Self-assembly Of Macromolecules Research Articles

Structural basis of the mycobacterial stress-response RNA polymerase auto-inhibition via oligomerization

Self-assembly of macromolecules into higher-order symmetric structures is fundamental for the regulation of biological processes. Higher-order symmetric structure self-assembly by the gene expression machinery, such as bacterial DNA-dependent RNA polymerase (RNAP), has never been reported before. Here, we show that the stress-response σB factor from the human pathogen, Mycobacterium tuberculosis, induces the RNAP holoenzyme oligomerization into a supramolecular complex composed of eight RNAP units. Cryo-electron microscopy revealed a pseudo-symmetric structure of the RNAP octamer in which RNAP protomers are captured in an auto-inhibited state and display an open-clamp conformation. The structure shows that σB is sequestered by the RNAP flap and clamp domains. The transcriptional activator RbpA prevented octamer formation by promoting the initiation-competent RNAP conformation. Our results reveal that a non-conserved region of σ is an allosteric controller of transcription initiation and demonstrate how basal transcription factors can regulate gene expression by modulating the RNAP holoenzyme assembly and hibernation.

Evolution of hyperbranched polyglycerols as single-dopant carriers

The self-assembly of macromolecules with each carrying one phosphorus atom may allow us to manipulate individual dopants at large scale. In this work, we applied the ring-opening multibranching polymerization process to synthesize hyperbranched polyglycerols (hbPGs). Nuclear magnetic resonance (NMR), inductively coupled plasma-atomic emission spectroscopy (ICP-AES) and size exclusion chromatography with multi-angle light scattering (SEC/MALLS) are employed to characterize the hbPGs molecules. The results indicate that each hbPGs molecule carries only one phosphorus atom. To drive the dopants into silicon, a monolayer of these hbPGs molecular carriers was immobilized on silicon surfaces, followed by rapid thermal annealing. Second ion mass spectroscopy (SIMS) indicates that every two hbPGs molecules contribute one phosphorus dopant to the Si substrate by thermal diffusion. Strategies were suggested to improve the dopant incorporation efficiency and the electrical ionization rate of the P dopants in Si.

Stereocomplexation of Poly(Lactic Acid)s on Graphite Nanoplatelets: From Functionalized Nanoparticles to Self-assembled Nanostructures.

The control of nanostructuration of graphene and graphene related materials (GRM) into self-assembled structures is strictly related to the nanoflakes chemical functionalization, which may be obtained via covalent grafting of non-covalent interactions, mostly exploiting π-stacking. As the non-covalent functionalization does not affect the sp2 carbon structure, this is often exploited to preserve the thermal and electrical properties of the GRM and it is a well-known route to tailor the interaction between GRM and organic media. In this work, non-covalent functionalization of graphite nanoplatelets (GnP) was carried out with ad-hoc synthesized pyrene-terminated oligomers of polylactic acid (PLA), aiming at the modification of GnP nanopapers thermal properties. PLA was selected based on the possibility to self-assemble in crystalline domains via stereocomplexation of complementary poly(L-lactide) (PLLA) and poly(D-lactide) (PDLA) enantiomers. Pyrene-initiated PLLA and PDLA were indeed demonstrated to anchor to the GnP surface. Calorimetric and X-ray diffraction investigations highlighted the enantiomeric PLAs adsorbed on the surface of the nanoplatelets self-organize to produce highly crystalline stereocomplex domains. Most importantly, PLLA/PDLA stereocomplexation delivered a significantly higher efficiency in nanopapers heat transfer, in particular through the thickness of the nanopaper. This is explained by a thermal bridging effect of crystalline domains between overlapped GnP, promoting heat transfer across the nanoparticles contacts. This work demonstrates the possibility to enhance the physical properties of contacts within a percolating network of GRM via the self-assembly of macromolecules and opens a new way for the engineering of GRM-based nanostructures.

Self-assembly of macromolecules in a long and narrow tube

Many nature materials have hierarchical structure, and its last cascade is always on a molecule scale, e. g., double-stranded DNA, making the hierarchy effective with minimal building blocks. Now artificial hierarchy can begin with a nanoscale level to embody the material with remarkable and fascinating properties which can be never achieved using non-hierarchical structure. A strong desire to fabricate some biomimicking hierarchies from a molecule level has been stimulating scientists. Herein we show that molecular structure can be easily controlled by a long and narrow tube, and self-assembly of macromolecules can be achieved to improve its crystallinity with plenty of excellent properties. We anticipate this paper to be a starting point for more sophisticated fabrication of fibers with self-assembly of macromolecules.

Frank-Kasper and related quasicrystal spherical phases in macromolecules

Creation of diverse ordered nanostructures via self-assembly of macromolecules is a promising “bottom-up” approach towards next-generation nanofabrication technologies. It is therefore of critical importance to explore the possibilities to form new self-assembled phases in soft matter systems. In this review, we summarized recent advances on the identification of several unconventional spherical phases in the self-assembly of functional macromolecules, including Frank-Kasper (F-K) phases and quasicrystals originally observed in metal alloys. We believe that these results provide a new strategy towards the rational design of novel functional materials with hierarchically ordered structures.

