Debapratim Das

Supramolecular Peptide Amphiphile Vesicles through Host–Guest Complexation†

Single-tail peptide amphiphiles, have been explored as a new class of biomaterials in many fields including nanotechnology and tissue engineering. A typical peptide amphiphile molecule is linked through a covalent amide bond between a hydrophilic peptide sequence and a hydrophobic lipid of variable length. In an aqueous environment, these peptide amphiphiles undergo self-assembly into structures such as vesicles, both spherical and cylindrical micelles or nanotubes, and have been successfully applied in the biomedical sciences for biomaterial conjugation and as bioactive scaffolds for tissue engineering. Although covalent attachment of two components to form peptide amphiphiles has been extremely successful, the synthetic versatility and the ability to respond to external triggers remains limited. A supramolecular approach to form the peptide amphiphile by connecting two building blocks through a non-covalent interaction would represent a major advance, especially in designing stimuliresponsive systems capable of being targeted by specific triggers. Cucurbit[n]urils (CB[n]) are a family of macrocyclic hosts known to form inclusion complexes with selectivity and high binding affinity in aqueous media. One of the larger macrocycles in this family, CB[8], can be used as a “molecular handcuff” to join two molecules together in a non-covalent fashion, and has been applied to form biomaterials such as polymer–protein conjugation and protein dimerization. Additionally, CB[n] hosts have found great utility in “switch on/switch off” fluorescence assays by supramolecular complexation with various fluorescent guests. Pyrene and its derivatives have been widely used as fluorescence probes in a large number of complex systems, on account of their high fluorescence quantum yields, long excited state lifetimes and the ability to form excimers. Herein, we utilize a functional pyrene bearing an imidazolium group both as a fluorescence sensor and as a guest for CB[8] and linked it to a simple peptide sequence (1). Pyrene-functionalized peptide 1 is able to form the supramolecular peptide amphiphile complex 3 with viologen lipid 2 through CB[8] conjugation, as shown in Figure 1a. During the

Synthesis of the Rheb and K-Ras4B GTPases

K-Ras4B is the mostimportant isoform of the Ras proteins, which hold a centralposition in the transduction of growth-promoting signalsacross the plasma membrane to regulate cell growth anddifferentiation. Mutations in Ras that lead to misregulatedsignaling are found in approximately 30% of all humancancers.

Structures of RabGGTase-substrate/product complexes provide insights into the evolution of protein prenylation.

Post‐translational isoprenylation of proteins is carried out by three related enzymes: farnesyltransferase, geranylgeranyl transferase‐I, and Rab geranylgeranyl transferase (RabGGTase). Despite the fact that the last one is responsible for the largest number of individual protein prenylation events in the cell, no structural information is available on its interaction with substrates and products. Here, we present structural and biophysical analyses of RabGGTase in complex with phosphoisoprenoids as well as with the prenylated peptides that mimic the C terminus of Rab7 GTPase. The data demonstrate that, unlike other protein prenyl transferases, both RabGGTase and its substrate RabGTPases completely ‘outsource’ their specificity for each other to an accessory subunit, the Rab escort protein (REP). REP mediates the placement of the C terminus of RabGTPase into the active site of RabGGTase through a series protein–protein interactions of decreasing strength and selectivity. This arrangement enables RabGGTase to prenylate any cysteine‐containing sequence. On the basis of our structural and thermodynamic data, we propose that RabGGTase has evolved from a GGTase‐I‐like molecule that ‘learned’ to interact with a recycling factor (GDI) that, in turn, eventually gave rise to REP.

Self-assembly of peptide-amphiphile forming helical nanofibers and in situ template synthesis of uniform mesoporous single wall silica nanotubes.

