Mammalian Amino Acid Transport System y+ Revisited: Specificity and Cation Dependence of the Interaction with Neutral Amino Acids

A reevaluation of the specificity of system y⁺, the classical transporter for cationic amino acids is presented. System y⁺ has been defined as a transporter for cationic amino acids that binds neutral amino acids with lower affinity in the presence of Na⁺. The discovery of other transporters for cationic amino has suggested that some properties, originally attributed to system y⁺, may relate to other transport systems. Uncertainty concerns mainly, the affinity for neutral amino acids and the cation dependence of this interaction. Neutral amino acids (13 analogues tested) were found to bind to system y⁺ in human erythrocytes with very low affinity. Inhibition constants (K_iy, mm) ranged between 14.2 mm and >400 mm, and the strength of interaction was similar in the presence of Na⁺, K⁺ or Li⁺ (145 mm). In choline medium, no interaction was detected up to 20 mm of the neutral amino acid. Guanidinium ion (5 mm, osmolarity maintained with choline) potentiated neutral amino acid binding; the effect was most important in the case of l-norvaline which aligned with guanidinium ion is equivalent to arginine. This suggests cooperative interaction at the substrate site. The specificity of system y⁺ was shown to be clearly distinct from that of system y⁺L, a cationic amino acid transporter that accepts neutral amino acids with high affinity in the presence of Na⁺ and which influenced the classical definition of system y⁺. Received: 28 September 1998/Revised: 21 December 1998     

The Specificity of Peptide Chain Extension by N-Carboxyanhydrides

We have used amino acids activated by carbonyldiimidazole to study the enantiospecificity of peptide elongation in aqueoussolution. Peptide `primers' Glu₁₀ and Ala₃Glu₁₀were elongated with the enantiomers of arginine, glutamic acid,asparagine, phenylalanine, serine and valine. The homochiral addition was always the more efficient reaction; the enantiospecificity was large in some cases but very small in others. In every case Ala₃Glu₁₀ was elongated more efficiently than Glu₁₀.     

Cleavage of di- and tripeptides by Prevotella ruminicola

The final step in the conversion of protein to amino acids by the common Gram-negative rumen bacterium, Prevotella (formerly Bacteroides) ruminicola , is the cleavage of di- and tripeptides. Dipeptidase and tripeptidase activities were predominantly cytoplasmic, and toluene treatment increased the rate of Ala₂ and Ala₃ hydrolysis by whole cells, suggesting that transport limited the rate of hydrolysis of extracellular di- and tripeptides. The hydrolysis of Ala₂ and Ala₃ by whole cells was not affected by protonophores, ionophores or dicyclohexylcarbodiimide, but Ala₂ hydrolysis by EDTA-treated cells was inhibited by the Ca²⁺/H⁺ ionophore, tetronasin. Ala₃ hydrolysis was not affected by protonophores or ionophores in EDTA-treated cells. The dipeptidase of strain M384 was inhibited > 99% by 1,10-phenanthroline and 39% by EDTA but not other protease inhibitors, consistent with the enzyme being a metalloprotease. Tripeptidase was insensitive to protease inhibitors, except for a 33% inhibition by EDTA. Cleavage of tripeptides occurred at the bond adjacent to the N-terminal amino acid. Distinct di-, tri- and oligopeptidase peaks were obtained by anion-exchange liquid chromatography of disrupted cells. Banding patterns on native PAGE using activity staining also indicated that P. ruminicola M384 had separate single dipeptidase and tripeptidase enzymes which hydrolysed a range of peptides. The dipeptidase of strain M384 was different from other strains of P. ruminicola: strains GA33 and B₁4 had activities which ran at the same R_f; strain GA33 had another band of lower activity; strain 23 had two bands different from those of the other strains. The tripeptidases ran at the same R_f for the different strains. Dipeptidase activity of all strains was inhibited by 1,10-phenanthroline on gels. Gel permeation chromatography indicated that the M_r of the dipeptidases from strains M384 and B₁4 were 115 000 and 114 500 respectively, and 112 500 and 121 500 for the corresponding tripeptidases. Thus the metabolism of small peptides by P. ruminicola involves separate permeases and intracellular peptidases for di- and tripeptides.     

Effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+ and Zn2+) and water coordination on the structure and properties of l-histidine and zwitterionic l-histidine

Interactions between metal ions and amino acids are common both in solution and in the gas phase. The effect of metal ions and water on the structure of l-histidine is examined. The effect of metal ions (Li⁺, Na⁺, K⁺, Mg²⁺, Ca²⁺, Ni²⁺, Cu²⁺ and Zn²⁺) and water on structures of His·M(H₂O)m, m = 0.1 complexes have been determined theoretically employing density functional theories using extended basis sets. Of the five stable complexes investigated the relative stability of the gas-phase complexes computed with DFT methods (with one exception of K⁺ systems) suggest metallic complexes of the neutral l-histidine to be the most stable species. The calculations of monohydrated systems show that even one water molecule has a profound effect on the relative stability of individual complexes. Proton dissociation enthalpies and Gibbs energies of l-histidine in the presence of the metal cations Li⁺, Na⁺, K⁺, Mg²⁺, Ca²⁺, Ni²⁺, Cu²⁺ and Zn²⁺ were also computed. Its gas-phase acidity considerably increases upon chelation. Of the Lewis acids investigated, the strongest affinity to l-histidine is exhibited by the Cu²⁺ cation. The computed Gibbs energies ΔG are negative, span a rather broad energy interval (from ?130 to ?1,300 kJ/mol), and upon hydration are appreciably lowered.     

Structural and Functional Analysis of Transmembrane Segment VI of the NHE1 Isoform of the Na+/H+ Exchanger

The Na⁺/H⁺ exchanger isoform 1 is a ubiquitously expressed integral membrane protein. It resides on the plasma membrane of cells and regulates intracellular pH in mammals by extruding an intracellular H⁺ in exchange for one extracellular Na⁺. We characterized structural and functional aspects of the transmembrane segment (TM) VI (residues 227–249) by using cysteine scanning mutagenesis and high resolution NMR. Each residue of TM VI was mutated to cysteine in the background of the cysteineless NHE1 protein, and the sensitivity to water-soluble sulfhydryl-reactive compounds (2-(trimethylammonium)ethyl)methanethiosulfonate (MTSET) and (2-sulfonatoethyl)methanethiosulfonate (MTSES) was determined for those residues with significant activity remaining. Three residues were essentially inactive when mutated to Cys: Asp²³⁸, Pro²³⁹, and Glu²⁴⁷. Of the remaining residues, proteins with the mutations N227C, I233C, and L243C were strongly inhibited by MTSET, whereas amino acids Phe²³⁰, Gly²³¹, Ala²³⁶, Val²³⁷, Ala²⁴⁴, Val²⁴⁵, and Glu²⁴⁸ were partially inhibited by MTSET. MTSES did not affect the activity of the mutant NHE1 proteins. The structure of a peptide representing TM VI was determined using high resolution NMR spectroscopy in dodecylphosphocholine micelles. TM VI contains two helical regions oriented at an approximate right angle to each other (residues 229–236 and 239–250) surrounding a central unwound region. This structure bears a resemblance to TM IV of the Escherichia coli protein NhaA. The results demonstrate that TM VI of NHE1 is a discontinuous pore-lining helix with residues Asn²²⁷, Ile²³³, and Leu²⁴³ lining the translocation pore.     

A DFT study on the role of long range correlation interaction and solvent effects in homochiral and heterochiral cyclic trimerization of imidazole based heterocyclic amino acids

Using B3LYP and B97D functionals of density functional theory (DFT), homochiral and heterochiral cyclic trimerization of imidazole based heterocyclic amino acids are studied in gas phase and solvent phase, i. e., Acetonitrile. Both the functionals show that formation of homochiral cyclic tripeptide is thermodynamically and kinetically favorable over its heterochiral counterpart in gas phase. The functional, B97D, decreases the height of reaction barriers significantly compared to those predicted by the functional B3LYP. The reaction pathways explored using PCM implicit solvent model show reduced kinetic favorability for formation of the homochiral cyclic tripeptide over its heterochiral counterpart. The results are substantiated by structural aspects.     