Ion-macromolecule interactions studied with model polyurethanes

HypothesisThe solubility and self-assembly of macromolecules in solution can be tuned by the presence of different salts. Natural proteins have been long manipulated with the aid of salts, and natural silk is processed in the gland tip across a gradient of different salts which modifies its solubility. Hence, the comprehensive understanding of the role of ion-macromolecule interactions should pave the way towards a biomimetic processing of macromolecules. ExperimentsA model polyurethane catiomer (PU+) with high density of hydrogen donors and acceptors (similar to proteins) has been designed and synthesized in order to study ion-macromolecule interactions by means of dynamic light scattering (DLS), infrared spectroscopy (FTIR) and nuclear magnetic resonance (13C NMR). FindingsThe PU+ solubility in the presence of different salts exhibited a reversed anion Hofmeister series (i.e., the anion ability to precipitate the PU+ was F−<Cl−<Br−<NO3−<CH3COO−<H2PO4−<H2CO3−<I−<ClO4−<SCN−). The ordering of this series was found to be predicted, for the first time, by the Born-Landé-Ephraim-Fajans-Bjerrum model used here to estimate the degree of macromolecule-ion pairing in water solution. This work also helps understanding the role of cations and anions nature on their interaction with macromolecules backbone.

Probing the Nanoscopic Thermodynamic Fingerprint of Paramagnetic Ligands Interacting with Amphiphilic Macromolecules.

Self-assembly of macromolecules with ligands is an intricate dynamic process that depends on a wide variety of parameters and forms the basis of many essential biological processes. We elucidate the underlying energetic processes of self-assembly in a model system consisting of amphiphilic core-shell polymers interacting with paramagnetic, amphiphilic ligand molecules from temperature-dependent continuous wave electron paramagnetic resonance (CW EPR) spectroscopy subsequent to spectral simulation. The involved processes as observed from the ligands’ point of view are either based on temperature-dependent association constants (KA,j,k) or dynamic rotational regime interconversion (IC) constants (KIC,j,k). The interconversion process describes a transition from Brownian (b1) towards free (b2) diffusion of ligand. Both processes exhibit non-linear van’t Hoff (lnK vs. T−1) plots in the temperature range of liquid water and we retrieve decisive dynamic information of the system from the energetic fingerprints of ligands on the nanoscale, especially from the temperature-dependent interconversion heat capacity (∆C°P,IC).

Aqueous Self-Assembly of Purely Hydrophilic Block Copolymers into Giant Vesicles.

Self-assembly of macromolecules is fundamental to life itself, and historically, these systems have been primitively mimicked by the development of amphiphilic systems, driven by the hydrophobic effect. Herein, we demonstrate that self-assembly of purely hydrophilic systems can be readily achieved with similar ease and success. We have synthesized double hydrophilic block copolymers from polysaccharides and poly(ethylene oxide) or poly(sarcosine) to yield high molar mass diblock copolymers through oxime chemistry. These hydrophilic materials can easily assemble into nanosized (<500 nm) and microsized (>5 μm) polymeric vesicles depending on concentration and diblock composition. Because of the solely hydrophilic nature of these materials, we expect them to be extraordinarily water permeable systems that would be well suited for use as cellular mimics.

Polimery wykazujace samoorganizacje makroczasteczek jako systemy kontrolowanego uwalniania lekow

The paper is a literature review concerning the polymers capable of macromolecular self-assembly — an interesting group of materials possessing diverse properties, which found various, especially medical applications, as controlled release drug delivery systems. Spontaneous assembly of macromolecules in solutions leads to the formation of various structural forms such as micelles, micro/nanospheres or polymersomes, as a result of the presence of weak bonds and interactions, i.e. hydrogen bonds as well as van der Waals, electrostatic or hydrophobic interactions, between specific parts of macromolecules. Selected structural patterns formed by self-assembly of macromolecules in organic and aqueous solutions were presented. The polymers capable of forming self-assembled structures, methods of their synthesis as well as the examples of medical applications as drug delivery systems have been described.

Self-assembly and elastic instability in polymer flows

This paper is devoted to the discussion of problems related to elastic instability arising in polymer flows. A new model of the rotary dynamics of macromolecules in shear fields of different geometries is proposed. The model is based on the nonlinear finite-difference Schrodinger equation describing the process of self-assembly for the system of bonded macromolecules as rotators. It is shown that the self-assembly of macromolecules is accompanied by the chaos-order transition that creates prerequisites for the flow elastic instability obeying the bifurcation mechanism. The self-assembly of macromolecules in shear fields is accompanied by the growth of the space scale in the molecular correlation and can lead to formation of rheological spiral and fibril superlattices.

Many Reasons to Celebrate!

Many Reasons to Celebrate!

