ATP recognition and sensing with a phenanthroline-containing polyammonium receptor

A new polyammonium receptor is able to selectively recognise and sense ATP among triphosphate nucleotides, thanks to ATP-induced quantitative quenching of its fluorescence emission.     

Anion coordination chemistry in aqueous solution of polyammonium receptors

The behavior of polyamines as receptors of selected families of anions in water is explored. First metallocyanide interaction with saturated polyammonium hosts is analyzed both in solution and in the solid state. The utility of potentiometry, multinuclear NMR, microcalorimetry and cyclic voltammetry to describe solution features of this chemistry is described for selected systems. Sulfate, phosphate, polyphosphate and nucleotide interactions with large polyammonium receptors are then reviewed. Hydrogen bond formation is discussed from a thermodynamic point of view. The influence of the presence of aromatic fragments within the structure on the binding strength is discussed. Factors affecting ATP hydrolytic cleavage by macrocyclic polyammonium receptors is revisited. Metal complexes are analyzed as anion receptors through formation of mixed complexes. Finally, an example of the influence of anion in crystal growing is provided.     

Protonation of polyamines in NaCl aqueous solution and binding of Cl by polyammonium cations

Equilibrium constants relative to the binding of Cl⁻ by nine open chain polyammonium cations (di, tri and tetra) were determined by potentiometric measurements (H⁺-glass electrode), at T=25°C. To this end the protonation constants of these amines were measured in NaCl aqueous solutions, in the ionic strength range 0.1<I≤1 mol dm⁻³. The different amines (some of which are N-alkyl substituted) were chosen in order to consider several factors affecting the values of protonation constants, the chloride complex formation constants and the dependence on ionic strength of apparent protonation constants. As concerns these last two points, it was found that fully N-alkyl substituted amines behave in a very similar way, with respect to partially or non-substituted ones. Simple linear relationships are reported involving chloride formation constants, parameters for the dependence on ionic strength of protonation constants and charges in polyammonium cations. The complexes formed by two linear polyamines with NO₃⁻ have also been studied for comparison. Literature data are examined.     

Molecular recognition of insulin by a synthetic receptor

The discovery of molecules that bind tightly and selectively to desired proteins continues to drive innovation at the interface of chemistry and biology. This paper describes the binding of human insulin by the synthetic receptor cucurbit[7]uril (Q7) in vitro. Isothermal titration calorimetry and fluorescence spectroscopy experiments show that Q7 binds to insulin with an equilibrium association constant of 1.5 × 10(6) M(-1) and with 50-100-fold selectivity versus proteins that are much larger but lack an N-terminal aromatic residue, and with >1000-fold selectivity versus an insulin variant lacking the N-terminal phenylalanine (Phe) residue. The crystal structure of the Q7·insulin complex shows that binding occurs at the N-terminal Phe residue and that the N-terminus unfolds to enable binding. These findings suggest that site-selective recognition is based on the properties inherent to a protein terminus, including the unique chemical epitope presented by the terminal residue and the greater freedom of the terminus to unfold, like the end of a ball of string, to accommodate binding. Insulin recognition was predicted accurately from studies on short peptides and exemplifies an approach to protein recognition by targeting the terminus.     

合成受体的分子识别

系统地总结了我们近年来在超分子化学研究中的一些工作进展,着重介绍了一些合成受体(环糊精,冠醚,杯芳烃)的分子识别和组装研究。     

Charge-mediated recognition of N-terminal tryptophan in aqueous solution by a synthetic host

The molecular recognition of peptides and proteins in aqueous solution by designed molecules remains an elusive goal with broad implications for basic biochemical research and for sensors and separations technologies. This paper describes the recognition of N-terminal tryptophan in aqueous solution by the synthetic host cucurbit[8]uril (Q8). Q8 is known to form 1:1:1 heteroternary complexes with methyl viologen (MV) and a second aromatic guest. Here, the complexes of Q8.MV with (i) the four natural aromatic alpha-amino acids, (ii) four singly charged tryptophan derivatives, and (iii) four tryptophan-containing tripeptides were characterized by isothermal titration calorimetry, mass spectrometry, and UV-visible, fluorescence, and (1)H NMR spectroscopy. We find that Q8.MV binds Trp-Gly-Gly with high affinity (K(a) = 1.3 x 10(5) M(-1)), with 6-fold specificity over Gly-Trp-Gly, and with 40-fold specificity over Gly-Gly-Trp. Analysis of the nine indole-containing compounds suggests that peptide recognition is mediated by the electrostatic charge(s) proximal to the indole, and that the mode of binding is consistent for these compounds. Complex formation is accompanied by the growth of a visible charge-transfer band and the quenching of indole fluorescence. These optical properties, combined with the stability and selectivity of this system, are promising for applications in sensing and separating specific peptides.     