Structural studies of decavanadate compounds with organic molecules and inorganic ions in their crystal packing

The formation of decavanadates containing amine counter-ions is explored to get a better insight into the resulting crystal packing. From mixtures containing the Schiff base H₂(SO₃-sal)₂en and vanadate, two different compounds containing decavanadate units have been characterised by X-ray diffraction. The structure of 1 consists of [V₁₀O₂₈]⁶⁻ monomers united by K⁺, ethylenediamine cations and H₂O molecules, which act as bridging atoms between the layers, forming a three-dimensional array. The structure of 2 contains vanadium triprotonated decavanadate anions, [H₃V₁₀O₂₈]³⁻, in one-dimensional vertical chains, bonded by interdecavanadate hydrogen bonds. The interchain region is populated by (H₂en)²⁺ cations and H₂O molecules, which form a network of hydrogen bonds. From the filtrate solution of the reaction mixture containing V^IVOSO₄, d,l-diaminopropionic acid and salicylaldehyde, which also contained triethylamine, a diprotonated decavanadate 3 was obtained. Compound 3 consists of decavanadate vertical dimers, surrounded by triethylamonium cations that preclude the interaction between the dimers. Bond valence calculations were used to confirm the degree of protonation of the decavanadate anions.     

Au(III)-complexes of the alanyl-containing peptides glycylalanine and glycylalanylalanine - Synthesis, spectroscopic and structural characterization

As part of an investigation on the coordination ability of peptides, the dipeptide glycylalanine (H-Gly-Ala-OH), tripeptide glycylalanylalanine (H-Gly-Ala-Ala-OH) and their Au(III)-complexes have been characterized structurally. The quantum chemical calculations and linear-dichroic infrared (IR-LD) spectroscopy predict structures of the compound studied, which are compared with a single crystal X-ray diffraction of H-Gly-Ala-OH. The coordination processes with Au(III) are supported by data for ¹H NMR, ESI-MS, HPLC-MS-MS, TGV and DSC methods. The [Au(Gly-Ala)H₋₁Cl] and [Au(Gly-Ala-Ala)H₋₂] · 2H₂O complexes are formed via -NH₂, N⁻amide/s and groups of the peptides. One Cl⁻ ion is attached to the metal center as terminal ligand in the first complex. In both cases a near to square-planar geometry of the chromophors AuN₂OCl and AuN₃O is yielded.     

Partial structure and properties of the ferredoxin from Rhodymenia palmata

A ferredoxin of MW 11 000 was isolated from the marine alga Rhodymenia palmata (Palmaria palmata). In its oxidised form the ferredoxin had absorption maxima at 276, sh 281, 328, 423 and 465 nm, and contained a single [2Fe-2S] cluster. The midpoint potential of the ferredoxin was ?400 mV and it effectively mediated electron transport in NADP⁺-photoreduction by higher plant chloroplasts, and pyruvate decarboxylation by the phosphoroclastic system of an anacrobic bacterium. The amino acid composition was Lys₃, His₁, Arg₁, Asx₁₂, Thr₉, Ser₈, Glx₁₃, Pro₄, Gly₈, Ala₇, Cys₅, Val₈, Ile₄, Leu₉, Tyr₄, Phe₂; tryptophan and methionine were absent from the molecule. The N-terminal amino acid region consisting of ca half the total amino acid sequence was determined using an automatic sequencer.     

Theoretical study on the interactions between methanol and imidazolium-based ionic liquids

To better understand the property of the binary systems composing of imidazolium salt, [emim]⁺Aˉ (A=Clˉ, Brˉ, BF₄ˉ, and PF₆ˉ) and methanol, we have investigated in detail the interactions of methanol molecule with anions Aˉ, cation [emim]⁺, and ion pair [emim]⁺Aˉ of several ionic liquids (ILs) based on 1-ethyl-3-methylimidazolium cation by performing density functional theory calculations. It is found that H-bonds are universally involved in these systems, which may play an important role for the miscibility of methanol with imidazolium-based ILs. The interaction mechanisms of methanol molecule with anion and cation are found to be different in nature: the former mainly involves LP_X-s_{O - H}^* \sigma_{{O - H}}^{*} interaction, while the latter relates with the decisive orbital overlap of the type of LP_O-s_{C - H}^* \sigma_{{C - H}}^{*} . Based on the present calculations, we have provided some reasonable interpretations for properties of the binary mixtures of ILs and alcohol and revealed valuable information for the interaction details between ILs and alcohols, which is expected to be useful for the design of more efficient ILs to form superior solvent system with alcohol.     

