Proteomics and models for enzyme cooperativity.

Cooperativity is a phenomenon of universal importance in biological systems and has almost as much variety as it has ubiquity. In virtually all ecosystems the cooperativity of groups, species, and individual organisms is evident. The cooperativity known as “mutualism” is one in which one species provides a haven or a metabolic advantage to another species. On a more microscopic level is the “metabolic cooperativity” in which an enzyme or substrate of one pathway can cooperate with another pathway by providing a component that can act as a substrate or a regulator of that pathway. Delving deeper into the molecular realm we find the type of cooperativity that will be the focus of this review: “allosteric cooperativity” (1, 2). The term “allosteric” has been used to describe a ligand-enzyme interaction, which results in a measurable conformational change in proximal and distal regions of that protein. We will categorize as a subdivision of allosteric cooperativity the phenomenon of i cooperativity in which the three following conditions are met: (a) the binding of the ligand induces a conformational change in the protein; (b) the conformational changes are intramolecular in the subunits of a multisubunit enzyme; and (c) the sites are initially essentially identical to each other. This type of cooperativity, which has since been shown in many enzymes, receptors, and ion channels, is of critical importance to both evolution and the field of proteomics because it can serve as a general model for the way in which the networks of interacting enzymes of metabolic pathways are regulated. Because these networks of interactions explain a lot of the factors that control these ensembles of networks, they play a major role in the differences in organisms and the understanding of proteomics. Cooperativity was originally found by C. Bohr in hemoglobin (3); he observed the sigmoid binding curve of O2 to hemoglobin, which he explained by saying that the binding of the first O2 molecule made it easier for the next O2 to bind and hence could be called “cooperative.” The and chains of hemoglobin satisfy the “essentially identical” criteria for i cooperativity because the binding affinities, sequence homology, and/or structural similarity of the O2 binding sites reveal that they are nearly identical but not quite. After the importance of conformational changes was recognized, two different theories of the cooperative mechanism were postulated. One was the theory of Monod, Wyman, and Changeux (1), herein referred to as the MWC model (and also mentioned as the “symmetry” model, “concerted” model, or “the two-state” model), and the other was the theory of Koshland, Nemethy, and Filmer (2), herein referred to as the KNF model (and often mentioned as the “induced fit” model or the “sequential” model). The MWC model proposed that the subunits changed shape in a concerted manner to preserve the symmetry of the entire molecule as it was transformed from one conformation (T) to a second conformation (R) under the influence of ligand. The alternative KNF model postulated that each subunit changed shape as ligand bound, so that changes in one subunit led to distortions in the shape and/or interactions of other subunits of the protein. A mathematical examination of these theories showed that both gave sigmoid curves and could explain, within experimental error, how O2 bound to hemoglobin. Both theories were postulated to apply to many other enzymes that also gave sigmoid curves showing cooperativity. The KNF model, however, also predicted that in some cases the first ligand to bind could make it more difficult for subsequent ligands to bind. This was called “negative cooperativity” because there was (a) “cooperativity” between the subunits and (b) “negative” because binding of one ligand made the binding of subsequent ligands more difficult (4, 5). The MWC theory allowed no such alternative. Because only the KNF theory fit negatively cooperative enzymes, it is easy to select that model for such enzymes, but because both theories fit positively cooperative enzymes more sophisticated tools must be applied to such cases. However, positive cooperativity and negative cooperativity are easy to distinguish from each other and they are important to proteomics and evolution so we will address their significance first and the mechanism for achieving them next. To obtain an objective appraisal of the relative quantities of negatively and positively cooperative enzymes in nature, we first selected all publications that had cooperativity in their titles in the period 1980–1990. Tables 1–3 (see supplemental material) are a distillation from 7,316,007 documents in the Science Citation Index from the years 1980–1990 inclusive. Of these, 374 articles had “cooperativity” in the title. From there, articles focusing on enzymes consistent with i cooperativity were identified and are listed in Tables 1–3. Table 1 shows 29 of the 291 examples of protein cooperativity reported in the 1980–1990 period (Refs. 19–47), Table 2 shows 27 of the 215 examples of negative cooperativity reported in 1980–1990 (Refs. 48–75), and Table 3 shows 4 of the 61 examples of enzymes that show both negative and positive cooperativity in 1980–1990 (Refs. 76–79). As can be seen in the list of enzymes given in Tables 1 and 2, the number of negatively cooperative enzymes is approximately the same as the number of positively cooperative enzymes suggesting that the sensitivity capabilities listed above have about equal evolutionary value with a slight evolutionary advantage to positive cooperativity. To check these results, in Tables 4–6 in the supplement are positive cooperativity and negative cooperativity in the years 1991–1993 (Refs. 80–104). Because the relative ratios of enzymes and other proteins with positive and negative cooperativity are roughly the same in the two arbitrarily selected time periods, we can assume that they are probably a pretty good indication of the relative ratios for all enzymes, i.e. about 50% positive and 50% negative. To some this may seem unusual because positive cooperativity was discussed first in relation to hemoglobin and to many people * This minireview will be reprinted in the 2002 Minireview Compendium, which will be available in December, 2002. □S The on-line version of this article (available at http://www.jbc.org) contains Tables 1–6. ‡ To whom correspondence should be addressed. Tel.: 510-642-0416; Fax: 510-642-6396; E-mail: dek@uclink4.berkeley.edu. Minireview THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 277, No. 49, Issue of December 6, pp. 46841–46844, 2002 © 2002 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in U.S.A.