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The Concept of Allosteric Interaction and Its Consequences for the Chemistry of the Brain

2013; Elsevier BV; Volume: 288; Issue: 38 Linguagem: Inglês

10.1074/jbc.x113.503375

1083-351X

Jean‐Pierre Changeux,

Receptor Mechanisms and Signaling

Throughout this Reflections article, I have tried to follow up on the genesis in the 1960s and subsequent evolution of the concept of allosteric interaction and to examine its consequences within the past decades, essentially in the field of the neuroscience. The main conclusion is that allosteric mechanisms built on similar structural principles operate in bacterial regulatory enzymes, gene repressors (and the related nuclear receptors), rhodopsin, G-protein-coupled receptors, neurotransmitter receptors, ion channels, and so on from prokaryotes up to the human brain yet with important features of their own. Thus, future research on these basic cybernetic sensors is expected to develop in two major directions: at the elementary level, toward the atomic structure and molecular dynamics of the conformational changes involved in signal recognition and transduction, but also at a higher level of organization, the contribution of allosteric mechanisms to the modulation of brain functions. Throughout this Reflections article, I have tried to follow up on the genesis in the 1960s and subsequent evolution of the concept of allosteric interaction and to examine its consequences within the past decades, essentially in the field of the neuroscience. The main conclusion is that allosteric mechanisms built on similar structural principles operate in bacterial regulatory enzymes, gene repressors (and the related nuclear receptors), rhodopsin, G-protein-coupled receptors, neurotransmitter receptors, ion channels, and so on from prokaryotes up to the human brain yet with important features of their own. Thus, future research on these basic cybernetic sensors is expected to develop in two major directions: at the elementary level, toward the atomic structure and molecular dynamics of the conformational changes involved in signal recognition and transduction, but also at a higher level of organization, the contribution of allosteric mechanisms to the modulation of brain functions. In the physical sciences, there is a long tradition of theory and model building; the advancement of the discipline has relied and still relies on an active interplay between theory and experimental studies and between the development of novel technologies and conceptual invention. In the biological sciences, a similar tradition exists, but it is not as systematic. The frequent enthusiasm for new techniques without explicit theoretical perspectives often hides an impoverished theoretical landscape where original hypotheses or ideas are rare. In my view, the theoretical objectives should precede, or be concomitant with, the technological and experimental means. According to Claude Bernard, "the experimenter who does not know what he is looking for will not understand what he finds" (1Robin E.D. Claude Bernard. Pioneer of regulatory biology.JAMA. 1979; 242: 1283-1284Crossref PubMed Google Scholar). 1The full quote (see Ref. 255Grande F. Visscher M.B. Introduction. Claude Bernard and Experimental Medicine. Schenkman Publishing Co., Cambridge, MA1967Google Scholar) is, "Empiricism may serve to accumulate facts, but it will never build science. The experimenter who does not know what he is looking for will not understand what he finds." The reasons for the difficulties encountered with the biological sciences possibly lie in the fact that the objects of biology are highly differentiated with multiple, intricate levels of organization. The identification of common conceptual rules further hinges on the considerable structural and functional diversity of the biological objects. Thus, there is the constant dilemma, often split between scientists, about the universality or the singularity of the objects they investigate. In this context, I have selected as a tentative common rule the concept of allosteric interaction and its consequences on the molecular chemistry of proteins, going from bacterial regulatory enzymes up to the nervous system and, tentatively, the higher functions of the brain. The circumstances of my personal life have been such that as an adolescent, I was already exposed to theory through the teaching of an exceptional professor of natural sciences, Jean Bathellier, who introduced me to the idea of biological evolution. This experience deeply influenced my scientific career to the extent that until now, as we shall see, my thinking has been framed within the Darwinian evolutionary paradigm. My first laboratory work was in marine biology (2Changeux J.