Defining systems based on information exchange: structure from dynamics

Molecules as complex adaptative systems: constrained molecular properties and their biochemical significance

The first part of the paper describes molecular structure by considering form (geometrical structure), function (observable properties resulting from interaction with a probe) and fluctuation (dynamics). The fluctuation of form and function generates a number of molecular states, whose ensemble delineates a property space. This concept is central when examining the mutual interactions of a chemical compound with its molecular environment. Because of these interactions, a chemical compound and its molecular environment may form a complex system in its own right, which exhibits emergent properties (e.g., solubility and lipophilicity) that are non-existent (and meaningless) at the level of description of isolated molecules, and which are part of the property space of the compound. The emergence of these properties is accompanied by constraints on the property space of the constituents, and especially of the chemical compound. Some of these constraints are well known, e.g., conformational shifts as seen in induced fit and chameleonic behaviour. Such mutual adaptability between a compound and its environment is a fundamental but insufficiently recognized phenomenon in biochemistry, since it amplifies molecular complementarity and hence molecular recognition. In the second part of this paper, the results of an exploratory study are reported which show that contraints on the property space of constituents also occur when molecules are covalently incorporated into larger compounds. Using the GRID/VolSurf softwares, we bring evidence that when some amino acids become residues in peptides, they experience a modest increase in their polarity and a marked increase in their hydrophobicity (as assessed by their polarity field and hydrophobicity field, respectively). The biological and pharmacological implications of constraints on solutes, ligands and monomers could inspire new directions of research.