How enzyme economy shapes metabolic fluxes

Metabolic fluxes are governed by physical and economic principles. Stationarity constrains them to a subspace in flux space and thermodynamics makes them lead from higher to lower chemical potentials. At the same time, fluxes in cells represent a compromise between metabolic performance and enzyme cost. To capture this, some flux prediction methods penalise larger fluxes by heuristic cost terms. Economic flux analysis, in contrast, postulates a balance between enzyme costs and metabolic benefits as a necessary condition for fluxes to be realised by kinetic models with optimal enzyme levels. The constraints are formulated using economic potentials, state variables that capture the enzyme labour embodied in metabolites. Generally, fluxes must lead from lower to higher economic potentials. This principle, which resembles thermodynamic constraints, can complement stationarity and thermodynamic constraints in flux analysis. Futile modes, which would be incompatible with economic potentials, are defined algebraically and can be systematically removed from flux distributions. Enzymes that participate in potential futile modes are likely targets of regulation. Economic flux analysis can predict high-yield and low-yield strategies, and captures preemptive expression, multi-objective optimisation, and flux distributions across several cells living in symbiosis. Inspired by labour value theories in economics, it justifies and extends the principle of minimal fluxes and provides an intuitive framework to model the complex interplay of fluxes, metabolic control, and enzyme costs in cells

Bifurcation gaps in asymmetric and high-dimensional hypercycles

Hypercycles are catalytic systems with cyclic architecture. These systems have been suggested to play a key role in the maintenance and increase of information in prebiotic replicators. It is known that for a large enough number of hypercycle species (n>4 the coexistence of all hypercycle members is governed by a stable periodic orbit. Previous research has characterized saddle-node (s-n) bifurcations involving abrupt transitions from stable hypercycles to extinction of all hypercycle members, or, alternatively, involving the outcompetition of the hypercycle by so-called mutant sequences or parasites. Recently, the presence of a bifurcation gap between a s-n bifurcation of periodic orbits and a s-n of fixed points has been described for symmetric five-member hypercycles. This gap was found between the value of the replication quality factor Q from which the periodic orbit vanishes (QPO)and the value where two unstable (nonzero) equilibrium points collide (QSS). Here, we explore the persistence of this gap considering asymmetries in replication rates in five-member hypercycles as well as considering symmetric, larger hypercycles. Our results indicate that both the asymmetry in Malthusian replication constants and the increase in hypercycle members enlarge the size of this gap. The implications of this phenomenon are discussed in the context of delayed transitions associated to the so-called saddle remnants. Read More: https://www.worldscientific.com/doi/abs/10.1142/S021812741830001X Read More: https://www.worldscientific.com/doi/abs/10.1142/S021812741830001XPeer ReviewedPreprin

LAURA Users Manual: 5.6

This users manual provides in-depth information concerning installation and execution of Laura, version 5. Laura is a structured, multiblock, computational aerothermodynamic simulation code. Version 5 represents a major refactoring of the original Fortran 77 Laura code toward a modular structure afforded by Fortran 95. The refactoring improved usability and maintainability by eliminating the requirement for problem-dependent recompilations, providing more intuitive distribution of functionality, and simplifying inter- faces required for multi-physics coupling. As a result, Laura now shares gas-physics modules, MPI modules, and other low-level modules with the Fun3D unstructured-grid code. In addition to internal refactoring, several new features and capabilities have been added, e.g., a GNU-standard installation process, parallel load balancing, automatic trajectory point sequencing, free-energy minimization, and coupled ablation and flow field radiation

In silico prediction of mutant HIV-1 proteases cleaving a target sequence

HIV-1 protease represents an appealing system for directed enzyme re-design, since it has various different endogenous targets, a relatively simple structure and it is well studied. Recently Chaudhury and Gray (Structure (2009) 17: 1636 -- 1648) published a computational algorithm to discern the specificity determining residues of HIV-1 protease. In this paper we present two computational tools aimed at re-designing HIV-1 protease, derived from the algorithm of Chaudhuri and Gray. First, we present an energy-only based methodology to discriminate cleavable and non cleavable peptides for HIV-1 proteases, both wild type and mutant. Secondly, we show an algorithm we developed to predict mutant HIV-1 proteases capable of cleaving a new target substrate peptide, different from the natural targets of HIV-1 protease. The obtained in silico mutant enzymes were analyzed in terms of cleavability and specificity towards the target peptide using the energy-only methodology. We found two mutant proteases as best candidates for specificity and cleavability towards the target sequence

Accelerated X-ray Structure Elucidation of a 36 kDa Muramidase/Transglycosylase Using wARP

