Formation Of Transient Structures Research Articles

Guiding Transient Peptide Assemblies with Structural Elements Embedded in Abiotic Phosphate Fuels

AbstractDespite great progress in the construction of non‐equilibrium systems, most approaches do not consider the structure of the fuel as a critical element to control the processes. Herein, we show that the amino acid side chains (A, F, Nal) in the structure of abiotic phosphates can direct assembly and reactivity during transient structure formation. The fuels bind covalently to substrates and subsequently influence the structures in the assembly process. We focus on the ways in which the phosphate esters guide structure formation and how structures and reactivity cross regulate when constructing assemblies. Through the chemical functionalization of energy‐rich aminoacyl phosphate esters, we are able to control the yield of esters and thioesters upon adding dipeptides containing tyrosine or cysteine residues. The structural elements around the phosphate esters guide the lifetime of the structures formed and their supramolecular assemblies. These properties can be further influenced by the peptide sequence of substrates, incorporating anionic, aliphatic and aromatic residues. Furthermore, we illustrate that oligomerization of esters can be initiated from a single aminoacyl phosphate ester incorporating a tyrosine residue (Y). These findings suggest that activated amino acids with varying reactivity and energy contents can pave the way for designing and fabricating structured fuels.

Guiding Transient Peptide Assemblies with Structural Elements Embedded in Abiotic Phosphate Fuels.

Despite great progress in the construction of non-equilibrium systems, most approaches do not consider the structure of the fuel as a critical element to control the processes. Herein, we show that the amino acid side chains (A, F, Nal) in the structure of abiotic phosphates can direct assembly and reactivity during transient structure formation. The fuels bind covalently to substrates and subsequently influence the structures in the assembly process. We focus on the ways in which the phosphate esters guide structure formation and how structures and reactivity cross regulate when constructing assemblies. Through the chemical functionalization of energy-rich aminoacyl phosphate esters, we are able to control the yield of esters and thioesters upon adding dipeptides containing tyrosine or cysteine residues. The structural elements around the phosphate esters guide the lifetime of the structures formed and their supramolecular assemblies. These properties can be further influenced by the peptide sequence of substrates, incorporating anionic, aliphatic and aromatic residues. Furthermore, we illustrate that oligomerization of esters can be initiated from a single aminoacyl phosphate ester incorporating a tyrosine residue (Y). These findings suggest that activated amino acids with varying reactivity and energy contents can pave the way for designing and fabricating structured fuels.

Using a biocatalyzed reaction cycle for transient and pH-dependent host-guest supramolecular hydrogels.

The formation of transient structures plays important roles in biological processes, capturing temporary states of matter through influx of energy or biological reaction networks catalyzed by enzymes. These natural transient structures inspire efforts to mimic this elegant mechanism of structural control in synthetic analogues. Specifically, though traditional supramolecular materials are designed on the basis of equilibrium formation, recent efforts have explored out-of-equilibrium control of these materials using both direct and indirect mechanisms; the preponderance of such works has been in the area of low molecular weight gelators. Here, a transient supramolecular hydrogel is realized through cucurbit[7]uril host-guest physical crosslinking under indirect control from a biocatalyzed network that regulates and oscillates pH. The duration of transient hydrogel formation, and resulting mechanical properties, are tunable according to the dose of enzyme, substrate, or pH stimulus. This tunability enables control over emergent functions, such as the programmable burst release of encapsulated model macromolecular payloads.

Transient Self‐Assembled Materials with Controllable Lifespan for Programmable Fluorescence

AbstractTransient structures play a wide range of vital roles in biological systems. Different from static structures that form the skeleton of bio‐tissues, transient structures only occur at certain spatial and temporal scales to undertake their duties in the life circle. Despite the significant progress in the field of artificial molecular self‐assembly studies, it still remains challenging to construct functional transient structures. Herein, the shaping of transient coordinating self‐assembled structures and their fluorescence is reported via host‐guest interaction that disfavors the assembly. The host‐guest interaction between the luminescent ligand and cyclodextrin drastically changes the kinetics of the coordinating self‐assembly, enabling the formation of transient structures. Different from the static equilibrium one with typical monomer emission in the UV region, the transient self‐assembly forms excimers, leading to visible emission. More intriguingly, the life cycle of the transient structures can be easily modulated by varying the host‐guest ratio, ligand‐metal ratio, as well as temperature. This makes it possible to create living patterns that mimic the growth of plants at different life stages. It is therefore envisioned that the creation of transient molecular self‐assembly will open a new paradigm in the field of molecular self‐assembly featuring advanced materials with dynamic functions.

