Mapping the energy landscapes of supramolecular assembly by thermal hysteresis.
Ontology highlight
ABSTRACT:
SUBMITTER: Harkness V RW
PROVIDER: S-EPMC6082911 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:By means of two supramolecular systems--peptide amphiphiles engaged in hydrogen-bonded ?-sheets, and chromophore amphiphiles driven to assemble by ?-orbital overlaps--we show that the minima in the energy landscapes of supramolecular systems are defined by electrostatic repulsion and the ability of the dominant attractive forces to trap molecules in thermodynamically unfavourable configurations. These competing interactions can be selectively switched on and off, with the order of doing so determining the position of the final product in the energy landscape. Within the same energy landscape, the peptide-amphiphile system forms a thermodynamically favoured product characterized by long bundled fibres that promote biological cell adhesion and survival, and a metastable product characterized by short monodisperse fibres that interfere with adhesion and can lead to cell death. Our findings suggest that, in supramolecular systems, functions and energy landscapes are linked, superseding the more traditional connection between molecular design and function.
| S-EPMC4805452 | biostudies-literature
Project description:Complexity in supramolecular polymer systems arises from interactions between different components, including solvent molecules. By varying their concentration or temperature in such multicomponent systems, complex phenomena can occur such as thermally bisignate and dilution-induced assembly of supramolecular polymers. Herein, we demonstrate that both these phenomena emerge from the same underlying interaction mechanism between the components. As a model system, amide-decorated supramolecular polymers of porphyrins were investigated in combination with aliphatic alcohols as hydrogen-bond scavengers, and thermodynamic mass-balance models were applied to map the three-dimensional assembly landscapes. These studies unveiled that the interaction between hydrogen-bond scavengers and monomers is temperature-dependent and becomes dominant at high monomer concentrations. With these insights, we could exploit competitive monomer-alcohol interactions to prompt the dilution-induced assembly of various common monomers as well as bisignate assembly events. Moreover, kinetic insights were obtained by navigating through the assembly landscape. Similar to phase diagrams of covalent polymers, these assembly landscapes provide a comprehensive picture of supramolecular polymerizations, which helps to precisely regulate the system properties. The generality of this approach using assembly landscapes makes it relevant for any supramolecular system, and this enhanced control will open the door to build complex and functional supramolecular polymer systems.
| S-EPMC9951209 | biostudies-literature
Project description:Metal ions are crucial for nucleic acid folding. From the free energy landscapes, we investigate the detailed mechanism for ion-induced collapse for a paradigm system: loop-tethered short DNA helices. We find that Na+ and Mg2+ play distinctive roles in helix-helix assembly. High [Na+] (>0.3 M) causes a reduced helix-helix electrostatic repulsion and a subsequent disordered packing of helices. In contrast, Mg2+ of concentration >1 mM is predicted to induce helix-helix attraction and results in a more compact and ordered helix-helix packing. Mg2+ is much more efficient in causing nucleic acid compaction. In addition, the free energy landscape shows that the tethering loops between the helices also play a significant role. A flexible loop, such as a neutral loop or a polynucleotide loop in high salt concentration, enhances the close approach of the helices in order to gain the loop entropy. On the other hand, a rigid loop, such as a polynucleotide loop in low salt concentration, tends to de-compact the helices. Therefore, a polynucleotide loop significantly enhances the sharpness of the ion-induced compaction transition. Moreover, we find that a larger number of helices in the system or a smaller radius of the divalent ions can cause a more abrupt compaction transition and a more compact state at high ion concentration, and the ion size effect becomes more pronounced as the number of helices is increased.