-P. Some biological characters of a parasitic copepod from holothurians: allantogynus delamarei n.g.n.sp.C. R. Hebd. Seances Acad. Sci. 1958; 247: 961-964Google Scholar), but I felt rapidly unsatisfied by perspectives essentially limited to descriptive morphology. In the fall of 1958, I visited Jean Brachet's laboratory in Brussels, where I also attended Christian de Duve's lectures and became fascinated by their theoretical perspective that the solution of the great problems of biology had ultimately to be found in elementary biochemical mechanisms. My interest shifted to the more explanatory chemistry of embryonic development. In this context, I imagined a theory in which the enzyme activations that follow the entry of the spermatozoon in the egg were due to a release of enzymes hidden in subcellular particles referred to as lysosomes by Christian de Duve. Back in Paris, I tried to test this hypothesis. Confronted by concrete technical difficulties, I met, by chance, Jacques Monod, who offered to let me enter his laboratory at the Institut Pasteur on the strict condition I abandon my ideas on embryonic development and work with Escherichia coli. I drudgingly accepted his demand (3Changeux J.-P. On the biochemical expression of genetic determinants of Escherichia coli introduced to Salmonella typhimurium.C. R. Hebd. Seances Acad. Sci. 1960; 250: 1575-1577PubMed Google Scholar), keeping my theoretical interest in animal biology for the future! My fascination for theory once again was stimulated in the spring of 1959, when the moment came for the selection of the topic for my Ph.D. thesis. I met Jacques Monod and François Jacob (Fig. 1), who suggested several themes for my research, most of them dealing with their ongoing work on the regulation of gene expression and the operon model. They did not suit me since the theoretical insights and outcomes were already in their hands. An alternative, original topic, mentioned by François Jacob, held my attention. He had heard a talk by Edwin Umbarger, who had shown that in bacterial biosynthetic pathways, such as those for the biosynthesis of l-isoleucine or l-valine, the first enzyme is feedback-inhibited by the end product of the pathway (4Umbarger H.E. Evidence for a negative-feedback mechanism in the biosynthesis of isoleucine.Science. 1956; 123: 848Crossref PubMed Google Scholar). The issue was to understand the molecular mechanism of this "apparently competitive" regulatory interaction, a critical step in the cybernetics of the cell. This topic fitted with my first interest about enzyme activations during fertilization but with a much broader biological perspective. I adopted the theme for my thesis work. My first naive idea was that if a special molecular device mediated the feedback inhibition by the enzyme, one should be able to find a way to identify its molecular constituents, for instance, by dissociating the regulatory interaction from the catalytic activity in vitro. I first confirmed Umbarger's in vitro observations of the apparent competitive inhibition of l-threonine deaminase by l-isoleucine and its "bimolecular" cooperative kinetics toward both the substrate and the feedback inhibitor. I noticed that the sensitivity of enzyme preparations to l-isoleucine changed with the time of storage, purification, heating, and exposure to reagents for –SH groups, resulting in a loss of response to l-isoleucine without a significant decline in enzyme activity. Interestingly, the loss of l-isoleucine feedback inhibition was also accompanied by the abolition of the bimolecular kinetics of the enzyme toward its substrate. The paper I presented at the 26th Cold Spring Harbor Symposium on Quantitative Biology entitled "Cellular Regulatory Mechanisms" (5Changeux J.