Maria J. Schilstra

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

BioModels Database (), part of the international initiative BioModels.net, provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems. Each model is carefully curated to verify that it corresponds to the reference publication and gives the proper numerical results. Curators also annotate the components of the models with terms from controlled vocabularies and links to other relevant data resources. This allows the users to search accurately for the models they need. The models can currently be retrieved in the SBML format, and import/export facilities are being developed to extend the spectrum of formats supported by the resource.

Circular Dichroism and Its Application to the Study of Biomolecules

Circular dichroism (CD) is an excellent method for the study of the conformations adopted by proteins and nucleic acids in solution. Although not able to provide the beautifully detailed residue-specific information available from nuclearmagnetic resonance (NMR) and X-ray crystallography, CD measurements have two major advantages: they can be made on small amounts of material in physiological buffers and they provide one of the best methods for monitoring any structural alterations that might result from changes in environmental conditions, such as pH, temperature, and ionic strength. This chapter describes the important basic steps involved in obtaining reliable CD spectra: careful instrument and sample preparation, the selection of appropriate parameters for data collection, and methods for subsequent data processing. The principal features of protein and nucleic acid CD spectra are then described, and the main applications of CD are discussed. These include: methods for analyzing CD data to estimate the secondary structure composition of proteins, methods for following the unfolding of proteins as a function of temperature or added chemical denaturants, the study of the effects of mutations on protein structure and stability, and methods for studying macromolecule-ligand and macromolecule-macromolecule interactions.

A Lateral Cap model of microtubule dynamic instability

The co‐existence and interconversion of growing and shrinking microtubules have been termed ‘dynamic instability’, and have been directly observed to occur under a variety of conditions in vitro and in vivo. Previous modelling was based on the concept of an extensive, fluctuating cap of tubulin‐GTP to stabilise growing microtubules. A quantitative kinetic model is now presented in which only the terminal layer of the multi‐start helical microtubule lattice contains tubulin‐GTP molecules, comprising a ‘Lateral Cap’. In Monte Carlo numerical simulation, this model readily reproduces the decisive experimental evidence of microtubule dynamics, and predicts a co‐operative mechanism for microtubule transitions. The model also suggests how differing kinetic properties at opposite ends are the result of the intrinsic polarity of the microtubule lattice, reflecting the polarity of the tubutin α/β heterodimer.

CellML2SBML: conversion of CellML into SBML

UNLABELLED CellML and SBML are XML-based languages for storage and exchange of molecular biological and physiological reaction models. They use very similar subsets of MathML to specify the mathematical aspects of the models. CellML2SBML is implemented as a suite of XSLT stylesheets that, when applied consecutively, convert models expressed in CellML into SBML without significant loss of information. The converter is based on the most recent stable versions of the languages (CellML version 1.1; SBML Level 2 Version 1), and the XSLT used in the stylesheets adheres to the XSLT version 1.0 specification. Of all 306 models in the CellML repository in April 2005, CellML2SBML converted 91% automatically into SBML. Minor manual changes to the unit definitions in the originals raised the percentage of successful conversions to 96%. AVAILABILITY http://sbml.org/software/cellml2sbml/. SUPPLEMENTARY INFORMATION Instructions for use and further documentation available on http://sbml.org/software/cellml2sbml/

Bio-logic: Gene expression and the laws of combinatorial logic

At the heart of the development of fertilized eggs into fully formed organisms and the adaptation of cells to changed conditions are genetic regulatory networks (GRNs). In higher multicellular organisms, signal selection and multiplexing are performed at the cis-regulatory domains of genes, where combinations of transcription factors (TFs) regulate the rates at which the genes are transcribed into mRNA. To be able to act as activators or repressors of gene transcription, TFs must first bind to target sequences on the regulatory domains. Two TFs that act in concert may bind entirely independently of each other, but more often binding of the first one will alter the affinity of the other for its binding site. This article presents a systematic investigation into the effect of TF binding dependences on the predicted regulatory function of this bio-logic. Four extreme scenarios, commonly used to classify enzyme activation and inhibition patterns, for the binding of two TFs were explored: independent (the TFs bind without affecting each others affinities), competitive (the TFs compete for the same binding site), ordered (the TFs bind in a compulsory order), and joint binding (the TFs either bind as a preformed complex, or binding of one is virtually impossible in the absence of the other). The conclusions are: (1) the laws of combinatorial logic hold only for systems with independently binding TFs; (2) systems formed according to the other scenarios can mimic the functions of their Boolean logical counterparts, but cannot be combined or decomposed in the same way; and (3) the continuously scaled output of systems consisting of competitively binding activators and repressors can be controlled more robustly than that of single TF or (quasi-)logical multi-TF systems.

