Direct Participation of Solvent Molecules in the Formation of Supramolecular Polymers.

This article reports supramolecular polymerization of two bis-amide functionalized naphthalene-diimide (NDI) building blocks (NDI-L and NDI-C) in two solvents, namely n-heptane (Hep) and methylcyclohexane (MCH). NDI-L and NDI-C differ only by the peripheral hydrocarbon wedges, consisting of linear C7 chains or cyclic methylcyclohexane rings, respectively. UV/Vis and FTIR spectroscopy studies reveal distinct internal order and H-bonding pattern for NDI-L and NDI-C aggregates irrespective of the solvent system, indicating the dominant role of the intrinsic packing parameters of the individual building block, possibly influenced by the peripheral steric crowding. However, NDI-L produces a significantly stronger gel in Hep compared to MCH as evident from the rheological and thermal properties. In contrast, NDI-C exhibits a clear preference for MCH, producing gel with moderate strength but in Hep it fails to produce 1D morphology or gelation. All-atom molecular dynamics (MD) simulation studies corroborate with the experimental observation and provide the rationale for the observed solvent-shape effect by revealing a quantitative estimate regarding the thermodynamics of self-assembly in these four combinations. Such clear-cut shape-matching effect (between the peripheral hydrocarbon wedge and the solvent system) unambiguously support a direct participation of the solvent molecules during supramolecular polymerization and presence of a closely-adhered solvent shell around the supramolecular polymers, similar to the first layer of water molecules around the protein surface. Solvent induced CD experiments support this hypothesis as induced CD band was observed only from a chiral co-solvent of matching shape. This is reconfirmed by the higher de-solvation temperature of the shape-matching NDI/solvent system combination compared to the shape mis-match combination in variable temperature UV/Vis experiments, revealing transformation to a different aggregate at higher temperatures rather than disassembly to the monomer for all four combinations.

Externally Regulated Specific Molecular Recognition Driven Pathway Selectivity in Supramolecular Polymerization.

This article reveals 4-dimethylaminopyridine (DMAP) regulated pathway selectivity in the supramolecular polymerization of a naphthalene-diimide derivative (NDI-1), appended with a carboxylic acid group. In decane, NDI-1 produces ill-defined aggregate (Agg-1) due to different H-bonding motifs of the -COOH group. With one mole equivalent DMAP, the NDI-1/DMAP complex introduces new nucleation condition and exhibits a cooperative supramolecular polymerization producing J-aggregated fibrillar nanostructure (Agg-2). With 10 % DMAP and fast cooling (10 K/min), similar nucleation and open chain H-bonding with the free monomer in an anti-parallel arrangement produces identical J-aggregate (Agg-2a). With 2.5 % DMAP and slow cooling (1 K/min), a distinct nucleation and supramolecular polymerization pathway emerge leading to the thermodynamically controlled Agg-3 with face-to-face stacking and 2D-morphology. Slow cooling with 5-10 % DMAP produces a mixture of Agg-2a and Agg-3. Computational modelling studies provide valuable insights into the internal order and the pathway complexity.

Uncovering the structural stability of Magnaporthe oryzae effectors: a secretome-wide in silico analysis.

Rice blast, caused by the ascomycete fungus Magnaporthe oryzae, is a deadly disease and a major threat to global food security. The pathogen secretes small proteinaceous effectors, virulence factors, inside the host to manipulate and perturb the host immune system, allowing the pathogen to colonize and establish a successful infection. While the molecular functions of several effectors are characterized, very little is known about the structural stability of these effectors. We analyzed a total of 554 small secretory proteins (SSPs) from the M. oryzae secretome to decipher key features of intrinsic disorder (ID) and the structural dynamics of the selected putative effectors through thorough and systematic in silico studies. Our results suggest that out of the total SSPs, 66% were predicted as effector proteins, released either into the apoplast or cytoplasm of the host cell. Of these, 68% were found to be intrinsically disordered effector proteins (IDEPs). Among the six distinct classes of disordered effectors, we observed peculiar relationships between the localization of several effectors in the apoplast or cytoplasm and the degree of disorder. We determined the degree of structural disorder and its impact on protein foldability across all the putative small secretory effector proteins from the blast pathogen, further validated by molecular dynamics simulation studies. This study provides definite clues toward unraveling the mystery behind the importance of structural distortions in effectors and their impact on plant-pathogen interactions. The study of these dynamical segments may help identify new effectors as well.Communicated by Ramaswamy H. Sarma.

Explored secretome of M. oryzae for intrinsic disorder in effectorsClassified intrinsic disorder into six categoriesNoted varying degrees of disorder in apoplastic vs. cytoplasmic effectorsFound a correlation between intrinsic disorder and flexibilityDemonstrated flexibility patterns through molecular dynamics simulationsRevealed that intrinsic disorder influences effector interactionsIdentified an exceptional 100% disordered effector defying observed trends.

Supramolecular alternating copolymers with highly efficient fluorescence resonance energy transfer.

