Emergence of selectivity and specificity in a coarse-grained model of the nuclear pore complex with sequence-agnostic FG-Nups.

The role of hydrophobicity of phenylalanine-glycine nucleoporins (FG-Nups) in determining the transport of receptor-bound cargo across the nuclear pore complex (NPC) is investigated using Langevin dynamics simulations. A coarse-grained, minimal model of the NPC, comprising a cylindrical pore and hydrophobic-hydrophilic random copolymers for FG-Nups was employed. Karyopherin-bound receptor-cargo complexes (Kaps) were modeled as rigid, coarse-grained spheres without (inert) and with (patchy) FG-binding hydrophobic domains. With a sequence-agnostic description of FG-Nups and the absence of any anisotropies associated with either NPC or cargo, the model described tracer transport only as a function of FG-Nup hydrophobicity, f. The simulations showed the emergence of two important features of cargo transport, namely, NPC selectivity and specificity. NPC selectivity to patchy tracers emerged due to hydrophobic Kap-FG interactions and despite the sequence-agnostic description of FG-Nups. Furthermore, NPC selectivity was observed only in a specific range of FG-hydrophobic fraction, 0.05 ≤ f ≤ 0.20, resulting in specificity of NPC transport with respect to f. Significantly, this range corresponded to the number fraction of FG-repeats observed in both S. cerevisiae and H. sapiens NPCs. This established the central role of the FG-hydrophobic fraction in determining NPC transport, and provided a biophysical basis for conservation of the FG-Nup hydrophobic fraction across evolutionarily distant NPCs. Specificity in NPC transport emerged from the formation of a hydrogel-like network inside the pore with a characteristic mesh size dependent on f. This network rejected cargo for f > 0.2 based on size exclusion, which resulted in enhanced translocation probability for 0.05 ≤ f ≤ 0.20. Extended brush configurations outside the pore resulted in entropic repulsion and exclusion of inert cargo in this range. Thus, our minimal NPC model exhibited a hybrid cargo translocation mechanism, with aspects of both virtual gate and selective-phase models, in this range of FG-hydrophobic fraction.

Helical intermediate formation and its role in amyloids of an amphibian antimicrobial peptide.

Helical intermediates appear to be crucial in the amyloid formation of several amyloidogenic peptides, including Aß, that are implicated in different neurodegenerative diseases. Intermediate species of amyloid formation have been reported to be more toxic than mature amyloid fibrils. Hence, the current work focuses on understanding the mechanistic roles of the helical intermediates in the early stages of amyloid self-assembly in amyloidogenic peptides. Molecular dynamics (MD) simulations and the adaptive biasing force (ABF) method were utilized to investigate structural changes that lead to amyloid formation in amphibian peptide uperin-3.5 (U3.5), an antimicrobial and amyloidogenic peptide. Microsecond time-scale MD simulations revealed that peptide aggregation, into ß-sheet dominated aggregates, is centred on two important factors; evolution of α-helical intermediates and the critical role of local peptide concentration inside these aggregates. Electrostatic attraction between the oppositely charged aspartate (D) and arginine (R) residues located near the N-terminus induced hydrogen bonding resulting in the formation of precursor 310-helices close to the N-terminus. The 310-helices transitioned into α-helices, thereby imparting partial helical conformations to the peptides. In the initial stages of aggregation, U3.5 peptides with amphipathic, partial helices were driven closer by hydrophobic interactions to form small clusters of helical intermediates. These helices imparted stability to the helical intermediates, which promoted the growth of clusters by further addition of peptides. This led to an increase in the local peptide concentration, which enabled stronger peptide-peptide interactions and triggered a ß-sheet transition in these aggregates. Thus, this study emphasized that the helical intermediates may be crucial to the evolution of ß-sheet-rich amyloid structures.

Secondary Structure Transitions for a Family of Amyloidogenic, Antimicrobial Uperin 3 Peptides in Contact with Sodium Dodecyl Sulfate.