-P. The feedback control mechanisms of biosynthetic l-threonine deaminase by l-isoleucine.Cold Spring Harb. Symp. Quant. Biol. 1961; 26: 313-318Crossref PubMed Google Scholar), at the initiative of Jacques Monod, gave me the stimulating opportunity to theorize. I briefly discussed the two plausible models that might account for the apparently competitive antagonism between the feedback inhibitor l-isoleucine and the substrate l-threonine. According to the first model, the binding sites for the substrate and regulatory inhibitor are partially overlapping, so the interaction is a classical competition by steric hindrance. In the second "new" model, referred to as "no-overlapping," the two sites are separated from each other, and the interaction between ligands takes place between topographically distinct sites. I favored the second model, in which the substrate and regulatory effector were to bind topographically distinct sites, specifically on the basis of the argument that loss of feedback inhibition was accompanied by a normalization of the kinetics (5Changeux J.-P. The feedback control mechanisms of biosynthetic l-threonine deaminase by l-isoleucine.Cold Spring Harb. Symp. Quant. Biol. 1961; 26: 313-318Crossref PubMed Google Scholar). Following my presentation, the distinguished bacteriologist Bernard Davis mentioned the possible analogy between the properties of hemoglobin and those of threonine deaminase. As we shall see, it was a highly relevant and inspiring comment (6Davis B. Commentary to Changeux's presentation.Cold Spring Harbor Symp. Quant. Biol. 1961; 26: 318Crossref Google Scholar). In the oral presentation of the "General Conclusions" of the symposium, Jacques Monod reported my results and interpretation in the section dealing with the regulation of enzyme activity. He also wrote, "Closely similar observations have been made independently and simultaneously by Pardee (private communication) on another enzyme sensitive to end-product (aspartate-carbamyl-transferase)" (7Gerhart J.C. Pardee A.B. The enzymology of control by feedback inhibition.J. Biol. Chem. 1962; 237: 891-896Abstract Full Text PDF PubMed Google Scholar). In Monod and Jacob's subsequently written "General Conclusions," the word "allosteric" appears for the first time. It is composed of two Greek roots expressing the difference (allo-) in (stereo-) specificity of the two binding sites to qualify and generalize the no-overlapping sites mechanism of indirect interaction between stereospecifically distinct sites mediated by a conformational change of the protein (8Changeux J.-P. 50th anniversary of the word "allosteric.".Protein Sci. 2011; 20: 1119-1124Crossref PubMed Scopus (0) Google Scholar). This was the birth of the word allosteric and of its general definition, which is nowadays widely accepted (8Changeux J.-P. 50th anniversary of the word "allosteric.".Protein Sci. 2011; 20: 1119-1124Crossref PubMed Scopus (0) Google Scholar). The introduction of the concept created a major landmark in classical enzymology and the ill-defined notions of "un-competitive" or "non-competitive" inhibition (9Haldane J.B.S. Enzymes. Longmans, Green and Co., London1930Google Scholar) most often (but not always) assumed to take place in the neighborhood (or even at the level) of the active site. At this stage, the conformational change linking the topographically distinct sites was interpreted by us in terms of the "induced-fit" theory of Daniel Koshland (10Koshland Jr., D.E. Molecular geometry in enzyme action.J. Cell. Physiol. 1956; 47: 217-234Crossref Google Scholar, 11Koshland Jr., D.E. Enzyme flexibility and enzyme action.J. Cell. Comp. Physiol. 1959; 54: 245-258Crossref PubMed Scopus (108) Google Scholar) in the sense that the ligand "instructs" rather than "selects" the structural change (12Monod J. Changeux J.-P. Jacob F. Allosteric proteins and cellular control systems.J. Mol. Biol. 1963; 6: 306-329Crossref PubMed Google Scholar). At the time, Koshland's concern was not the regulation of enzyme activity by a metabolic signal but the specificity of enzyme action. His theory (11Koshland Jr., D.E. Enzyme flexibility and enzyme action.J. Cell. Comp. Physiol. 