An elastically tethered viscous load imposes a regular gait on the motion of myosin-V. Simulation of the effect of transient force relaxation on a stochastic process

Myosin-V is a processive molecular motor that moves membrane vesicles along actin tracks. In the simple model for motor and cargo motion investigated here, an elastic connection between motor and cargo transiently absorbs the abrupt mechanical transitions of the motor, and allows smooth relaxation of the cargo to a new position. We use a stochastic description to model motor stepping, with kinetics that depends on the instantaneous force exerted on the motor through the elastic connection. Tether relaxation is modelled as a continuous process, in which the rate is determined by the viscous drag of the cargo and the stiffness profile of the connection. Quantitative combined stochastic–continuous simulation of the dynamics of this system shows that bulky loads can impose a highly regular gait on the motor. If the characteristics of the elastic connection are similar to those of the myosin-II coiled-coil domain, the myosin-V motor, tether and cargo form a true escapement, in which the motor only escapes from its current position after one or more force thresholds have been crossed. Multiple thresholds limit the variation in tether length to values below that of the total step size.

Effect of Nonionic Detergents on Lipoxygenase Catalysis

In many studies on lipoxygenase catalysis, nonionic detergents are used to obtain an optically transparent solution of the fatty acid substrate. In order to resolve some controversies that exist with regard to the interpretation of kinetic data obtained with solutions containing nonionic detergents, a systematic investigation was undertaken into the effects of Lubrol, Tween-20 and Triton X-100 (0–0.8 g/L) on the kinetics of linoleate (2.5–110 μM) dioxygenation, catalyzed by lipoxygenase-1 or lipoxygenase-2 from soybean, at pH 9 or 10, at 25°C. Under most conditions, it was found that the detergents slowed down the reaction. However, at high linoleate concentrations, where substrate inhibition of lipoxygenase is significant, small amounts of detergent increased the dioxygenation rate. In a quantitative analysis of the results, a kinetic model in which the incorporation of linoleate in the detergent micelles is formulated as a simple reversible equilibrium, and in which both lipoxygenase-1 and-2 interact with free linoleate, but not with linoleate incorporated in the micelles, appeared to be sufficient to predict experimental results over a wide range of experimental conditions. According to this model, the changes in the dioxygenation kinetics caused by the presence of nonionic detergents are similar (but not equal) to those caused by competitive inhibitors. The conclusions that monomeric, nonmicellar linoleate is the preferred substrate for lipoxygenase and that the observed inhibition and stimulation are solely due to changes in the effective linoleate concentration strongly corroborate the earlier observations by Galpin and Allen [Biochim. Biophys. Acta 488 (1977), 392–401].

Immunocytochemical localization of the elongation factor Tu in E. coli cells.

The localization of the elongation factor Tu (EF‐Tu) in ultrathin cryosections of E. coli cells was determined with the electron microscope using a highly specific immunological labellin technique. EF‐Tu is distributed almost homogeneously throughout the cytoplasm. Although it has often been suggested that EF‐Tu could be part of a putative prokaryotic cytoskeleton, we did not find any evidence for supramolecular assemblies, such as fibres or filaments, containing a large amount of EF‐Tu. EF‐Tu was not observed in association with the outer cell membrane and periplasmic space. A topological relationship with the inner membrane is not apparent in our micrographs. In cells in which the EF‐Tu level is raised significantly, the protein piles up in discrete cell regions.

An electron microscopic investigation of the structure of Alfalfa mosaic virus

Original article can be found at: http://www.sciencedirect.com/science/journal/00222836 Copyright Elsevier Ltd. DOI: 10.1016/0022-2836(81)90544-1 [Full text of this article is not available in the UHRA]

Genetic regulatory network models of biological clocks: Evolutionary history matters

We study the evolvability and dynamics of artificial genetic regulatory networks (GRNs), as active control systems, realizing simple models of biological clocks that have evolved to respond to periodic environmental stimuli of various kinds with appropriate periodic behaviors. GRN models may differ in the evolvability of expressive regulatory dynamics. A new class of artificial GRNs with an evolvable number of complex cis-regulatory control sites—each involving a finite number of inhibitory and activatory binding factors—is introduced, allowing realization of complex regulatory logic. Previous work on biological clocks in nature has noted the capacity of clocks to oscillate in the absence of environmental stimuli, putting forth several candidate explanations for their observed behavior, related to anticipation of environmental conditions, compartmentation of activities in time, and robustness to perturbations of various kinds or to unselected accidents of neutral selection. Several of these hypotheses are explored by evolving GRNs with and without (Gaussian) noise and blackout periods for environmental stimulation. Robustness to certain types of perturbation appears to account for some, but not all, dynamical properties of the evolved networks. Unselected abilities, also observed for biological clocks, include the capacity to adapt to change in wavelength of environmental stimulus and to clock resetting.