Intrinsic proclivity of left-handed conformation in large Nest motif peptides inferred from molecular dynamics

The 'Nest' motif plays a functional role in protein owing to its ligand binding potential aided by geometric concavity. The presence of less favored left-handed conformation (L-state) in its structure makes this concavity possible and in shaping the native chemical environment amenable to stable binding interactions. To understand the persistent appearance of L-state torsion in the Nest motif, we analyzed 0.5μs Molecular Dynamics (MD) simulation trajectories of 35 six-residue peptides (out of a total of 50 large Nest sequences of ≥6 residues) identified in our previous study. Analysis of the MD trajectories of the individual peptides reveals initial L-state in 60% of the peptides persists for >40% of the trajectory. Further, Nests with different sequences appear to adopt a specific conformational state driven by the neighboring L-state residues. The sequences also possess short secondary structures and amino acid repeats, suggesting evolutionary conservation and the specific role of amino acids in locally predisposing the torsion angle to the L-state. These findings help us to understand how L-state conformation is an essential prerequisite in stabilizing the Nest motif and shed light on the sequence-structure-function paradigm in the rational design of peptides and peptidomimetics for therapeutics.Communicated by Ramaswamy H. Sarma.

Thermodynamics of anion binding to zwitterionic sulfobetaine micelles

One of the most intriguing aspects of zwitterionic surfactant micelles is their propensity to exhibit selectivity in the binding of the anions of added salts. In this work we examine the thermodynamics of the interaction of the strongly bound perchlorate ion and the more weakly bound bromide ion with micelles of N-tetradecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (SB3-14) in aqueous solution employing enthalpies derived from isothermal titration calorimetry combined with Gibbs free energies derived from literature data for the binding equilibria. In both cases, the binding is exothermic and enthalpy driven, but entropically unfavorable, with only modest changes in the Gibbs free energy as a function of the extent of anion binding. Likewise, perchlorate ion binding was found to have little or no effect on the aggregation numbers of SB3-14 micelles determined by time-resolved fluorescence quenching of pyrene by the N-hexadecylpyridinium cation. The results are interpreted within the context of the factors involved in the ion-pairing between the anions and the positive charge center of the zwitterion headgroup and the interplay between electrostatics, solvent reorganization and a net loss of translational degrees of freedom that accompany anion binding.

Entropy Versus Enthalpy Controlled Temperature/Redox Dual-Triggered Cages for Selective Anion Encapsulation and Release

New C₃ -symmetric imidazole ligands were designed with phosphine and phosphine oxide linkers (L^P and L^PO , respectively) to demonstrate a dual-triggered dynamic closed coordination cage. Both L^P and L^PO form discrete Zn₄ L₄ -closed cages (1^P and 1^PO , respectively) with excellent selectively for BPh₄ ^- , whereas 1^P and 1^PO encapsulate neither a slightly larger size anion [B(C₆ H₄ CH₃ )₄ ^- ] nor smaller size anions (BF₄ ^- , PF₆ ^- , SbF₆ ^- , and OSO₂ CF₃ ^- ). 1^PO exhibits more negative enthalpy and entropy changes upon anion encapsulation, thus releasing almost all of the encapsulated anions at high temperature (343 K) (trigger 1: BPh₄ ^- ⊂1^PO ← → 1^PO +BPh₄ ^- ). In contrast 1^P has less negative enthalpy and entropy changes, thus preserving the captured anion over a wide range of temperatures (298 K to 343 K). The 1^P cage can be quantitatively oxidized to the 1^PO cage by a mild oxidant (Ox.=H₂ O₂ ), and therefore the captured anion can be released by a redox triggering event (trigger 2: BPh₄ ^- ⊂1^P +Ox.→1^PO +BPh₄ ^- ).

