We propose a mathematical model for mitochondria-dependent apoptosis, in which kinetic cooperativity in formation of the apoptosome is a key element ensuring bistability. We examine the role of Bax and Bcl-2 synthesis and degradation rates, as well as the number of mitochondrial permeability transition pores (MPTPs), on the cell response to apoptotic stimuli. Our analysis suggests that cooperative apoptosome formation is a mechanism for inducing bistability, much more robust than that induced by other mechanisms, such as inhibition of caspase-3 by the inhibitor of apoptosis (IAP). Simulations predict a pathological state in which cells will exhibit a monostable cell survival if Bax degradation rate is above a threshold value, or if Bax expression rate is below a threshold value. Otherwise, cell death or survival occur depending on initial caspase-3 levels. We show that high expression rates of Bcl-2 can counteract the effects of Bax. Our simulations also demonstrate a monostable (pathological) apoptotic response if the number of MPTPs exceeds a threshold value. This study supports our contention, based on mathematical modeling, that cooperativity in apoptosome formation is critically important for determining the healthy responses to apoptotic stimuli, and helps define the roles of Bax, Bcl-2, and MPTP vis-à-vis apoptosome formation.

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Despite the suitability of various lattice geometries for coarse-grained modeling of proteins, the actual packing geometry of residues in folded structures has remained largely unexplored. A strong tendency to assume a regular packing geometry is shown here by optimally reorienting and superimposing clusters of neighboring residues from databank structures examined on a coarsegrained (single-site-per-residue) scale. The orientation function (or order parameter) of the examined coordination clusters with respect to fcc lattice directions is found to be 0.82. The observed geometry, which may be termed an incomplete distorted face-centered cubic (fcc) packing, is apparently favored by the drive to maximize packing density, in a fashion analogous to the way identical spheres pack densely and follow fcc geometry. About 2/3 of all residues obey this packing geometry, while the remainder occupy other context-dependent positions. The preferred coordination directions show relatively small variations over the various amino acid types, consistent with uniform residue viewpoint. Both the extremes of solvent-exposed and completely buried residue neighborhoods approximate the same generic packing, the only difference being in the numbers (and not the orientations) of coordination sites that are occupied (or left void for solvent occupancy). We observe the prevalence of a rather uniform (tight) residue packing density throughout the structure, including even the residues packed near solvent-exposed regions. The observed orientation distribution reveals an underlying, intrinsic orientation lattice for proteins. Proteins 2003;52:56 -67.

The high packing density of residues in proteins ought to be manifested in some order; to date this packing order has not been thoroughly characterized. The packing regularity in proteins is important because the internal organization of proteins can have a dominant effect on functional dynamics, and it can aid in the design, simulation and evaluation of structures. Packing metrics could also inform us about normal sequence variability, an issue that, with the accumulating genome data, becomes increasingly important. Other studies, indicating a possible correlation between packing density, sequence conservation, and folding nucleation ͓O. B. Ptitsyn, J. Mol. Biol. 278, 655 ͑1998͔͒, have emphasized the importance of packing. Here, residue clusters from protein databank structures, each comprised of a central residue and all neighbors located within the first coordination shell, have been rigidly re-oriented and superimposed in a self-consistent optimization. About two-thirds of residues are found to follow approximately the relative orientation preferences of face-centered-cubic packing, when examined on a coarse-grained scale ͑one site per residue͒, while the remaining one-third occupy random positions. The observed regularity, which becomes more pronounced after optimal superimposition of core residues, appears to be the result of uniform sampling of the coordination space around each residue on a coarse-grained scale with hydrophobic clustering and volume exclusion, to achieve packing densities close to that of the universal closest packing of identical spheres.