Design and chance in the self-assembly of macromolecules

The principles of self-assembly are described for naturally occurring macromolecules and for complex assemblies formed from simple synthetic constituents. Many biological molecules owe their function and specificity to their three-dimensional folds, and, in many cases, these folds are specified entirely by the sequence of the constituent amino acids or nucleic acids, and without the requirement for additional machinery to guide the formation of the structure. Thus sequence may often be sufficient to guide the assembly process, starting from denatured components having little or no folds, to the completion state with the stable, equilibrium fold that encompasses functional activity. Self-assembly of homopolymeric structures does not necessarily preserve symmetry, and some polymeric assemblies are organized so that their chemically identical subunits pack stably in geometrically non-equivalent ways. Self-assembly can also involve scaffolds that lack structure, as seen in the multi-enzyme assembly, the degradosome. The stable self-assembly of lipids into dynamic membraneous sheets is also described, and an example is shown in which a synthetic detergent can assemble into membrane layers.

Network structures in solutions of rigid-chain polyelectrolytes: Computer simulation

The results of molecular dynamics simulation of solutions of highly charged rigid-chain polymers in the presence of multivalent counterions are presented. The processes of self-assembly of macromolecules that occur during the condensation of counterions and depend on temperature, the dielectric permittivity of the medium, and the charge of counterions were studied. Various conformational rearrangements induced by changing the parameters of the medium were examined. The conditions that lead to the formation of network superstructures composed of aggregating polymer chains were found. Size distribution functions for free-volume holes were constructed and the average dimensions of voids in the network structures formed were calculated.

Nanostructured biointerfaces

Colloidal lithography is used to create nanostructured interfaces suitable for studying and interacting with cellular biosystems. Large areas of patterned surface can be produced. We investigate the use of plasma etching for transfer of the pattern of individual colloidal particles into the substrates to create short-range ordered arrays of topographic and/or chemical nanostructures. Colloidal masks perform differently to traditional photoresist masks and local redeposition of material around the particle has significant impact on the resultant structures. The colloidal particles can be reshaped to allow the fabrication of flat-topped structures. Topographic and chemical nanostructures can be used to template the self assembly of macromolecules. The phase separation of thin films of PS-PMMA symmetric block copolymers above nanostructure sites is aligned at the surface nanostructure by topographic features. PLL-PEG assembly at alkanethiol-modified nanoscale chemical patterns of gold/silicon allows the production of nanoscale protein patterns. Patterns of ferritin 100 nm in diameter are demonstrated.

Roles of partly unfolded conformations in macromolecular self-assembly.

From genes to cells there are many steps of hierarchical increments in building up complex frameworks that provide intricate networks of macromolecular interactions, through which cellular activities such as gene expression, signal processing, energy transduction and material conversion are dynamically organized and regulated. The self-assembly of macromolecules into large complexes is one such important step, but this process is by no means a simple aggregation of macromolecules with predefined, rigid complementary structures. In many cases the component molecules undergo either domain rearrangements or folding of disordered portions, which occurs only following binding to their correct partners. The partial disorder is used in some cases to prevent spontaneous assembly at inappropriate times or locations. It is also often used for finely tuning the equilibrium and activation energy of reversible binding. In other cases, such as protein translocation across membranes, an unfolded terminus appears to be the prerequisite for the process as an initiation signal, as well as the physical necessity to be taken into narrow channels. Self-assembly processes of viruses and bacterial flagella are typical examples where the induced folding of disordered chains plays a key role in regulating the addition of new components to a growing assembly. Various aspects of mechanistic roles of natively unfolded conformations of proteins are overviewed and discussed in this short review.

Evaluation of Single-Stranded Nucleic Acids as Carriers in the DNA-Directed Assembly of Macromolecules

Current developments in nanosciences indicate that the self-assembly of macromolecules, such as proteins or metallic nanoclusters, can be conveniently achieved by means of nucleic acid hybridization. Within this context, we here report on the evaluation of single-stranded nucleic acids to be utilized as carrier backbones in DNA-directed self-assembly. A microplate solid-phase hybridization assay is described which allows rapid experimental determination of the hybridization efficiencies of various sequence stretches within a given nucleic acid carrier strand. As demonstrated for two DNA fragments of different sequence, the binding efficiencies of several oligonucleotides depend on the formation of specific secondary structure elements within the carrier molecule. A correlation of sequence-specific hybridization capability with modeled secondary structure is also obvious from experiments using the fluorescence gel-shift analysis. Electrophoretic studies on the employment of helper oligonucleotides in the formation of supramolecular conjugates of several oligonu-cleotide-tagged proteins indicate, that structural constraints can be minimized by disruption of intramolecular secondary structures of the carrier molecule. To estimate the influences of the chemical nature of the carrier, gel-shift experiments are carried out to compare a 170mer RNA molecule with its DNA analogue. Ternary aggregates, containing two protein components bound to the carrier, are formed with a greater efficiency on the DNA instead of the RNA carrier backbone.