Emergence of life:Physical chemistry changes the paradigm

Origin of life research has been slow to advance not only because of its complex evolutionary nature (Franklin Harold: In Search of Cell History, 2014) but also because of the lack of agreement on fundamental concepts, including the question of 'what is life?'. To re-energize the research and define a new experimental paradigm, we advance four premises to better understand the physicochemical complexities of life's emergence: (1) Chemical and Darwinian (biological) evolutions are distinct, but become continuous with the appearance of heredity. (2) Earth's chemical evolution is driven by energies of cycling (diurnal) disequilibria and by energies of hydrothermal vents. (3) Earth's overall chemical complexity must be high at the origin of life for a subset of (complex) chemicals to phase separate and evolve into living states. (4) Macromolecular crowding in aqueous electrolytes under confined conditions enables evolution of molecular recognition and cellular self-organization. We discuss these premises in relation to current 'constructive' (non-evolutionary) paradigm of origins research - the process of complexification of chemical matter 'from the simple to the complex'. This paradigm artificially avoids planetary chemical complexity and the natural tendency of molecular compositions toward maximum disorder embodied in the second law of thermodynamics. Our four premises suggest an empirical program of experiments involving complex chemical compositions under cycling gradients of temperature, water activity and electromagnetic radiation.</p

Smartness, culture and local authority ICT awareness: an empirical enquiry for a province in Poland

The paper reports on a sequence of analyses of the local self-governmental authority website-related features in conjunction with the socio-economic characteristics of the respective administrative units (counties and municipalities). These analyses had two objectives: (a) assessment of the local authority websites, their content and functionality, also in a dynamic perspective, and (b) inquiry into the potential interrelations between the specific features of the websites and the nature of the local unit, with special emphasis on the local development in the rural areas and its forward path. The study has been carried out for the capital province of Mazowsze in Poland, but some hints as to a quasi-comparative international study are also provided. First of all, substantial progress between 2003 and 2008 in the quality of the local authority websites is shown. Further, the conclusions from the study imply a rather loose connection between the characteristics of these websites and the socio-economic profile of the unit, including the characterisation along the urban-rural dimension. At the same time, though, an important role becomes apparent, played by the broadly conceived local culture, including the ‘smartness’ aspect, as perceived by the present authors. This role of culture and ‘smartness’ is visible in the very clear divergences from the general regularities observed, and is partly also associated with the socio-economic function of the respective local unit, as distinguished from the, say, income and education level characteristics of the local population

The Cellular Environment Stabilizes Adenine Riboswitch RNA Structure

There are large differences between the intracellular environment and the conditions widely used to study RNA structure and function in vitro. To assess the effects of the crowded cellular environment on RNA, we examined the structure and ligand-binding function of the adenine riboswitch aptamer domain in healthy, growing Escherichia coli cells at single-nucleotide resolution on the minute timescale using SHAPE. The ligand-bound aptamer structure is essentially the same in cells and in buffer at 1 mM Mg2+, the approximate Mg2+ concentration we measured in cells. In contrast, the in-cell conformation of the ligand-free aptamer is much more similar to the fully folded ligand-bound state. Even adding high Mg2+ concentrations to the buffer used for in vitro analyses did not yield the conformation observed for the free aptamer in cells. The cellular environment thus stabilizes the aptamer significantly more than does Mg2+ alone. Our results show that the intracellular environment has a large effect on RNA structure that ultimately favors highly organized conformations

Disordered proteins mitigate the temperature dependence of site-specific binding free energies

Biophysical characterization of protein-protein interactions involving disordered proteins is challenging. A common simplification is to measure the thermodynamics and kinetics of disordered site binding using peptides containing only the minimum residues necessary. We should not assume, however, that these few residues tell the whole story. Son of sevenless (Sos), a multidomain signaling protein from Drosophila melanogaster, is critical to the mitogen-activated protein kinase pathway, passing an external signal to Ras, which leads to cellular responses. The disordered 55 kDa C-terminal domain of Sos is an auto-inhibitor that blocks guanidine exchange factor activity. Activation requires another protein, Downstream of receptor kinase (Drk), which contains two Src homology 3 (SH3) domains. Here, we utilize nuclear magnetic resonance spectroscopy and isothermal titration calorimetry to quantify the thermodynamics and kinetics of the N-terminal SH3 domain binding to the strongest sites incorporated into the flanking disordered sequences. Comparing these results to those for isolated peptides provides information about how the larger domain affects binding. The affinities of sites on the disordered domain are like those of the peptides at low temperatures but less sensitive to temperature. Our results, combined with observations showing that IDPs become more compact with increasing temperature, suggest a mechanism for this effect

Second-Order Nonlinear Optical Properties of Multiaddressable Indolinooxazolidine Derivatives: Joint Computational and Hyper-Rayleigh Scattering Investigations

The linear and nonlinear optical (NLO) properties of two indolinooxazolidine derivatives acting as multiaddressable switches are reported. The second-order hyperpolarizability contrasts upon commutation between their closed and open forms are characterized using hyper-Rayleigh scattering (HRS) measurements, and rationalized by means of density functional theory and post Hartree–Fock ab initio calculations. It is evidenced that the addition of a withdrawing substituent on the indolinic subunit leads to a more effective photoinduced charge transfer while decreasing the transition energy of the S0 → S1 transition, which induces a significant enhancement of the HRS response of the open form. This substitution is however detrimental to the NLO contrast, due to the concomitant increase of the HRS response of the closed form

An osmolyte mitigates the destabilizing effect of protein crowding: Crowding & Osmolytes

Most theories predict that macromolecular crowding stabilizes globular proteins, but recent studies show that weak attractive interactions can result in crowding-induced destabilization. Osmolytes are ubiquitous in biology and help protect cells against stress. Given that dehydration stress adds to the crowded nature of the cytoplasm, we speculated that cells might use osmolytes to overcome the destabilization caused by the increased weak interactions that accompany desiccation. We used NMR-detected amide proton exchange experiments to measure the stability of the test protein chymotrypsin inhibitor 2 under physiologically relevant crowded conditions in the presence and absence of the osmolyte glycine betaine. The osmolyte overcame the destabilizing effect of the cytosol. This result provides a physiologically relevant explanation for the accumulation of osmolytes by dehydration-stressed cells

An upper limit for macromolecular crowding effects

<p>Abstract</p> <p>Background</p> <p>Solutions containing high macromolecule concentrations are predicted to affect a number of protein properties compared to those properties in dilute solution. In cells, these macromolecular crowders have a large range of sizes and can occupy 30% or more of the available volume. We chose to study the stability and ps-ns internal dynamics of a globular protein whose radius is ~2 nm when crowded by a synthetic microgel composed of poly(<it>N</it>-isopropylacrylamide-<it>co</it>-acrylic acid) with particle radii of ~300 nm.</p> <p>Results</p> <p>Our studies revealed no change in protein rotational or ps-ns backbone dynamics and only mild (~0.5 kcal/mol at 37°C, pH 5.4) stabilization at a volume occupancy of 70%, which approaches the occupancy of closely packing spheres. The lack of change in rotational dynamics indicates the absence of strong crowder-protein interactions.</p> <p>Conclusions</p> <p>Our observations are explained by the large size discrepancy between the protein and crowders and by the internal structure of the microgels, which provide interstitial spaces and internal pores where the protein can exist in a dilute solution-like environment. In summary, microgels that interact weakly with proteins do not strongly influence protein dynamics or stability because these large microgels constitute an upper size limit on crowding effects.</p