Self-replication of Aß42 aggregates occurs on small and isolated fibril sites.

Self-replication of amyloid fibrils via secondary nucleation is an intriguing physicochemical phenomenon in which existing fibrils catalyze the formation of their own copies. The molecular events behind this fibril surface-mediated process remain largely inaccessible to current structural and imaging techniques. Using statistical mechanics, computer modeling, and chemical kinetics, we show that the catalytic structure of the fibril surface can be inferred from the aggregation behavior in the presence and absence of a fibril-binding inhibitor. We apply our approach to the case of Alzheimer's A[Formula: see text] amyloid fibrils formed in the presence of proSP-C Brichos inhibitors. We find that self-replication of A[Formula: see text] fibrils occurs on small catalytic sites on the fibril surface, which are far apart from each other, and each of which can be covered by a single Brichos inhibitor.

How an overlooked gene in coenzyme a synthesis solved an enzyme mechanism predicament.

Coenzyme A (CoA) is an essential cofactor throughout biology. The first committed step in the CoA synthetic pathway is synthesis of ß-alanine from aspartate. In Escherichia coli and Salmonella enterica panD encodes the responsible enzyme, aspartate-1-decarboxylase, as a proenzyme. To become active, the E. coli and S. enterica PanD proenzymes must undergo an autocatalytic cleavage to form the pyruvyl cofactor that catalyzes decarboxylation. A problem was that the autocatalytic cleavage was too slow to support growth. A long-neglected gene (now called panZ) was belatedly found to encode the protein that increases autocatalytic cleavage of the PanD proenzyme to a physiologically relevant rate. PanZ must bind CoA or acetyl-CoA to interact with the PanD proenzyme and accelerate cleavage. The CoA/acetyl-CoA dependence has led to proposals that the PanD-PanZ CoA/acetyl-CoA interaction regulates CoA synthesis. Unfortunately, regulation of ß-alanine synthesis is very weak or absent. However, the PanD-PanZ interaction provides an explanation for the toxicity of the CoA anti-metabolite, N5-pentyl pantothenamide.

Autocatalysis in Eschenmoser Coupling Reactions.

The Eschenmoser coupling reaction (ECR) of thioamides with electrophiles is believed to proceed via thiirane intermediates. However, little is known about converting the intermediates into ECR products. Previous mechanistic studies involved external thiophiles to remove the sulfur atom from the intermediates. In this work, an ECR proceeding without any thiophilic agent or base is studied by electrospray ionization-mass spectrometry. ESI-MS enables the detection of the so-far elusive polysulfide species Sn , with n ranging from 2 to 16 sulfur atoms, proposed to be the key species leading to product formation. Integrating observations from ion mobility spectrometry, ion spectroscopy, and reaction monitoring via flow chemistry coupled with mass spectrometry provides a comprehensive understanding of the reaction mechanism and uncovers the autocatalytic nature of the ECR reaction.

On the exclusion of exponential autocatalysts by sub-exponential autocatalysts.

Selection among autocatalytic species fundamentally depends on their growth law: exponential species, whose number of copies grows exponentially, are mutually exclusive, while sub-exponential ones, whose number of copies grows polynomially, can coexist. Here we consider competitions between autocatalytic species with different growth laws and make the simple yet counterintuitive observation that sub-exponential species can exclude exponential ones while the reverse is, in principle, impossible. This observation has implications for scenarios pertaining to the emergence of natural selection.

Achiral 2-pyridone and 4-aminopyridine act as chiral inducers of asymmetric autocatalysis with amplification of enantiomeric excess via the formation of chiral crystals.

Enantiomorphous crystals of achiral 2-pyridone and 4-aminopyridine served as sources of chirality, to induce the asymmetric autocatalysis of 5-pyrimidyl alkanol during the asymmetric addition of diisopropylzinc to the corresponding pyrimidine-5-carbaldehyde, that is, the Soai reaction. Following a significant amplification of enantiomeric excess through asymmetric autocatalysis, highly enantioenriched 5-pyrimidyl alkanol could be synthesized with their corresponding absolute configurations to those of chiral crystals of 2-pyridone and 4-aminopyridine.

