Special Issue "Quantitative Modelling in Molecular System Bioenergetics"

Guest Editor
Dr. Valdur Saks
Laboratory of Bioenergetics, INSERM U884, Joseph Fourier University, Grenoble, France
E-Mail:
Interests: bioenergetics; systems biology; biophysics; enzymology; cell physiology

Dear Colleagues,

The new Special Issue of IJMS continues description of developments in new area of the research - Molecular System Bioenergetics, which was begun by publication of a book “Molecular System Bioenergetics. Energy for Life” by Wiley-VCH in 2007 (http://www3.interscience.wiley.com/cgi-bin/bookhome/117349267) and followed by publication in 2009 of Special Issue of IJMS “Molecular System Bioenergetics” (http://www.mdpi.com/journal/ijms/special_issues/molecular_system_bioenergetics). The way of life of cells is metabolism by exchanging mass and energy with surrounding medium, and understanding its mechanisms needs knowledge of the complex interactions between cellular systems and components. Understanding of the mechanisms of regulation of metabolic and energy fluxes is one of the important aims of Molecular System Bioenergetics, a part of Systems Biology. An important tool in these investigations is the use of quantitative, mathematical models for description, analysis and prediction of the behavior of the complex, integrated systems. While there is abundant literature on quantitative aspects of Systems Biology, network theories etc, important area of metabolic research is still full of contradictions, especially regarding the mathematical description of intracellular metabolic systems and energy metabolism of the cells. Here, two opposite approaches are used with conflicting results, as it has been described in details in a recent review by Saks et al., Int. J. Mol. Sci. 2008, 9, 751-767. One part of investigators ignores the information of complex cell structure and intracellular interactions; these are not interesting for this Special Issue. The aim of this Issue is discussion of problems of modelling of real intracellular metabolic systems functioning in non-equilibrium steady state, taking into account compartmentation of metabolites and enzymes, metabolic channeling, restrictions of intracellular diffusion, direct interaction of enzymes within multienzyme complexes, formation and behavior of dissipative metabolic networks etc. This is a new challenge for Molecular System Bioenergetics.

Prof. Dr. Valdur Saks
Guest Editor

Related Special Issues in 2009

Molecular System Bioenergetics in IJMS

Submission

All manuscripts should be submitted to ijms@mdpi.org with a copy to the Guest Editor. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. The International Journal of Molecular Sciences is an international peer-reviewed Open Access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this Open Access journal is 1000 CHF per accepted paper.

• mathematical modelling
• metabolism
• cellular bioenergetics
• compartmentation
• metabolic channeling
• dissipative metabolic networks
• non-equilibrium steady state kinetics
• feedback regulation

Feature Papers

Type of Paper: Review
Title: Computational Mitochondrial Energetics: A Review of Modelling Approaches
Authors: Ardo Illaste and Marko Vendelin
Affiliation: Laboratory of Systems Biology, Institute of Cybernetics, Tallinn University of Technology, kadeemia 21, 12618 Tallinn, Estonia; E-Mail: markov@sysbio.ioc.ee (M.V.)
Abstract: Mitochondria are responsible for providing red muscle cells with ATP, the chemical energy of which is converted to mechanical work by sarcomeres. Just as the organism needs to cope with different levels of activity, energy production rate in mitochondria has to be able to adjust to changes in demand. A complex regulatory system allows energy production in mitochondria to keep up with demand. This system can be studied with the aid of computational models, giving insights and predictions unavailable through in vitro procedures. Several approaches have been published over the years, differing in their philosophy, level of detail and focus of interest. This review discusses these various models and how they are applied to study mitochondrial energy metabolism.

Type of Paper: Review
Title: The Chemical Master Equation Approach to Nonequilibrium Steady-State of Open Biochemical Systems: Linear Single-Molecule Enzyme Kinetics and Nonlinear Biochemical Reaction Networks
Authors: Melissa Vellela and Hong Qian
Affiliation: Department of Applied Mathematics, National Simulation Resource, 415E Guggenheimer Hall, Department of Bioengineering, University of Washington, Box357962 Seattle, WA 98195-2420, USA; E-Mail: qian@amath.washington.edu (H.Q.)
Abstract: We develop the stochastic, chemical master equation as a unifying approach to biochemical reaction kinetics in nonequilibrium steady state. We discuss the linear, unimolecular single-molecule enzyme kinetics, phosphorylation-dephosphorylation cycle with bistability, and network exhibiting oscillations.

Type of Paper: Review
Title: The Analysis of Compartmentalized Energy Metabolism Based on Simulations of Stable Isotope Tracer Data
Author: Vitaly A. Selivanov^1,2
Affiliations: ¹ Department of Biochemistry and Molecular Biology, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
² A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 199899 Moscow, Russia; E-Mail: selivanov@ub.edu
Abstract: Stable isotope labeling is now used for the metabolic flux profile estimation in various areas of cell and tissue biology. Detected using various mass spectrometry or nuclear magnetic resonance methods, the distributions of isotopic isomers of intracellular metabolites provide information about the distribution of fluxes in metabolic networks. The extraction of complete information from meets some difficulties, in part because of huge number of various isotopic isomers produced be cellular metabolism. Until recently such analysis of metabolic fluxes was restricted by isotopic steady state and assumption of the existence of only one intracellular compartment. Recently we developed software that in automated manner constructs huge system of differential equations, which describes the evolution of all isotopic isomers and which takes into account compartmentalization of intracellular metabolism. The analysis of isotopic isomer distribution using such tool is helpful in understanding the structure of cellular metabolism and its functioning in various environmental conditions.

Type of Paper: Review
Title: Quantitative Analysis of Cellular Metabolic Dissipative Structures
Author: Ildefonso Mtz. de la Fuente Mtz.
Affiliation: Universidad del País Vasco, Facultad de Ciencia y Tecnología, Departamento de Matemáticas, E-48940 Bilbao, Vizcaya, Spain; E-Mail: mtpmadei@ehu.es
Abstract: One of the most important goals of the postgenomic era is understanding the dynamic metabolic processes and the functional structures generated by them. Extensive studies during the last three decades have shown that the dissipative self-organization of the functional enzymatic associations, the catalytic reactions produced during the metabolite channelling, the microcompartmentation of these metabolic processes and the emergence of dissipative networks are the fundamental elements of the dynamical organization of cell metabolism.
Here we present an overview of how mathematical models can be used to address the properties of dissipative metabolic structures at different organizational levels, both for individual enzymatic associations and for enzymatic modular metabolic networks. Recent analyses performed with dissipative metabolic networks have shown that unicellular organisms display a singular global enzymatic structure common to all living cellular organisms which seems to be an intrinsic property of the functional metabolism as a whole. Mathematical models firmly based on experiments, with corresponding computational approaches are needed to fully grasp the molecular mechanisms of metabolic dynamical processes. They are necessary to make possible the quantitative and qualitative analysis of the cellular catalytic reactions and also to help to comprehend the conditions under which the structural dynamical phenomena and biological rhythms arise. Understanding the molecular mechanisms responsible for the metabolic dissipative structures is crucial for unravelling the dynamics of cellular life.