Secondary structure changes are an inherent part of antimicrobial (AMP) and amyloidogenic peptide activity, especially in close proximity to membranes, and impact the peptides' function and dysfunction roles. The formation, and stability of α-helical components are regarded as essential 'intermediates' for both these functions. To illuminate the conformational transitions leading to amyloid formation we use short cationic AMPs, from an Australian toadlet, Uperoleia mjobergii, (Uperin 3 family, U3) and assess the impact on secondary structural elements in the presence of a membrane mimetic surfactant, sodium dodecyl sulfate (SDS). Specifically, Uperin 3.x, where x=4, 5, 6 wild-type peptides and position seven variants for each, R7A or K7A, were investigated using a combination of experimental and simulation approaches. In water, U3 peptides remain largely unstructured as random coils, with the addition of salts initiating structural transitions leading to assembly towards amyloid. Solution NMR data show that an unstructured U3.5 wt peptide transitions in the presence of SDS to a well-defined α-helical structure that spans nearly the entire sequence. Circular dichroism (CD) and ThT fluorescence studies show that all six U3 peptides aggregate in solution, albeit with vastly varying rates, and a dynamic equilibrium between soluble aggregates rich in either α-helices or ß-sheets may exist in solution. However, the addition of SDS leads to a rapid disaggregation for all peptides and stabilisation of predominantly α-helical content in all the U3 peptides. Molecular dynamics (MD) simulations show that the adsorption of U3.5 wt/R7A peptides onto the SDS micelle is driven by Coulombic attraction between peptide cationic residues and the negatively charged sulfate head-groups on SDS. Simulating the interactions of various kinds of ß-sheet dimers (of both U3.5 wt and its variant U3.5 R7A) with SDS micelles confirmed ß-sheet content decreases in the dimers after their attachment to the SDS micelle. Adsorbed peptides interact favourably with the hydrophobic core of the micelle, promoting intramolecular hydrogen bonds leading to stabilisation of the α-helical structure in peptides, and resulting in a corresponding decrease in intermolecular hydrogen bonds responsible for ß-sheets.

Deagglomeration of multi-walled carbon nanotubes via an organic modifier: structure and mechanism.

We have investigated the agglomeration behaviour of two types of multi-walled carbon nanotubes (MWNTs; N-MWNTs and D-MWNTs), which have different chemical functionalities, average diameter, varying extent of agglomeration and agglomerations. The properties were altered by varying the agglomerated structure. The strength of the MWNT agglomerates was estimated via nanoindentation. The work done to indent D-MWNT agglomerates (3910.3 × 10(-8) erg) was higher than for N-MWNTs agglomerates (2316.4 × 10(-8) erg). An organic modifier, the Li salt of 6-aminohexanoic acid (Li-AHA), was used to deagglomerate the MWNTs in an aqueous medium. The stability of the aqueous dispersion of Li-AHA-modified MWNTs was analyzed by UV-vis spectroscopy and zeta potential measurements. An increase in Li-AHA concentration increased the dispersion of MWNTs in the aqueous medium. Furthermore, the mechanism of dispersion of the two types of MWNTs in the aqueous medium in the presence of Li-AHA was determined based on the electrostatic charge repulsion between the negatively charged species. A fluorescence-activated cell sorting technique was used to assess the debundling of MWNT agglomerates in the aqueous medium. We examined the morphology-property relationship in Li-AHA-modified MWNTs.

Exoelectrogens Leading to Precise Reduction of Graphene Oxide by Flexibly Switching Their Environment during Respiration.

Reduced graphene oxide (RGO) has been prepared by a simple, cost-effective, and green route. In this work, graphene oxide (GO) has been reduced using Gram-negative facultative anaerobe S. dysenteriae, having exogenic properties of electron transfer via electron shuttling. Apparently, different concentrations of GO were successfully reduced with almost complete mass recovery. An effective role of lipopolysaccharide has been observed while comparing RGO reduced by S. dysenteriae and S. aureus. It was observed that the absence of lipopolysaccharide in Gram-positive S. aureus leads to a disrupted cell wall and that S.aureus could not survive in the presence of GO, leading to poor and inefficient reduction of GO, as shown in our results. However, S. dysenteriae having an outer lipopolysaccharide layer on its cell membrane reduced GO efficiently and the reduction process was extracellular for it. RGO prepared in our work has been characterized by X-ray diffraction, ζ potential, X-ray photoelectron spectroscopy, and Raman spectroscopy techniques, and the results were found to be in good agreement with those of chemically reduced GO. As agglomeration of RGO is the major issue to overcome while chemically reducing GO, we observed that RGO prepared by a bacterial route in our work has ζ potential value of -26.62 mV, good enough to avoid restacking of RGO. The role of exoelectrogens in electron transfer in the extracellular space has been depicted. Toxin released extracellularly during the process paves the way for reduction of GO due to its affinity towards oxygen.