N-Confused Porphyrin - A Unique "Turn-On" Chemosensor for CN- and F- ions and "Turn-Off" Sensor for ClO4 - ions

N-Confused meso-tetrakis(4-carbomethoxyphenyl)porphyrin (1) and its Ni(II) complex (1 a) have been synthesized and utilized for anion sensing studies, and the results are compared with N-confused meso-tetraphenylporphyrin (NCTPP). Anion susceptibilities of 1 and 1 a were investigated using spectroscopic, electrochemical, and DFT studies. Porphyrins 1 and 1 a were able to detect CN^- , F^- , and ClO₄ ^- ions selectively over the tested set of anions even at ppm level. Interestingly, the addition of ClO₄ ^- ions resulted in fluorescence quenching (turn off) whereas the addition of F^- or CN^- resulted in fluorescence enhancement (turn on). Notably, the TFA addition resulted in fluorescence quenching, whereas the fluorescence enhancement was observed while adding TBAOH. The higher association constant (K_a ) values with anions, lower detection limit, and shifts in redox potentials are due to the electron-withdrawing effect of the -COOCH₃ group at the para-position of the meso-phenyl ring. This electron-withdrawing nature is crucial for the higher affinity towards anions. The anion sensing description in this article may not only unveil the built-in nature of N-confused porphyrins, but may also provide a general proposal for the development of novel anion sensors based on porphyrinoids. The electron-deficient porphyrin framework, large polarisable π-system, and anion binding through the outer NH or a combination of the above factors serve as a foundation for N-confused porphyrin to act as an anion sensor.

Metal-based optical chemosensors for CN- detection

This critical review focuses on recent advances (2010-2015) in the detection of cyanide anion via metal-based optical chemosensors in which a change in colour and/or fluorescence intensity (or emission wavelength) of a molecular metal complex is determined by the direct interaction of the metal centre with this anion.

Solution and structural binding studies of phosphate with thiophene-based azamacrocycles

Two thiophene-based monocyclic receptors L1 and L2 have been studied for phosphate binding in solutions (D2O and DMSO-d6 ) by 1H NMR and 31P NMR titrations, and in the solid state by single crystal X-ray analysis. Results from 1H NMR titrations suggest that the ligands bind phosphate anions in a 1:2 binding mode in DMSO-d6 , with the binding constants of 5.25 and 4.20 (in log K), respectively. The binding of phosphate to L1 and L2 was further supported by 31P NMR in D2O at pH = 5.2. The crystal structure of the phosphate complex of L1 reveals unambiguous proof for the formation of a ditopic complex via multiple hydrogen bonds from NH···O and CH···O interactions.

Exploratory studies towards various anion recognition chemistry by two different sized cleft shaped organic ligands

Indole and urea based two organic receptors have been synthesized by an easy synthetic process. These two receptors have strong sensitivity and selectivity for several bio-relevant anions. Receptor 1 and 2 were synthesized from indole-2-carboxylic acid and p-anisidine respectively, which are low cost starting materials. Receptor 1 can selectively sense anions like F(-), OAc(-) and H2PO4(-), while receptor 2 can only sense F(-) and H2PO4(-). Both receptors are silent toward anions like Cl(-), Br(-), I(-) and NO3(-). It is the difference in their shape and size which are responsible for different anion sensing. The nature of these host-guest type interactions was analyzed by convenient spectrophotometric techniques like UV-Vis, fluorescence, (1)H NMR, FT-IR studies and also confirmed by electrochemical techniques like cyclic voltammetry studies of the two ligand receptors with convenient anions. Between receptor 1 and 2, receptor 2 was crystallographically characterized also.

Phosphate binding with a thiophene-based azamacrocycle in water

Structural characterization of the phosphate complex with a thiophene-based macrocycle suggests that two dihydrogen phosphates in a dimeric form are encapsulated in the cavity via several hydrogen bonds from NH···O and CH···O interactions. In the lattice framework, the two dimers are linearly hydrogen-bonded to form a tetramer. ¹H NMR titrations suggest that the host forms a 1:1 complex with phosphate, showing an association constant of 120 M^-1 in D₂O at pH = 5.5. The host guest complexation was further confirmed by ESI-MS in a gas phase.