A lysine based peptide amphiphile (PA) is designed and synthesized for efficient water immobilization. The PA with a minimum gelation concentration (MGC) of 1% w/v in water shows prolonged stability and can also efficiently immobilize aqueous mixtures of some other organic solvents. The presence of a free amine induced pH dependency of the gelation as the PA could form hydrogel at a pH range of 1-8 but failed to do so above that pH. Various spectroscopic and microscopic experiments such as steady state fluorescence, NMR, IR, CD, and FESEM reveal the presence of hydrophobic interaction, hydrogen bond, and π-π stacking interaction in the self-assembly process. The self-aggregation has been correlated with the design of the molecule to show the involvement of supramolecular forces and the hierarchical pathway. While the L analogue formed left-handed helical nanofibers, the other enantiomer showed opposite helicity. Interestingly the equimolar mixture of the isomers failed to form any fibrous aggregate. Although fibers formed at a subgel concentration, no helical nature was observed at this stage. The length and thickness of the fibers increased with increase in the gelator concentration. The nanofibers formed by the gelator are used as a template to prepare mesoporous single wall silica nanotubes (SWSNTs) in situ in plain water without the requirement of any organic solvent as well as any external hydrolyzing agent. The SWSNTs formed are open at both ends, are few micrometers in length, and have an average diameter of ~10 nm. The BET isotherm showed a type IV hysteresis loop suggesting mesoporous nature of the nanotubes.

Dual Self-Sorting by Cucurbit[8]uril To Transform a Mixed Micelle to Vesicle

A systematic study on the cucurbit[8]uril (CB[8]) assisted transformation of a mixed micellar system of CTAB and a viologen surfactant to vesicles is depicted. The micelle to vesicle transformation is assisted by a charge transfer complex mediated ternary complexation between the viologen group of the surfactant, CB[8], and 2,6-dihydroxynaphthalene. In the presence of CB[8], both the surfactants formed U-shaped binary inclusion complexes inside the CB[8] cavity, and no selective binding is observed. Upon addition of DHN, CB[8] showed two different self-sorting mechanisms. The U-shaped binary complex with CTAB breaks down, and CB[8] moves toward the viologen headgroup of the other surfactant to form a stable ternary complex. In the case of the viologen surfactant, CB[8] moved toward the headgroup leaving the hydrophobic tail free in order to form the ternary complex. The mechanistic detail of this micelle to vesicle transformation is revealed through methodical studies using (1)H and DOSY NMR, ESI-MS, ITC, and other instrumental techniques.

Physicochemical analysis of mixed micelles of a viologen surfactant: extended to water-in-oil (w/o) microemulsion and cucurbit[8]uril-assisted vesicle formation.

A systematic study of the self-assembly process of a viologen-containing surfactant in aqueous medium is reported. Dodecyl-ethyl-viologendibromide (DDEV) is mixed in different proportions with dodecyltrimethylammonium bromide (DTAB), and the physicochemical properties of micellization are evaluated in order to find a suitable combination which does not interfere with the micellar properties of DTAB but introduces the characteristic properties of viologen. In this process, 1% doping of DDEV with DTAB was found to be the most appropriate, as negligible changes were observed in the physicochemical behavior of this system with respect to that of pure DTAB. The 1% DDEV-doped DTAB mixed micellar system showed the characteristic two-step reduction process for the viologen units at the interface as revealed by CV experiments. 1% mixing of DDEV with DTAB also allowed us to prepare stable w/o microemulsions containing viologen units at the interface which is otherwise unattainable with pure viologen surfactants. The charge-transfer capability of the viologen unit to the electron-rich 2,6-dihydroxynaphthalene (DHN) moiety inside the macrocyclic host, cucurbit[8]uril (CB[8]) is also evaluated for this system, and surprisingly even at this very low concentration, the ternary complex of DDEV-DHN@CB[8] transformed the micellar assembly to uniform vesicles. All of these properties have been further extended to other tetraalkylammonium surfactants, and similar effects were observed.

Flexible and General Synthesis of Functionalized Phosphoisoprenoids for the Study of Prenylation in vivo and in vitro

Protein modification with isoprenoid lipids affects hundreds of signaling proteins in eukaryotic cells. Modification of isoprenoids with reporter groups is the main approach for the creation of probes for the analysis of protein prenylation in vitro and in vivo. Here, we describe a new strategy for the synthesis of functionalized phosphoisoprenoids that uses an aminederivatized isoprenoid scaffold as a starting point for the synthesis of functionalized phosphoisoprenoid libraries. This overcomes a long‐standing problem in the field, where multistep synthesis had to be carried out for each individual isoprenoid analogue. The described approach enabled us to synthesize a range of new compounds, including two novel fluorescent isoprenoids that previously could not be generated by conventional means. The fluorescent probes that were developed using the described approach possess significant spectroscopic advantages to all previously generated fluorescent isoprenoid analogue. Using these analogues for flow cytometry and cell imaging, we analyzed the uptake of isoprenoids by mammalian cells and zebrafish embryos. Furthermore, we demonstrate that derivatization of the scaffold can be coupled in a one‐pot reaction to enzymatic incorporation of the resulting isoprenoid group into proteins. This enables rapid evaluation of functional groups for compatibility with individual prenyltransferases and identification of the prenyltransferase specific substrates.

