Effect of metal ion and water coordination on the structure of a gas-phase amino acid

pH-dependent interactions of biologically important metal ions with hen egg white lysozyme based on its hydration properties: Thermodynamic and mechanistic insights

Importance of metal ion selectivity in biomolecules and their key role in proteins are widely explored. However, understanding the thermodynamics of how hydrated metal ions alter the protein hydration and their conformation is also important. In this study, the interaction of some biologically important Ca2+, Mn2+, Co2+, Cu2+, and Zn2+ ions with hen egg white lysozyme at pH 2.1, 3.0, 4.5 and 7.4 has been investigated. Intrinsic fluorescence studies have been employed for metal ion-induced protein conformational changes analysis. Thermostability based on protein hydration has been investigated using differential scanning calorimetry (DSC). Thermodynamic parameters emphasizing on metal ion-protein binding mechanistic insights have been well discussed using isothermal titration calorimetry (ITC). Overall, these experiments have reported that their interactions are pH-dependent and entropically driven. This research also reports the strongly hydrated metal ions as water structure breaker unlike osmolytes based on DSC studies. These experimental results have highlighted higher concentrations of different metal ions effect on the protein hydration and thermostability which might be helpful in understanding their interactions in aqueous solutions.

Aqueous Solution Enhanced Room Temperature Phosphorescence through Coordination-Induced Structural Rigidity

Achieving aqueous solution enhanced room temperature phosphorescence (RTP) is critical for the applications of RTP materials in solution phase, but which faces a great challenge. Herein, for the first time, a strategy of coordination-induced structural rigidity is proposed to achieve enhanced quantum efficiency of aluminum/scandium-doped phosphorescent microcubes (Al/Sc-PMCs) in aqueous solution. The Al/Sc-PMCs in a dry state exhibit a nearly invisible blue RTP. However, they emit a strong RTP emission in aqueous solution with a RTP intensity increase of up to 22.16-times, which is opposite to common solution-quenched RTP. The RTP enhancement mechanism is attributed to the abundant metal sites (Al3+ and Sc3+ ions) on the Al/Sc-PMCs surface that can tightly combine with water molecules through the strong coordination. Subsequently, these coordinated water molecules as the bridging agent can bind with surface groups by hydrogen bonding interaction, thereby rigidifying chemical groups and inhibiting their motions, resulting in the transition from the nonradiative decay to the radiative decay, which greatly enhances the RTP efficiency of the Al/Sc-PMCs. This work not only develops a coordination rigidity strategy to enhance RTP intensity in aqueous solution, but also constructs a phosphorescent probe to achieve reliable and accurate determination of analyte in complex biological matrices.

Interaction of Cysteine with Li+ and LiF in the Presence of (H2O) n (n = 0-6) Clusters

The interaction between cysteine with Li⁺ and LiF in the microcosmic water environment was investigated to elucidate how ions interact with amino acids and the cation-anion correlation effect involved. The structures of Cys·Li⁺(H₂O) _n and Cys·LiF(H₂O) _n (n = 0-6) were characterized using ab initio calculations. Our studies show that the water preferentially interacts with Li⁺/LiF. In Cys·Li⁺(H₂O)_0-6, Li⁺ interacts with amino nitrogen, carbonyl oxygen, and hydrophobic sulfur of Cys to form a tridentate mode, whereas in Cys·LiF(H₂O) _n , Li⁺ and F^- work in cooperation and interact with carbonyl oxygen and hydroxyl hydrogen of Cys to form a bidentate type. The neutral and zwitterionic forms are essentially isoenergetic when the water number reaches three in the presence of Li⁺, whereas this occurs at four water molecules in the presence of LiF. Further research revealed that the interaction between Li⁺/LiF and Cys was mainly electrostatic, followed by dispersion, and the weakest interaction occurs at the transition from the neutral form to zwitterionic form. Natural population analysis charge analyses show that for Cys·Li⁺(H₂O) _n , the positive charge is mostly concentrated on Li⁺ except for the system containing three water molecules. For Cys·LiF(H₂O) _n , the positive charge is centered on the LiF unit in the range n = 0-6, and at n = 5, electron transfer from Cys to water occurs. Our study shows that the contribution of anions in zwitterionic state stabilization should be addressed more generally along with cations.