Purification and Properties of Sarcosine Oxidase from Cylindrocarpon didymum M–1

Sarcosine oxidase was purified to homogeneity from the cell extract of Cylindrocarpon didymum M–1, aerobically grown in medium containing choline as the carbon source. The molecular weight of the enzyme was estimated to be 45,000 by gel filtration method and 48,000 by the sodium dodecylsulfate disc gel electrophoresis method. The enzyme exhibited an absorption spectrum with maxima at 277 and 450 run and shoulders at 370 and 470 nm. The anaerobic addition of sarcosine to the enzyme resulted in the disappearance of the peak at 450 nm. The enzyme contained one mol of covalently bound FAD per mol of enzyme. Enzyme activity was inhibited by Ag⁺, Cu²⁺, Hg²⁺, p-chloromercuribenzoate and iodoacetate. The enzyme oxidized sarcosine but was inert toward choline, betaine, dimethylglycine and N-methyl amino acids. Km and V_max values for sarcosine were 1.8 ihm and 26.2 μmol/min/mg, respectively. The enzyme catalyzed the following reaction: Sarcosine+O₂+H₂O→glycine +formaldehyde+H₂O₂.     

Theoretical studies on protein-nucleic acid interactions. I. Interaction of positively charged amino acids with nucleic acid fragments

Coulombic interactions between the side chains of charged amino acids (Arg⁺, Lys⁺, and His⁺) and negatively charged phosphate groups of nucleic acid fragments have been studied theoretically. Diribose monophosphate and dideoxyribose monophosphate are chosen as model systems for single-stranded RNA and DNA, respectively. The interaction energies have been calculated by second-order perturbation theory using simplified formulas for individual terms. The interaction energy in this formalism is a sum of electrostatic, polarization, dispersion, and repulsive energies. Our results show that about 90% of the total interaction energy is contributed by the electrostatic term alone. Contribution from the repulsive term exceeds that from the dispersion term. Calculated interaction energies suggest that Lys⁺ and His⁺ form more stable complexes with RNA than with single-stranded DNA. On the other hand, Arg⁺ has a higher affinity for DNA than for RNA. The affinity of nucleic acids for the three amino acids is in the order Lys⁺ > His⁺ > Arg⁺. Further, the basic amino acid residues form more stable complexes with A-DNA than with B-DNA. The role of the Coulombic interactions in the specific recognition of nucleic acids by proteins is discussed.     

Histidine 352 (His352) and Tryptophan 355 (Trp355) Are Essential for Flax UGT74S1 Glucosylation Activity toward Secoisolariciresinol

Flax secoisolariciresinol diglucoside (SDG) lignan is a natural phytoestrogen for which a positive role in metabolic diseases is emerging. Until recently however, much less was known about SDG and its monoglucoside (SMG) biosynthesis. Lately, flax UGT74S1 was identified and characterized as an enzyme sequentially glucosylating secoisolariciresinol (SECO) into SMG and SDG when expressed in yeast. However, the amino acids critical for UGT74S1 glucosyltransferase activity were unknown. A 3D structural modeling and docking, site-directed mutagenesis of five amino acids in the plant secondary product glycosyltransferase (PSPG) motif, and enzyme assays were conducted. UGT74S1 appeared to be structurally similar to the Arabidopsis thaliana UGT72B1 model. The ligand docking predicted Ser³⁵⁷ and Trp³⁵⁵ as binding to the phosphate and hydroxyl groups of UDP-glucose, whereas Cys³³⁵, Gln³³⁷ and Trp³⁵⁵ were predicted to bind the 7-OH, 2-OCH₃ and 17-OCH₃ of SECO. Site-directed mutagenesis of Cys³³⁵, Gln³³⁷, His³⁵², Trp³⁵⁵ and Ser³⁵⁷_, and enzyme assays revealed an alteration of these binding sites and a significant reduction of UGT74S1 glucosyltransferase catalytic activity towards SECO and UDP-glucose in all mutants. A complete abolition of UGT74S1 activity was observed when Trp³⁵⁵ was substituted to Ala³⁵⁵ and Gly³⁵⁵ or when changing His³⁵² to Asp³⁵²_, and an altered metabolite profile was observed in Cys335Ala, Gln337Ala, and Ser357Ala mutants. This study provided for the first time evidence that Trp³⁵⁵ and His³⁵² are critical for UGT74S1’s glucosylation activity toward SECO and suggested the possibility for SMG production in vitro.     

