Reduced kinetic models of facilitative transport.
In spite of the highly complex structural dynamics of globular proteins, the processes mediated by them can usually be described in terms of relatively simple kinetic diagrams. How do complex proteins, characterized by undergoing transitions among a possibly very large number of intermediate states, exhibit functional properties that can be interpreted in terms of kinetic diagrams consisting of only a small number of states? One possible way of explaining this apparent contradiction is that, under some conditions, a reduction of the actual complete kinetic diagram that describes all of the macromolecular states and transitions takes place. In this work, we contribute with a formal basis to this interpretation, by generalizing the procedure of diagram reduction to the case of multicyclic kinetic diagrams. As an example, we apply the procedure to a complex kinetic model of facilitative transport. We develop Monte Carlo simulations to obtain the kinetic parameters of the complex model and we compare them with the ones analytically obtained from the reduced model. We confirm that, under some conditions, the kinetic behavior of the complex transporter is indistinguishable from the one of a four-state simple carrier model, derived from the former by diagram reduction. Besides introducing some novel methodological aspects, this work further contributes to the idea that, under many physiological and experimental conditions, a reduction occurs of the complete kinetic diagram that describes the dynamics of a globular protein.
Hernández
Julio A
JA
Sección Biofísica, Facultad de Ciencias, Universidad de la República, Iguá s/n esq. Mataojo, 11400 Montevideo, Uruguay. jahern@fcien.edu.uy
Valle Lisboa
Juan Carlos
JC
D002352:Carrier Proteins / Q000737:chemistry*; D007700:Kinetics; D046911:Macromolecular Substances; D008956:Models, Chemical; D009010:Monte Carlo Method; D011487:Protein Conformation
D002352:Carrier Proteins; D046911:Macromolecular Substances