What Wilhelm Ostwald meant by "Autokatalyse" and its significance to origins-of-life research: Facilitating the search for chemical pathways underlying abiogenesis by reviving Ostwald's thought that reactants may also be autocatalysts: Facilitating the search for chemical pathways underlying abiogenesis by reviving Ostwald's thought that reactants may also be autocatalysts.

A closer look at Wilhelm Ostwald's articles that originally proposed the concept of autocatalysis reveals that he accepted reactants, not just products, as potential autocatalysts. Therefore, that a process is catalyzed by some of its products, which is the common definition of autocatalysis, is only a proper subset of what Ostwald meant by "Autokatalyse." As a result, it is necessary to reconsider the definition of autocatalysis, which is especially important for origins-of-life research because autocatalysis provides an abiotic mechanism that yields reproduction-like dynamics. Here, we translate and briefly review the two key publications on autocatalysis by Ostwald to revive his understanding of autocatalysis, and we introduce the concepts of recessive and expansive autocatalysis. Then we discuss the twofold significance of such a revival: first, facilitating the search for candidate processes underlying the origins of life, and second, updating our view of autocatalysis in complex reaction networks and metabolism.

A unifying autocatalytic network-based framework for bacterial growth laws.

Recently discovered simple quantitative relations, known as bacterial growth laws, hint at the existence of simple underlying principles at the heart of bacterial growth. In this work, we provide a unifying picture of how these known relations, as well as relations that we derive, stem from a universal autocatalytic network common to all bacteria, facilitating balanced exponential growth of individual cells. We show that the core of the cellular autocatalytic network is the transcription-translation machinery-in itself an autocatalytic network comprising several coupled autocatalytic cycles, including the ribosome, RNA polymerase, and transfer RNA (tRNA) charging cycles. We derive two types of growth laws per autocatalytic cycle, one relating growth rate to the relative fraction of the catalyst and its catalysis rate and the other relating growth rate to all the time scales in the cycle. The structure of the autocatalytic network generates numerous regimes in state space, determined by the limiting components, while the number of growth laws can be much smaller. We also derive a growth law that accounts for the RNA polymerase autocatalytic cycle, which we use to explain how growth rate depends on the inducible expression of the rpoB and rpoC genes, which code for the RpoB and C protein subunits of RNA polymerase, and how the concentration of rifampicin, which targets RNA polymerase, affects growth rate without changing the RNA-to-protein ratio. We derive growth laws for tRNA synthesis and charging and predict how growth rate depends on temperature, perturbation to ribosome assembly, and membrane synthesis.

The Autocatalytic Chemical Reaction of a Soluble Biopolymer Derived from Municipal Biowaste.

The paper discusses the perspectives of further implementation of the autocatalytic properties of a soluble biopolymer (SBP) derived from municipal biowastes for the realisation of a biorefinery producing value-added bio-products for consumer use. The reaction of an SBP and water is reported to cause the depolymerisation and oxidation of the pristine SBP organic matter with the formation of carboxyl-functionalised polymers having lower molecular weight and CO2. These findings demonstrate the oxidation of the SBP via water, which could only occur through the production of O and OH radicals catalysed by the SBP. According to the adopted experimental plan, the anaerobic digestate supplied by an Italian municipal biowaste treatment plant was hydrolysed in pH 13 water at 60 °C. The dry product was re-dissolved in plain water at pH 10 and used as a control against the same solution with hydrogen peroxide at 0.1-3 H2O2 moles per SBP carbon mole added. The control and test solutions were kept at room temperature, in the dark or in a climatic chamber under irradiation with simulated solar light, until the pH of the solutions remained constant. Afterwards, the solutions were processed to recover and analyse the crude soluble products. The present work reports the results obtained for the control solution and for the test solutions treated in the presence and absence of H2O2, with and without pH control, in the dark and under irradiation with simulated solar light.

The Role of Hydrogen Bonds in Thermally Responsive Crystallization-Driven Template Autocatalysis.