Effect of extracellular potassium on amino acid transport and membrane potential in fetal human fibroblasts

The distribution ratio of the lipophilic cation tetraphenylphosphonium (TPP⁺) has been used to estimate the electrical potential difference across the plasma membrane in cultured human fibroblasts. These cells exhibit a membrane potential markedly influenced by the diffusion potential of K⁺. High extracellular potassium concentrations depolarize human fibroblasts and depress the activity of transport systems A, ASC (both serving for zwitterionic amino acids), X_AG⁻ (for anionic amino acids), and y⁺ (for cationic amino acids). High doses (100 μM) of the K⁺-ionophore valinomycin hyperpolarize the cells. This condition enhances the activity of systems A, ASC and y⁺. Transport systems L (for neutral amino acids) and x_C⁻ (for anionic amino acids) are insensitive to changes in extracellular K⁺ or to valinomycin. System X_AG⁻ is inhibited by the addition of 100 μM valinomycin, but the effect of the ionophore appears to be potential-independent. These results indicate that: (a) the activity of systems L and x_C⁻ is potential-independent and (b) the activity of systems A, ASC, X_AG⁻ and y⁺ is sensitive to alterations of external [K⁺] associated to changes in membrane potential.     

Packing interactions of aib-containing helices: Molecular modeling of parallel dimers of simple hydrophobic helices and of alamethicin

α-Aminoisobutyric acid (Aib) is a helicogenic α,α-dimethyl amino acid found in channel-forming peptaibols such as alamethicin. Possible effects of Aib on helix–helix packing are analyzed. Simulated annealing via restrained molecular dynamics is used to generate ensembles of approximately parallel helix dimers. Analysis of variations in geometrical and energetic parameters within ensembles defines how tightly a pair of helices interact. Simple hydrophobic helix dimers are compared: Ala₂₀, Leu₂₀, Aib₂₀, and P20, the latter a simple channel-forming peptide [G. Menestrina, K. P. Voges, G, Jung, and G. Boheim (1986) Journal of Membrane Biology, Vol. 93, pp. 111–132]. Ala₂₀ and Leu₂₀ dimers exhibit well-defined ridges-in-grooves packing with helix crossing angles (Ω) of the order of +20°. Aib₂₀ α-helix dimers are much more loosely packed, as evidenced by a wide range of Ω values and small helix-helix interaction energies. However, when in a 3₁₀ conformation Aib₂₀ helices pack in three well-defined parallel modes, with Ω ca. ?15°, +5°, and 10°. Comparison of helix–helix interaction energies suggests that dimerization may favor the 3₁₀ conformation. P20, with 8 Aib residues, also shows looser packing of α-helices. The results of these studies of hydrophobic helix dimers are analyzed in the context of the ridges-in-grooves packing model. Simulations are extended to dimers of alamethicin, and of an alamethicin derivative in which all Aib residues are replaced by Leu. This substitution has little effect on helix–helix packing. Rather, such interactions appear to be sensitive to interactions between polar side chains. Overall, the results suggest that Aib may modulate the packing of simple hydrophobic helices, in favor of looser interactions. For more complex amphipathic helices, interactions between polar side chains may be more critical. © 1995 John Wiley & Sons, Inc.     