Phosphorylation-dependent regulation of the transcriptional activity of Arabidopsis SOG1.

Eukaryotic organisms rely on the evolutionary conserved DNA damage response (DDR) mechanism to maintain genome integrity. Despite sharing many DDR components, plants lack the key mammalian DDR regulator called tumour suppressor P53. They use the functionally equivalent but otherwise unrelated plant-specific transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1) instead. Outside the conserved folded DNA-binding NAC domain, SOG1 is disordered and carries a net negative charge in its C-terminal tail. Using a high-throughput screening method in yeast, we located three putative SOG1 transcription activation domains (TAD). Two out of three are located in a C-terminal region and both comply with the Acidic Exposure Model of TAD function. In addition, those TADs are flanked by phosphorylation sites whose phosphorylation state contribute to the TAD's activity. The TADs biophysical properties are being determined and linked to their putative role as protein-protein interaction interfaces. Special interest goes out to the potential formation of transient structures in the disordered SOG1 C-terminus and its functional implications.

Mechanism of temperature-induced asymmetric swelling and shrinking kinetics in self-healing hydrogels

Understanding the physical principle that governs the stimuli-induced swelling and shrinking kinetics of hydrogels is indispensable for their applications. Here, we show that the shrinking and swelling kinetics of self-healing hydrogels could be intrinsically asymmetric. The structure frustration, formed by the large difference in the heat and solvent diffusions, remarkably slows down the shrinking kinetics. The plateau modulus of viscoelastic gels is found to be a key parameter governing the formation of structure frustration and, in turn, the asymmetric swelling and shrinking kinetics. This work provides fundamental understandings on the temperature-triggered transient structure formation in self-healing hydrogels. Our findings will find broad use in diverse applications of self-healing hydrogels, where cooperative diffusion of water and gel network is involved. Our findings should also give insight into the molecular diffusion in biological systems that possess macromolecular crowding environments similar to self-healing hydrogels.

Temperature-Driven Anchoring Transitions at Liquid Crystal/Water Interfaces.

Controlling the anchoring of liquid crystal molecules at an interface with a water solution influences the entire organization of the underlying liquid crystal phase, which is crucial for many applications. The simplest way to stabilize such interfaces is by fabricating liquid crystal droplets in water; however, a greater sensitivity to interfacial effects can be achieved using liquid crystal shells, that is, spherical films of liquid crystal suspended in water. Anchoring transitions on those systems are traditionally triggered by the adsorption of surfactant molecules onto the interface, which is neither an instantaneous nor a reversible process. In this study, we report the ability to change the anchoring of 4-cyano-4'-pentylbiphenyl (5CB), one of the most widely used liquid crystals, at the interface with dilute water solutions of polyvinyl alcohol (PVA), a polymer commonly used for stabilizing liquid crystal shells, simply by controlling the temperature in the close vicinity of the liquid crystal clearing point. A quasi-static increase in temperature triggers an instantaneous reorientation of the molecules from parallel to perpendicular to the interfaces, owing to the local disordering effect of PVA on 5CB, prior to the phase transition of the bulk 5CB. We study this anchoring transition on both flat suspended films and spherical shells of liquid crystals. Switching anchoring entails a series of structural transformations involving the formation of transient structures in which topological defects are stabilized. The type of defect structure depends on the topology of the film. This method has the ability to influence both interfaces of the film nearly at the same time and can be applied to transform an initially polydisperse group of nematic shells into a monodisperse population of bivalent shells.

Deconstructing Vibrational Motions on the Potential Energy Surfaces of Hydrogen-Bonded Complexes

Internal vibrations underlie transient structure formation, spectroscopy, and dynamics. However, at least two challenges exist when aiming to elucidate the contributions of vibrational motions on t...