Influence of hybrid nano-filler on the crystallization behaviour and interfacial interaction in polyamide 6 based hybrid nano-composites.

Expanded graphite (EG) and multiwalled carbon nanotubes (MWNTs) based hybrid nano-composites were prepared with polyamide 6 (PA6) matrix via melt-mixing technique using a conical twin-screw micro-compounder. A novel organic modifier (lithium salt of 6-aminohexanoic acid; Li-AHA) was employed to modify MWNTs, which was utilized to intercalate Li-AHA modified MWNTs into the partially exfoliated EG gallery. Morphological investigation showed the intercalation of Li-AHA modified MWNTs into a partially exfoliated EG gallery in an EG/MWNTs-m2h hybrid, whereas the unmodified EG/MWNTs-h hybrid mixture exhibited a separate identity in the mixture. Improved interaction via melt-interfacial reaction between the acid end group of PA6 and the amine functionality of Li-AHA in the EG/MWNTs-m2h hybrid filler was confirmed by Fourier transform infrared spectroscopic analysis. The extent of melt-interfacial reaction was increased as a function of Li-AHA concentration in the filler. Wide angle X-ray diffraction analysis showed the existence of the α-crystalline phase of PA6. The incorporation of MWNTs, EG and EG/MWNTs hybrid in the PA6 matrix has favoured an α-crystalline structure of the PA6 phase. Crystallization studies have indicated a significant increase in the bulk crystallization temperature of the PA6 phase in the presence of MWNTs, EG and the EG/MWNTs hybrid filler. Moreover, the formation of PA6 'trans-crystalline lamellae' on the MWNTs surface was facilitated in the case of composites with MWNTs and the EG/MWNTs hybrid filler. An attempt has been made to investigate the role of the EG/MWNTs hybrid filler in influencing the crystallization behaviour of the PA6 phase in the hybrid nano-composites.

Influence of non-covalent modification of multiwalled carbon nanotubes on the crystallization behaviour of binary blends of polypropylene and polyamide 6.

Blends of polypropylene (PP) and polyamide 6 (PA6) with multiwalled carbon nanotubes (MWNTs) were prepared using different processing strategies in a twin-screw micro-compounder. The effect of MWNTs on the crystallization behaviour of the PP phase and the PA6 phase of the blend has been investigated through non-isothermal crystallization studies by differential scanning calorimetric analysis. Furthermore, the effect of the addition of the compatibilizer (PP-g-MA) and the modification of MWNTs (m-MWNTs) with a non-covalent organic modifier (Li-salt of 6 amino hexanoic acid, Li-AHA) has also been studied in context to the crystallization behaviour of the PP and PA6 phase in the blend. The crystallization studies have indicated a significant increase in bulk crystallization temperature of the PP phase in the blend in the presence of MWNTs. Moreover, the formation of 'trans-lamellar crystalline' structure consisting of PA6 'trans-crystalline lamellae' on MWNTs surface was facilitated in the case of blends prepared via 'protocol 2' as compared to the corresponding blends prepared via 'protocol 1'. Wide angle X-ray diffraction analysis has showed the existence of a ß-polymorph of the PP phase due to incorporation of the PA6 phase in the blend. Addition of MWNTs in the blends has facilitated further ß-crystalline structure formation of the PP phase. In the presence of m-MWNTs, a higher ß-fraction was observed in the PP phase as compared to the blend with pristine MWNTs. Addition of PP-g-MA has suppressed the ß-phase formation in the PP phase in the blend. X-ray bulk texture analysis revealed that incorporation of PA6 as well as pristine/modified MWNTs has influenced the extent of orientation of the PP chains towards specific crystalline planes in various blend compositions of PP and PA6.

Influence of noncovalent modification on dispersion state of multiwalled carbon nanotubes in melt-mixed immiscible polymer blends.

