6-Strand to Stable 10/12 Helix Conformational Switch by Incorporating Flexible ß-hGly in the Homooligomers of Camphor Derived ß-Amino Acid: NMR and X-Ray Crystallographic Evidence.

Rational design of unnatural amino acid building blocks capable of stabilizing predictable secondary structures similar to protein fragments is pivotal for foldamer chemistry/catalysis. Here, we introduce novel ß-amino acid building blocks: [1S,2R,4R]exoCDA and [1S,2S,4R]endoCDA, derived from the abundantly available R(+)-camphor, which is traditionally known for its medicinal value. Further, we demonstrate that the homooligomers of exoCDA adopt 6-strand conformation, which switches to a robust 10/12-helix simply by inserting flexible ß-hGly spacer at alternate positions (1 : 1 ß-hGly/exoCDA heterooligomers), as evident by DFT-calculations, solution-state NMR spectroscopy and X-ray crystallography. To the best of our knowledge, this is the first example of crystalline-state structure of left-handed 10/12-mixed helix, that is free from the conventional approach of employing ß-amino acids of either alternate chirality or alternate ß2/ß3 substitutions, to access the 10/12-helix. The results also show that the homooligomers of heterochiral exoCDA don't adopt helical fold, instead exhibit banana-shaped strands, whereas the homodimers of the other diastereomer endoCDA, nucleate 8-membered turns. Furthermore, the homo-exoCDA and hetero-[ß-hGly-exoCDA] oligomers are found to exhibit self-association properties with distinct morphological features. Overall, the results offer new possibilties of constructing discrete stable secondary and tertiary structures based on CDAs, which can accommodate flexible residues with desired side-chain substitutions.

The narrow escape problem of a chiral active particle (CAP): an optimal scheme.

We report a simulation study on the narrow escape kinetics of a chiral active particle (CAP) confined to a circular domain with a narrow escape opening. The study's main objective is to optimize the CAP's escape chances as a function of the relevant parameters, such as translational and rotational speeds of the CAP, domain size, etc. We identified three regimes in the escape kinetics, namely the noise-dominated regime, the optimal regime, and the chiral activity-dominated regime. In particular, the optimal regime is characterized by an escape scheme that involves a direct passage to the domain boundary at first and then a unidirectional drift along the boundary towards the exit. Furthermore, we propose a non-dimensionalization approach to optimize the escape performance across microorganisms with varying motile characteristics. Additionally, we explore the influence of the translational and rotational noise on the CAP's escape kinetics.

Revealing the deterministic components in active avalanche-like dynamics.

Avalanche dynamics in an ensemble of self-propelled camphor boats are studied. The self-propelled agents are camphor infused circular paper disks moving on the surface of water. The ensemble exhibits bursts of activity in the autonomous state triggered by stochastic fluctuations. This type of dynamics has been previously reported in a slightly different system (J. Phys. Soc. Jpn., 2015, 84, 034802). Fourier analysis of the autonomous ensemble's average speed reveals a unimodal spectrum, indicating the presence of a preferred time scale in the dynamics. We therefor, entrain such an ensemble by external forcing by using periodic air perturbations on the surface of the water. This forcing is able to replace the stochastic fluctuations which trigger a burst in the autonomous ensemble, thus entraining the system. Upon varying the periodic forcing frequency, an optimal frequency is revealed at which the quality of entrainment of the ensemble by the forcing is augmented. This optimal frequency is found to be in the vicinity of the Fourier spectrum peak of the autonomous ensemble's average speed. This indicates the existence of an underlying deterministic component in the apparent aperiodic bursts of motion of the autonomous ensemble of active particles. A qualitative reasoning for the observed phenomenon is presented.

Total Synthesis and Structural Revision of Greensporone F and Dechlorogreensporone F.

The first asymmetric total syntheses of the real isolation product (2S,5R,8R)-greensporone F and (2S,5R,8R)-dechlorogreensporone F, 14-membered resorcylic acid lactones with a cis-2,5-disubstituted tetrahydrofuran ring system, was accomplished. The synthesis features a late-stage Lewis acid-catalyzed stereoselective intramolecular oxa-Michael reaction, E-selective ring-closing metathesis, De Brabander's esterification, and Jacobsen's hydrolytic kinetic resolution as the key steps. Synthesis of both real isolation and erroneously proposed structure necessitated the revision of the absolute configuration of greensporone F and dechlorogreensporone F. The erroneous representation of (2S,5S,8S)-configuration in greensporone F and dechlorogreensporone F was assigned to be (2S,5R,8R) by comparison with the NMR data and specific rotation of the synthetic compounds with that of the reported data.