1959; 54: 245-258Crossref PubMed Scopus (108) Google Scholar, 13Koshland Jr., D.E. The role of flexibility in enzyme action.Cold Spring Harbor Symp. Quant. Biol. 1963; 28: 473-482Crossref Google Scholar) was that a local steric fit seemed essential for the reaction to occur "only after a change in shape of the enzyme molecule had been induced by the substrate" (13Koshland Jr., D.E. The role of flexibility in enzyme action.Cold Spring Harbor Symp. Quant. Biol. 1963; 28: 473-482Crossref Google Scholar). We suggested the extension of the idea to a higher level long-range and distant allosteric interaction between active and regulatory sites (12Monod J. Changeux J.-P. Jacob F. Allosteric proteins and cellular control systems.J. Mol. Biol. 1963; 6: 306-329Crossref PubMed Google Scholar). Without being aware of it, we were following the widely accepted tradition of Karl Landsteiner and Linus Pauling's empiricist ideology, viewing the local environment as directly instructing structural changes within biological organisms. A paradigmatic change from instruction to selection occurred with the Monod-Wyman-Changeux (MWC) model (14Monod J. Wyman J. Changeux J.-P. On the nature of allosteric transitions: a plausible model.J. Mol. Biol. 1965; 12: 88-118Crossref PubMed Google Scholar). Quite surprisingly, in my opinion, it did not emerge from a deliberate shift of theoretical position by any one of us, but from experimental observations. At the end of 1963, I handed Jacques Monod the first typed version of my thesis work (15Changeux J.-P. On the allosteric properties of l-threonine deaminase. I. Methods of studying biosynthetic l-threonine deaminase.Bull. Soc. Chim. Biol. 1964; 46: 927-946PubMed Google Scholar, 73Changeux J.-P. On the allosteric properties of biosynthetic l-threonine deaminase. VI. General discussion.Bull. Soc. Chim. Biol. 1965; 47: 281-300PubMed Google Scholar, 251Changeux J.-P. On the allosteric properties of biosynthetic l-threonine deaminase. II. Kinetics of action of biosynthetic l-threonine deaminase with respect to the natural substrate and inhibitor.Bull. Soc. Chim. Biol. 1964; 46: 947-961PubMed Google Scholar, 252Changeux J.-P. On the allosteric properties of biosynthetic l-threonine deaminase. III. Interpretation of the inhibitory effect of l-isoleucine: steric hindrance or allosteric effect.Bull. Soc. Chim. Biol. 1964; 46: 1151-1173PubMed Google Scholar, 253Changeux J.-P. On the allosteric properties of biosynthetic l-threonine deaminase. IV. The desensitization phenomenon.Bull. Soc. Chim. Biol. 1965; 47: 113-139PubMed Google Scholar, 254Changeux J.-P. On the allosteric properties of biosynthetic l-threonine deaminase. V. The allosteric transition.Bull. Soc. Chim. Biol. 1965; 47: 267-280PubMed Google Scholar). Of the many observations I had made, he became especially interested by the experiments I did in 1962 on the effects of urea (16Changeux J.-P. Allosteric interactions on biosynthetic l-threonine deaminase from E. coli K12.Cold Spring Harb. Symp. Quant. Biol. 1963; 28: 497-504Crossref Google Scholar). At an adequate concentration, urea reversibly inactivates l-threonine deaminase, an inactivation interpreted as a split of the enzyme into subunits. Interestingly, in this system, allosteric activators, such as l-norleucine, l-valine, and l-allo-threonine, facilitated inactivation and thus subunit dissociation; feedback inhibitors, such as isoleucine, protected against inactivation and thus strengthened the assembly of the subunits in the protein. To formally account for the observed effects, I mentioned the possibility of three possible conformational states, one for each experimental condition (presence of activator, presence of inhibitor, and no effector). Jacques Monod pressed me to systematically adopt in my theoretical reasoning the rule to reduce the number of hypotheses to the strict minimum. Two states should suffice! I immediately agreed and further documented the experimental consequences of the two states with a tight (T) or relaxed (R) mode of packing of the subunits, each state pre-existing the binding of ligand and exhibiting different intrinsic affinities for both substrate and allosteric effectors. In my opinion, this was the birth of the two-state mechanism of pre-existing conformational states (R ↔ T), a consequence of a selective, rather than an instructive, effect of the ligands. These views were the start of many debates and theoretical developments that, after many successive writings of the paper by Jacques Monod (17Buc H. Interactions between Jacques Monod and Jeffries Wyman (or the burdens of co-authorship).Rendiconti Lincei. 