| S-EPMC1751542 | biostudies-literature
Project description:The assembly/disassembly of biological macromolecules plays an important role in their biological functionalities. Although the dynamics of tubulin polymers and their super-assembly into microtubule structures is critical for many cellular processes, details of their cyclical polymerization/depolymerization are not fully understood. Here, we use a specially designed light scattering technique to continuously examine the effects of temperature cycling on the process of microtubule assembly/disassembly. We observe a thermal hysteresis loop during tubulin assembly/disassembly, consistently with earlier reports on the coexistence of tubulin and microtubules as a phase transition. In a cyclical process, the structural hysteresis has a kinetic component that depends on the rate of temperature change but also an intrinsic thermodynamic component that depends on the protein topology, possibly related to irreversible processes. Analyzing the evolution of such thermal hysteresis loops over successive cycles, we found that the assembly/disassembly ceases after some time, which is indicative of protein aging leading to its inability to self-assemble after a finite number of temperature cycles. The emergence of assembly-incompetent tubulin could have major consequences for human pathologies related to microtubules, including aging, neurodegenerative diseases and cancer.
| S-EPMC8749447 | biostudies-literature
Project description:As molecular self-assembled systems increase in complexity, due to a large number of participating entities and/or the establishment of multiple competing equilibria, their full understanding becomes likewise more complicated, and the use of diverse analytical techniques that can afford complementary information is required. We demonstrate in this work that resonance excitation energy transfer phenomena, measured by fluorescence spectroscopy in combination with other optical spectroscopies, can be a valuable tool to obtain supplementary thermodynamic data about complex supramolecular landscapes that other methods fail to provide. In particular, noncovalent macrocyclization processes of lipophilic dinucleosides are studied here by setting up a competition between intra- and intermolecular association processes of Watson-Crick H-bonding pairs. Multiwavelength analysis of the monomer emission changes allowed us to determine cyclotetramerization constants and to quantify chelate cooperativity, which was confirmed to be substantially larger for the G-C than for the A-U pair. Furthermore, when bithiophene-BODIPY donor-acceptor energy transfer probes are employed in these competition experiments, fluorescence and circular dichroism spectroscopy measurements in different regions of the visible spectrum additionally reveal intermolecular interactions occurring simultaneously at both sides of the macrocyclization reaction: the cyclic product, acting as a host for the competitor, and the monomer reactant, ultimately leading to macrocycle denaturation.
| S-EPMC6194488 | biostudies-literature
Project description:Peptide-drug conjugates that self-assemble into supramolecular nanomaterials have promise for uses in drug delivery. These discrete molecular species offer high and precise drug loading, affording efficient carriers for various therapeutic agents. Their peptide modules, meanwhile, enable biological targeting and stimuli-responsive function while also ordering the assembled nanostructure. The often hydrophobic drug payload likewise acts as a directive for self-assembly in aqueous media. Though accessible synthetic methods have allowed for extensive exploration of the peptide design space, the specific contributions of the drug molecule and its linker to the resulting assembly have been less explored. Hydrophobic drugs frequently have planar domains, conjugated π-systems, and isolated polar groups, which in turn can lead to specific and directional self-interactions. These energies of interaction affect the free energy landscape of self-assembly and may impact the form and assembly process of the desired nanomaterial. Here, two model supramolecular peptide-drug conjugates (sPDCs) are explored, composed of the corticosteroid dexamethasone conjugated to a conserved peptide sequence via two different linker chemistries. The choice of linker, which alters the orientation, rotational freedom, and number of stereoisomers of the prodrug in the final sPDC, impacts the mechanism and energetic barrier of assembly as well as the nano/macroscale properties of the resultant supramolecular materials. Accordingly, this work demonstrates the nonzero energetic contributions of the drug and its linker to sPDC self-assembly, provides a quantitative exploration of the sPDC free energy landscape, and suggests design principles for the enhanced control of sPDC nanomaterials to inform future applications as therapeutic drug carriers.