Solvent Assisted Tuning of Morphology of a Peptide-Perylenediimide Conjugate: Helical Fibers to Nano-Rings and their Differential Semiconductivity

Understanding the regulatory factors of self-assembly processes is a necessity in order to modulate the nano-structures and their properties. Here, the self-assembly mechanism of a peptide-perylenediimide (P-1) conjugate in mixed solvent systems of THF/water is studied and the semiconducting properties are correlated with the morphology. In THF, right handed helical fibers are formed while in 10% THF-water, the morphology changes to nano-rings along with a switch in the helicity to left-handed orientation. Experimental results combined with DFT calculations reveal the critical role of thermodynamic and kinetic factors to control these differential self-assembly processes. In THF, P-1 forms right handed helical fibers in a kinetically controlled fashion. In case of 10% THF-water, the initial nucleation of the aggregate is controlled kinetically. Due to differential solubility of the molecule in these two solvents, elongation of the nuclei into fibers is restricted after a critical length leading to the formation of nano-rings which is governed by the thermodynamics. The helical fibers show superior semi-conducting property to the nano-rings as confirmed by conducting-AFM and conventional I-V characteristics.

Redox controlled reversible transformation of a supramolecular alternating copolymer to a radical cation containing homo-polymer

Research in the area of supramolecular polymeric materials has grown substantially in recent years owing to their potential applications in drug delivery, sensing, and catalysis. In this work, a supramolecular polymer has been prepared using the hetero-ternary complexation of cucurbit[8]uril (CB[8]). The CB[8] mediated ternary complexation of a viologen dimer and a tryptophan dimer led to the formation of a supramolecular alternating copolymer of (AB)n type. The polymer was characterized using UV-visible, fluorescence, 1H and DOSY NMR, DLS, and microscopy techniques. The copolymer led to the formation of well dispersed micro-globules of average diameter between 150 and 250 nm. Upon reduction of the viologen units of the copolymer, viologen radical cations were formed in the solution. These viologen radical cations displaced the second guest (tryptophan units) and formed dimers inside the CB[8] cavity. This complexation by viologen radical cations eventually led to the formation of a homo-polymer of (A)n type. The degree of polymerization was calculated to be approximately three times that of the copolymer, and larger micro-globules (∼950 nm) were obtained. Upon oxidation of the homo-polymer, the system reverted to the original co-polymer system. The reversible transformation can be achieved several times by controlling the redox reaction. A similar homo-polymer was also obtained by reducing the viologen dimer in the presence of CB[8].

A Viologen-Perylenediimide Conjugate as an Efficient Base Sensor with Solvatochromic Property.

A viologen-perylenediimide conjugate, denoted PDEV, is prepared for efficient base sensing. The conjugate shows solvatochromic behavior as well. The base sensitivity of viologen is purposefully coupled with the emission property of perylenediimide (PDI) to lower the detection limit. PDEV shows base-sensing ability at the ppb level, which is at least three orders of magnitude lower than those of previously reported sensors. The probe is sensitive toward solvent polarity and generates different shades of colors according to the polarity of the medium (solvent). The photophysical properties show a linear correlation with the solvent polarity, and this makes it an efficient solvatochromic agent. On the other hand, the generation of viologen radical cations by bases affects the aggregation and consequently the absorption and emission behavior of the PDI core. The effect of bases can also be visualized, because the probe generates different colors in the presence of bases, both under normal and under UV light. Organic amines can be detected even in the crystalline state, since the dark red color of the PDEV crystals changes to purple in a reversible fashion on exposure to amine vapors. An easy and practical paper-based tool created by using the probe can efficiently be used to detect solvent polarity and presence of bases optically.