2006; 17: 31-49Crossref Scopus (11) Google Scholar, 18Buc H. The design of an enzyme: a chronology on the controversy.J. Mol. Biol. 2013; 425: 1407-1409Crossref PubMed Scopus (3) Google Scholar), led to the final version of the MWC model (14Monod J. Wyman J. Changeux J.-P. On the nature of allosteric transitions: a plausible model.J. Mol. Biol. 1965; 12: 88-118Crossref PubMed Google Scholar). The model was originally planned to conclude my thesis work with the aim to formally establish a causal link between the structural organization of the known regulatory proteins and their signal transduction properties (Fig. 2). The problem was risky because at that time, the only known three-dimensional structures of proteins were those of hemoglobin (19Perutz M.F. Rossmann M.G. Cullis A.F. Muirhead H. Will G. North A.C.T. Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5-Å resolution, obtained by x-ray analysis.Nature. 1960; 185: 416-422Crossref PubMed Scopus (690) Google Scholar) and myoglobin (20Kendrew J.C. Structure and function in myoglobin and other proteins.Fed. Proc. 1959; 18: 740-751PubMed Google Scholar). Emphasis was placed on the cooperative binding of ligands, a property found frequently associated with the ability to transduce regulatory signals. An essential postulate for us was that cooperativity between ligand-binding sites relies upon the structural cooperativity existing between several subunits in a regulatory protein. In other words, the quaternary assembly of the subunits into a cooperative symmetrical oligomers is critical (although exceptions exist where single folded polypeptides that form several binding sites for different ligands may display allosteric interactions) (21Changeux J.-P. Allostery and the Monod-Wyman-Changeux model after 50 years.Annu. Rev. Biophys. 2012; 41: 103-133Crossref PubMed Scopus (242) Google Scholar). Max Perutz's structural model of hemoglobin (22Perutz M.F. X-ray analysis of hemoglobin.Science. 1963; 140: 863-869Crossref PubMed Scopus (0) Google Scholar, 23Muirhead H. Perutz M.F. Structure of haemoglobin. A three-dimensional Fourier synthesis of reduced human haemoglobin at 5–5 Å resolution.Nature. 1963; 199: 633-638Crossref PubMed Scopus (0) Google Scholar) revealed the symmetries of the α2β2-tetramer and the 25–36-Å distance between hemes, together with the evidence that the conformational change that takes place upon O2 binding primarily concerns the quaternary organization of the molecule. Through several visits, Jeffries Wyman made us aware about his views that the symmetry properties of the O2 saturation function for hemoglobin reveal the existence of elements of structural symmetry (24Wyman Jr., J. Heme Proteins.Adv. Protein Chem. 1948; 4: 407-531Crossref PubMed Scopus (354) Google Scholar). Additional analysis of the assembly of protein oligomers and their symmetry properties was carried out in parallel by Jacques Monod himself and was included in the text. Along these lines, the MWC model introduces the important notion that signal transduction requires a particular flexibility of protein structure associated with a quaternary constraint established between the subunits within the oligomer, which affects their tertiary organization (and vice versa) (14Monod J. Wyman J. Changeux J.-P. On the nature of allosteric transitions: a plausible model.J. Mol. Biol. 1965; 12: 88-118Crossref PubMed Google Scholar, 21Changeux J.-P. Allostery and the Monod-Wyman-Changeux model after 50 years.Annu. Rev. Biophys. 2012; 41: 103-133Crossref PubMed Scopus (242) Google Scholar, 25Changeux J.