Transient Structure Formation Kinetics of Monomeric Alpha-Synuclein Derived from MD Simulations

Transient Structure Formation Kinetics of Monomeric Alpha-Synuclein Derived from MD Simulations

Observational Evidence for the Associated Formation of Blobs and Raining Inflows in the Solar Corona

Abstract The origin of the slow solar wind is still a topic of much debate. The continual emergence of small transient structures from helmet streamers is thought to constitute one of the main sources of the slow wind. Determining the height at which these transients are released is an important factor in determining the conditions under which the slow solar wind forms. To this end, we have carried out a multipoint analysis of small transient structures released from a north–south tilted helmet streamer into the slow solar wind over a broad range of position angles during Carrington Rotation 2137. Combining the remote-sensing observations taken by the Solar-TErrestrial RElations Observatory (STEREO) mission with coronagraphic observations from the SOlar and Heliospheric Observatory (SOHO) spacecraft, we show that the release of such small transient structures (often called blobs), which subsequently move away from the Sun, is associated with the concomitant formation of transient structures collapsing back toward the Sun; the latter have been referred to by previous authors as “raining inflows.” This is the first direct association between outflowing blobs and raining inflows, which locates the formation of blobs above the helmet streamers and gives strong support that the blobs are released by magnetic reconnection.

Effect of waveform of the driving field on electroconvection near the dielectric inversion frequency.

This paper concerns the instability behavior of a nematic liquid crystal in the region of dielectric inversion frequency for different waveforms of the exciting electric field. The critical frequency separating the regimes of dielectric and electroconvective primary bifurcation states shows a notable dependence on the waveform. In particular, it is found to undergo a large downshift for square-wave and sawtooth-wave fields as compared to sine-wave and triangle-wave fields. This seems to underscore the significance of harmonics in nonsinusoidal fields for the evolution of patterned electroconvective states. The study also deals with the flow pattern associated with the periodic state and the sequence of secondary instabilities occurring at higher fields to emphasize the role of the Carr-Helfrich mechanism for the instabilities in this region. The relevance of dielectric heating to the formation of transient structures is also pointed out.

Resolving the Heterogeneity of the Ensemble of Unfolded States by a Combination of Fluorescence Spectroscopic Methods

Intense debate exists on the possibility that unfolded proteins show, to certain extent, residual secondary structure. Transient structure formation might facilitate folding (nucleation site) and/ or enhance binding to ligands. Some proteins such as those categorized as intrinsically disordered proteins take advantage of these features. Here, we used the model enzyme lysozyme from the phage T4 (T4L), a simple two subdomain protein, which already exists in an equilibrium of at least three conformations under native conditions. We created a set of 24 double mutants of the cysteine-free pseudo-wild type by inserting an unnatural amino acid and a cysteine mutation and site-specifically labeled them using orthogonal chemistry with a Forster resonance energy transfer (FRET) dye pair. Our set of variants allows us to build up a network of distances spanning the enzyme in order to monitor the ensemble of conformations. The behavior of the protein under highly denaturing conditions was observed by a combination of ensemble (ensemble time-resolved fluorescence lifetime and anisotropy) and single-molecule spectroscopic (multiparameter fluorescence detection, photon distribution analysis, (filtered) fluorescence correlation spectroscopy) methods. Our network covered all possible directions over the whole protein allowing us to map specifically the local motions (dye mobility) and global changes. We identified regions with residual structure which exist even under highly denaturing conditions. Additionally, the combination of ensemble and single-molecule methods allows us to resolve the full heterogeneity of the proteins’ denatured conformations.

Understanding anisotropic growth behavior of hexagonal ice on a molecular scale: A molecular dynamics simulation study

Although distinct growth behaviors on different faces of hexagonal ice have long been suggested, their understanding on a molecular scale has been hampered due to experimental difficulties near interfaces. We present a molecular dynamics simulation study to unravel the molecular origin of anisotropy in the growth kinetics of hexagonal ice by visualizing the formation of transient water structures in the growing ice interface. During ice growth, the formation of transient structures and their rearrangement to the final ice configuration are observed irrespective of growth direction. However, we find that their structure and duration differ significantly depending on growth direction. In the direction perpendicular to the basal face of hexagonal ice along which growth occurs most slowly, a two-dimensional transient structure, which is formed by competing hexagonal and cubic arrangements within the same layer, persists for a significant period of time, contrasted with short-lived transient structures in other directions. This observation of such transient water structures and their rearrangement during ice growth provides a clear explanation of different growth rates on each face of hexagonal ice on a molecular scale.

Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing.

We combined rapid microfluidic mixing with single-molecule Förster Resonance Energy Transfer to study the folding kinetics of the intrinsically disordered human protein α-synuclein. The time-resolution of 0.2 ms revealed initial collapse of the unfolded protein induced by binding with lipid-mimics and subsequent rapid formation of transient structures within the encounter complex. The method also enabled study of rapid dissociation and unfolding of weakly bound complexes triggered by massive dilution.

Conserved structural and dynamics features in the denatured states of drosophila SUMO, human SUMO and ubiquitin proteins: Implications to sequence‐folding paradigm

We have characterized here the structural and dynamics properties of urea-denatured state of dSmt3 by multidimensional NMR at 27 degrees C and pH 5.6. The various results suggest that hydrophobic clusters as well as different native and non-native secondary structural elements are transiently formed. The backbone in the regions Gln26-Lys31 and Gly47-Gln60 shows conformationally restricted motions. The AABUF profile of the sequence reflected that this region has the highest tendency to undergo hydrophobic clustering and may thus assist the formation of transient structures. The secondary chemical shifts and coupling constants indicated that this region has strong tendency to occupy the broad beta-domain of (phi,psi) space. A number of NMR parameters indicated that the region Asp58-Gln60 (corresponding to beta3-beta4 turn in the folded state) has residual turn-like structure. The present structural and dynamics results on urea-denatured dSmt3 have been compared with the previously published results on denatured states of similar fold proteins e.g. human SUMO-1 (55% homologous), ubiquitin (13.8% homologous) and GB1. Although the sequence homology is rather poor between them, the residual structure in all cases seems to be largely native type. The implications of these to sequence-folding paradigm and initial folding processes have been discussed.

Practical application of thixotropic suspension models

The practical implementation of several thixotropic rheological models has been evaluated for a prototypical industrial application. We have studied the ability of the models to predict both steady and transient rheology of a suspension of alumina particles and the suitability of those models for full transient finite element calculations. The constitutive models for thixotropic materials examined include the Carreau-Yasuda model and first and second-order indirect structure models. While all of these models were able to predict the shear-thinning behavior of the steady viscosity, the first and second-order structure models were also able to capture some aspects of the transient structure formation and fluid history. However, they were not able to predict some more complex transient behavior observed in step shear experiments. For most thixotropic suspensions, the time constant required to form structure is longer than the time constant to break it down. For this suspension, the time constant at a given shear rate was also dependent on the previous shear rate. If the previous shear rate was high, the time required to reach equilibrium was longer than if the previous shear rate was lower. This behavior was not captured by the simple initial structure dependence in the previous models. By adding an additional dependence on the initial suspension structure, the prediction of the transient rheology was substantially improved while maintaining an excellent agreement with the steady shear viscosity. Finite element results are presented for extrusion of a suspension to form a fiber. This model two-dimensional problem contains many of the same complexities as practical three-dimensional mold filling simulations (i.e., nonviscometric and mobile free surface). Our results show that these direct structure models exhibit oscillations near the stick-slip point in finite element calculations similar to many polymeric constitutive equations, but are otherwise suitable for implementation in complex industrial modeling applications.

Short-pulse Laser Induced Transient Structure Formation and Ablation Studied with Time-resolved Coherent XUV-scattering

AbstractThe structural dynamics of short-pulse laser irradiated surfaces and nano-structures has been studied with nm spatial and ultrafast temporal resolution by means of single-shot coherent XUV-scattering techniques. The experiments allowed us to time-resolve the formation of laser-induced periodic surface structures, and to follow the expansion and disintegration of nano-objects during laser ablation.