Effect of Transition-Metal Ions on the Conformation of Encephalin Investigated by Hydrogen/Deuterium Exchange and Theoretical Calculations

We have studied the effects of different 3d orbitals in divalent transition-metal ions [G²⁺ = Mn²⁺ (d⁵), Fe²⁺ (d⁶), Co²⁺ (d⁷), Ni²⁺ (d⁸), Cu²⁺ (d⁹), or Zn²⁺ (d¹⁰)] on the conformations of leucine encephalin (LE) and methionine encephalin (ME) in the gas phase using hydrogen/deuterium exchange mass spectrometry (HDX-MS) and theoretical calculations at the molecular level. The HDX-MS reveals a 1:1 stoichiometric monovalent complex of [LE/ME + G - H]⁺ and observed that the different HDX reactivities follow the trend Fe²⁺ < Co²⁺ < Ni²⁺ < Mn²⁺ < Cu²⁺ ≈ Zn²⁺ and that [ME + Mn/Cu/Zn - H]⁺ > [LE + Mn/Cu/Zn - H]⁺, while [LE + Fe/Co/Ni - H]⁺ > [ME + Fe/Co/Ni - H]⁺. We cross-correlated the collision-induced dissociation energies of the complexes with the HDX results and found that the more stable the complex, the harder it is for it to undergo HDX. Furthermore, we used theoretical calculations to optimize the favorable conformations of the complexes and found the same interaction structure of G²⁺ coordination with the five carbonyl oxygens of LE/ME that have different bond lengths. Finally, we calculated the proton affinity (PA) values of the optimized complexes in order to interpret the HDX observations that the higher the PA values, the more difficult it is for the complex to undergo HDX. Overall, both the experiments and the theoretical calculations show that the six metal ions have different effects on the LE/ME conformation, with the low-energy stability of the G²⁺ 3d orbitals corresponding to more dramatic effects on the LE/ME conformation. In addition, the hardness of the ionic acid corresponding to the fully filled Mn²⁺ and half-filled Zn²⁺ orbitals also contributes strongly to the coordination effect; the conformation effect of Fe²⁺/Co²⁺/Ni²⁺ on LE is greater than that on ME, whereas the conformation effect of Mn²⁺/Cu²⁺/Zn²⁺ on ME is greater than that on LE.

Metal ion assisted interface re-engineering of a ferritin nanocage for enhanced biofunctions and cancer therapy

The bottom-up self-assembly of protein subunits into supramolecular nanoarchitectures is ubiquitously exploited to recapitulate and expand the features of natural proteins to advance nanoscience in medicine. Various chemical and biological re-engineering approaches are available to render diverse functions in the given proteins. They are, unfortunately, capable of compromising protein integrity and stability after extensive modifications. In this study, we introduce a new protein re-engineering method, metal ion assisted interface re-engineering (MAIR), to serve as a robust and universal strategy to extend the functions of self-assembly proteins by boosting structural features to advance their diverse biomedical applications. In particular, the MAIR strategy was applied to a widely used natural protein, ferritin, as a model protein to coordinate with copper ions in its mutagenic artificial metal binding domain. Structure directed rational protein mutagenesis was carried out at the C2 interface amino acid residues of the ferritin subunit for metal ion coordination site optimization. Copper binding at the artificial binding pocket was highly specific over the other divalent ions present in physiological fluids, and the structurally embedded copper ion in turn strengthened the overall protein integrity and stability. In the presence of isotopic copper-64, the interface re-engineered ferritin worked as a chelator-free molecular nanoprobe with an extraordinarily high specific activity to allow PET imaging of tumors in live animals. We also found that the re-engineered ferritin coordinating with copper ions demonstrates high drug loading capacity of a widely used anti-cancer agent, doxorubicin (DOX), to achieve significant drug retention at the tumor site and enhance tumor regression for improved anti-cancer effects. The MAIR approach, thus, exploited the copper ion to facilitate efficient one-step labeling of mutant ferritin derivatives for simultaneous molecular imaging and drug delivery. The reported interface re-engineering strategy provides an unparalleled opportunity to expand protein biofunctions to serve as a new theranostic agent in cancer research.

