MOLECULAR SWITCH
Historical dogma teaches that ATP hydrolysis provides the energy that drives biological processes. This dogma is based on the large Gibbs free-energy associated with release of the ATP γ-phosphate (~7 kcal/mol). Yet, the rate of γ-phosphate hydrolysis appears to be at least 1000-time slower than Brownian Motion. This means that for most processes (and clearly for diffusion controlled biochemical reactions/interactions), vibrational Brownian contact and loss-of-contact between substrate and enzyme (or protein and protein) may occur up to 1000-times during a single ATP hydrolysis event. Such rapid nano-scale motions make it unlikely that ATP hydrolysis could direct a unidirectionally biological process.
Understanding the concept of molecular switches may solve this dilemma. Molecular switches are grounded in GTP binding proteins (G proteins). G proteins cycle through conformational states that act as gates for protein-protein interaction(s) and downstream cellular processes (for review see: Fishel, Gen Dev 1998). Historically, the first recognized G-protein was the E.coli EF-Tu subunit, which promotes the correct positioning of an aminoacyl-tRNA on an mRNA within the ribosome. Following peptidyl-transferase, a second G-protein, EF-G, induces the translocation of a growing peptidyl-tRNA prior to EF-Tu recruitment of the next aminoacyl-tRNA. However, it was the Ras oncogene that focused attention on the switch functions of G-proteins. In general, G-proteins use the binding energy of GTP (tightly controlled by GDP GTP exchange) to induce conformational transitions in "switch regions" that enhance their interaction with downstream effectors (the definition of a Molecular Switch). The hydrolysis of GTP to GDP+Pi then resets the switch.
A-Proteins
The mechanics of G proteins may be easily adapted to ATP binding/hydrolysis proteins (A-Proteins). Similar ATP-dependent protein conformational transitions have been long known to drive biological processes such as myosin movement along actin filaments, flagellar motions, F1/F0 ATPase and kinesin movement along microtubules. Textbooks suggest that it is the hydrolysis of the gamma-phosphate that provoked the relevant conformational transitions. However, one could easily reverse this coin and propose that ATP binding (ADP for ATP exchange) provokes the relevant conformational transitions, which then biases naturally occurring molecular collisions (termed: Rectified Brownian Motion). In this view, Brownian collision of a MutS homolog (MSH) with a mismatch provokes ADP for ATP exchange, which results in a conformational transition that results in the stable formation of a sliding clamp (see Section on Mismatch Repair). In the case of the directional movement of kinesin down a microtubule, ATP binding by one subunit is transmitted through a "linker region" that is remarkably similar to "switch" regions identified in G proteins. This conformational transition biases the Brownian movement of the second subunit such that the only productive collision occurs with a nearby ß-tubulin in the direction of movement. In this model, ATP hydrolysis allows the release (recycling) of the "back foot" such that the new "front foot" may bind ATP in a second step of biased Brownian movement. The concept of a Molecular Switch as the fundamental control for many A-proteins suggests regulation and specificity to the ADP for ATP exchange process. One of our overriding interests is to understand the biophysical processes that control A-protein Molecular Switches in DNA repair.
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