Autocatalysis has been recognized to be involved in the emergence of life and intrinsic to biomolecular replication. Recently, an efficient template autocatalysis driven by solvent-free crystallization has been reported. Herein, we unveil the role of intermolecular hydrogen bonds formed by amides in crystallization-driven template autocatalysis (CDTA), which involves the autocatalytic activity, template selectivity, and thermal responsiveness. We found that the thermal-induced cis-trans isomerization of amides possibly affects the H-bonding-mediated template ability of products for autocatalytic transformation. As a result, CDTA can be reversibly inhibited and activated by tuning the reaction temperatures. Our work sheds light on the significance of noncovalent H-bonding interactions in artificial self-replicators.

In-Situ Fabrication of Sustainable-N-Doped-Carbon-Nanotube-Encapsulated CoNi Heterogenous Nanocomposites for High-Efficiency Electromagnetic Wave Absorption.

Developing carbon encapsulated magnetic composites with rational design of microstructure for achieving high-performance electromagnetic wave (EMW) absorption in a facile, sustainable, and energy-efficiency approach is highly demanded yet remains challenging. Here, a type of N-doped carbon nanotube (CNT) encapsulated CoNi alloy nanocomposites with diverse heterostructures are synthesized via the facile, sustainable autocatalytic pyrolysis of porous CoNi-layered double hydroxide/melamine. Specifically, the formation mechanism of the encapsulated structure and the effects of heterogenous microstructure and composition on the EMW absorption performance are ascertained. With the presence of melamine, CoNi alloy emerges its autocatalysis effect to generate N-doped CNTs, leading to unique heterostructure and high oxidation stability. The abundant heterogeneous interfaces induce strong interfacial polarization to EMWs and optimize impedance matching characteristic. Combined with the inherent high conductive and magnetic loss capabilities, the nanocomposites accomplish a high-efficiency EMW absorption performance even at a low filling ratio. The minimum reflection loss of -84.0 dB at the thickness of 3.2 mm and a maximum effective bandwidth of 4.3 GHz are obtained, comparable to the best EMW absorbers. Integrated with the facile, controllable, and sustainable preparation approach of the heterogenous nanocomposites, the work shows a great promise of the nanocarbon encapsulation protocol for achieving lightweight, high-performance EMW absorption materials.

On the Mechanism of the Formal [2+2] Cycloaddition - Retro-electrocyclization (CA-RE) Reaction.

The [2+2] cycloaddition - retro-electrocyclization (CA-RE) reaction is a "click-like" protocol for facile synthesis of donor-acceptor chromophores from an alkyne and tetracyanoethylene. Herein we shed light on the mechanism of this reaction by detailed kinetics studies using 1 H NMR spectroscopy. By considering several experiments simultaneously, a variety of mechanistic models was evaluated. Surprisingly, a model in which the final 1,1,4,4-tetracyanobuta-1,3-diene product promoted the first step was the only one that described well the experimental data. This autocatalysis model also involved a non-concerted, stepwise formation of the cyclobutene cycloaddition adduct. By proper choice of conditions, we were able to generate the transient cyclobutene in sufficient amount to verify it as an intermediate using 13 C NMR spectroscopy. For its final retro-electrocyclization step, simple first-order kinetics was observed and only minor solvent dependence, which indicates a concerted reaction.

Use of the redox-dependent intein system for enhancing production of the cyclic green fluorescent protein.

To expand the reported redox-dependent intein system application, in this work, we used the split intein variant with highly trans-splicing efficiency and minimal extein dependence to cyclize the green fluorescent protein variant reporter in vitro. The CPG residues were introduced adjacent to the intein's catalytic cysteine for reversible formation of a disulfide bond to retard the trans-splicing reaction under the oxidative environment. The cyclized reporter protein in Escherichia coli cells was easily prepared by organic extraction and identified by the exopeptidase digestion. The amounts of extracted cyclized protein reporter in BL21 (DE3) cells were higher than those in hyperoxic SHuffle T7 coexpression system for facilitating the disulfide bond formation. The double His6-tagged precursor was purified for in vitro cyclization of the protein for 3 h. Compared with the purified linear counterpart, the cyclic reporter showed about twofold increase in fluorescence intensity, exhibited thermal and hydrolytic stability, and displayed better folding efficiency in BL21 (DE3) cells at the elevated temperature. Taken together, the developed redox-dependent intein system will be used for producing other cyclic disulfide-free proteins. The cyclic reporter is a potential candidate applied in certain thermophilic aerobes.

