Formamide and the origin of life

The complexity of life boils down to the definition: “self-sustained chemical system capable of undergoing Darwinian evolution” (Joyce, 1994) [1]. The term “self-sustained” implies a set of chemical reactions capable of harnessing energy from the environment, using it to carry out programmed anabolic and catabolic functions. We briefly present our opinion on the general validity of this definition.Running anabolic and catabolic functions entails complex chemical information whose stability, reproducibility and evolution constitute the core of what is dubbed genetics.Life as-we-know-it is made of the intimate interaction of metabolism and genetics, both built around the chemistry of the most common elements of the Universe (hydrogen, oxygen, nitrogen, carbon). Other elements like phosphorus and sulphur play important but ancillary and potentially replaceable roles.The reproducible interaction of metabolic and genetic cycles results in the hypercycles of organization and de-organization of chemical information that we consider living entities. In order to approach the problem of the origin of life it is therefore reasonable to start from the assumption that both metabolism and genetics had a common origin, shared a common chemical frame, were embedded in physical–chemical conditions favourable for the onset of both.The most abundant three-atoms organic compound in interstellar environment is hydrogen cyanide HCN, the most abundant three-atoms inorganic compound is water H₂O. The combination of the two results in the formation of formamide H₂NCOH. We have explored the chemistry of formamide in conditions compatible with the synthesis and the stability of compounds of potential pre-genetic and pre-metabolic interest. We discuss evidence showing (i) that all the compounds necessary for the build-up of nucleic acids are easily obtained abiotically, (ii) that essentially all the steps leading to the spontaneous generation of RNA are abiotically possible, (iii) that the key compounds of extant metabolic cycles are obtained in the same chemical frame, often in the same test tube.How close are these observations to a plausible scenario for the origin of life?     

Transport of self-propelling bacteria in micro-channel flow

Understanding the collective motion of self-propelling organisms in confined geometries, such as that of narrow channels, is of great theoretical and practical importance. By means of numerical simulations we study the motion of model bacteria in 2D channels under different flow conditions: fluid at rest, steady and unsteady flow. We find aggregation of bacteria near channel walls and, in the presence of external flow, also upstream swimming, which turns out to be a very robust result. Detailed analysis of bacterial velocity and orientation fields allows us to quantify the phenomenon by varying cell density, channel width and fluid velocity. The tumbling mechanism turns out to have strong influence on velocity profiles and particle flow, resulting in a net upstream flow in the case of non-tumbling organisms. Finally we demonstrate that upstream flow can be enhanced by a suitable choice of an unsteady flow pattern.     

7Li quasi-free scattering off the α-cluster in 9Be nucleus

Spectra of coincident charged particles from the reactions induced by a 52 MeV ⁷Li beam incident on a beryllium target were measured. Strong contributions of the ⁷Li quasi-free scattering off the α-cluster in ⁹Be nucleus were observed. This observation supports the conclusions from the study of complete fusion of weakly bound light nuclei at low energies that the “fragility” of the nuclei makes their fusion less probable. Received: 1 June 1998     

Source of entropy decrease in biosystems

Summary Entropy changes are evaluated for all possible coupled reactions which define the overall biochemical processes. Predictions are well supported by all known data. The results show that biochemical process in animal systems yield a net decrease of entropy thanks to respiration. It is shown also that the respiration is the primary source of entropy decrease in vegetal systems.

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Riassunto Si valutano le variazioni di entropia per tutte le possibili reazioni accoppiate che definiscono l'intera sequenza di un completo processo biochimico. I valori previsti sono in buon accordo con tutti i dati da noi conosciuti. I risultati mostrano che i processi biochimici inducono una diminuzione netta di entropia all'interno dei sistemi animali grazie al processo di respirazione. Si mostra inoltre che anche nei sistemi vegetali la variazione negativa di entropia è prevalentemente determinata dal processo di respirazione.

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Резюме Оцениваются изменения энтропии для всех возможных связанных реакций, которые полностью определяют биохимические поцессы. Предсказания хорощо согласуются со всеми известными данными. Полученные результаты покзывают, что биохимические процессы в животных системах приводят к результирующему уменьшению энтропии вследствие дыхания. Показывается, что дыхание представляет первичный источник уменьшения энтропии также в растительных системах.

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To speed up publication, the authors of this paper have agreed to not receive the proofs for correction.     

Toward the de novo design of a catalytically active helix bundle: a substrate-accessible carboxylate-bridged dinuclear metal center.

De novo design of proteins provides an attractive approach to uncover the essential features required for their functions. Previously, we described the design and crystal structure determination of a di-Zn(II) complex of "due-ferri-1" (DF1), a protein patterned after the diiron-dimanganese class of redox-active proteins [Lombardi, A.; Summa, C.; Geremia, S.; Randaccio, L.; Pavone, V.; DeGrado, W. F. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 6298-6305]. The overall structure of DF1, which contains a carboxylate-bridged dinuclear metal site, agrees well with the intended design. However, access to this dimetal site is blocked by a pair of hydrophobic leucine residues (L13 and L13'), which prevent facile entry of metal ions and small molecules. We have now taken the next step in the eventual construction of a catalytically active metalloenzyme by engineering an active site cavity into DF1 through the replacement of these two leucine residues with smaller residues. The crystal structure of the dimanganous form of L13A-DF1 indeed shows a substrate access channel to the dimetal center. In the crystal structure, water molecules and a ligating dimethyl sulfoxide molecule, which forms a monatomic bridge between the metal ions, occupy the cavity. Furthermore, the diferric form of a derivative of L13A-DF1, DF2, is shown to bind azide, acetate, and small aromatic molecules.