Structural enzymology studies with the substrate 3S-hydroxybutanoyl-CoA: bifunctional MFE1 is a less efficient dehydrogenase than monofunctional HAD

Multifunctional enzyme, type-1 (MFE1) catalyzes the second and third step of the β-oxidation cycle, being, respectively, the 2E-enoyl-CoA hydratase (ECH) reaction (N-terminal part, crotonase fold) and the NAD+-dependent, 3S-hydroxyacyl-CoA dehydrogenase (HAD) reaction (C-terminal part, HAD fold). Structural enzymological properties of rat MFE1 (RnMFE1) as well as of two of its variants, namely the E123A variant (a glutamate of the ECH active site is mutated into alanine) and the BCDE variant (without domain A of the ECH part), were studied, using as substrate 3S-hydroxybutanoyl-CoA. Protein crystallographic binding studies show the hydrogen bond interactions of 3S-hydroxybutanoyl-CoA as well as of its 3-keto, oxidized form, acetoacetyl-CoA, with the catalytic glutamates in the ECH active site. Pre-steady state binding experiments with NAD+ and NADH show that the kon and koff rate constants of the HAD active site of monomeric RnMFE1 and the homologous human, dimeric 3S-hydroxyacyl-CoA dehydrogenase (HsHAD) for NAD+ and NADH are very similar, being the same as those observed for the E123A and BCDE variants. However, steady state and pre-steady state kinetic data concerning the HAD-catalyzed dehydrogenation reaction of the substrate 3S-hydroxybutanoyl-CoA show that, respectively, the kcat and kchem rate constants for conversion into acetoacetyl-CoA by RnMFE1 (and its two variants) are about 10 fold lower as when catalyzed by HsHAD. The dynamical properties of dehydrogenases are known to be important for their catalytic efficiency, and it is discussed that the greater complexity of the RnMFE1 fold correlates with the observation that RnMFE1 is a slower dehydrogenase than HsHAD.

Numerical Modeling of the Dynamic Elastic Modulus of Concrete

This article introduces simulations of theoretical material with controlled properties for the evaluation of the effect of key parameters, as volumetric fractions, elastic properties of each phase and transition zone on the effective dynamic elastic modulus. The accuracy level of classical homogenization models was checked regarding the prediction of dynamic elastic modulus. Numerical simulations were performed with the finite element method for evaluations of the natural frequencies and their correlation with E_d through frequency equations. An acoustic test validated the numerical results and obtained the elastic modulus of concretes and mortars at 0.3, 0.5 and 0.7 water-cement ratios. Hirsch calibrated according to the numerical simulation (x = 0.27) exhibited a realistic behavior for concretes of w/c = 0.3 and 0.5, with a 5% error. However, when the water-to-cement ratio (w/c) was set to 0.7, Young's modulus displayed a resemblance to the Reuss model, akin to the simulated theoretical triphasic materials, considering matrix, coarse aggregate and a transition zone. Hashin-Shtrikman bounds is not perfectly applied to theoretical biphasic materials under dynamic situations.

Bow-tie architecture of gene regulatory networks in species of varying complexity

The gene regulatory network (GRN) architecture plays a key role in explaining the biological differences between species. We aim to understand species differences in terms of some universally present dynamical properties of their gene regulatory systems. A network architectural feature associated with controlling system-level dynamical properties is the bow-tie, identified by a strongly connected subnetwork, the core layer, between two sets of nodes, the in and the out layers. Though a bow-tie architecture has been observed in many networks, its existence has not been extensively investigated in GRNs of species of widely varying biological complexity. We analyse publicly available GRNs of several well-studied species from prokaryotes to unicellular eukaryotes to multicellular organisms. In their GRNs, we find the existence of a bow-tie architecture with a distinct largest strongly connected core layer. We show that the bow-tie architecture is a characteristic feature of GRNs. We observe an increasing trend in the relative core size with species complexity. Using studied relationships of the core size with dynamical properties like robustness and fragility, flexibility, criticality, controllability and evolvability, we hypothesize how these regulatory system properties have emerged differently with biological complexity, based on the observed differences of the GRN bow-tie architectures.