| S-EPMC10019486 | biostudies-literature
Project description:Herein, we exploit coordination geometry as a new tool to regulate the non-covalent interactions, photophysical properties and energy landscape of supramolecular polymers. To this end, we have designed two self-assembled Pt(ii) complexes 1 and 2 that feature an identical aromatic surface, but differ in the coordination and molecular geometry (linear vs. V-shaped) as a result of judicious ligand choice (monodentate pyridine vs. bidentate bipyridine). Even though both complexes form cooperative supramolecular polymers in methylcyclohexane, their supramolecular and photophysical behaviour differ significantly: while the high preorganization of the bipyridine-based complex 1 enables an H-type 1D stacking with short Pt⋯Pt contacts via a two-step consecutive process, the existence of increased steric effects for the pyridyl-based derivative 2 hinders the formation of metal-metal contacts and induces a single aggregation process into large bundles of fibers. Ultimately, this fine control of Pt⋯Pt distances leads to tuneable luminescence-red for 1 vs. blue for 2, which highlights the relevance of coordination geometry for the development of functional supramolecular materials.
| S-EPMC8179630 | biostudies-literature
Project description:Topologically complex proteins fold by multiple routes as a result of hard-to-fold regions of the proteins. Oftentimes these regions are introduced into the protein scaffold for function and increase frustration in the otherwise smooth-funneled landscape. Interestingly, while functional regions add complexity to folding landscapes, they may also contribute to a unique behavior referred to as hysteresis. While hysteresis is predicted to be rare, it is observed in various proteins, including proteins containing a unique peptide cyclization to form a fluorescent chromophore as well as proteins containing a knotted topology in their native fold. Here, hysteresis is demonstrated to be a consequence of the decoupling of unfolding events from the isomerization or hula-twist of a chromophore in one protein and the untying of the knot in a second protein system. The question now is- can hysteresis be a marker for the interplay of landscapes where complex folding and functional regions overlap?
| S-EPMC3601837 | biostudies-literature
Project description:Cotranslational folding (CTF) is a fundamental molecular process that ensures efficient protein biosynthesis and minimizes the formation of misfolded states. However, the complexity of this process makes it extremely challenging to obtain structural characterizations of CTF pathways. Here, we correlate observations of translationally arrested nascent chains with those of a systematic C-terminal truncation strategy. We create a detailed description of chain length-dependent free energy landscapes associated with folding of the FLN5 filamin domain, in isolation and on the ribosome, and thus, quantify a substantial destabilization of the native structure on the ribosome. We identify and characterize two folding intermediates formed in isolation, including a partially folded intermediate associated with the isomerization of a conserved cis proline residue. The slow folding associated with this process raises the prospect that neighboring unfolded domains might accumulate and misfold during biosynthesis. We develop a simple model to quantify the risk of misfolding in this situation and show that catalysis of folding by peptidyl-prolyl isomerases is sufficient to eliminate this hazard.
| S-EPMC6166796 | biostudies-literature
Project description:MCMap is a tool particularly well-suited for analyzing energy landscapes of transient macromolecular complexes. The program applies a Monte Carlo strategy, where the ligand moves randomly in the electrostatic field of the receptor. By applying importance sampling, the major interaction sites are mapped, resulting in a global distribution of ligand-receptor complexes. This approach displays the dynamic character of transiently interacting protein complexes where not a single complex but an ensemble of complexes better describes the protein interactions. The software provides a broad range of analysis options which allow for relating the simulations to experimental data and for interpreting them on a structural level. The application of MCMap is exemplified by the electron-transfer complex of cytochrome c peroxidase and cytochrome c from baker's yeast. The functionality of MCMap and the visualization of simulation data are in particular demonstrated by studying the dependence of the association on ionic strength and on the oxidation state of the binding partner. Furthermore, microscopically, a repulsion of a second ligand can be seen in the ternary complex upon the change of the oxidation state of the bound cytochrome c. The software is made available as open source software together with the example and can be downloaded free of charge from http://www.bisb.uni-bayreuth.de/index.php?page=downloads.
| S-EPMC6644659 | biostudies-literature