Self-assembling Dimeric and Trimeric Aggregates Based on Solvophobic and Charge-pairing Interactions

Self-assembly processes based on shape complementarity and noncovalent binding interactions are widely recognized as a fundamental principle in nature. Besides charge pairing and hydrogen bonding, hydrophobic interactions play a crucial role in water. Here we report the self-assembly of structurally simple monomers to yield defined dimeric and trimeric aggregates in highly polar media, based on ionic and solvophobic interactions. NMR, mass spectrometry and curve fitting were used to characterize these supramolecular assemblies in water–methanol solutions.     

Possible factors influencing the separation mechanism of diastereomeric amino acid derivatives obtained from s-triazine type reagents

Diastereomeric derivatives prepared from an amino acid and an amino amide using trichloro s-triazine as a coupling platform are known to produce good chromatographic diastereoselectivity for many amino acid analytes. The chromatographic diastereoselectivity of these derivatives is difficult to rationalize based on the possibility of four possible conformational isomers, which can interconvert by rotation about the C-N bonds between the amino substituents and the triazine ring. The observed diastereoselectivity implicates an unobvious but significant driving force which causes one of several conformations to be favored over the others. Several possibilities are discussed. Intramolecular hydrogen bonding between acid and amide substituents was explored using computer aided molecular modeling. While such hydrogen bonding may be geometrically possible between the amino acid and the amide substituents, it does not explain why derivatives produced from other chiral compounds which are not capable of the same hydrogen bonding interaction nevertheless exhibit substantial diastereoselectivity. Two other more general effects, steric hindrance to solvation and ion pairing, are therefore suggested as possible contributing factors to the chromatographic diastereoselectivity. Based on the conformational equilibrium behavior of related triazine compounds as reported in the literature, either one of these effects could influence the conformation of the diastereomeric derivatives even in the absence of intramolecular hydrogen bonding interactions between the two chiral substituents, and these effects may therefore be a contributing factor for the observed elution order of the diastereomers.     

Amino Acid Modified RNA Bases as Building Blocks of an Early Earth RNA-Peptide World

Fossils of extinct species allow us to reconstruct the process of Darwinian evolution that led to the species diversity we see on Earth today. The origin of the first functional molecules able to undergo molecular evolution and thus eventually able to create life, are largely unknown. The most prominent idea in the field posits that biology was preceded by an era of molecular evolution, in which RNA molecules encoded information and catalysed their own replication. This RNA world concept stands against other hypotheses, that argue for example that life may have begun with catalytic peptides and primitive metabolic cycles. The question whether RNA or peptides were first is addressed by the RNA-peptide world concept, which postulates a parallel existence of both molecular species. A plausible experimental model of how such an RNA-peptide world may have looked like, however, is absent. Here we report the synthesis and physicochemical evaluation of amino acid containing adenosine bases, which are closely related to molecules that are found today in the anticodon stem-loop of tRNAs from all three kingdoms of life. We show that these adenosines lose their base pairing properties, which allow them to equip RNA with amino acids independent of the sequence context. As such we may consider them to be living molecular fossils of an extinct molecular RNA-peptide world.     

Study of the behaviour of amino acids in aqueous solution by time-domain NMR and high-resolution NMR

The study of protein hydration by time-domain NMR is complicated by the great number of interactions involved, resulting from the presence of several amino acids and the possible modifications produced by the various structures. Moreover, a good comprehension of the molecular interactions of the simple amino acids in solution is essential to elucidate the mechanism of the biological functions of proteins. Measurements of transverse relaxation rates of the protons of water (R(2) = 1/T(2)) in aqueous solutions of amino acids such as L-glycine, L-asparagine, L-arginine and L-tryptophan were carried out in order to study the effects of chemical exchange and molecular diffusion on the amplitude of R(2). The values of R(2) measured by the Carr-Purcell-Meiboom-Gill (CPMG) sequence were studied while varying the solution pH and the parameters of the CPMG sequence. The dependence of R(2) on pH and tau (inter-pulse delay between the first and the second pulses of the CPMG sequence) is interpreted in terms of chemical exchange between the protons of water and those of the labile amino acid groups. This interpretation was confirmed by the analysis of the proton spectra acquired using a 300 MHz NMR spectrometer.     

