Circuit Topology Analysis of Polymer Folding Reactions.
Ontology highlight
ABSTRACT:
SUBMITTER: Heidari M
PROVIDER: S-EPMC7318069 | biostudies-literature | 2020 Jun
REPOSITORIES: biostudies-literature
Publications
Circuit Topology Analysis of Polymer Folding Reactions.
Heidari Maziar M Schiessel Helmut H Mashaghi Alireza A
ACS central science 20200512 6
Circuit topology is emerging as a versatile measure to classify the internal structures of folded linear polymers such as proteins and nucleic acids. The topology framework can be applied to a wide range of problems, most notably molecular folding reactions that are central to biology and molecular engineering. In this Outlook, we discuss the state-of-the art of the technology and elaborate on the opportunities and challenges that lie ahead. ...[more]
Similar Datasets
Project description:We present a braided circuit topology framework for investigating topology and structural phase transitions in aggregates of semiflexible polymers. In the conventional approach to circuit topology, which specifically applies to single isolated folded linear chains, the number and arrangement of contacts within the circuitry of a folded chain give rise to increasingly complex fold topologies. Another avenue for achieving complexity is through the interaction and entanglement of two or more folded linear chains. The braided circuit topology approach describes the topology of such multiple-chain systems and offers topological measures such as writhe, complexity, braid length, and isotopy class. This extension of circuit topology to multichains reveals the interplay between collapse, aggregation, and entanglement. In this work, we show that circuit topological motif fractions are ideally suited order parameters to characterize structural phase transitions in entangled systems that can detect structural re-ordering other measures cannot.
| S-EPMC10867648 | biostudies-literature
Project description:Intrinsically disordered proteins (IDPs) lack a stable native conformation, making it challenging to characterize their structure and dynamics. Key topological motifs with fundamental biological relevance are often hidden in the conformational noise, eluding detection. Here, we develop a circuit topology toolbox to extract conformational patterns, critical contacts, and timescales from simulated dynamics of intrinsically disordered proteins. We follow the dynamics of IDPs by providing a smart low-dimensionality representation of their three-dimensional (3D) configuration in the topology space. Such an approach allows us to quantify topological similarity in dynamic systems, therefore providing a pipeline for structural comparison of IDPs.
| S-EPMC10131221 | biostudies-literature
Project description:The contact topology of a protein determines important aspects of the folding process. The topological measure of contact order has been shown to be predictive of the rate of folding. Circuit topology is emerging as another fundamental descriptor of biomolecular structure, with predicted effects on the folding rate. We analyze the residue-based circuit topological environments of 21 K mutations labeled as pathogenic or benign. Multiple statistical lines of reasoning support the conclusion that the number of contacts in two specific circuit topological arrangements, namely inverse parallel and cross relations, with contacts involving the mutated residue have discriminatory value in determining the pathogenicity of human variants. We investigate how results vary with residue type and according to whether the gene is essential. We further explore the relationship to a number of structural features and find that circuit topology provides nonredundant information on protein structures and pathogenicity of mutations. Results may have implications for the polymer physics of protein folding and suggest that "local" topological information, including residue-based circuit topology and residue contact order, could be useful in improving state-of-the-art machine learning algorithms for pathogenicity prediction.
| S-EPMC9543832 | biostudies-literature
Project description:Reciprocal regulation of genome topology and function is a fundamental and enduring puzzle in biology. The wealth of data provided by Hi-C libraries offers the opportunity to unravel this relationship. However, there is a need for a comprehensive theoretical framework in order to extract topological information for genome characterization and comparison. Here, we develop a toolbox for topological analysis based on Circuit Topology, allowing for the quantification of inter- and intracellular genomic heterogeneity, at various levels of fold complexity: pairwise contact arrangement, higher-order contact arrangement, and topological fractal dimension. Single-cell Hi-C data were analyzed and characterized based on topological content, revealing not only a strong multiscale heterogeneity but also highly conserved features such as a characteristic topological length scale and topological signature motifs in the genome. We propose that these motifs inform on the topological state of the nucleus and indicate the presence of active loop extrusion.
| S-EPMC8861635 | biostudies-literature
Project description:We investigate aspects of topology in protein folding. For this we numerically simulate the temperature driven folding and unfolding of the slipknotted archaeal virus protein AFV3-109. Due to knottiness the (un)folding is a topological process, it engages the entire backbone in a collective fashion. Accordingly we introduce a topological approach to model the process. Our simulations reveal that the (un)folding of AFV3-109 slipknot proceeds through a folding intermediate that has the topology of a trefoil knot. We observe that the final slipknot causes a slight swelling of the folded AFV3-109 structure. We disclose the relative stability of the strands and helices during both the folding and unfolding processes. We confirm results from previous studies that pointed out that it can be very demanding to simulate the formation of knotty self-entanglement, and we explain how the problems are circumvented: The slipknotted AFV3-109 protein is a very slow folder with a topologically demanding pathway, which needs to be properly accounted for in a simulation description. When we either increase the relative stiffness of bending, or when we decrease the speed of ambient cooling, the rate of slipknot formation rapidly increases.