In Situ Regulation of MnO2 Structural Characteristics by Oxyanions to Boost Permanganate Autocatalysis for Phenol Removal.

Oxyanions, a class of constituents naturally occurring in water, have been widely demonstrated to enhance permanganate (Mn(VII)) decontamination efficiency. However, the detailed mechanism remains ambiguous, mainly because the role of oxyanions in regulating the structural parameters of colloidal MnO2 to control the autocatalytic activity of Mn(VII) has received little attention. Herein, the origin of oxyanion-induced enhancement is systematically studied using theoretical calculations, electrochemical tests, and structure-activity relation analysis. Using bicarbonate (HCO3-) as an example, the results indicate that HCO3- can accelerate the degradation of phenol by Mn(VII) by improving its autocatalytic process. Specifically, HCO3- plays a significant role in regulating the structure of in situ produced MnO2 colloids, i.e., increasing the surface Mn(III)s content and restricting particle growth. These structural changes in MnO2 facilitate its strong binding to Mn(VII), thereby triggering interfacial electron transfer. The resultant surface-activated Mn(VII)* complexes demonstrate excellent degrading activity via directly seizing one electron from phenol. Further, other oxyanions with appropriate ionic potentials (i.e., borate, acetate, metasilicate, molybdate, and phosphate) exhibit favorable influences on the oxidative capability of Mn(VII) through an activation mechanism similar to that of HCO3-. These findings considerably improve our fundamental understanding of the oxidation behavior of Mn(VII) in actual water environments and provide a theoretical foundation for designing autocatalytically boosted Mn(VII) oxidation systems.

Universal motifs and the diversity of autocatalytic systems.

Autocatalysis is essential for the origin of life and chemical evolution. However, the lack of a unified framework so far prevents a systematic study of autocatalysis. Here, we derive, from basic principles, general stoichiometric conditions for catalysis and autocatalysis in chemical reaction networks. This allows for a classification of minimal autocatalytic motifs called cores. While all known autocatalytic systems indeed contain minimal motifs, the classification also reveals hitherto unidentified motifs. We further examine conditions for kinetic viability of such networks, which depends on the autocatalytic motifs they contain and is notably increased by internal catalytic cycles. Finally, we show how this framework extends the range of conceivable autocatalytic systems, by applying our stoichiometric and kinetic analysis to autocatalysis emerging from coupled compartments. The unified approach to autocatalysis presented in this work lays a foundation toward the building of a systems-level theory of chemical evolution.

Spontaneous formation of autocatalytic sets with self-replicating inorganic metal oxide clusters.

Here we show how a simple inorganic salt can spontaneously form autocatalytic sets of replicating inorganic molecules that work via molecular recognition based on the {PMo12} ≡ [PMo12O40]3- Keggin ion, and {Mo36} ≡ [H3Mo57M6(NO)6O183(H2O)18]22- cluster. These small clusters are able to catalyze their own formation via an autocatalytic network, which subsequently template the assembly of gigantic molybdenum-blue wheel {Mo154} ≡ [Mo154O462H14(H2O)70]14-, {Mo132} ≡ [MoVI72MoV60O372(CH3COO)30(H2O)72]42- ball-shaped species containing 154 and 132 molybdenum atoms, and a {PMo12}⊂{Mo124Ce4} ≡ [H16MoVI100MoV24Ce4O376(H2O)56 (PMoVI10MoV2O40)(C6H12N2O4S2)4]5- nanostructure. Kinetic investigations revealed key traits of autocatalytic systems including molecular recognition and kinetic saturation. A stochastic model confirms the presence of an autocatalytic network involving molecular recognition and assembly processes, where the larger clusters are the only products stabilized by the cycle, isolated due to a critical transition in the network.

The Reduction of Carbonyl Compounds with Dicyclopentylzinc: A New Example of Asymmetric Amplifying Autocatalysis.

