Direct transfer (channeling): ... E1.I + E2 --> E1.I.E2 --> E1 + E2.I --> ...
Release/rebinding ('normal'): ... E1.I --> E1+ I and then E2 + I --> E2.I --> ...
The occurence of channeling or direct transfer through transient association of enzymes during activity has important kinetic as well as regulatory implications. Indeed, in contrast with the 'normal mechanism', the metabolite 'I' is forced to go on through E2 rather than being available as a substrate to another enzyme 'En' in a different (competing?) pathway.
An extreme case for channeling is the permanent organization of enzymes in a pathway into a 'multi-enzyme complex', in which the intermediates are restricted into a common internal active locus. The complex represents a black box into which a substrate enters, is sequentially processed in isolation from the medium, and only the final product comes out and become available to further catalysis by other systems. A famous example for that is the pyruvate dehydrogenase complex of bacteria and mitochondria.
The use of localized probes to monitor the concentration of reactants in the immediate vicinity of the catalyst(s) helps to resolve the contribution of physical processes (diffusion, chemical or electrostatic partition, local changes in pH, etc.) to the observed behavior of heterogeneous systems.
In view of the inherently crowded nature of the intracellular milieu, most macromolecules are likely to be in physical contact with each other. Since all the components in a cell have evolved in parallel, they had ample opportunity to adapt to such environment (to the advantage of the organism) through molecular evolution. It is believed that confined macromolecules in each cell have reached mutual recognition for a better organization and coordinated function.
Cell biologists increasingly realize the importance of molecular recognition, and this topics is currently a favored subject of multidisciplinary research.
Macromolecular recognition (as protein folding) is determined by the sequence, 3D structure and the environment. It is effected by building blocks occuring at the surface of macromolecules, being complementary in terms of:
geometric fit: match at the surface needed to achieve maximal packing density;
hydrophobic fit: surface patches matching needed for water exclusion;
hydrogen bonding/electrostatic fit: for further stabilization of the associated molecules.
Most these factors are predictable through computer analysis of known 3D structures or existing models of macromolecules suspected to interact and the simulation of their mutual docking. Other (wet) approaches to detect macromolecular interaction are non-denaturating separation methods (ultracentrifugation, gel exclusion or electrophoresis), or recombinant DNA methods (e.g., yeast double hybrid system).
Mitochondrial outer membrane protein, also referred to as VDAC (Voltage Dependent Anion Channel). Represents a regulated gate between the cytosol and intramitochondrial compartments for the exchange of metabolites. Believed to occur as a dimer, this mostly beta sheet transmembrane protein forms a hydrophilic pore in the outer membrane allowing neutral molecules (up to 5 kDa) to diffuse in and out the mitochondrion.
The mutual affinity of protein pairs is encoded in their respective sequences and structures, while their potential association or separation is effected through simple physico-chemical determinants of their local environment. The latter are believed to be achieved through the 'interpretation' of variable signals in the global environment (extra- or intra-cellular) by proper signal transduction.