In Silico and In Vitro Studies on the Protein-Protein Interactions between Brugia malayi Immunomodulatory Protein Calreticulin and Human C1q

Filarial parasites modulate effective immune response of their host by releasing a variety of immunomodulatory molecules, which help in the long persistence of the parasite within the host. The present study was aimed to characterize an immunomodulatory protein of Brugia malayi and its interaction with the host immune component at the structural and functional level. Our findings showed that Brugia malayi Calreticulin (BmCRT) is responsible for the prevention of classical complement pathway activation via its interaction with the first component C1q of the human host. This was confirmed by inhibition of C1q dependent lysis of immunoglobulin-sensitized Red Blood Cells (S-RBCs). This is possibly the first report which predicts CRT-C1q interaction on the structural content of proteins to explain how BmCRT inhibits this pathway. The molecular docking of BmCRT-C1q complex indicated that C1qB chain (IgG/M and CRP binding sites on C1q) played a major role in the interaction with conserved and non-conserved regions of N and P domain of BmCRT. Out of 37 amino acids of BmCRT involved in the interaction, nine amino acids (Pro¹²⁶, Glu¹³², His¹⁴⁷, Arg¹⁵¹, His¹⁵³, Met¹⁵⁴, Lys¹⁵⁶, Ala¹⁹⁶ and Lys²¹²) are absent in human CRT. Both ELISA and in silico analysis showed the significant role of Ca⁺² in BmCRT-HuC1q complex formation and deactivation of C1r₂–C1s₂. Molecular dynamics studies of BmCRT-HuC1q complex showed a deviation from ∼0.4 nm to ∼1.0 nm. CD analyses indicated that BmCRT is composed of 49.6% α helix, 9.6% β sheet and 43.6% random coil. These findings provided valuable information on the architecture and chemistry of BmCRT-C1q interaction and supported the hypothesis that BmCRT binds with huC1q at their targets (IgG/M, CRP) binding sites. This interaction enables the parasite to interfere with the initial stage of host complement activation, which might be helpful in parasites establishment. These results might be utilized for help in blocking the C1q/CRT interaction and preventing parasite infection.     

Energy-linked conformational change of the mitochondrial membrane measured with the NH2-modifying reagent,acrolein

Application of the NH₂-modifying reagent, acrolein (2-propenal, CH₂ = CHCHO), to the mitochondrial membrane gave the information that amino groups in the mitochondrial membrane in the energized state are more accessible to acrolein than those in the non-energized state. This finding was supported by the following experimental results. Addition of acrolein to the respiring mitochondria gives rise to rapid H⁺ production, which is caused by the reaction of the amino groups in the membrane with acrolein, followed by a slow H⁺ consumption, whereas resting mitochondria produce little H⁺. The H⁺ production is stopped by the addition of NaN₃, antimycin A and 2-thenoyltrifluoroacetone but not by oligomycin. During the course of H⁺ production, O₂ consumption and Ca²⁺ uptake remain completely active, indicating that mitochondrial function is unaffected. The subsequent H⁺ consumption may be closely related to the destruction of the transmembrane proton gradient formed by mitochondrial respiration.     

Chromium(III) complexes and their relationship to the glucose tolerance factor. Part II. Structure and biological activity of amino acid complexes

A number of octahedral chromium complexes with amino acids are ligands have been prepared and their structures assigned on the basis of their chromatographic and spectral properties. These include complexes with the general structure Cr(AA)₂(H₂O)₂ where the amino acids glycine, glutamic acid and glutamine act as bidentate ligands. The analogous compound with cysteine as ligand is stable at low pH, but at high pH a terdentate cysteine complex, Cr(cysteine)₂^?, is formed. These complexes, as well as a solution of monodentate glycine aquo complexes, and Cr-nicotinic acid-glycine and Cr-nicotinic acid-cysteine complexes of undetermined structure, have been assayed for glucose tolerance factor activity using a yeast assay. Only Cr(glutamine)₂- (H₂O)₂⁺, Cr-nicotinic acid-glycine and the mixture of complexes Cr(glycine)_n(H₂O)_6-n⁺³ showed significant activity. It is proposed that a trans arrangement of the non-coordinated nitrogen atoms in the ligands of these complexes can mimic the structural features of the glucose tolerance factor which are essential for biological activity.     

