential for N,N-Me(2)PheH(+)(H(2)O), N-MePheH(+)(H(2)O), and PheH(+)(H(2)O). Relative populations of ions with water molecules attached at various binding sites are determined from fitting these kinetic data, and relative energies for hydration of these competitive binding sites at 133 K are obtained from these experimental values.

Secondary structure in de novo designed peptides induced by electrostatic interaction with a lipid bilayer membrane

We show that it is possible to induce a defined secondary structure in de novo designed peptides upon electrostatic attachment to negatively charged lipid bilayer vesicles without partitioning of the peptides into the membrane, and that the secondary structure can be varied via small changes in the primary amino acid sequence of the peptides. The peptides have a random-coil conformation in solution, and results from far-UV circular dichroism spectroscopy demonstrate that the structure induced by the interaction with silica nanoparticles is solely alpha-helical and also strongly pH-dependent. The present study shows that negatively charged vesicles, to which the peptides are electrostatically adsorbed via cationic amino acid residues, induce either alpha-helices or beta-sheets and that the conformation is dependent on both lipid composition and variations in peptide primary structure. The pH-dependence of the vesicle-induced peptide secondary structure is weak, which correlates well with small differences in the vesicles' electrophoretic mobility, and thus the surface charge, as the pH is varied.