Colorimetric sensor for ATP in aqueous solution

A new chromogenic complex 1.Zn has been synthesized, and its interactions with different biologically important phosphates have been investigated in aqueous solution (pH approximately 7.2). A visual color change can be detected on binding of ATP to 1.Zn, whereas no such change is observed when other biologically related anions (AMP, ADP, PPi, or Phosphate) are used. Complex 1.Zn can also be used as a staining agent for yeast cells allowing detection under normal light microscopy.     

A supramolecular optic receptor for selective recognition CDP in neutral aqueous solution

We designed and synthesized a Cu-coordination complex based on a seven-membered amide cycle and studied its binding ability with nucleotides (cytidine 5′-monophosphate (CMP), cytidine 5′-diphosphate (CDP), cytidine 5′-triphosphate (CTP), cytidine d-5′-monophosphate (dCMP), and thymidine d-5′-monophosphate (dTMP)) by UV-Vis spectroscopy. Results indicate that the compound shows the highest binding ability with CDP among the studied nucleotides and can selectively and strongly bind nucleotides in neutral aqueous solution. The compound can be used as optical receptor for the detection of CDP.     

水溶液中的氨基酸桥联环糊精二聚体的分子识别

采用荧光偏光方法研究了用2-氨基-L-1,5-戊二酸衍生物和(1R,3R)-1-氨基-1,3-二羧基环戊烷衍生物桥联的环糊精二聚体1和2(主体),在298K、pH=7.4时,与四个低分子量的多肽(客体,H-Trp-Trp-Arg-Arg-NH23;Adm-Trp-Arg-Arg-NH24;Adm-D-Trp-Arg-Arg-NH25;H-Trp-Trp-Trp-Trp-Arg-Arg-NH26)之间的相互作用。研究结果表明,二聚体环糊精对于多肽的分子识别作用,就主体而言,即便是主体作用位点以外部分基团结构的改变,对主-客体之间的分子识别也有重要影响,并且两个空腔在组装客体过程中相互之间产生协同作用,就客体而言,多肽分子的链长、疏水性及其嵌入基团的极性、大小、形状等对包合物的形成与稳定均起重要作用。主-客体组装过程中产生负的焓变和正的熵变,表明范德华-伦敦色散力、氢键和疏水相互作用是本文研究体系的主要包合驱动力。     

Interaction of l-malic acid with alkaline metals and open chain polyammonium cations in aqueous solution

This work reports a potentiometric, calorimetric and spectropolarimetric ultraviolet circular dichroism (UV/CD) study of the interaction of l-malic acid with alkaline metals or (poly)ammonium (methylamine, ethylenediamine, diethylenetriamine, triethylenetetramine, spermine, tetraethylenepentamine and pentaethylenehexamine) cations. Stability data (logK, DeltaG(0)) were obtained potentiometrically for the l-malic acid with (poly)ammonium cations systems; calorimetric measurements (25 degrees C) made it possible to obtain DeltaH(0) and TDeltaS(0) values for the complexes formed in the systems under examination. logK values calculated (for the reaction: H(i)A(i+)+H(j)L((j-z))=ALH(r)((i+j-z)), with r=i+j) range between 0.8 and 4.6, i.e., the interactions are from weak to fairly strong while maximum stability for each system is given by the species with the highest z(anion)xz(cation) (z=charge) value. Enthalpy changes associated with reactions H(n)A(n+)+L(2-)=ALH(n)((n-2)) and H(n)A(n+)+HL(-)=ALH(n+1)((n-1)) are always positive and increase progressively with n. The same is valid for T DeltaS(0) values, which indicate that these species are entropically stabilized, as expected for electrostatic interactions. It was verified that the UV/CD signal depends on both ionic medium and ionic strength value; for comparison, we used the l-malic acid signal recorded in tetramethylammonium chloride as baseline background salt (as in potentiometry). UV/CD spectra were recorded for solutions containing both cationic and anionic species. When the cation was a protonated polyamine, CD spectra calculations were performed for most stable ion pairs: the results show remarkable differences in Deltaepsilon (dm(3) mol(-1) cm(-1)) values at 205 nm (which is the l-malate UV/CD lambda(max)) between the chiral ligand and its complex with a polyamine.     