-P. The origins of allostery: from personal memories to material for the future.J. Mol. Biol. 2013; 425: 1396-1406Crossref PubMed Scopus (13) Google Scholar). Its principal consequence is the all-or-none character of the molecular switch between discrete conformational states, without intermediate hybrid states, associated with cooperative ligand binding. The statement then enunciated put forward that regulatory proteins spontaneously form closed and symmetrical oligomers (or microcrystals) that exist in a few discrete (all-or-none) and symmetrical (R, T…) conformations in thermal equilibrium in the absence of a regulatory signal. The regulatory ligands do not instruct any new adaptative conformations, but merely shift the spontaneous equilibrium between the conformations, selectively stabilizing the one that displays the biological activity and the highest affinity. The model fundamentally distinguishes a function of state "R," which describes the spontaneous conformational equilibrium (defined by its intrinsic equilibrium constant L0), and a binding function, "Y," which describes the occupation of the binding sites and distinctly evolves as a function of ligand concentration. Several of these statements have since then been reformulated and discussed by several groups in terms of "conformational shift" or "shape shifting" (21Changeux J.-P. Allostery and the Monod-Wyman-Changeux model after 50 years.Annu. Rev. Biophys. 2012; 41: 103-133Crossref PubMed Scopus (242) Google Scholar, 26Boehr D.D. Nussinov R. Wright P.E. The role of dynamic conformational ensembles in biomolecular recognition.Nat. Chem. Biol. 2009; 5: 789-796Crossref PubMed Scopus (1261) Google Scholar, 27Deupi X. Kobilka B.K. Energy landscapes as a tool to integrate GPCR structure, dynamics, and function.Physiology. 2010; 25: 293-303Crossref PubMed Scopus (195) Google Scholar, 28Hammes G.G. Chang Y.C. Oas T.G. Conformational selection or induced fit: a flux description of reaction mechanism.Proc. Natl. Acad. Sci. U.S.A. 2009; 106: 13737-13741Crossref PubMed Scopus (356) Google Scholar, 29Cui Q. Karplus M. Allostery and cooperativity revisited.Protein Sci. 2008; 17: 1295-1307Crossref PubMed Scopus (464) Google Scholar). They created a theoretical landmark in biochemical thinking by opposing a selectionist model to the traditional induced-fit scheme. A year following the MWC publication, Koshland, Némethy, and Filmer attempted to rehabilitate the Pauling scheme for O2 cooperativity in hemoglobin (30Pauling L. The oxygen equilibrium of hemoglobin and its structural interpretation.Proc. Natl. Acad. Sci. U.S.A. 1935; 21: 186-191Crossref PubMed Google Scholar) by proposing an instructive model (KNF) (31Koshland Jr., D.E. Némethy G. Filmer D. Comparison of experimental binding data and theoretical models in proteins containing subunits.Biochemistry. 1966; 5: 365-385Crossref PubMed Google Scholar) that implied a gradual induced change of biophysical parameters with abundant intermediate hybrid states accompanied by the superimposition of the state and binding functions. I took the opportunity to test this prediction during a postdoctoral position with John Gerhart and Howard Schachman. First, I extended the formulation of the MWC model to account for nonexclusive binding of regulatory ligands to both R and T states with the help of Merry Rubin, a computational scientist from the laboratory (32Rubin M.M. Changeux J.-P. On the nature of allosteric transitions: implications of non-exclusive ligand binding.J. Mol. Biol. 1966; 21: 265-274Crossref PubMed Google Scholar). Then making use of the high amounts of purified aspartate transcarbamylase (7Gerhart J.C. Pardee A.B. The enzymology of control by feedback inhibition.J. Biol. Chem. 1962; 237: 891-896Abstract Full Text PDF PubMed Google Scholar, 33Gerhart J.C. Pardee A.B. Aspartate transcarbamylase, an enzyme designed for feedback inhibition.Fed. Proc. 1964; 23: 727-735PubMed Google Scholar) available for binding experiments (34Changeux J.-P. Gerhart J.C. Schachman H.K. Allosteric interactions in aspartate transcarbamylase. I. Binding of specific ligands to the native enzyme and its isolated subunits.Biochemistry. 1968; 7: 531-538Crossref PubMed Google Scholar), together with simultaneously collected conformational data (35Gerhart J.C. Schachman H.K. Allosteric interactions in aspartate transcarbamylase. II. Evidence for different conformational states of the protein in the presence and absence of specific ligands.Biochemistry. 1968; 7: 538-552Crossref PubMed Google Scholar), we were able to demonstrate unambiguous differences between the state and binding functions. Moreover, the aspartate transcarbamylase data could be fitted with the general equation of the MWC model (Ref. 36Changeux J.-P. Rubin M.M. Allosteric interactions in aspartate transcarbamylase. III. Interpretations of experimental data in terms of the model of Monod, Wyman, and Changeux.Biochemistry. 