An innovative in situ method of creating hybrid dendrimer nano-assembly: An efficient next generation dendritic platform for drug delivery.

Dendrimers have proven to be effective for drug delivery and their biodisposition varies with change on their surface, generation and core. In an effort to understand the role of critical nanoscale design parameters, we developed a novel hybrid dendrimer approach to harness unique features of individual dendrimers and create a nano-assembly. We report an easy in situ method of creating hybrid dendrimer nano-assembly by mixing G4.0 PAMAM (-NH2) and G3.5 PAMAM (-COONa) dendrimers with a chemotherapeutic drug docetaxel (DTX). Zeta potential, HR-TEM, 1H-NMR proved the formation of nano-assembly. In vitro dissolution, release studies revealed pH dependent dissolution and sustained drug release. Cellular uptake, cytotoxicity, and flow cytometric analysis in human/mouse glioblastoma cells indicated the effectiveness of hybrid dendrimers. The oral administration of the hybrid dendrimers showed pharmacokinetic equivalence to intravenous injection of commercially available Taxotere®. Hybrid dendrimer concept provides much needed fine-tuning to create multistage next-generation dendritic platform in nanomedicine.

Phase separation in binary fluid mixtures with symmetric and asymmetric Schmidt numbers: A DPD study.

We investigate the effect of the Schmidt number (Sc) on phase separation dynamics of two immiscible fluids in a two-dimensional periodic box using dissipative particle dynamics. The range of Sc investigated spans liquid-liquid separation processes. Phase separation is characterized by a domain size r(t), which typically follows a power law tß in time t, where ß is a characteristic exponent corresponding to the coarsening mechanism at play. The phase separation dynamics is studied for strongly (deep quench) separating mixtures. We consider cases of critical (ϕ ∼ 0.5) and off-critical (ϕ < 0.5) mixtures of fluids A and B for both ScA = ScB and ScA ≠ ScB. In all cases, the growth dynamics slow down with the increasing Schmidt number of either fluid. We observe the power law exponent ß = 0.5 for symmetric (ScA = ScB) critical mixtures and ß = 0.33 for all other cases. However, for off-critical mixtures, the exponent is 0.33 irrespective of the Schmidt number ratio of the two fluids. We explain these results from an analysis of the competition between diffusive effects vis-á-vis dynamical forces.

Rotational synchronization of camphor ribbons.

Experiments on interacting pinned self-propelled rotators are presented. The rotators are made from paper with camphor infused in its matrix. The ribbons rotate due to Marangoni effect driven forces arising by virtue of surface tension gradients. Two such self-rotating camphor ribbons are observed to experience a repulsive coupling via the camphor layer in the common water medium. Lag synchronization in both corotating (same sense of rotation) and counterrotating (opposite sense of rotation) ribbons is reported for the experiments. This synchronization is found to be dependent on the pivot to pivot distance l. For distances less than the span of both the ribbons, l_{c}, the rotators successfully synchronize. Furthermore, it is experimentally perceived that synchronization in the counterrotating ribbons is more robust than in the corotating ribbons. We rationalize the mechanism of this synchronization via a theoretical model involving a Yukawa type interaction which is analyzed numerically.

Force distributions in frictional granular media.

We report a joint experimental and theoretical investigation of the probability distribution functions (PDFs) of the normal and tangential (frictional) forces in amorphous frictional media. We consider both the joint PDF of normal and tangential forces together, and the marginal PDFs of normal forces separately and tangential forces separately. A maximum entropy formalism is utilized for all these cases after identifying the appropriate constraints. Excellent agreements with both experimental and simulation data are reported. The proposed joint PDF predicts giant slip events at low pressures, again in agreement with observations.

Roccellatol, a new ß-orcinol based metabolite from the lichen Roccella montagnei.