| S-EPMC7806123 | biostudies-literature
Project description:Folding one-dimensional polymer chains into well-defined topologies represents an important organization process for proteins, but replicating this process for supramolecular polymers remains a challenging task. We report supramolecular polymers that can fold into protein-like topologies. Our approach is based on curvature-forming supramolecular rosettes, which affords kinetic control over the extent of helical folding in the resulting supramolecular fibers by changing the cooling rate for polymerization. When using a slow cooling rate, we obtained misfolded fibers containing a minor amount of helical domains that folded on a time scale of days into unique topologies reminiscent of the protein tertiary structures. Thermodynamic analysis of fibers with varying degrees of folding revealed that the folding is accompanied by a large enthalpic gain. The self-folding proceeds via ordering of misfolded domains in the main chain using helical domains as templates, as fully misfolded fibers prepared by a fast cooling rate do not self-fold.
| S-EPMC6128674 | biostudies-literature
Project description:Spike synchronization underlies information processing and storage in the brain. But how can neurons synchronize in a noisy network? By exploiting a high-speed (500-2,000 fps) multineuron imaging technique and a large-scale synapse mapping method, we directly compared spontaneous activity patterns and anatomical connectivity in hippocampal CA3 networks ex vivo. As compared to unconnected pairs, synaptically coupled neurons shared more common presynaptic neurons, received more correlated excitatory synaptic inputs, and emitted synchronized spikes with approximately 10(7) times higher probability. Importantly, common presynaptic parents per se synchronized more than unshared upstream neurons. Consistent with this, dynamic-clamp stimulation revealed that common inputs alone could not account for the realistic degree of synchronization unless presynaptic spikes synchronized among common parents. On a macroscopic scale, network activity was coordinated by a power-law scaling of synchronization, which engaged varying sets of densely interwired (thus highly synchronized) neuron groups. Thus, locally coherent activity converges on specific cell assemblies, thereby yielding complex ensemble dynamics. These segmentally synchronized pulse packets may serve as information modules that flow in associatively parallel network channels.
| S-EPMC2890467 | biostudies-literature
Project description:The ability to describe the topology of a folded protein conformation is critically important for functional analysis, protein engineering, and drug design. Circuit topology is a unique topological framework which is widely applicable to protein analysis, yet a state-of-the art implementation of this concept is lacking. Here, we present an open-source Python-implemented circuit topology tool called ProteinCT. The platform provides a method for acquiring, visualizing, analyzing, and quantifying circuit topology data from proteins of interest. We mapped the universe of human proteins to a circuit topology space using conventional hardware within a few hours, demonstrating the performance of ProteinCT. In brief,•A Python-implemented circuit topology tool is developed to extract global and local topological information from a protein structure file.•Modules are developed to combine topological information with geometric and energetic information.•It is demonstrated that the method can be efficiently applied to a large set of proteins, opening a wide range of possibilities for structural proteomics research.
| S-EPMC9520010 | biostudies-literature
Project description:Disordered mechanical systems, when strongly deformed, have complex configuration spaces with multiple stable states and pathways connecting them. The topology of such pathways determines which states are smoothly accessible from any part of configuration space. Controlling this topology would allow us to limit access to undesired states and select desired behaviors in metamaterials. Here, we show that the topology of such pathways, as captured by bifurcation diagrams, can be tuned using imperfections such as stiff hinges in elastic networks and creased thin sheets. We derive Linear Programming-like equations for designing desirable pathway topologies. These ideas are applied to eliminate the exponentially many ways of misfolding self-folding sheets by making some creases stiffer than others. Our approach allows robust folding by entire classes of external folding forces. Finally, we find that the bifurcation diagram makes pathways accessible only at specific folding speeds, enabling speed-dependent selection of different folded states.
| S-EPMC6191449 | biostudies-literature
Project description:Shape plays an important role in defining the function of materials, particularly those found in nature. Several strategies exist to program materials to change from one shape to another; however, few can temporally and spatially control the shape. Programming the sequence of shape transformation with temporal control has been driven by the desire to generate complex shapes with high yield and to create multiple shapes from the same starting material. This paper demonstrates a markedly simple strategy for programmed self-folding of two-dimensional (2D) polymer sheets into 3D objects in a sequential manner using external light. Printed ink on the surface of the polymer sheets discriminately absorbs light on the basis of the wavelength of the light and the color of the ink that defines the hinge about which the sheet folds. The absorbed light gradually heats the underlying polymer across the thickness of the sheet, which causes relief of strain to induce folding. These color patterns can be designed to absorb only specific wavelengths of light (or to absorb differently at the same wavelength using color hues), thereby providing control of sheet folding with respect to time and space. This type of shape programming may have numerous applications, including reconfigurable electronics, actuators, sensors, implantable devices, smart packaging, and deployable structures.
| S-EPMC5336351 | biostudies-literature