The Conformations of Amino Acids on a Gold(111) Surface

The interactions of amino acids with inorganic surfaces are of interest for biologists and biotechnologists alike. However, the structural determinants of peptide–surface interactions have remained elusive, but are important for a structural understanding of the interactions of biomolecules with gold surfaces. Molecular dynamics simulations are a tool to analyze structures of amino acids on surfaces. However, such an approach is challenging due to lacking parameterization for many surfaces and the polarizability of metal surfaces. Herein, we report DFT calculations of amino acid fragments in vacuo and molecular dynamics simulations of the interaction of all amino acids with a gold(111) surface in explicit solvent, using the recently introduced polarizable gold force field GolP. We describe preferred orientations of the amino acids on the metal surface. We find that all amino acids preferably interact with the gold surface at least partially with their backbone, underlining an unfolding propensity of gold surfaces.     

Adsorption of alpha amino acids at the water/goethite interface

The adsorption of amino acids onto mineral surfaces plays an important role in a wide range of areas, e.g., low-temperature aqueous geochemistry, bone formation and protein-bone interactions. In this work, the adsorption of three alpha aminoacids (sarcosine, MIDA and EDDA) onto goethite (alpha-FeOOH) was studied as a function of pH and background electrolyte concentration at 25.0 degrees C, and the molecular structures of the surface complexes formed were analyzed by means of ATR-FTIR spectroscopy. The results showed that adsorption of alpha amino acids were strongly dependent on the functionality and structure of the ligands. No adsorption was detected for the zwitterionic sarcosine indicating that simple alpha amino acids without other ionizable and/or functional groups display insignificant affinity for mineral surfaces such as goethite. With respect to the more complex amino acids, which are surface reactive, the number and relative positions of carboxylate and amine groups determine the types of surface interactions. These interactions range from non-specific outer-sphere to specific inner-sphere interactions as shown by the MIDA and EDDA results, respectively. The results presented herein suggest that isomerically-selective adsorption might only occur for amino acids that are capable of specific surface interactions, either through site-specific hydrogen bonding or inner-sphere complexation.     

Electrospray ionization mass spectrometric study of encapsulation of amino acids by cyclodextrins

Electrospray ionization (ESI) mass spectrometry has been used to study inclusion (host-guest) complexes of cyclodextrins (CDs) with amino acids. Host-guest complexes formed in solution are stable for characterization by ESI mass spectrometry: The relative abundances and the stoichiometry of the complexes formed in solution can, thus, be determined in the gas phase. The studies verified that β- and γ-cyclodextrin better accommodate protonated amino acids than α-cyclodextrin, and that chemically modified cyclodextrins such as heptakis(2,6-di-O-methyl)-β-cyclodextrin (DM-β-CD) may show profound improvement in complexation. The preferential formation of DM-β-CD-aromatic amino acid over DM-β-CD-aliphatic amino acid complexes is confirmed by the experiments, and the relative gas-phase stabilities determined by repeller-collimator collision-induced dissociation show an identical trend to the complexation in solution. Although molecular mechanics studies also may predict the encapsulation preference of protonated amino acids by cyclodextrins, only small differences in the total complexation energies are obtained because of the inability of the calculations to consider hydrophobic interactions. An experimental approach based on ESI mass spectrometry is, therefore, more reliable in predicting host-guest interactions that involve cyclodextrins and amino acids than the theoretical calculations that employ molecular mechanics models.     

