Computer-based analysis of the binding steps in protein complex formation

Abstract

Computer models were used to examine whether and under what conditions the multimeric protein complex is inhibited by high concentrations of one of its components-an effect analogous to the prozone phenomenon in precipitin tests. A series of idealized simple ''ball-and-stick'' structures representing small oligomeric complexes of protein molecules formed by reversible binding reactions were analyzed to determine the binding steps leading to each structure. The equilibrium state of each system was then determined over a range of starting concentrations and K d s and the steady-state concentration of structurally complete oligomer calculated for each situation. A strong inhibitory effect at high concentrations was shown by any protein molecule forming a bridge between two or more separable parts of the complex. By contrast, proteins linked to the outside of the complex by a single bond showed no inhibition whatsoever at any concentration. Nonbridging, multivalent proteins in the body of the complex could show an inhibitory effect or not depending on the structure of the complex and the strength of its bonds. On the basis of this study, we suggest that the prozone phenomenon will occur widely in living cells and that it could be a crucial factor in the regulation of protein complex formation.In the precipitin reaction widely used by immunologists, increasing amounts of soluble antigen are added to a series of tubes each containing a fixed amount of antibody-containing serum. As the antigen increases, the quantity of precipitate also increases up to a maximum and then declines. The basis for this phenomenon, for which the term ''prozone'' was originally used (1, 2), is well understood and depends on the fact that the precipitates are made from a three-dimensional lattice of antigen and antibody molecules (3). Macroscopic precipitates form only when antibody and antigen are in optimal proportions, and if either molecule is present in excess, small soluble complexes are produced instead. With excess antigen, for example, the soluble complexes consist of antibody molecules surrounded by multiple molecules of antigen.There is reason to think that a similar effect may occur in the formation of multimeric protein complexes in living cells. Many if not most protein molecules in a living cell are part of multiprotein assemblies held together by noncovalent bonds, such as multimeric enzymes and receptor complexes (4-8). Such complexes have a definite structure and composition, and their formation depends in part on a series of diffusion-limited binding reactions influenced by the concentrations of participating protein molecules and their binding affinities for each other. Thus, if one species is present at much higher levels than the others, we might anticipate that something similar to the prozone phenomenon could operate. That is, we might find that formation of the structurally complete complex would be suppressed at the expense of smaller, incomplete clusters of proteins. Because the function of most protein com...

Undesired usage and the robust self-assembly of heterogeneous structures

“…The problem of incomplete structures has been argued to be central to both DNA brick assembly 9,34-36 and protein complexes 27,37 . Indeed, before the experiments of ref.…”

Molecular Binding Interactions: Their Estimation and Rationalization in QSARs in Terms of Theoretically Derived Parameters

“…Hydrogen bonding can be considered as a special case of dipole-dipole interaction that is usually stronger due to the relatively short distance ranges (2.5 to 3.5 Å) and angle constraints brought about as a result of the directional nature of nonbonding (lone pair) electron orbitals. The energy range for dipole-dipole interactions is about -3 to -5 kJ.mol -1 or between -0.7 and -1.2 kcal.mol -1 , whereas hydrogen bonding energies lie between -8 and -32 kJ.mol -1 , corresponding to between -2 and -8 kcal.mol -1 , although lower values have been reported in some cases [25]. As a particular example, the dipolar energy between tyrosine and camphor at an orientation found in the active site of cytochrome P450 cam (the enzyme which specifically mediates camphor 5-hydroxylation) can be calculated to be between -3.5 and -4.6 kcal.mol -1 depending on whether the experimental or calculated dipole moments are employed.…”

Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties

“…Because of the pro-zone (combinatorial inhibition) effect, the concentration of functional complexes before signaling can be shown to have a maximum (28). However, the existence of a maximum for MAPK activation and its position cannot be inferred directly from this effect, because phosphorylation reactions increase the number of possible complexes, and free rather than bound MAPK-PP represents the signaling output.…”

“…A detailed study of this ''pro-zone'' effect has been reported recently (28). The pro-zone effect (''combinatorial inhibition'' can be proposed as a more descriptive term) in terms of the scaffold-mediated MAPK activation means that at low scaffold concentration, when both kinases are in excess, formation of a functional complex containing both kinases is likely, whereas in excess of the scaffold, nonfunctional complexes containing none or only one of the kinases become relatively more abundant.…”