Roccellatol, a new (2'R,3'S)-erythrityl-2,6-dihydroxy-4-methylbenzoate was isolated along with nine known compounds from the fruticose lichen, Roccella montagnei Bel. em. D.D. Awasthi. The structure of the new compound was elucidated by detailed spectroscopic analysis (1H, 13C, DEPT and HRMS). The present isolation of roccellatol (10) assumes significance as the esters of p-orcellinic acid are rare in lichens. Interestingly, among the known compounds, (+)-montagnetol (9) was now isolated in very large quantity (4.66%).

Multiple Ligand-Bound States of a Phosphohexomutase Revealed by Principal Component Analysis of NMR Peak Shifts.

Enzymes sample multiple conformations during their catalytic cycles. Chemical shifts from Nuclear Magnetic Resonance (NMR) are hypersensitive to conformational changes and ensembles in solution. Phosphomannomutase/phosphoglucomutase (PMM/PGM) is a ubiquitous four-domain enzyme that catalyzes phosphoryl transfer across phosphohexose substrates. We compared states the enzyme visits during its catalytic cycle. Collective responses of Pseudomonas PMM/PGM to phosphosugar substrates and inhibitor were assessed using NMR-detected titrations. Affinities were estimated from binding isotherms obtained by principal component analysis (PCA). Relationships among phosphosugar-enzyme associations emerge from PCA comparisons of the titrations. COordiNated Chemical Shifts bEhavior (CONCISE) analysis provides novel discrimination of three ligand-bound states of PMM/PGM harboring a mutation that suppresses activity. Enzyme phosphorylation and phosphosugar binding appear to drive the open dephosphorylated enzyme to the free phosphorylated state, and on toward ligand-closed states. Domain 4 appears central to collective responses to substrate and inhibitor binding. Hydrogen exchange reveals that binding of a substrate analogue enhances folding stability of the domains to a uniform level, establishing a globally unified structure. CONCISE and PCA of NMR spectra have discovered novel states of a well-studied enzyme and appear ready to discriminate other enzyme and ligand binding states.

Solvent-Directed Switch of a Left-Handed 10/12-Helix into a Right-Handed 12/10-Helix in Mixed ß-Peptides.

Present study describes the synthesis and conformational analysis of ß-peptides from C-linked carbo-ß-amino acids [ß-Caa(l)] with a d-lyxo furanoside side chain and ß-hGly in 1:1 alternation. NMR and CD investigations on peptides with an (S)-ß-Caa(l) monomer at the N-terminus revealed a right-handed 10/12-mixed helix. An unprecedented solvent-directed "switch" both in helical pattern and handedness was observed when the sequence begins with a ß-hGly residue instead of a (S)-ß-Caa(l) constituent. NMR studies on these peptides in chloroform indicated a left-handed 10/12-helix, while the CD spectrum in methanol inferred a right-handed secondary structure. The NMR data for these peptides in CD3OH showed the presence of a right-handed 12/10-helix. NMR investigations in acetonitrile indicated the coexistence of both helix types. Quantum chemical studies predicted a small energy difference of 0.3 kcal/mol between the two helix types, which may explain the possibility of solvent influence. Examples for a solvent-directed switch of both the H-bonding pattern and the handedness of foldamer helices are rare so far. A comparable solvent effect was not found in the corresponding peptides with (R)-ß-Caa(l) residues, where right-handed 12/10-helices are predominating.

Hydrodynamic Signatures of Stationary Marangoni-Driven Surfactant Transport.

We experimentally study steady Marangoni-driven surfactant transport on the interface of a deep water layer. Using hydrodynamic measurements, and without using any knowledge of the surfactant physicochemical properties, we show that sodium dodecyl sulphate and Tergitol 15-S-9 introduced in low concentrations result in a flow driven by adsorbed surfactant. At higher surfactant concentration, the flow is dominated by the dissolved surfactant. Using camphoric acid, whose properties are a priori unknown, we demonstrate this method's efficacy by showing its spreading is adsorption dominated.

Self gelating isoracemosol A, new racemosaceramide A, and racemosol E from Barringtonia racemosa.

