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Briefings in Bioinformatics Advance Access published online on July 18, 2007
Briefings in Bioinformatics, doi:10.1093/bib/bbm034
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© The Author 2007. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Towards a calculus of biomolecular complexes at equilibrium

Eric Mjolsness

Corresponding author. Eric Mjolsness, Department of Computer Science, University of California, Irvine, CA 92617, USA. Tel: 949 824 3533; Fax: 949 824 4056; E-mail: emj{at}uci.edu

An overview is presented of the construction and use of algebraic partition functions to represent the equilibrium statistical mechanics of multimolecular complexes and their action within a larger regulatory network. Unlike many applications of equilibrium statistical mechanics, multimolecular complexes may operate with various subsets of their components present and connected to the others, the rest remaining in solution. Thus they are variable-structure systems. This aspect of their behavior may be accounted for by the use of ‘fugacity’ variables as a representation within the partition functions.

Four principles are proposed by which the combinatorics of molecular complex construction can be reflected in the construction of their partition functions. The corresponding algebraic operations on partition functions are multiplication, addition, function composition and a less commonly used operation called contraction. Each has a natural interpretation in terms of probability distributions on multimolecular structures. Possible generalizations to nonequilibrium statistical mechanics are briefly discussed.

Keywords: biomolecular complex, allosteric enzyme, transcription complex, statistical mechanics, equilibrium, partition function, fugacity, composition, contraction

Submitted: April 16, 2007. Received (in revised form): June 18, 2007.


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