Amine vs. carboxylic acid protonation in ortho-, meta-, and para-aminobenzoic acid: An IRMPD spectroscopy study

Infrared multiple photon dissociation (IRMPD) spectroscopy and computational chemistry are applied to the ortho-, meta-, and para- positional isomers of aminobenzoic acid to investigate whether the amine or the carboxylic acid are the favored sites of proton attachment in the gas phase. The NH and OH stretching modes yield distinct patterns that establish the carboxylic acid as the site of protonation in para-aminobenzoic acid, as opposed to the amine group in ortho- and meta-aminobenzoic acid, in agreement with computed thermochemistries. The trends for para- and meta-substitutions can be rationalized simplistically by inductive effects and resonant stabilization, and will be discussed in light of computed charge distributions based from electrostatic potentials. In ortho-aminobenzoic acid, the close proximity of the amine and acid groups allow a simultaneous interaction of the proton with both groups, thus stabilizing and delocalizing the charge more effectively, and compensating for some of the resonance stabilization effects.

Distal Stereocontrol Using Guanidinylated Peptides as Multifunctional Ligands: Desymmetrization of Diarylmethanes via Ullman Cross-Coupling

We report the development of a new class of guanidine-containing peptides as multifunctional ligands for transition-metal catalysis and its application in the remote desymmetrization of diarylmethanes via copper-catalyzed Ullman cross-coupling. Through design of these peptides, high levels of enantioinduction and good isolated yields were achieved in the long-range asymmetric cross-coupling (up to 93:7 er and 76% yield) between aryl bromides and malonates. Our mechanistic studies suggest that distal stereocontrol is achieved through a Cs-bridged interaction between the Lewis-basic C-terminal carboxylate of the peptides with the distal arene of the substrate.

Calcium Binding to Amino Acids and Small Glycine Peptides in Aqueous Solution: Toward Peptide Design for Better Calcium Bioavailability

Deprotonation of amino acids as occurs during transfer from stomach to intestines during food digestion was found by comparison of complex formation constants as determined electrochemically for increasing pH to increase calcium binding (i) by a factor of around 6 for the neutral amino acids, (ii) by a factor of around 4 for anions of the acidic amino acids aspartic and glutamic acid, and (iii) by a factor of around 5.5 for basic amino acids. Optimized structures of the 1:1 complexes and ΔHbinding for calcium binding as calculated by density functional theory (DFT) confirmed in all complexes a stronger calcium binding and shorter calcium-oxygen bond length in the deprotonated form. In addition, the stronger calcium binding was also accompanied by a binding site shift from carboxylate binding to chelation by α-amino group and carboxylate oxygen for leucine, aspartate, glutamate, alanine, and asparagine. For binary amino acid mixtures, the calcium-binding constant was close to the predicted geometric mean of the individual amino acid binding constants indicating separate binding of calcium to two amino acids when present together in solution. At high pH, corresponding to conditions for calcium absorption, the binding affinity increased in the order Lys < Arg < Cys < Gln < Gly ∼ Ala < Asn < His < Leu < Glu< Asp. In a series of glycine peptides, calcium-binding affinity was found to increase in the order Gly-Leu ∼ Gly-Gly < Ala-Gly < Gly-His ∼ Gly-Lys-Gly < Glu-Cys-Gly < Gly-Glu, an ordering confirmed by DFT calculations for the dipeptides and which also accounted for large synergistic effects in calcium binding for up to 6 kJ/mol when compared to the corresponding amino acid mixtures.