Secondary Structures in Synthetic Poly(Amino Acids): Homo- and Copolymers of Poly(Aib), Poly(Glu), and Poly(Asp)

The secondary structure of poly(amino acids) is an excellent tool for controlling and understanding the functionality and properties of proteins. In this perspective article the secondary structures of the homopolymers of oligo- and poly-glutamic acid (Glu), aspartic acid (Asp), and α-aminoisobutyric acid (Aib) are discussed. Information on external and internal factors, such as the nature of side groups, interactions with solvents and interactions between chains is reviewed. A special focus is directed on the folding in hybrid-polymers consisting of oligo(amino acids) and synthetic polymers. Being part of the SFB TRR 102 “Polymers under multiple constraints: restricted and controlled molecular order and mobility” this overview is embedded into the cross section of protein fibrillation and supramolecular polymers. As polymer- and amino acid folding is an important step for the utilization and design of future biomolecules these principles guide to a deeper understanding of amyloid fibrillation.     

Serine octamers: cluster formation, reactions, and implications for biomolecule homochirality

The emergence of homochirality continues to be one of the most challenging topics associated with the origin of life. One possible scenario is that aggregates of amino acids might have been involved in a sequence of chemical events that led to chiral biomolecules in self-replicating systems, that is, to homochirogenesis. Serine is the amino acid of principal interest, since it forms "magic-number" ionic clusters composed of eight amino acid units, and the clusters have a remarkable preference for homochirality. These serine octamer clusters (Ser8) can be generated under simulated prebiotic conditions and react selectively with other biomolecules. These observations led to the hypothesis that serine reactions were responsible for the first chiral selection in nature which was then passed through chemical reactions to other amino acids, saccharides, and peptides. This Review evaluates the chemistry of Ser8 clusters and the experimental evidence that supports their possible role in homochirogenesis.     

Effects of hydrogen-bonding and stacking interactions with amino acids on the acidity of uracil

The effects of hydrogen-bonding interactions with amino acids on the (N1) acidity of uracil are evaluated using (B3LYP) density functional theory. Many different binding arrangements of each amino acid to three uracil binding sites are considered. The effects on the uracil acidity are found to significantly depend upon the nature of the amino acid and the binding orientation, but weakly depend on the binding site. Our results reveal that in some instances small models for the amino acids can be used, while for other amino acids larger models are required to properly describe the binding to uracil. The gas-phase acidity of uracil is found to increase by up to approximately 60 kJ mol(-1) due to discrete hydrogen-bonding interactions. Although (MP2) stacking interactions with aromatic amino acids decrease the acidity of uracil, unexpected increases in the acidity are found when any of the aromatic amino acids, or the backbone, hydrogen bond to uracil. Consideration of enzymatic and aqueous environments leads to decreases in the effects of the amino acids on the acidity of uracil. However, we find that the magnitude of the decrease varies with the nature of the molecule bound, as well as the (gas-phase) binding orientations and strengths, and therefore solvation effects should be considered on a case-by-case basis in future work. Nevertheless, the effects of amino acid interactions within enzymatic environments are as much as approximately 35 kJ mol(-1). The present study has general implications for understanding the nature of active site amino acids in enzymes, such as DNA repair enzymes, that catalyze reactions involving anionic nucleobase intermediates.     

Development of modified force field for cation–amino acid interactions: Ab initio-derived empirical correction terms with comments on cation–π interactions

The modeling of voltage-gated ion-channel proteins is a continuing challenge for force-field calculations because of the diverse range of interactions involved. In particular, current force fields are not parameterized for either ion–amino acid or amino acid–electric field interactions. To address the parameterization of ion–amino acid interactions, we have tested the use of empirical correction terms, derived from ab initio calculations of single amino acids (representing the peptide backbone) interacting with K⁺ ions. Having demonstrated the utility of such an approach, we then extended the application to the amino acid side chains. The calculation of the interaction of K⁺ with serine, cysteine, methionine, lysine, arginine, aspartate, histidine (uncharged), tyrosine, tryptophan, and phenylalanine, both completes the parameterization of the molecular environments contained in the amino acids, and allows specific comment on these ion–functional group interactions. The cation–π interactions were of particular interest, given recent proposals in the literature and the fear that force fields would not be able to treat such interactions. We present a comprehensive comparison of the ab initio (DFT [BLYP], 6-311 G**) and force field (CHARMm22.0) assessments of these interactions. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1515–1525, 1998     