Local Structural Preferences and Dynamics Restrictions in the Urea-Denatured State of SUMO-1: NMR Characterization

We have investigated by multidimensional NMR the structural and dynamic characteristics of the urea-denatured state of activated SUMO-1, a 97-residue protein belonging to the growing family of ubiquitin-like proteins involved in post-translational modifications. Complete backbone amide and 15N resonance assignments were obtained in the denatured state by using HNN and HN(C)N experiments. These enabled other proton assignments from TOCSY-HSQC spectra. Secondary H α chemical shifts and 1H- 1H NOE indicate that the protein chain in the denatured state has structural preferences in the broad β-domain for many residues. Several of these are seen to populate the ( ϕ, ψ) space belonging to polyproline II structure. Although there is no evidence for any persistent structures, many contiguous stretches of three or more residues exhibit structural propensities suggesting possibilities of short-range transient structure formation. The hetero-nuclear 1H- 15N NOEs are extremely weak for most residues, except for a few at the C-terminal, and the 15N relaxation rates show sequence-wise variation. Some of the regions of slow motions coincide with those of structural preferences and these are interspersed by highly flexible residues. The implications of these observations for the early folding events starting from the urea-denatured state of activated SUMO-1 have been discussed.

Erratum: The chemistry of transient molecular cloud cores

We assume that some, but not all, of the structure observed in molecular clouds is associated with transient features which are not bound by self-gravity. We investigate the chemistry of a transient density fluctuation, with properties similar to those of a core within a molecular cloud. We run a multipoint chemical code through a core's condensation from a diffuse medium to its eventual dispersion, over a period of ∼1 Myr. The dynamical description adopted for our study is based on an understanding of a particular mechanism, involving slow-mode wave excitation, for transient structure formation which so far has been studied in detail only with plane-parallel models in which self-gravity has not been included. We find a significant enhancement of the chemical composition of the core material on its return to diffuse conditions, whilst the expansion of the core as it disperses moves this material out to large distances from the core centre. This process transports molecular species formed in the high-density regions out into the diffuse medium. Chemical enrichment of the cloud as a whole also occurs, as other cores of various sizes, life-spans and separations evolve throughout. Enrichment is strongly affected by freeze-out on to dust grains, which takes place in high-density, high visual extinction regions. As the core disperses after reaching its peak density and the visual extinction drops below a critical value, grain mantles are evaporated back into the gas phase, initiating more chemistry. The influence of the sizes, masses and cycle periods of cores will be large both for the level of chemical enrichment of a dark cloud and ultimately for the low-mass star formation rate. The cores in which stars form are almost certainly bound by their self-gravity and are not transient in the sense that the cores on which most of our study is focused are transient. Obviously, enrichment of the chemistry of low-density material will not take place if self-gravity prevents the re-expansion of a core. We also consider the case of a self-gravitating core, by holding its peak density conditions for a further 0.4 Myr. We find that the differences near the peak densities between transient and gravitationally bound cores are generally small, and the resultant column densities for objects near the peak densities do not provide definitive criteria for discriminating between transient and bound cores. However, increases in fractional abundances due to reinjection of mantle-borne species may provide a criterion for detection of a non-bound core.

Co-transcriptional folding is encoded within RNA genes

BackgroundMost of the existing RNA structure prediction programs fold a completely synthesized RNA molecule. However, within the cell, RNA molecules emerge sequentially during the directed process of transcription. Dedicated experiments with individual RNA molecules have shown that RNA folds while it is being transcribed and that its correct folding can also depend on the proper speed of transcription.MethodsThe main aim of this work is to study if and how co-transcriptional folding is encoded within the primary and secondary structure of RNA genes. In order to achieve this, we study the known primary and secondary structures of a comprehensive data set of 361 RNA genes as well as a set of 48 RNA sequences that are known to differ from the originally transcribed sequence units. We detect co-transcriptional folding by defining two measures of directedness which quantify the extend of asymmetry between alternative helices that lie 5' and those that lie 3' of the known helices with which they compete.ResultsWe show with statistical significance that co-transcriptional folding strongly influences RNA sequences in two ways: (1) alternative helices that would compete with the formation of the functional structure during co-transcriptional folding are suppressed and (2) the formation of transient structures which may serve as guidelines for the co-transcriptional folding pathway is encouraged.ConclusionsThese findings have a number of implications for RNA secondary structure prediction methods and the detection of RNA genes.