A previously unknown reduction of carbonyl compounds with dicyclopentylzinc is reported. Aldehydes react in mild conditions yielding corresponding primary alcohols and cyclopentene. Although cyclohexanone and acetophenone are inert to dicyclopentylzinc, a variety of heterocyclic ketones reacted readily, yielding reasonable to high yields of corresponding secondary alcohols. When the reaction was catalyzed with (-)-(1R,2S)-ephedrine, 3-acetylpyridine (10) resulted in a high yield of (S)-1-(pyridin-3-yl)ethanol (19) with >99% ee. 5-Acetyl-2-bromopyridine (11) also provided the corresponding optically active alcohol 20, albeit with a much lower optical yield. When 10% of 19 with 92% ee was used as an autocatalyst, 55% yield of the same compound was obtained, with 95% ee and 96% ee in two independent experiments. A three-stage reaction sequence starting from "no chirality" reaction yielded 19 with 6% ee. Thus, amplifying autocatalysis was detected in the reaction of ketone 10 with dicylopentylzinc.

Anion-π catalysis on carbon allotropes.

Anion-π catalysis, introduced in 2013, stands for the stabilization of anionic transition states on π-acidic aromatic surfaces. Anion-π catalysis on carbon allotropes is particularly attractive because high polarizability promises access to really strong anion-π interactions. With these expectations, anion-π catalysis on fullerenes has been introduced in 2017, followed by carbon nanotubes in 2019. Consistent with expectations from theory, anion-π catalysis on carbon allotropes generally increases with polarizability. Realized examples reach from enolate addition chemistry to asymmetric Diels-Alder reactions and autocatalytic ether cyclizations. Currently, anion-π catalysis on carbon allotropes gains momentum because the combination with electric-field-assisted catalysis promises transformative impact on organic synthesis.

History Dependence in a Chemical Reaction Network Enables Dynamic Switching.

This work describes an enzymatic autocatalytic network capable of dynamic switching under out-of-equilibrium conditions. The network, wherein a molecular fuel (trypsinogen) and an inhibitor (soybean trypsin inhibitor) compete for a catalyst (trypsin), is kept from reaching equilibria using a continuous flow stirred tank reactor. A so-called 'linear inhibition sweep' is developed (i.e., a molecular analogue of linear sweep voltammetry) to intentionally perturb the competition between autocatalysis and inhibition, and used to demonstrate that a simple molecular system, comprising only three components, is already capable of a variety of essential neuromorphic behaviors (hysteresis, synchronization, resonance, and adaptation). This research provides the first steps in the development of a strategy that uses the principles in systems chemistry to transform chemical reaction networks into platforms capable of neural network computing.

The limits of metabolic heredity in protocells.

The universal core of metabolism could have emerged from thermodynamically favoured prebiotic pathways at the origin of life. Starting with H2 and CO2, the synthesis of amino acids and mixed fatty acids, which self-assemble into protocells, is favoured under warm anoxic conditions. Here, we address whether it is possible for protocells to evolve greater metabolic complexity, through positive feedbacks involving nucleotide catalysis. Using mathematical simulations to model metabolic heredity in protocells, based on branch points in protometabolic flux, we show that nucleotide catalysis can indeed promote protocell growth. This outcome only occurs when nucleotides directly catalyse CO2 fixation. Strong nucleotide catalysis of other pathways (e.g. fatty acids and amino acids) generally unbalances metabolism and slows down protocell growth, and when there is competition between catalytic functions cell growth collapses. Autocatalysis of nucleotide synthesis can promote growth but only if nucleotides also catalyse CO2 fixation; autocatalysis alone leads to the accumulation of nucleotides at the expense of CO2 fixation and protocell growth rate. Our findings offer a new framework for the emergence of greater metabolic complexity, in which nucleotides catalyse broad-spectrum processes such as CO2 fixation, hydrogenation and phosphorylation important to the emergence of genetic heredity at the origin of life.

Prebiotically Plausible Autocatalytic Peptide Amyloids.

The prebiotic emergence of molecules capable both of self-replication and of storing information was a defining event at the dawn of life. Still, no plausible prebiotic self-replication of biologically relevant molecules has been demonstrated. Building upon the known templating nature of amyloids, we present two systems in which the products of a peptide-bond-forming reaction act as self-replicators to enhance the yield and stereoselectivity of their formation. This first report of an amino acid condensation that can undergo autocatalysis further supports the potential role of amyloids in prebiotic molecular evolution as an environment-responsive and information-coding system capable of self-replication.