Partitioning behavior of amino acids in aqueous two-phase systems containing polyethylene glycol and phosphate buffer

The partitioning behavior of four amino acids, cysteine, phenylalanine, methionine, and lysine in 15 aqueous two-phase systems (ATPSs) with different polyethylene glycol (PEG) molecular weights and phosphate buffers has been studied in the present paper. The phase diagrams of the systems are investigated together with the effect of the PEG molecular weight and pH of the phosphate solutions. The composition of these systems and some parameters such as density and refractive index are determined. The influences of salts in ATPSs, side chain structure of the amino acids, pH of ATPSs, and the PEG molecular weight on the distribution ratios of the amino acids have been studied. This work is useful for the purification of amino acids and the separation of some proteins whose main surface exposed amino acid residues are these four amino acids, respectively.     

Metal ligand aromatic cation-pi interactions in metalloproteins: ligands coordinated to metal interact with aromatic residues

Cation-pi interactions between aromatic residues and cationic amino groups in side chains and have been recognized as noncovalent bonding interactions relevant for molecular recognition and for stabilization and definition of the native structure of proteins. We propose a novel type of cation-pi interaction in metalloproteins; namely interaction between ligands coordinated to a metal cation--which gain positive charge from the metal--and aromatic groups in amino acid side chains. Investigation of crystal structures of metalloproteins in the Protein Data Bank (PDB) has revealed that there exist quite a number of metalloproteins in which aromatic rings of phenylalanine, tyrosine, and tryptophan are situated close to a metal center interacting with coordinated ligands. Among these ligands are amino acids such as asparagine, aspartate, glutamate, histidine, and threonine, but also water and substrates like ethanol. These interactions play a role in the stability and conformation of metalloproteins, and in some cases may also be directly involved in the mechanism of enzymatic reactions, which occur at the metal center. For the enzyme superoxide dismutase, we used quantum chemical computation to calculate that Trp163 has an interaction energy of 10.09 kcal mol(-1) with the ligands coordinated to iron.     

Speciation and structural aspects of interactions of Al(III) with small biomolecules

Complexes formed with low molecular mass biomolecules are the ‘dynamic or mobile units’ of Al(III), which may be involved in the absorption and transport processes of this toxic element in organisms. This paper reviews the interactions of Al(III), from speciation and structural aspects, with biologically relevant endogenous and exogenous small biomolecules such as inorganic ligands (hydroxide, fluoride, (oligo)phosphates and silicic acid), amino acids, phosphorylated amino acids, oligopeptides, biophosphates including nucleotides, phosphonates, hydroxamates, and aromatic and aliphatic hydroxycarboxylates. The importance of time in biospeciation is demonstrated on the examples of binary and ternary systems involving Al(III) and citric acid. Examples are also given for the implications of the speciation of Al(III) with such small biomolecules in biology.     

Separation of Cobalt (III) Bis(ethylenediamine) Amino Acid Complexes by Reversed Phase HPLC

Abstract

Methods for the rapid analysis of amino acid cobalt (III) bis(ethylenediamine) complexes by reversed phase high performance liquid chromatography (HPLC) are described with mobile phases containing the pairing ions, p-toluenesulphonate and hexanesulphonate. Under these conditions, the amino acid cobalt (III) bis(ethylenediamine) complexes elute in order of the relative hydrophobicities of the parent amino acids which suggests that the amino acid side chain makes a significant contribution to the retention mechanism. At high sample loadings, these complexes shows a concentration dependent peak splitting effect divergent to that normally experienced with inadequate buffering capacity of the pairing ion reagent.     