Multiwalled carbon nanotubes (MWNTs) were melt-mixed with polyamide6 (PA6) and acrylonitrile butadiene styrene copolymer (ABS) to obtain electrically conducting composites. MWNTs were noncovalently modified with sodium salt of 6-aminocaproic acid (MWNTs-m1) and 3-pyrenealdehyde (MWNTs-m2) to 'deagglomerate' MWNTs. Raman spectroscopic analysis indicated a G-band shift from ∼1581.9 cm(-1) for pristine MWNTs to ∼1590.2 cm(-1) for MWNTs-m1 and ∼1588.8 cm(-1) for MWNTs-m2, indicating the interaction between MWNTs and the respective modifier molecules. Blends showed 'co-continuous' morphology on the addition of MWNTs. TEM observations showed that a higher population of pristine MWNTs exhibited a 'nanoagglomerated' state in PA6 and ABS phases in the case of a 40/60 PA6/ABS blend, unlike a 60/40 blend, which depicted a higher population of 'individualized' MWNTs. Further, the corresponding blends with MWNTs-m1 and MWNTs-m2 showed 'nanoagglomerated' and 'individualized' MWNTs. Blends with pristine MWNTs showed an increase in DC electrical conductivity with an increase in PA6 concentration in the blend. Moreover, the corresponding blends with MWNTs-m1 and MWNTs-m2 exhibited an increased DC electrical conductivity value as compared to the corresponding blend with pristine MWNTs. Ratio of the intensity (H1/H2) of the crystallization peak at lower temperature (H1) to the intensity of the crystallization peak at higher temperature (H2) depicted lower values for blends with pristine MWNTs as compared to the corresponding blends with MWNTs-m1 and MWNTs-m2. TGA studies indicated the formation of a thicker 'interphase' involving MWNTs and the interacting polymer chains.

Enzyme-modulated DNA translocation through a nanopore.

We present a Langevin dynamics simulation study of enzyme-modulated translocation of a single-stranded DNA molecule through a cylindrical nanopore. The toroidal-shaped enzyme placed along the axis of the pore, threads a DNA molecule at a constant rate. As a result of this controlled release process, the length of DNA available for translocation varies with time. We examine the effect of time-dependent conformational entropy of the DNA on the translocation process. In addition, we also examine the effects of both the separation between the exonuclease and the pore, and the rate at which DNA is released by the enzyme. Our results indicate that the separation distance primarily influences the entry of the DNA into the pore. The length of the DNA released by the exonuclease that is most likely to enter the pore is nearly equal to separation distance between the pore and the exonuclease despite the flexibility of the polymer. However, the speed at which the DNA translocates through the nanopore is solely determined by the rate at which the exonuclease releases the DNA. We find that the translocation velocity is directly proportional to the rate of release.

Brownian dynamics simulations of polyelectrolyte adsorption in shear flow.

Brownian dynamics simulations are used to study the adsorption of an isolated polyelectrolyte molecule onto an oppositely charged flat surface in the absence and the presence of an imposed shear flow. The polyelectrolyte is modeled as a freely jointed bead-rod chain where excluded volume interactions are incorporated by using a hard-sphere potential. The total charge along the backbone is distributed uniformly among all the beads, and the beads are allowed to interact with one another and the charged surface through screened Coulombic interactions. The simulations are performed by placing the molecule a fixed distance above the surface, and the adsorption behavior is then studied as a function of screening length. In the absence of an imposed flow, the chain is found to lie flat and extended on the adsorbing surface in the limit of weak screening, whereas in the limit of strong screening it desorbs from the surface and attains free-solution behavior. For intermediate screening, only a small portion of the chain adsorbs and it becomes highly extended in the direction normal to the surface. An imposed shear flow tends to orient the chain in the direction of flow and also leads to increased contact of the chain with the surface.

Electrophoresis of a bead-rod chain through a narrow slit: a Brownian dynamics study.

We use two-dimensional Brownian dynamics simulations to study the electrophoresis of a bead-rod chain through a narrow slit. A constant electric field is assumed to act inside and outside of the slit, and each bead on the chain is assigned a constant uniform charge. We calculate the dependence of the polymer transit velocity on chain length, slit dimensions (width-to-length ratio), and electric-field strength. For sufficiently narrow slits, the transit velocity increases nonlinearly with the applied field for low-field strengths, whereas it increases linearly for high-field strengths. In the low-field strength region and for sufficiently narrow slits, the transit velocity decreases rapidly for small chain lengths and then decreases slowly beyond a critical chain length. As the slit width increases, the transit velocity decreases with chain length in more continuous manner, and for sufficiently large slits the transit velocity becomes independent of chain length as expected. Distributions of the chain end-to-end distances and the translocation times depend strongly on the relative size of the chain to the slit. These results show the sensitivity of the transit velocity vs chain length relationship to the slit dimensions and applied electric-field strength, and suggest that there may be an optimal slit width for a given field strength and vice versa. The results may be useful for microfluidic separations and for understanding the motion of biological polymers through narrow constrictions.