Molecular dynamics of a vanadate-dipeptide complex in aqueous solution

Static geometry optimizations and Car-Parrinello molecular dynamics simulations with the BP86 density functional, as well as NMR chemical shift calculations at the GIAO-B3LYP level, have been used to assess structure, speciation, and dynamics of aqueous solutions of the vanadate-glycylglycine complex. According to the simulations, this complex should be formulated as five-coordinate, anionic [VO2(GlyGly')]- (GlyGly' = H2N-CH2-C(O)-N-CH2-CO2). The neutral conjugate acid is unstable in water, where it is deprotonated within a few picoseconds. Six-coordinate structural alternatives, [VO(OH)2(GlyGly')]-, are disfavored energetically and/or entropically. The hydration shell around [VO2(GlyGly')]- in water is characterized in terms of suitable pair correlation functions.     

Metal-ion-assisted hydrolysis of dipeptides involving a serine residue in a neutral aqueous solution

Dipeptides having a serine residue at the C-terminus, X-Ser, where X is an appropriate amino acid residue, were efficiently hydrolyzed in the presence of ZnCl2 at pH 7.0. The rapid hydrolysis of X-Ser is due to an autocatalysis of the hydroxy group in the serine residue, and is found to be accelerated by a metal ion, in particular by ZnCl2. Roles of the metal ion in the hydrolysis of peptides involving a serine residue, in relation to the recently reported protein cleavages, are discussed.     

Molecular simulation of a concentrated aqueous KCl solution

A 1.0 M aqueous KCl solution was studied by molecular dynamics simulations at 293 K in order to study the influence of the ionic concentration on the hydration structure of the ions as well as the formation of ion clusters. The hydration structures of the ions are almost independent of the ionic concentration unless in respect to the perturbation that appears due to ionic clustering. Fractions equal to 31.9% of the anions and 37.8% of the cations are associated. Clusters constituted by two, three and four ions were detected. Their mean lifetimes are always affected by thermal effects, reorientational relaxation while the longest lifetimes are a consequence of ionic cloud relaxations. The pairs constituted by two anions or two cations are stabilized by water molecules belonging to the solvation shells of both ions. The neutral K⁺Cl⁻ pairs are formed under the influence of the electrostatic attraction that, however, is small due to the ionic radii of these ions. Consequently, this kind of pairs contains only 8.8% of the ions while the fraction of ions in the negative and positive pairs are equal to 29.2 and 39.3%, respectively, when the same ion can pertain to more than one pair.     

Bis- and tris-naphthoimidazolium derivatives for the fluorescent recognition of ATP and GTP in 100% aqueous solution

Naphthoimidazolium groups can form unique ionic hydrogen bonds with anions as imidazolium moieties, and in addition, they are fluorescent, so no further elaborative synthesis is needed to introduce a fluorescent group. In this paper, three naphthoimidazolium derivatives were synthesized and studied for the recognition of nucleotides. Compound 1 composed of a single naphthoimidazolium group and quaternary ammonium group did not show any significant fluorescent changes with various anions and nucleotides, such as ATP, GTP, CTP, TTP, UTP, ADP and AMP. A tripodal compound 3 bearing three naphthoimidazolium groups and three quaternary ammonium groups, respectively, showed large fluorescence enhancements with UTP, CTP and TTP and moderate fluorescence enhancements with ATP and pyrophosphate and a fluorescence quenching effect with GTP. On the other hand, compound 2 bearing two naphthoimidazolium groups and two quaternary ammonium groups displayed a selective fluorescence enhancement with ATP and a selective fluorescence quenching effect with GTP in 100% aqueous solution.     

Molecular shape of palytoxin in aqueous solution

Palytoxin, one of the most toxic non-peptide substances, formed an associated dimer of 5 nm length in aqueous solution.     

A self-assembled receptor for the recognition of phosphate and acetate anions in neutral aqueous solution

The reaction of [(benzene)RuCl(2)](2) with a piperazine-bridged bis(dihydroxypyridine) ligand and LiOH leads to the formation of an expanded helicate, which is able to bind phosphate and acetate in aqueous solution at neutral pH.