Dynamical factors in protein-protein association

Abstract Although the conformational fluctuations of proteins in solution are not yet well characterized, there is ample evidence that some have amplitudes signficant with respect to the surface roughness of proteins and the distance-dependence of van der Waals potential-energy functions. It thus becomes necessary to examine the ways fluctuations may influence protein-protein association processes and the communication between associated proteins which makes free-energy management possible. This contribution is a first step in this examination. The dynamical possibilities are grouped into two dynamical factors both of which are sensitive to the degree of matching of the dynamical spectra of the associated proteins. A mechanism for free-energy storage and redistribution based on alterations of dynamic spectra is elaborated in some detail using hemoglobin as a model, since the mechanism appears to be responsible for linkage in that protein. However, hemoglobin may not be an entirely satisfactory prototype for some other kinds of proteins, e.g., enzymes, which are built using the knot-matrix principle, since there are good reasons for suspecting that hemoglobin folding is based on a different construction principle. Some consequences of the two principles for fluctuation behavior are discussed particularly as they influence activated free-volume rearrangements, which appear to form the most important class of fluctuation phenomena. Knot-matrix proteins probably have fewer substates and fewer large-amplitude fluctuations, but the limited experimental information suggests that the dynamical factors are important for this class as well. The participation of the dynamical factors in single-subunit and multiple-subunit enzymes is examined in terms of the redistributions of free energy and free volume which are associated with the closing of the cleft between two domains. It is shown that the high degree of specificity in protein-protein associations and substrate selection can be established by adjustments of conformational fluctuations, adjustments made by residue changes and thus available for evolutionary experiments by simple changes in DNA. Strictly speaking thermodynamics can be applied only to dynamics at equilibrium but these may include fluctuations into most of the conformational states involved in enzymic catalysis. Thermodynamic fluctuation theory is introduced to examine the consequences of this simplification; e.g., linear-response behavior, fractal-like probability distributions. These form a basis for integration of empirical information about protein dynamics chemical species is an active participant. Perhaps this complexity can be achieved without utilization of the fluctuation behavior of the species but it is more likely that some supplement to the chemical natures and average geometries of the species is necessary. Conformational fluctuation behavior appears to be the only supplement available. To be useful the fluctuation behavior of the other macromolecules and structured arrays must be utilized in the same ways we propose for proteins. Membranes, for example, as a result of weak first-order phase changes develop near the midpoints of these transitions resonance conditions in which free-volume fluctuations are very large. Such fluctuations appear to labilize transport enzymes in the membranes72 and probably regulate passive permeation. Since the conformations and assembly of all biological macrospecies depend on secondary interactions, they must have similar dynamic spectra. It is thus likely that if dynamic matching is important for proteins, it is also important for other macrospecies in their assembly, functions and communication with other macrospecies. The three major requirements for tissue assembly are recognition, stability in association and cooperativity. As has been shown here all three can rest on a single dynamical basis. The additional requirement of mutability is automatically satisfied because the adjustments in all three are made by changes in DNA. The importance of dynamical behavior in biology has been appreciated for a very long time. To many readers the proposal that conformational fluctuations are a major source of such behavior is novel only in the mechanisms we propose. Conformations have the dynamical characteristics necessary to support the dynamical factors we have discussed but the quantitative significance of these factors may be insignificant. On the other hand, they may be so large that many biological mechanisms cannot be better understood until conformational fluctuations are better characterized.