Gene Regulation in the Pi Calculus: Simulating Cooperativity at the Lambda Switch

Part of the Lecture Notes in Computer Science book series (LNCS, volume 4230).Also part of the Lecture Notes in Bioinformatics book sub series (volume 4230).International audienceWe propose to model the dynamics of gene regulatory networks as concurrent processes in the stochastic pi calculus. As a first case study, we show how to express the control of transcription initiation at the lambda switch, a prototypical example where cooperative enhancement is crucial. This requires concurrent programming techniques that are new to systems biology, and necessitates stochastic parameters that we derive from the literature. We test all components of our model by exhaustive stochastic simulations. A comparison with previous results reported in the literature, experimental and simulation based, confirms the appropriateness of our modeling approach

Thermodynamic stability of the asymmetric doubly-ligated hemoglobin tetramer (alpha+CNbeta+CN)(alphabeta) : methodological and mechanistic issues

Free energy contributions to cooperativity by the eight ligation intermediates of human hemoglobin (Hb) have been characterized extensively using six oxygenation analogs [cf. Huang et al. (1996) Biophys. J. 71, 2094-2105, Table 2]. These unprecedented data bases have strongly supported the molecular code mechanism of Hb cooperativity [Ackers et al. (1992) Science 255, 54-83]. The present study addresses a recent argument against this work [Shibayama et al. (1997) Biochemistry 36, 4375-4381] based on "free energy" determinations for a doubly-ligated species of the CN-met analog. Shibayama et al. (1997) have claimed that, in the hybridization experiments that have been used to determine free energy of the asymmetric "species [21]" tetramer, a portion of the bound cyanide is allegedly released from CN-met Hb during the incubation with deoxy Hb that is used to achieve hybrid equilibrium. These authors have claimed that cyanide release has resulted in extensive electron exchange between heme sites of the hybridizing sample, leading to incorrect evaluation of the equilibrium species population by the cryogenic techniques that have been employed. In this report, we demonstrate that neither appreciable cyanide loss nor electron exchange occurs with the methods that have been used extensively by our two laboratories for these equilibrium determinations [Perrella et al. (1990) Biophys. Chem. 35, 97-103; Daugherty et al. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 1110-1114]. An alternative experiment, which Shibayama et al. (1997) have carried out to illustrate their claim, does not evaluate a thermodynamic equilibrium property of the species [21] hybrid. The relevance of their newly-estimated "free energy" is therefore unclear. Nevertheless, Shibayama et al. (1997) have claimed that their proposed "free energy" (which is ~1.3 kcal more positive than the free energy of -11.4 kcal found independently by our two laboratories) renders invalid the molecular code mechanism of hemoglobin cooperativity. This representation is utterly without foundation since a free energy even more positive than suggested by Shibayama et al. (1997) would be fully consistent with the molecular code mechanism

Thermodynamics of the protein translocation

Many proteins synthesized in bacteria are secreted from the cytoplasm into the periplasm to function in the cell envelope or in the extracellular medium. The Sec translocase is a primary and evolutionary conserved secretion pathway in bacteria. It catalyzes the translocation of unfolded proteins across the cytoplasmic membrane via the pore-forming SecYEG complex. This process is driven by the proton motive force and ATP hydrolysis facilitated by the SecA motor protein. Current insights in the mechanism of protein translocation are largely based on elaborate multidisciplinary studies performed during the last three decades. To understand the process dynamics, the thermodynamic principles of translocation and the subunit interactions need to be addressed. Isothermal titration calorimetry has been widely applied to study thermodynamics of biological interactions, their stability, and driving forces. Here, we describe the examples that exploit this method to investigate key interactions among components of the Sec translocase and suggest further potential applications of calorimetry

It's a small world: managing human resources in small business

It has become widely acknowledged that, during the past decade or so, large mainstream companies in the UK have adopted a new agenda for managing people. Relatively little is known about the impact of this new agenda on small businesses. The small business sector has been long regarded as the natural home for ‘bleak house’ employment relations practices typified by direct management control, poor terms and conditions, high staff turnover and little training. In March 1993, however, a large survey of 560 companies in Leicestershire revealed a surprisingly high take-up and awareness of new management ideas among small business managers. These findings are at odds with a crude ‘bleak house’ scenario. This large-scale telephone survey was then followed up with detailed case study research. This article presents and reflects upon the evidence and reformulates ideas about people management in small businesses

Automated abstraction methodology for genetic regulatory networks

Abstract. In order to efficiently analyze the complicated regulatory systems often encountered in biological settings, abstraction is essential. This paper presents an automated abstraction methodology that systematically reduces the small-scale complexity found in genetic regulatory network models, while broadly preserving the large-scale system behavior. Our method first reduces the number of reactions by using rapid equilibrium and quasi-steady-state approximations as well as a number of other stoichiometry-simplifying techniques, which together result in substantially shortened simulation time. To further reduce analysis time, our method can represent the molecular state of the system by a set of scaled Boolean (or n-ary) discrete levels. This results in a chemical master equation that is approximated by a Markov chain with a much smaller state space providing significant analysis time acceleration and computability gains.