X-ray crystallographic signature of supramolecular triple helix formation from a water soluble synthetic tetrapeptide

Single crystal X-ray diffraction studies on the water soluble, synthetic tetrapeptide Tyr(1)-Aib(2)-Tyr(3)-Val(4) with a non-coded amino acid residue (Aib: [small alpha]-amino isobutyric acid) reveal that the peptide adopts an "S"-shaped molecular structure which self-assembles to form a supramolecular triple helix using various non-covalent interactions including water mediated hydrogen bonds in the solid state.     

Substoichiometric determination of mercury by neutron activation analysis

A method has been developed for the substoichiometric determination of mercury by thermal neutron activation analysis, based on the selective extraction of the Hg(II)—Bindschedler's Green complex into 1,2-dichloroethane. The method has been applied for the determination of trace amounts of mercury in geological standards such as W-1, GR, Sye-1, and T-1, meteorite Allende de Publito, and biological materials such as kale, IR1 standard tobacco, and human blood serum.     

The role of the disulfide bond in amyloid-like fibrillogenesis in a model peptide system

Three terminally protected short peptides Bis[Boc-D-Leu1-Cys2-OMe] 1, Bis[Boc-Leu1-Cys2-OMe] and Bis[Boc-Val1-Cys2-OMe] 3 exhibit amyloid-like fibrillar morphology. Single crystal X-ray diffraction analysis of peptide 1 clearly demonstrates that it adopts an overall extended backbone molecular conformation that self-assembles to form an intermolecular hydrogen-bonded antiparallel supramolecular beta-sheet structure in crystals. Scanning electron microscopic (SEM) images, transmission electron microscopic (TEM) images and Congo red binding studies vividly demonstrate the amyloid-like fibril formation of peptides 1, 2 and 3. However, after reduction of the disulfide bridge of peptides 1, 2 and 3, three newly generated peptides Boc-D-Leu1-Cys2-OMe 4, Boc-Leu1-Cys2-OMe 5 and Boc-Val1-Cys2-OMe 6 are formed and all of them failed to form any kind of fibril under the same conditions, indicating the important role of the disulfide bond in amyloid-like fibrillogenesis in a peptide model system.     

Spectroscopic investigation on the interaction of ICT probe 3-acetyl-4-oxo-6,7-dihydro-12H Indolo-[2,3-a] quinolizine with serum albumins

Interaction of 3-acetyl-4-oxo-6,7-dihydro-12H indolo-[2,3-a] quinolizine (AODIQ), a biologically active molecule, with model transport proteins, bovine serum albumin (BSA) and human serum albumin (HSA) have been studied using steady state and picosecond time-resolved fluorescence and fluorescence anisotropy. The polarity dependent intramolecular charge transfer (ICT) process is responsible for the remarkable sensitivity of this biological fluorophore to the protein environments. The CT fluorescence exhibits appreciable hypsochromic shift along with an enhancement in the fluorescence yield, fluorescence anisotropy (r) and fluorescence lifetime upon binding with the proteins. The reduction in the rate of ICT within the hydrophobic interior of albumins leads to an increase in the fluorescence yield and lifetime. Marked increase in the fluorescence anisotropy indicates that the probe molecule is located in a motionally constrained environment within the proteins. Micropolarities in the two proteinous environments have been determined following the polarity sensitivity of the CT emission. Addition of urea to the protein-bound systems leads to a reduction in the fluorescence anisotropy indicating the denaturation of the proteins. Polarity measurements and fluorescence resonance energy transfer (FRET) studies throw light in assessing the location of the fluorophore within the two proteinous media.     

Can a consecutive double turn conformation be considered as a peptide based molecular scaffold for supramolecular helix in the solid state?

Helices and sheets are ubiquitous in nature. However, there are also some examples of self-assembling molecules forming supramolecular helices and sheets in unnatural systems. Unlike supramolecular sheets there are a very few examples of peptide sub-units that can be used to construct supramolecular helical architectures using the backbone hydrogen bonding functionalities of peptides. In this report we describe the design and synthesis of two single turn/bend forming peptides (Boc-Phe-Aib-Ile-OMe 1 and Boc-Ala-Leu-Aib-OMe 2) (Aib: α-aminoisobutyric acid) and a series of double-turn forming peptides (Boc-Phe-Aib-Ile-Aib-OMe 3, Boc-Leu-Aib-Gly-Aib-OMe 4 and Boc-γ-Abu-Aib-Leu-Aib-OMe 5) (γ-Abu: γ-aminobutyric acid). It has been found that, in crystals, on self-assembly, single turn/bend forming peptides form either a supramolecular sheet (peptide 1) or a supramolecular helix (peptide 2), unlike self-associating double turn forming peptides, which have only the option of forming supramolecular helical assemblages.     