Boronic acid building blocks: tools for sensing and separation

In this feature article the use of boronic acids to monitor, identify and isolate analytes within physiological, environmental and industrial scenarios is discussed. Boronic acids recognise diol motifs through boronic ester formation and interact with anions generating boronates, as such they have been exploited in sensing and separation protocols for diol appended molecules such as saccharides and anions alike. Therefore robust molecular sensors with the capacity to detect chosen molecules selectively and signal their presence continues to attract substantial attention, and boronic acids have been exploited with some success to monitor the presence of various analytes. Reversible boronic acid-diol interactions have also been exploited in boron affinity chromatography realising new separation domains through the same binding events. Boronic acid diol and anion interactions pertaining to sensing and separation are surveyed.     

Diphenylalanine Motif Drives Self-Assembling in Hybrid PNA-Peptide Conjugates

Peptides and nucleic acids can self-assemble to give supramolecular structures that find application in different fields, ranging from the delivery of drugs to the obtainment of materials endowed with optical properties. Forces that stabilize the “suprastructures” typically are hydrogen bonds or aromatic interactions; in case of nucleic acids, Watson-Crick pairing drives self-assembly while, in case of peptides, backbone hydrogen bonds and interactions between aromatic side chains trigger the formation of structures, such as nanotubes or ribbons. Molecules containing both aromatic peptides and nucleic acids could in principle exploit different forces to self-assemble. In this work we meant to investigate the self-assembly of mixed systems, with the aim to understand which forces play a major role and determine formation/structure of aggregates. We therefore synthesized conjugates of the peptide FF to the peptide nucleic acid dimer “gc” and characterized their aggregates by different spectroscopic techniques, including NMR, CD and fluorescence.     

Molecular recognition effects in polyaniline

Polyaniline (PANI) is known to dissolve in strong acids, such as sulphonic acids. PANI, in its electrically conductive form, is generally regarded to be poorly soluble in low-acidic solvents and to be infusible, closely resembling fully aromatic rigid rod polymers. We show that “less” acidic solvents and plasticizers can be found based on phenyl-phenyl interactions in combination with hydrogen bonding. The requirement is that the interactions are strong enough and, importantly, sterically match the complementary moieties of the sulphonic acid doped PANI. Dihydroxybenzenes and bisphenols are examples of such low-acidic compounds. This type of molecular recognition allows solution and melt processibility of PANI doped by generic sulphonic acid, such as methanesulphonic acid or alkylbenzenesulphonic acid. Molecular recognition is also offered as an explanation for the previously observed high solubility of camphorsulphonic acid (CSA) doped PANI in phenols.     

Vibronic interactions and possible electron pairing in the photoinduced excited electronic States in molecular systems: a theoretical study

Electron-phonon interactions in the photoinduced excited electronic states in molecular systems such as phenanthrene-edge-type hydrocarbons are discussed and compared with those in the monoanions and cations. The complete phase patterns difference between the highest occupied molecular orbitals (HOMO) and the lowest unoccupied molecular orbitals (LUMO) (the atomic orbitals between two neighboring carbon atoms combined in phase (out of phase) in the HOMO are combined out of phase (in phase) in the LUMO) are the main reason that the C-C stretching modes around 1500 cm(-1) afford much larger electron-phonon coupling constants in the excited electronic states than in the charged electronic states. The frequencies of the vibrational modes that play an essential role in the electron-phonon interactions for the excited electronic states are similar to those for the monoanions and cations in phenanthrene-edge-type hydrocarbons. Possible electron pairing and Bose-Einstein condensation in the photoinduced excited electronic states as well as those in the monoanions and cations in molecular systems such as phenanthrene-edge-type hydrocarbons are also discussed.     

Mechanism of selectivity in ion-pair high-performance liquid chromatography of aminoglycoside antibiotics using perfluorinated pairing ions

The behaviour of perfluorinated carboxylic acids as pairing ions for the chromatography of the aminoglycoside antibiotics was studied. As with perhydrogenated pairing ions, the capacity factor can be modified according to the percentage of organic modifier and the nature and concentration of perfluorinated pairing ion in the mobile phase. The special selectivity effect observed with trifluoroacetic acid was investigated and interpreted as a concerted mechanism involving ionic and hydrophobic interactions.