Phytochemical investigation into the CHCl3 extract of the fruits of Barringtonia racemosa resulted in the isolation of two new metabolites along with isoracemosol A and betulinic acid as known metabolites. The new compounds were characterised as phytosphingosine-type ceramide [(2S,3S,4R)-2-[(2R)-2-hydroxyhexadecanoyl amino]-hexacos-8(E)-ene-1,3,4-triol, 1] and racemosol E [21ß-acetoxy-22α-(2-methylbutyroxy)-olean-12-ene-3ß,16α,28-triol, 2] on the basis of extensive spectroscopic data analysis and chemical modifications. In addition, the self-gelating property of isoracemosol A (3) was investigated for the first time, which leads to the unexpected agglomerated porous-like morphology.

Synthesis of rebaudioside-A by enzymatic transglycosylation of stevioside present in the leaves of Stevia rebaudiana Bertoni.

Rebaudioside-A is the second most abundant sweet diterpene glycoside (1-3%) present in the leaves of Stevia rebaudiana Bertoni, and is now being considered as a possible sucrose substitute due to its pleasant organoleptic properties and associated health benefits. In the present study, a novel in situ enzymatic transglycosylation of stevioside has been developed by pre-treating the stevia leaves with cellulase and adding soluble starch as the glucosyl donor. The results confirm that the transglycosylation of stevioside led to an enrichment in the rebaudioside-A content from 4% to 66%. This was further purified by multiple column chromatography to obtain 95% pure rebaudioside-A. The isolated rebaudioside-A showed concentration-dependent α-glucosidase inhibitory activity with IC50=35.01 µg/ml. Thus the study highlights the biotransformation of stevioside present in stevia leaves to rebaudioside-A by a simple, inexpensive and eco-friendly process that has commercial potential.

Epimeric Excolides from the Stems of Excoecaria agallocha and Structural Revision of Rhizophorin A.

Excolides A-B (1-4) represent the first examples of a new class of secolabdanoids with an unprecedented framework, which were isolated from the stems of Excoecaria agallocha. Their structures were determined by spectroscopic analysis, chemical modifications, CD, and single-crystal X-ray analysis (1 and 4) as excolide A (1), 11-epi-excolide A (2), 11,13-di-epi-excolide A (3), and excolide B (4). In addition, the structure of rhizophorin A (7), a novel bicyclic secolabdanoid, was revised as excolide A (1).

Investigation of anion-π interactions involving thiophene walls incorporated calix[4]pyrroles.

Thiophene containing "two-wall" aryl extended calix[4]pyrroles were synthesized for the first time, through acid catalyzed condensation of 2-acetylthiophenes with pyrrole. Isomeric "two-walled" calix[4]pyrroles (8a-10a and 8b-10b) were obtained in satisfactory yields and their halide anion binding strengths were investigated in the solution phase by (1)H NMR and in the gas phase by computational methods and mass spectrometry. Change in the chemical shifts of thiophene -CH-protons during the course of NMR titrations entailed participation of the thiophene rings in anion binding; this fact was further substantiated by computational methods. The α,α-(cis)-isomers (8a, 9a, and 10a) showed strong binding toward F(-) and Cl(-) anions when compared to their isomeric α,ß-(trans)-isomer (8b, 9b, and 10b). In both isomers, binding with F(-) anion was found to be stronger than that with Cl(-) anion. Both the solution-phase and gas-phase results revealed that the thiophene rings stabilize the anions through anion-π interactions.

Design and synthesis of peptides with hybrid helix-turn-helix (HTH) motif and their conformational study.

The present study is aimed at the design and synthesis of peptides with hybrid helix-turn-helix (HTH) motif and their conformational analysis (NMR, MD, and CD studies). The requisite peptides with heterogeneous backbones were prepared from ß-, γ-, and δ-amino acids with carbohydrate side chains and α-amino acid, L-Ala. The α/ß-peptides were prepared from (S)-ß-Caa(l) (C-linked carbo-ß-amino acid with D-lyxo furanoside side chain) and L-Ala with a 1:1 alternation. The α/ß-peptides with "helix-turn" motif displayed a 11/9-helix nucleating a 13-atom H-bonding turn. The α/ß-octapeptides showed the presence of HTH structures with bifurcated 11/15-H-bonded turn. Further, the α/ß-hexapeptide with HT motif, independently on coupling with γ/α/γ/α- and δ/α/δ/α-tetrapeptides at the C-terminus provided access to the decapeptides with "hybrid HTH" motifs. The decapeptide ("α-ß-α-ß-α-ß-γ-α-γ-α") showed a hybrid HTH with "11/9/11/9/11/16/9/12/10" H-bonding, while the decapeptide ("α-ß-α-ß-α-ß-δ-α-δ-α") revealed the presence of a "11/9/11/9/11/17/9/13/11" helical pattern. The above peptides thus have shown compatibility between different types of helices and serendipitous bifurcated 11/16- and 11/17-turns. The present study thus provided the first opportunity for the design and study of "hybrid HTH" motifs with more than one kind of helical structures in them.