Stepwise Hydration of 2-Aminooxazole: Theoretical Insight into the Structure, Finite Temperature Behavior and Proton-Induced Charge Transfer

It was recently suggested that 2-aminooxazole (AO) could contribute to the formation of RNA nucleotides on primitive earth. In this article we have considered by means of computational modeling the influence of microhydration on the structural and spectral properties of this potential prebiotic molecule. The stable structures of AO(H2O)n were obtained first by sampling the potential energy landscapes of clusters containing up to n = 20 water molecules, using a simple but reasonably accurate force field and replica-exchange molecular dynamics simulations. Through reoptimization using an explicit description of electronic structure at the level of density functional theory with the M06-2X functional, the formation energies, ionization energies and electron affinities were determined in the vertical and adiabatic treatments, as well as vibrational and optical spectra covering the far-IR, mid-IR, and lower part of the UV ranges. The results generally show a clear segregation between the aminooxazole solute and the water molecules, a water cluster being formed near the nitrogen and amino group side leaving the hydrocarbon side dry even at temperatures corresponding to the liquid state. The spectral signatures generally concur and show distinct contributions of the solute and solvent, spectral shifts to lower energies being in agreement with earlier calculations in bulk solvent. We have also investigated the importance of microhydration on the charge transfer cross section upon collision with a proton, thereby extending an earlier investigation on the bare AO molecule. The presence of water molecules generally reduces the propensity for charge transfer at small sizes, but the influence of the solvent steadily decreases in larger droplets.

An insight into the interaction of L-proline with the transition metal cations Fe(2+), Co(2+), Ni(2+): a gas phase theoretical study

The interaction of Fe(2+), Co(2+), and Ni(2+) with L-proline has been studied. Three modes of interaction have been considered: salt bridged (SB), involving binding in a bi-dentate manner through the carboxylate group of L-proline, charge solvated 1 (CS1) involving carbonyl and hydroxyl oxygen, and charge solvated 2 (CS2) involving carbonyl oxygen and the lone pair of the nitrogen atom. All calculations including geometry optimization, metal ion affinities (MIAs), and frequency calculations of the binding structures of Fe(2+), Co(2+), and Ni(2+) to L-proline were calculated using the hybrid density functional theory (DFT-B3LYP) method. All three cations were found to bind preferentially in a zwitterionic (SB) coordination pattern with the metal ion affinity in the order Ni(2+) ˃ Co(2+) ˃ Fe(2+) in all binding forms. The nature of the binding interaction between metal cations and L-proline was found to be mainly electrostatic. Comparison of the infrared vibrations of the C=O, the N-H and the O-H groups of free L-proline with L-proline-M(2+) in both CS1 and CS2 complex structures indicated a considerable shift to lower frequency during complexation. In order to gain more insight into the nature of the interaction of L-proline with group VIIIB metal ions, comparison of the interaction of L-proline with other cations such as (Li(+), Na(+), K(+), Be(2+), Mg(2+), and Ca(2+)) was made. Graphical Abstract L-proline with the transition metal cations Fe(2+), Co(2+), Ni(2.)

Nanohydration of uracil: emergence of three-dimensional structures and proton-induced charge transfer

Stepwise hydration of uracil proceeds three dimensionally above three molecules and qualitatively changes the response to proton damage.

Host-guest chemistry in the gas phase: complex formation of cucurbit[6]uril with proton-bound water dimer

The hydration of cucurbit[6]uril (CB[6]) in the gas phase is investigated using electrospray ionization traveling wave ion mobility mass spectrometry (ESI-TWIM-MS). Highly abundant dihydrated and tetrahydrated species of diprotonated CB[6] are found in the ESI-TWIM-MS spectrum. The hydration patterns of the CB[6] ion and the dissociation patterns of the hydrated CB[6] ion indicate that two water molecules are bound to each other, forming a water dimer in the CB[6] complex. Ion mobility studies combined with the structures calculated by density functional theory suggest that the proton-bound water dimer is present as a Zundel-like structure in the CB[6] portal, forming a hydrogen bond network with carbonyl groups of the CB[6]. When a large guest molecule is bound to a CB[6] portal, water molecules cannot bind to the portal. In addition, the strong binding energy of the water dimer blocks the portal, hindering the insertion of the long alkyl chain of the guest molecule into the CB[6] cavity. With small alkali metal cations, such as Li(+) and Na(+), a single water molecule interacts with the CB[6] portal, forming hydrogen bonds with the carbonyl groups of CB[6]. A highly stable Zundel-like structure of the proton-bound water dimer or a metal-bound water molecule at the CB[6] portal is suggested as an initial hydration process for CB[6], which is only dissolved in aqueous solution with acid or alkali metal ions.