Enhanced sampling molecular dynamics simulations correctly predict the diverse activities of a series of stiff-stilbene G-quadruplex DNA ligands

Ligands with the capability to bind G-quadruplexes (G4s) specifically, and to control G4 structure and behaviour, offer great potential in the development of novel therapies, technologies and functional materials. Most known ligands bind to a pre-formed topology, but G4s are highly dynamic and a small number of ligands have been discovered that influence these folding equilibria. Such ligands may be useful as probes to understand the dynamic nature of G4 in vivo, or to exploit the polymorphism of G4 in the development of molecular devices. To date, these fascinating molecules have been discovered serendipitously. There is a need for tools to predict such effects to drive ligand design and development, and for molecular-level understanding of ligand binding mechanisms and associated topological perturbation of G4 structures. Here we study the G4 binding mechanisms of a family of stiff-stilbene G4 ligands to human telomeric DNA using molecular dynamics (MD) and enhanced sampling (metadynamics) MD simulations. The simulations predict a variety of binding mechanisms and effects on G4 structure for the different ligands in the series. In parallel, we characterize the binding of the ligands to the G4 target experimentally using NMR and CD spectroscopy. The results show good agreement between the simulated and experimentally observed binding modes, binding affinities and ligand-induced perturbation of the G4 structure. The simulations correctly predict ligands that perturb G4 topology. Metadynamics simulations are shown to be a powerful tool to aid development of molecules to influence G4 structure, both in interpreting experiments and to help in the design of these chemotypes.

Enhanced sampling molecular dynamics simulations and solution-phase experiments come together to demonstrate the diverse effects of G4-interactive small molecules.     

Thermodynamics of micellization of multiheaded single-chain cationic surfactants

The energetics of micelle formation of three single-chain cationic surfactants bearing single (h = 1), double (h = 2), and triple (h = 3) trimethylammonium [(+)N(CH(3))(3)] headgroups have been investigated by microcalorimetry. The results were compared with the microcalorimetric data obtained from well-known cationic surfactant, cetyl trimethylammonium bromide (CTAB), bearing a single chain and single headgroup. The critical micellar concentrations (cmc's) and the degrees of counterion dissociation (alpha) of micelles of these surfactants were also determined by conductometry. The cmc and the alpha values increased with the increase in the number of headgroups of the surfactant. The relationship between the cmc of the surfactant in solution and its free energy of micellization (DeltaG(m)) was derived for each surfactant. Exothermic enthalpies of micellization (DeltaH(m)) and positive entropies of micellization (DeltaS(m)) were observed for all the surfactants. Negative DeltaH(m) values increased from CTAB to h = 1 to h = 2 and decreased for h = 3 whereas DeltaS(m) values decreased with increase in the number of headgroups. The DeltaG(m) values progressively became less negative with the increase in the number of headgroups. This implies that micelle formation becomes progressively less favorable as more headgroups are incorporated in the surfactant. From the steady-state fluorescence measurements using pyrene as a probe, the micropolarities sensed by the probe inside various micelles were determined. These studies suggest that the micelles are more hydrated with multiheaded surfactants and the micropolarity of micelles increases with the increase in the number of headgroups.     

First crystallographic signature of an acyclic peptide nanorod: molecular mechanism of nanorod formation by a self-assembled tetrapeptide

A terminally protected acyclic tetrapeptide Boc-Aib-Val-Aib-beta-Ala-OMe 1 (Aib: alpha-aminoisobutyric acid, beta-Ala: beta-Alanine) self-assembles into a continuous hydrogen-bonded supramolecular helix with an average diameter of 10 A (1 nm) starting from a double bend molecular conformation in crystals and further self-assembly of this supramolecular architecture leads to the formation of polydisperse nanorods of diameters 10-40 nm.     

A new motif in the formation of peptide nanotubes: the crystallographic signature

Terminally protected acyclic tripeptides Boc-Tyr(1)-Val(2)-Tyr(3)-OMe 1 and Boc-Tyr(1)-Ile(2)-Tyr(3)-OMe 2 self-assemble into nanotubes in crystals through various noncovalent interactions with an average internal diameter of 5 A (0.5 nm), and the tubular ensemble is developed through the hydrogen-bonded side chains of tyrosine residues. The inside of the hollow nanotubular structures is hydrophilic; however, no solvent molecules have been crystallographically detected. [structure: see text]     

Conformational heterogeneity of tripeptides containing Boc-Leu-Aib as corner residues in the solid state

A critical analysis of single crystal X-ray diffraction studies on a series of terminally protected tripeptides containing a centrally positioned Aib (α-aminoisobutyric acid) residue has been reported. For the tripeptide series containing Boc-Ala-Aib as corner residues, all the reported peptides formed distorted type II β-turn structures. Moreover, a series of Phe substituted analogues (tripeptides with Boc-Phe-Aib) have also shown different β-turn conformations. However, the Leu-modified analogues (tripeptides with Boc-Leu-Aib) disrupt the concept of β-turn formation and adopt various conformations in the solid state. X-ray crystallography sheds some light on the conformational heterogeneity at atomic resolution.