The X-ray structure of the 36kDa soluble lytic transglycosylase from Escherichia coli has been determined starting with the multiple isomorphous replacement method with inclusion of anomalous scattering at 2.7 Å resolution. Subsequently, before any model building was carried out, phases were extended to 1.7 Å, resolution with the weighted automated refinement procedure wARP, which gave a dramatic improvement in the phases. The electron-density maps from wARP were of outstanding quality for both the main chain and the side chains of the protein, which allowed the time spent on the tracing, interpretation and building of the X-ray structure to be substantially shortened. The structure of the soluble lyric transglycosylase was refined at 1.7 Å, resolution with X-PLOR to a final crystallographic R factor of 18.9%. Analysis of the wARP procedure revealed that the use of the maximum-likelihood refinement in wARP gave much better phases than least-squares refinement, provided that the ratio of reflections to protein atom parameters was approximately 1.8 or higher. Furthermore, setting aside 5% of the data for an Rfree test set had a negative effect on the phase improvement. The mean WwARP, a weight determined at the end of the wARP procedure and based on the variance of structure factors from six individually refined wARP models, proved to be a better indicator than the Rfree factor to judge different phase improvement protocols. The elongated Slt35 structure has three domains named the alpha, beta and core domains. The alpha domain contains mainly α-helices, while the beta domain consists of a five-stranded antiparallel β-sheet flanked by a short α-helix. Sandwiched between the alpha and beta domains is the core domain, which bears some resemblance to the fold of the catalytic domain of the previously elucidated 70 kDa soluble lytic transglycosylase from E. coli. The putative active site is at the bottom of a large deep groove in the core domain.

High-Latitude Communications Satellite (HILACS)

The Naval Postgraduate School in the AE 4871 Advanced Spacecraft Design course designed a communications satellite (HILACS) that will provide a continuous UHF communications link between stations located north of the region covered by geosynchronous communications satellites. The communications payload will operate only for that portion of the orbit necessary to provide specific coverage. The satellite orbit is elliptic with perigee at 1204 km in the Southern Hemisphere and an apogee at 14,930 km with 63.4 degrees inclination. Analysis and design of each of the subsystems was done to the extent possible within the constraints of an eleven week quarter and the design and analysis tools available. Work was completed in orbital analysis, the reaction control system, attitude control subsystem, electric power subsystem, telemetry, tracking, and control, thermal control subsystem, and the structures subsystem. The design team consisted of 12 students. Additional support was provided by the Jet Propulsion Laboratory and the Naval Research Laboratory

Steady state and (bi-) stability evaluation of simple protease signalling networks

Signal transduction networks are complex, as are their mathematical models. Gaining a deeper understanding requires a system analysis. Important aspects are the number, location and stability of steady states. In particular, bistability has been recognised as an important feature to achieve molecular switching. This paper compares different model structures and analysis methods particularly useful for bistability analysis. The biological applications include proteolytic cascades as, for example, encountered in the apoptotic signalling pathway or in the blood clotting system. We compare three model structures containing zero-order, inhibitor and cooperative ultrasensitive reactions, all known to achieve bistability. The combination of phase plane and bifurcation analysis provides an illustrative and comprehensive understanding of how bistability can be achieved and indicates how robust this behaviour is. Experimentally, some so-called “inactive” components were shown to have a residual activity. This has been mostly ignored in mathematical models. Our analysis reveals that bistability is only mildly affected in the case of zero-order or inhibitor ultrasensitivity. However, the case where bistability is achieved by cooperative ultrasensitivity is severely affected by this perturbation

From bench scale to pilot plant: A 150x scaled-up configuration of a microwave-driven structured reactor for methane dehydroaromatization

Microwave-assisted gas-phase conversion on structured catalysts is emerging as a promising process intensifi-cation technology in the field of heterogeneous catalysis. The combination of selective heating and structured catalytic materials induces a temperature difference between the heated catalytic sample and the surrounding void regions to avoid non-selective gas-phase reactions. This operational principle allowed inhibiting thermal cracking in alkane dehydrogenation processes as well as retarding catalyst deactivation by coking in methane dehydroaromatization (MDA) processes. However, its effectiveness has not been reported so far out of the lab-oratory scale conditions. This work addresses the scaling of the microwave-assisted MDA process from lab scale experiments to a scaled-up configuration capable of stable operation with a 150-fold higher feeding rate. The scaling-up potential and main obstacles to overcome for this technology are critically discussed. In addition, a techno-economic assessment of the MW-MDA process is presented. The catalytic activity was kept for seven consecutive reaction cycles, i.e. 35 h MW-MDA, prior to a progressive decay due to permanent deactivation caused by zeolite dealumination and active metal loss. The scaled set-up operated for up to 295 consecutive hours under unmanned operation conducting 4 -h MDA-regeneration cycles on Mo/ZSM-5@SiC monoliths and resulting in 125-fold increase of converted methane and a 450-fold increase of benzene (0.17 LC6H6/h) in comparison with the laboratory scale tests. Scaled set-up experiments were run using only a 6-fold microwave input power, thus, highlighting the non-linearity between energy consumption and scaling factor for this tech-nology and the importance of microwave cavity design

An assembly oriented design framework for product structure engineering and assembly sequence planning

The paper describes a novel framework for an assembly-oriented design (AOD) approach as a new functional product lifecycle management (PLM) strategy, by considering product design and assembly sequence planning phases concurrently. Integration issues of product life cycle into the product development process have received much attention over the last two decades, especially at the detailed design stage. The main objective of the research is to define assembly sequence into preliminary design stages by introducing and applying assembly process knowledge in order to provide an assembly context knowledge to support life-oriented product development process, particularly for product structuring. The proposed framework highlights a novel algorithm based on a mathematical model integrating boundary conditions related to DFA rules, engineering decisions for assembly sequence and the product structure definition. This framework has been implemented in a new system called PEGASUS considered as an AOD module for a PLM system. A case study of applying the framework to a catalytic-converter and diesel particulate filter sub-system, belonging to an exhaust system from an industrial automotive supplier, is introduced to illustrate the efficiency of the proposed AOD methodology