1968; 7: 553-561Crossref PubMed Google Scholar; also see Ref. 37Blangy D. Buc H. Monod J. Kinetics of the allosteric interactions of phosphofructokinase from Escherichia coli.J. Mol. Biol. 1968; 31: 13-35Crossref PubMed Google Scholar with phosphofructokinase). Since the 1960s, abundant structural studies have confirmed the MWC statement that many regulatory devices possess a symmetrical oligomeric structure and undergo the predicted conformational changes (21Changeux J.-P. Allostery and the Monod-Wyman-Changeux model after 50 years.Annu. Rev. Biophys. 2012; 41: 103-133Crossref PubMed Scopus (242) Google Scholar). The MWC model has also elicited new structural and molecular dynamics investigations in hemoglobin (38Perutz M.F. Wilkinson A.J. Paoli M. Dodson G.G. The stereochemical mechanism of the cooperative effects in hemoglobin revisited.Annu. Rev. Biophys. Biomol. Struct. 1998; 27: 1-34Crossref PubMed Scopus (449) Google Scholar, 39Edelstein S.J. Extensions of the allosteric model for haemoglobin.Nature. 1971; 230: 224-227Crossref PubMed Scopus (0) Google Scholar, 40Cammarata M. Levantino M. Wulff M. Cupane A. Unveiling the timescale of the R-T transition in human hemoglobin.J. Mol. Biol. 2010; 400: 951-962Crossref PubMed Scopus (41) Google Scholar, 41Fischer S. Olsen K.W. Nam K. Karplus M. Unsuspected pathway of the allosteric transition in hemoglobin.Proc. Natl. Acad. Sci. U.S.A. 2011; 108: 5608-5613Crossref PubMed Scopus (0) Google Scholar, 42Levantino M. Spilotros A. Cammarata M. Schirò G. Ardiccioni C. Vallone B. Brunori M. Cupane A. The Monod-Wyman-Changeux allosteric model accounts for the quaternary transition dynamics in wild type and a recombinant mutant human hemoglobin.Proc. Natl. Acad. Sci. U.S.A. 2012; 109: 14894-14899Crossref PubMed Scopus (0) Google Scholar, 43Tekpinar M. Zheng W. Coarse-grained and all-atom modeling of structural states and transitions in hemoglobin.Proteins. 2013; 81: 240-252Crossref PubMed Scopus (17) Google Scholar) and was extended to gene repressors (44Lewis M. The lac repressor.C. R. Biol. 2005; 328: 521-548Crossref PubMed Scopus (161) Google Scholar, 45Lewis M. A tale of two repressors.J. Mol. Biol. 2011; 409: 14-27Crossref PubMed Scopus (25) Google Scholar), together with the superfamily of nuclear receptors (46Gronemeyer H. Gustafsson J.A. Laudet V. Principles for modulation of the nuclear receptor superfamily.Nat. Rev. Drug Discov. 2004; 3: 950-964Crossref PubMed Scopus (862) Google Scholar, 47Chandra V. Huang P. Hamuro Y. Raghuram S. Wang Y. Burris T.P. Rastinejad F. Structure of the intact PPAR-γ-RXR-α nuclear receptor complex on DNA.Nature. 2008; 456: 350-356Crossref PubMed Scopus (521) Google Scholar, 48Huang P. Chandra V. Rastinejad F. Structural overview of the nuclear receptor superfamily: insights into physiology and therapeutics.Annu. Rev. Physiol. 2010; 72: 247-272Crossref PubMed Scopus (312) Google Scholar). We shall see that it was also extended to ion channel-linked (49Corringer P.J. Poitevin F. Prevost M.S. Sauguet L. Delarue M. Changeux J.-P. Structure and pharmacology of pentameric receptor channels: from bacteria to brain.Structure. 2012; 20: 941-956Abstract Full Text Full Text PDF PubMed Scopus (155) Google Scholar) and G-protein-linked (50Canals M. Lane J.R. Wen A. Scammells P.J. Sexton P.M. Christopoulos A. A Monod-Wyman-Changeux mechanism can explain G protein-coupled receptor (GPCR) allosteric modulation.J. Biol. Chem. 2012; 287: 650-659Abstract Full Text Full Text PDF PubMed Scopus (89) Google Scholar) membrane receptors. As any scientific theory, the MWC model did not aim to give an exhaustive description of physical reality. It has intrinsic limitations introduced, in particular, by its founding postulates. The formal model was limited to a minimum of two main conformational states, which, as we shall see, are often more numerous (51Prevost M.S. Sauguet L. Nury H. Van Renterghem C. Huon C. Poitevin F. Baaden M. Delarue M. Corringer P.J. A locally closed conformation of a bacterial pentameric proton-gated ion channel.Nat. Struct Mol. Biol. 2012; 19: 642-649Crossref PubMed Scopus (111) Google Scholar, 52Nygaard R. Zou Y. Dror R.O. Mildorf T.J. Arlow D.H. Manglik A. Pan A.C. Liu C.W. Fung J.J. Bokoch M.P. Thian F.S. Kobilka T.S. Shaw D.