Bioinspired Self‐Assembly II: Principles of Cooperativity in Bioinspired Self‐Assembling Systems

Ercolani, Gianfranco; Schiaffino, Luca

doi:10.1002/9781118310083.ch3

Cited by 6 publications

(4 citation statements)

References 54 publications

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“…Cooperativity is a key organizing principle in biology that represents a fundamental mechanism for accomplishing molecular interdependencies [ 63 – 69 ]. We here define cooperativity as the dependence of the binding affinity of one molecule on the state of the matrix in terms of other molecules already bound to it.…”

Section: Resultsmentioning

confidence: 99%

“…Cooperativity is a ubiquitous and crucial regulation mechanism in a large variety of processes, including molecular recognition, enzyme catalysis, membrane transport, protein folding, and self-assembly of supramolecular complexes [ 63 – 69 ]. In the context of synaptic biology, cooperativity plays key roles not only in the formation of multi-molecular scaffolds (e.g.…”

Section: Discussionmentioning

confidence: 99%

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Cooperative stochastic binding and unbinding explain synaptic size dynamics and statistics

et al. 2017

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Synapses are dynamic molecular assemblies whose sizes fluctuate significantly over time-scales of hours and days. In the current study, we examined the possibility that the spontaneous microscopic dynamics exhibited by synaptic molecules can explain the macroscopic size fluctuations of individual synapses and the statistical properties of synaptic populations. We present a mesoscopic model, which ties the two levels. Its basic premise is that synaptic size fluctuations reflect cooperative assimilation and removal of molecules at a patch of postsynaptic membrane. The introduction of cooperativity to both assimilation and removal in a stochastic biophysical model of these processes, gives rise to features qualitatively similar to those measured experimentally: nanoclusters of synaptic scaffolds, fluctuations in synaptic sizes, skewed, stable size distributions and their scaling in response to perturbations. Our model thus points to the potentially fundamental role of cooperativity in dictating synaptic remodeling dynamics and offers a conceptual understanding of these dynamics in terms of central microscopic features and processes.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Cooperative stochastic binding and unbinding explain synaptic size dynamics and statistics

et al. 2017

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“…Let us consider a long Gaussian chain M 1 endowed with two end functional groups capable of reacting with each other in a reversible addition reaction. The monomer, present in solution at the initial concentration [M 1 ] 0 , is converted at equilibrium into a mixture of a virtually infinite number of oligomeric chains M i , rings C i , and [2]catenanes CC ij with i ≥ j , so that the mass balance equation can be written as eq . If it is assumed, as usual, that the equilibrium constant for linear propagation, K , is independent of the length of the chains to which the end groups are attached (eq ), then it can be easily demonstrated that the equilibrium concentration of any linear i -mer is given by eq , where x is the extent of reaction in the chain fraction. , The equilibrium effective molarity (EM i ), ,− also known as the molar cyclization constant, is a measure of the propensity of a given chain to undergo cyclization. It is defined as the equilibrium constant of the back-biting process in which a linear oligomer, say M i + j , splits into a cyclic oligomer C i and a linear oligomer M j (eq ).…”

Section: Resultsmentioning

confidence: 99%

Statistical Ring Catenation under Thermodynamic Control: Should the Jacobson–Stockmayer Cyclization Theory Take into Account Catenane Formation?

Stefano

Ercolani

2017

J. Phys. Chem. B

Self Cite

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An extension of the Jacobson−Stockmayer theory is presented to include the reversible formation of [2]catenanes in a ring−chain system under thermodynamic control. The extended theory is based on the molar catenation constant, measuring the ease of catenation of two ring oligomers, whose expression was obtained in a previous work. Two scenarios have been considered: that of "thick" (hydrocarbon-like) chains and that of "thin" (DNA-like) chains. In the case of "thick" chains, the formation of catenanes can be neglected, unless in the unlikely case of a very large value of the equilibrium constant for linear propagation (K ≈ 10 8 mol −1 L, or larger). For K tending to infinity, the system becomes a chain-free system where only ring−catenane equilibria occur. Under this condition, there is a critical concentration below which only rings are present at equilibrium and above which the ring fraction remains constant, and the excess monomer is converted only into catenanes. In the case of "thin" chains, the formation of catenanes cannot be neglected even for values of K as low as 10 2 mol −1 L, thus justifying the use of the extended theory.

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“…Cooperativity plays a key role in biological and synthetic systems to govern self‐assembly, determine selective molecular recognition, and regulate the behavior of complex systems [1–5] . Cooperativity is seen as the deviation of the behavior of multiple binding events from the hypothetical case in which these binding events would add up independently [6–9] .…”

Section: Introductionmentioning

confidence: 99%

Dinucleoside‐Based Macrocycles Displaying Unusually Large Chelate Cooperativities

Serrano-Molina

Juan

González‐Rodríguez

2020

The Chemical Record

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High‐fidelity production of a single self‐assembled species in competition with others relies on achieving strong chelate cooperativities, which can be quantified by the effective molarity parameter. Therefore, supramolecular systems displaying very high effective molarities are reliably formed in a wide range of experimental conditions and exhibit “all‐or‐none” phenomena, meaning that the assembly is either fully formed or fully dissociated into the corresponding monomeric components. We summarize here our efforts in the study and characterization of one of these synthetic systems exhibiting record chelate cooperativities: the self‐assembly of rod‐like dinucleoside molecules into tetrameric macrocycles through hydrogen‐bonding Watson‐Crick interactions.

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Bioinspired Self‐Assembly II: Principles of Cooperativity in Bioinspired Self‐Assembling Systems

Abstract: [No abstract available

Cited by 6 publications

References 54 publications

Cooperative stochastic binding and unbinding explain synaptic size dynamics and statistics

Cooperative stochastic binding and unbinding explain synaptic size dynamics and statistics

Statistical Ring Catenation under Thermodynamic Control: Should the Jacobson–Stockmayer Cyclization Theory Take into Account Catenane Formation?

Dinucleoside‐Based Macrocycles Displaying Unusually Large Chelate Cooperativities

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