Potassium ions are more effective than sodium ions in salt induced peptide formation

Prebiotic peptide formation under aqueous conditions in the presence of metal ions is one of the plausible triggers of the emergence of life. The salt-induced peptide formation reaction has been suggested as being prebiotically relevant and was examined for the formation of peptides in NaCl solutions. In previous work we have argued that the first protocell could have emerged in KCl solution. Using HPLC-MS/MS analysis, we found that K⁺ is more than an order of magnitude more effective in the L-glutamic acid oligomerization with 1,1'-carbonyldiimidazole in aqueous solutions than the same concentration of Na⁺, which is consistent with the diffusion theory calculations. We anticipate that prebiotic peptides could have formed with K⁺ as the driving force, not Na⁺, as commonly believed.

Extensive computational study on coordination of transition metal cations and water molecules to glutamic acid

On the basis of the conformations of glutamic acid (Glu) and analysis of possible metal cation coordination and hydration modes, conformations of Glu metalated with transition metal cations (TMCs), Cu(+/2+), Zn(+/2+), and Fe(+/2+/3+) and hydrations of Glu-Cu(+/2+) and Glu-Zn(+/2+) complexes by up to three water molecules are determined by extensive computational searches. The BHandHLYP functional is chosen as the main computational method as its overall performance for treating the spin multiplicity of TMCs is similar to that of CCSD(T) and better than that of MP2 and B3LYP. All mono- and divalent TMCs prefer tridentate coordination to canonical Glu, while Fe(3+) favors a bidentate coordination to zwitterionic Glu. The ground state of Glu-Fe(+) is found to be a spin sextet. Metal ion affinities of Glu for the TMCs are determined, and an excellent agreement with the experiment for Cu(+) may be obtained if the entropic effect is properly accounted for. Effects of hydration on the stabilities of different Glu-Cu(+/2+)/Zn(+/2+) structures are discussed, and the hydration energies for up to three water molecules are obtained. For the global minimum to take the zwitterionic form, Glu-Zn(+) requires only monohydration, Glu-Zn(2+) needs to be trihydrated, while Glu-Cu(+/2) should be hydrated with four or more water molecules.

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.

DFT STUDY ON GAS-PHASE INTERACTION BETWEEN HISTIDINE AND ALKALI METAL IONS (Li+, Na+, K+); AND INFLUENCE OF THESE IONS ON HISTIDINE ACIDITY

The gas-phase metal affinities of histidine Li +, Na + and K + ions have been determined theoretically employing the hybrid B3LYP exchange–correlation functional and using 6-311++G** basis sets. All computations indicate that the metal ion affinity decreases on going from Li + to Na + and K + for the considered amino acid. Different types of M + coordinations on several histidine conformers/tautomers were considered in detail.

The optimized structures indicate that Li + and Na + prefer a tri-dentate coordination, bonding with a nitrogen atom of imidazole ring ( N τ), – NH 2, and an oxygen atom of a carbonyl, while in the K +-histidine lowest-energy conformer, the cation appears to be bi-coordinated to both oxygen atoms of the zwitterionic form by the energy values not too far from that of tri-coordination. We also performed the DFT calculations for proton dissociation energy of histidine both in the presence and absence of alkali metal ions. Our results also reveal that the acidity of histidine dramatically increases upon metal ion complexation.

Thermochemistry of microhydration of sodiated and potassiated monosaccharides

The thermochemical properties ΔH(o)(n), ΔS(o)(n), and ΔG(o)(n) for the hydration of sodiated and potassiated monosaccharides (Ara = arabinose, Xyl = xylose, Rib = ribose, Glc = glucose, and Gal = galactose) have been experimentally studied in the gas phase at 10 mbar by equilibria measurements using an electrospray high-pressure mass spectrometer equipped with a pulsed ion beam reaction chamber. The hydration enthalpies for sodiated complexes were found to be between -46.4 and -57.7 kJ/mol for the first, and -42.7 and -52.3 kJ/mol for the second water molecule. For potassiated complexes, the water binding enthalpies were similar for all studied systems and varied between -48.5 and -52.7 kJ/mol. The thermochemical values for each system correspond to a mixture of the α and β anomeric forms of monosaccharide structures involved in their cationized complexes.