A segment of cold shock protein directs the folding of a combinatorial protein

It has been suggested that protein domains evolved by the non-homologous recombination of building blocks of subdomain size. In earlier work we attempted to recapitulate domain evolution in vitro. We took a polypeptide segment comprising three beta-strands in the monomeric, five-stranded beta-barrel cold shock protein (CspA) of Escherichia coli as a building block. This segment corresponds to a complete exon in homologous eukaryotic proteins and includes residues that nucleate folding in CspA. We recombined this segment at random with fragments of natural proteins and succeeded in generating a range of folded chimaeric proteins. We now present the crystal structure of one such combinatorial protein, 1b11, a 103-residue polypeptide that includes segments from CspA and the S1 domain of the 30S ribosomal subunit of E. coli. The structure reveals a segment-swapped, six-stranded beta-barrel of unique architecture that assembles to a tetramer. Surprisingly, the CspA segment retains its structural identity in 1b11, recapitulating its original fold and deforming the structure of the S1 segment as necessary to complete a barrel. Our work provides structural evidence that (i) random shuffling of nonhomologous polypeptide segments can lead to folded proteins and unique architectures, (ii) many structural features of the segments are retained, and (iii) some segments can act as templates around which the rest of the protein folds.     

The metabolic effects of sodium dichloroacetate in the suckling newborn rat

Summary Subcutaneous injection of sodium dichloroacetate (1 mg/g body wt every 3 h) in suckling newborn rats caused in 6 h a fall of 2.5 mmol/l in blood glucose concentrations, and a rise of 2.4 mmol/ l in total blood ketone body levels, but no change in the high levels of plasma non esterified fatty acids. Glucose utilization, measured after intraperitoneal injection of D-glucose (2 mg/g body wt), was not increased in newborns injected with dichloroacetate. The hypoglycaemia resulted from a decrease in gluconeogenic rate, secondarily to a lowering effect of dichloroacetate on blood levels of lactate, pyruvate and alanine. The hypoglycaemia induced by dichloroacetate was completely reversed by injecting newborn rats with a mixture of gluconeogenic precursors (lactate, pyruvate and alanine). It is concluded that the high rate of gluconeogenesis observed in suckling newborn rats in sustained by an increased release of lactate and, to a much smaller extent of pyruvate and alanine, by peripheral tissues. This probably resulted from the low pyruvate dehydrogenase activity found in peripheral tissues of the newborn rat. The hyperketonaemia induced by dichloroacetate could result from an increased ketogenesis and/or a decreased ketone body utilization.     

Clathrin light chains function in mannose phosphate receptor trafficking via regulation of actin assembly

Clathrin-coated vesicles (CCVs) are major carriers for endocytic cargo and mediate important intracellular trafficking events at the trans-Golgi network (TGN) and endosomes. Whereas clathrin heavy chain provides the structural backbone of the clathrin coat, the role of clathrin light chains (CLCs) is poorly understood. We now demonstrate that CLCs are not required for clathrin-mediated endocytosis but are critical for clathrin-mediated trafficking between the TGN and the endosomal system. Specifically, CLC knockdown (KD) causes the cation-independent mannose-6 phosphate receptor (CI-MPR) to cluster near the TGN leading to a delay in processing of the lysosomal hydrolase cathepsin D. A recently identified binding partner for CLCs is huntingtin-interacting protein 1-related (HIP1R), which is required for productive interactions of CCVs with the actin cytoskeleton. CLC KD causes mislocalization of HIP1R and overassembly of actin, which accumulates in patches around the clustered CI-MPR. A dominant-negative CLC construct that disrupts HIP1R/CLC interactions causes similar alterations in CI-MPR trafficking and actin assembly. Thus, in mammalian cells CLCs function in intracellular membrane trafficking by acting as recruitment proteins for HIP1R, enabling HIP1R to regulate actin assembly on clathrin-coated structures.     