A Monte Carlo simulation study to predict the solubility of H2S in ionic liquids with 1-butyl-3-methylimidazolium ([C4mim+]) cation and tetrafluoroborate ([BF4−]), hexaflorophosphate ([PF6−]) and bis(trifluoromethanesulfonyl)amide ([Tf2N−]) anions

The solubilities of H₂S in ionic liquids, 1-butyl-3-methylimidazolium tetrafluoroborate ([C₄mim⁺][BF₄^?]), 1-butyl-3-methylimidazolium hexaflorophosphate ([C₄mim⁺][PF₆^?]) and -butyl-3-methylimidazolium tetrafluoroborate bis(trifluoromethanesulphonyl)amide ([C₄mim⁺][Tf₂N^?]) are predicted using isothermal–isobaric Gibbs ensemble Monte Carlo method (NPT-GEMC) at temperatures ranging from 333 to 453 K and pressure up to 20 bar. The low pressure points (up to 3 bar) of the absorption isotherms are fitted to a straight line to get a rough estimation of the Henry’s law constants. The van’t Hoff relationship is used to estimate the partial molar enthalpy of the absorption. The obtained results are in a good agreement with Jou and Mather [18], and Jalili et al. [13]. When comparing the solubility in ILs, it is found that H₂S solubility is highest for [C₄mim⁺][Tf₂N^?], followed by [C₄mim⁺][PF₆^?]. The lowest solubility is observed in [C₄mim⁺][BF₄^?]. The highest solubility in [C₄mim⁺][Tf₂N^?] is consistent with Jalili et al. [13]. However, their results indicate slightly higher solubility in [C₄mim⁺][BF₄^?] than in [C₄mim⁺][PF₆^?], and do not agree with the predictions. Upon absorption, the molar volumes of the mixtures decrease linearly, showing only small changes in volume. The effect of H₂S absorption on ILs is further studied by calculating the radial distribution functions between the ions. The results indicate that the solute molecules accommodate themselves in the cavities without significantly disturbing the ionic arrangement of the ions, similar to CO₂ absorption in ILs. The spatial distribution functions show similar spatial distribution for H₂S around cation in all of the studied ILs, whereas the distribution around anion depends on the shape and flexibility of the anion. The mechanism of H₂S absorption is studied by computing the van der Waals (VDW) and electrostatic (ELEC) energies. It is observed that the solubility of H₂S in the studied ILs is primarily controlled by VDW interaction. When comparing the interaction of H₂S with the ions, it is found that solute molecules interact with cations mainly due to VDW interaction. Both VDW and ELEC energies contribute in the interaction between H₂S and anions.     

Exploring Strong Interactions in Proteins with Quantum Chemistry and Examples of Their Applications in Drug Design

Objectives

Three strong interactions between amino acid side chains (salt bridge, cation-π, and amide bridge) are studied that are stronger than (or comparable to) the common hydrogen bond interactions, and play important roles in protein-protein interactions.

Methods

Quantum chemical methods MP2 and CCSD(T) are used in calculations of interaction energies and structural optimizations.

Results

The energies of three types of amino acid side chain interactions in gaseous phase and in aqueous solutions are calculated using high level quantum chemical methods and basis sets. Typical examples of amino acid salt bridge, cation-π, and amide bridge interactions are analyzed, including the inhibitor design targeting neuraminidase (NA) enzyme of influenza A virus, and the ligand binding interactions in the HCV p7 ion channel. The inhibition mechanism of the M2 proton channel in the influenza A virus is analyzed based on strong amino acid interactions.

Conclusion

(1) The salt bridge interactions between acidic amino acids (Glu^- and Asp^-) and alkaline amino acids (Arg⁺, Lys⁺ and His⁺) are the strongest residue-residue interactions. However, this type of interaction may be weakened by solvation effects and broken by lower pH conditions. (2) The cation- interactions between protonated amino acids (Arg⁺, Lys⁺ and His⁺) and aromatic amino acids (Phe, Tyr, Trp and His) are 2.5 to 5-fold stronger than common hydrogen bond interactions and are less affected by the solvation environment. (3) The amide bridge interactions between the two amide-containing amino acids (Asn and Gln) are three times stronger than hydrogen bond interactions, which are less influenced by the pH of the solution. (4) Ten of the twenty natural amino acids are involved in salt bridge, or cation-, or amide bridge interactions that often play important roles in protein-protein, protein-peptide, protein-ligand, and protein-DNA interactions.