This article reports alternating supramolecular copolymerization of two naphthalene-diimide (NDI)-derived building blocks (NDI-1 and NDI-2) under thermodynamic control. Both monomers contain a central NDI chromophore, attached to a hydrocarbon-chain and a carboxylic-acid group. The NDI core in NDI-2 is symmetrically substituted with two butane-thiol groups, which makes it distinct from NDI-1. In decane, a 1 : 1 mixture of NDI-1 and NDI-2 shows spontaneous gelation and a typical fibrillar network, unlike the behavior of either of the components individually. The solvent-dependent UV/vis spectrum of the mixed sample in decane shows bathochromically shifted sharp absorption bands and a sharp emission band (holds a mirror-image relationship) with a significantly small Stokes shift compared to those in CHCl3, indicating J-aggregation. In contrast, the aggregated spectra of the individual monomers show broad structureless features, suggesting ill-defined aggregates. Cooling curves derived from the temperature-dependent UV/vis spectroscopy studies revealed early nucleation and a signature of well-defined cooperative polymerization for the mixed sample, unlike either of the individual components. Molecular dynamics simulations predicted the greatest dimer formation tendency for the NDI-1 + NDI-2 (1 : 1), followed by pure NDI-1 and NDI-2. Theoretical studies further revealed a partial positive charge in the NDI ring of NDI-1 when compared to NDI-2, promoting the alternating stacking propensity, which is also favored by the steric factor as NDI-2 is core-substituted with alkyl thiols. Such theoretical predictions fully corroborate with the experimental results showing 1 : 1 stoichiometry (from Job's plot) of the two monomers, indicating alternate stacking sequences in the H-bonded (syn-syn catemer type) supramolecular copolymer. Such alternating supramolecular copolymers showed highly efficient (>93%) fluorescence resonance energy transfer (FRET).

Role of metabolites in flower development and discovery of compounds controlling flowering time.

Flowering is one of the most important physiological processes of plants that ensures continuity of genetic flow from one generation to the next and also maintains food security. Therefore, impact of various climate-related abiotic stresses on flowering have been assessed to evaluate the long-term impact of global climate change. In contrast to the enormous volume of research that has been conducted at the genetic, transcriptional, post-transcriptional, and protein level, much less attention has been paid to understand the role of various metabolites in flower induction and floral organ development during normal growth or in stressed environmental condition. This review article aims at summarizing information on various primary (e.g., carbohydrates, lipids, fatty acid derivatives, protein and amino acids) and secondary metabolites (e.g., polyamines, phenolics, neuro-indoles, phenylpropanoid, flavonoids and terpenes) that have so far been identified either during flower induction or in individual floral organs implying their possible role in organ development. Specialized metabolites responsible for flower colour, scent and shape to support plant-pollinator interaction have been extensively reviewed by many research groups and hence are not considered in this article. Many of the metabolites discussed here may be used as metabolomarkers to identify tolerant crop genotypes. Several agrochemicals have been successfully used to release endodormancy in temperate trees. Along the same line, a strategy that combines metabolite profiling, screening of small-molecule libraries, and structural alteration of selected compounds has been proposed in order to identify novel lead compounds that can regulate flowering time when applied exogenously.

Mycoherbicides for the Noxious Meddlesome: Can Colletotrichum be a Budding Candidate?

Invasive plant species are a major threat to biodiversity and agricultural productivity. Hence, efforts to manage these menace involves extensive and effective use of chemical herbicides amongst others. However, not only is the impact of control with chemical herbicides short-lived but also leads to negative impact on human health and environment due to non-target herbicide-drift and runoff from the sprayed areas. This has ushed in much-anticipated nature-based potential regulators of weed species, in an attempt to lower the utilisation of chemical herbicides. Mycoherbicides have been seen as a benign, eco-friendly, host-specific, and replacement for chemical herbicides. There are several noteworthy genera of fungus that have been proved to be effective against weeds. They either produce strong phytotoxins or are often used as spore/conidia-based solutions and applied as a spray in growth media. One of such potential genera is Colletotrichum Corda 1831. Compared to other potent fungal genera, with well-established roles in conferring herbicidal activities by producing competent phytotoxins, only a few species under genus Colletotrichum are known to produce fungal metabolites be used as phytotoxins. This article elucidates the current understanding of using spore suspension/phytotoxin of Colletotrichum as a weedicide. We also discuss the interaction between fungal metabolites release and Colletotrichum-target plant, from a molecular and biochemical point of view. This review article has been written to accentuate on the potency of Colletotrichum, and to serve as an eye-opener to consider this genus for further fruitful investigations. However, inconsistency associated with mycoherbicides in terms of viability and efficacy under field conditions, production of bioactive compound, slow natural dispersal ability, etc., have often reduced their utility. Hence, our study emphasizes on the need to do extensive research in elucidating more phytotoxins from necrotrophic phytopathogenic microorganisms with novel mode of action for field application.

Organobase triggered controlled supramolecular ring opening polymerization and 2D assembly.

A carboxylic acid appended naphthalene-diimide (NDI) derivative spontaneously aggregates in decane to generate a kinetically controlled product with irregular fibrillar morphology. By fine-tuning the sample preparation conditions, the carboxylic acid group can be trapped by intra-molecular H-bonds with the adjacent imide carbonyl, which retards the spontaneous aggregation. In the presence of a catalytic amount of a non-nucleophilic organic base (DBU or DMAP), the meta-stable monomer exhibits supramolecular polymerization through a thermodynamically controlled pathway involving simultaneous H-bonding and π-stacking and generates ultra-thin 2D nano-sheets. DMAP/DBU helps in ring-opening of the intra-molecularly H-bonded monomer and in situ breeds the free acid, which, beyond a critical concentration, initiates controlled supramolecular ring opening polymerization (SROP) via the chain-growth mechanism. The 2D polymer acts as a macro-initiator for subsequent two cycles of SROP and produces laterally extended ultra-thin nano-sheets.