Chemical shift assignments of domain 4 from the phosphohexomutase from Pseudomonas aeruginosa suggest that freeing perturbs its coevolved domain interface.

A domain needed for the catalytic efficiency of an enzyme model of simple processivity and domain-domain interactions has been characterized by NMR. This domain 4 from phosphomannomutase/phosphoglucomutase (PMM/PGM) closes upon glucose phosphate and mannose phosphate ligands in the active site, and can modestly reconstitute activity of enzyme truncated to domains 1-3. This enzyme supports biosynthesis of the saccharide-derived virulence factors (rhamnolipids, lipopolysaccharides, and alginate) of the opportunistic bacterial pathogen Pseudomonas aeruginosa. (1)H, (13)C, and (15)N NMR chemical shift assignments of domain 4 of PMM/PGM suggest preservation and independence of its structure when separated from domains 1-3. The face of domain 4 that packs with domain 3 is perturbed in NMR spectra without disrupting this fold. The perturbed residues overlap both the most highly coevolved positions in the interface and residues lining a cavity at the domain interface.

A male-predominant cuticular hydrocarbon, 7-methyltricosane, is used as a contact pheromone in the western flower thrips Frankliniella occidentalis.

In a laboratory bioassay, adult female Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae) spent more time near filter paper disks that had been exposed to adult males than near unexposed disks; this effect was not observed on disks exposed to adult females. The response could only partly be explained by the known male-produced aggregation pheromone, neryl (S)-2-methylbutanoate, suggesting the presence of an unknown male-produced compound. In gas chromatography/mass spectrometry analyses, 7-methyltricosane was detected on disks exposed to males, but not on disks exposed to females. Extracts of cuticular lipids also showed relatively large amounts of 7-methyltricosane on males, whereas only trace amounts were found on females and none on larvae. Bioassays of synthetic 7-methyltricosane showed that adults responded only after contact. The response to this compound was clearly different from that to n-tricosane or hexane-only controls. Females that contacted 7-methyltricosane on glass beads stayed in the vicinity and frequently raised the abdomen, a behavior that rejects mating attempts by males. Males stayed in the vicinity and wagged the abdomen sideways, a behavior used in fighting between males. This is the first identification of a contact pheromone in the order Thysanoptera.

Solution NMR of a 463-residue phosphohexomutase: domain 4 mobility, substates, and phosphoryl transfer defect.

Phosphomannomutase/phosphoglucomutase contributes to the infectivity of Pseudomonas aeruginosa, retains and reorients its intermediate by 180°, and rotates domain 4 to close the deep catalytic cleft. Nuclear magnetic resonance (NMR) spectra of the backbone of wild-type and S108C-inactivated enzymes were assigned to at least 90%. (13)C secondary chemical shifts report excellent agreement of solution and crystallographic structure over the 14 α-helices, C-capping motifs, and 20 of the 22 ß-strands. Major and minor NMR peaks implicate substates affecting 28% of assigned residues. These can be attributed to the phosphorylation state and possibly to conformational interconversions. The S108C substitution of the phosphoryl donor and acceptor slowed transformation of the glucose 1-phosphate substrate by impairing k(cat). Addition of the glucose 1,6-bisphosphate intermediate accelerated this reaction by 2-3 orders of magnitude, somewhat bypassing the defect and apparently relieving substrate inhibition. The S108C mutation perturbs the NMR spectra and electron density map around the catalytic cleft while preserving the secondary structure in solution. Diminished peak heights and faster (15)N relaxation suggest line broadening and millisecond fluctuations within four loops that can contact phosphosugars. (15)N NMR relaxation and peak heights suggest that domain 4 reorients slightly faster in solution than domains 1-3, and with a different principal axis of diffusion. This adds to the crystallographic evidence of domain 4 rotations in the enzyme, which were previously suggested to couple to reorientation of the intermediate, substrate binding, and product release.