(Finite) statistical size effects on compressive strength

The larger structures are, the lower their mechanical strength. Already discussed by Leonardo da Vinci and Edmé Mariotte several centuries ago, size effects on strength remain of crucial importance in modern engineering for the elaboration of safety regulations in structural design or the extrapolation of laboratory results to geophysical field scales. Under tensile loading, statistical size effects are traditionally modeled with a weakest-link approach. One of its prominent results is a prediction of vanishing strength at large scales that can be quantified in the framework of extreme value statistics. Despite a frequent use outside its range of validity, this approach remains the dominant tool in the field of statistical size effects. Here we focus on compressive failure, which concerns a wide range of geophysical and geotechnical situations. We show on historical and recent experimental data that weakest-link predictions are not obeyed. In particular, the mechanical strength saturates at a nonzero value toward large scales. Accounting explicitly for the elastic interactions between defects during the damage process, we build a formal analogy of compressive failure with the depinning transition of an elastic manifold. This critical transition interpretation naturally entails finite-size scaling laws for the mean strength and its associated variability. Theoretical predictions are in remarkable agreement with measurements reported for various materials such as rocks, ice, coal, or concrete. This formalism, which can also be extended to the flowing instability of granular media under multiaxial compression, has important practical consequences for future design rules.Owing to its importance for structural design (1), the elaboration of safety regulations (2), or the extrapolation of laboratory results to geophysical field scales (3), the size effects on strength of materials are one of the oldest problems in engineering, already discussed by Leonardo da Vinci and Edmé Mariotte (4) several centuries ago, but still an active field of research (5, 6). As early as 1686, Mariotte (4) qualitatively introduced the weakest-link concept to account for size effects on mechanical strength, a phenomenon evidenced by Leonardo da Vinci almost two centuries earlier. This idea, which states that the larger the system considered is, the larger the probability to find a particularly faulty place that will be at the origin of global failure, was formalized much later by Weibull (7). Considering a chain of elementary independent links, the failure of the chain is obtained as soon as one link happens to break. By virtue of the independence between the potential breaking events, the survival probability of a chain of N links is obtained by the simple multiplication of the N elementary probabilities. Depending on the properties of the latter, the global survival probability converges toward one of the three limit distributions identified by Weibull (7), Gumbel (8), and Fréchet (8), respectively. Together with Fisher and Tippett (9), these authors pioneered the field of extreme value statistics.This purely statistical argument, undoubtedly valid in 1D, was extended by Weibull (7, 10) to account for the risk of failure of 3D samples or structures. Besides the hypothesis of independence, it thus requires an additional hypothesis of brittleness: The nucleation of any elementary crack at the microscopic scale from a preexisting flaw is assumed to immediately induce the failure at the macroscale. More specifically, following linear elastic fracture mechanics (LEFM) stating that crack initiation from a flaw of size s occurs at a stress , one gets a probability of failure of a system of size L under an applied stress σ, , that depends on the distribution of preexisting defect sizes. Assuming a power law tail for this distribution, Weibull statistics are expected(7), , whereas Gumbel statistics are expected for any distribution of defect sizes whose the tail falls faster than that of a power law (8, 11, 12), , where m is the so-called Weibull’s modulus, d is the topological dimension, and L₀ and σ_u are normalizing constants. For Weibull statistics, the mean strength and the associated SD δ(σ_f) then scale with sample size L as . This approach has been successfully applied to the statistics of brittle failure strength under tension (7, 13), with m in the range 6–30 (14). It implies a vanishing strength for L → +∞, although this decrease can be rather shallow, owing to the large values of m often reported.Although relying on strong hypotheses, this weakest-link statistical approach was almost systematically invoked until the 1970s to account for size effects on strength whatever the material and/or the loading conditions. However, as shown by Bazant (1, 5), in many situations the hypothesis of brittleness is not obeyed. This is in particular the case when the size of the fracture process zone (FPZ) becomes nonnegligible with respect to the system size. In this so-called quasi-brittle case, an energetic, nonstatistical size effect applies (15), which has been shown to account for a large variety of situations (5). Toward large scales, i.e., L → +∞, the FPZ becomes negligible compared with L, and the hypothesis of brittleness should therefore be recovered and statistical size effects should dominate. Statistical numerical models of fracture of heterogeneous media also revealed deviations from the extreme value statistics predictions (16) but, as stated by Alava et al. (ref. 11, p. 9), “the role of damage accumulation for fracture size effects in unnotched samples still remains unclear.” As shown below, compressive failure results from such progressive damage accumulation.In what follows, we do not consider (deterministic) energetic size effects and explore a situation, compressive failure, where both the hypotheses of brittleness (in the sense given above) and independence are not fulfilled, up to very large scales. Relaxing these initial hypotheses of the weakest-link theory, our statistical physics approach remains statistical by nature and relies on the interplay between internal disorder and stress redistributions. It is based on a mapping of brittle compressive failure onto the critical depinning transition of an elastic manifold, a class of models widely used in nonequilibrium statistical physics characterized by a dynamic phase transition (17). This approach does not consider a sample’s shape effects (18), only statistical size effects. The critical scaling laws associated to this phase transition naturally predict a saturation of the compressive strength at a large scale and are in remarkable agreement with measurements reported for various materials such as rocks, ice, coal, or concrete.