Abstract
Homo-multimeric proteins that can come apart, change shape, and reassemble differently with functional consequences have been called morpheeins and/or transformers; these provide a largely unexplored context for understanding disease and developing allosteric therapeutics. This article describes such proteins within the context of protein structure dynamics, provides one detailed example related to an inborn error of metabolism and potential herbicide development, and describes the context for applying these ideas for understanding disease and designing bioactive molecules, such as therapeutics.
Introduction
A great number of medically relevant proteins are homo-multimers, some of which exist as an equilibrium of alternate assemblies that are both non-additive and functionally distinct. The phenomenon wherein protein homo-multimers can come apart, change shape while dissociated, and reassemble into an architecturally and functionally different assembly has been called the morpheein model of protein allostery (; see Morpheein in Wikipedia1). A key to this protein structure dynamic is that the required conformational change is spatially forbidden within the context of either assembly. Proteins with this capacity can be called morpheeins and the alternate assemblies can be called morpheein forms. The dynamic process of dissociation and association makes this mode of allostery distinct from the classic Monod-Wyman-Changeux and Koshland-Nemethy-Filmer models; it provides a conceptually distinct approach to understanding normal protein function, disease-associated protein dysfunction, drug action, and approaches to drug design. This article describes the morpheein model for allosteric regulation, provides a disease relevant example in the protein porphobilinogen synthase, and considers current and future research intended to capitalize on targeting quaternary structure shape shifting in many different proteins as a way to understand disease and develop therapies. Because there are so few well characterized examples, even the most comprehensive treatments of allosteric drug discovery do not address proteins that are established to sample a dynamic equilibrium of assemblies comprised of alternate protomer conformations whose interconversion is forbidden within the assemblies (,).
Morpheeins Within the Context of Protein Structure Dynamics
The existence of morpheeins is one of many protein structure dynamic phenomena that falls outside the classic one sequence – one structure – one function paradigm. Consequently, such discoveries have been surprising (e.g., ; ; ), often serendipitous, and have been accompanied by the introduction of alternate related nomenclature such as transformers and metamorphic proteins (e.g., ; ; ; ). These refer to a continuum of quaternary structure dynamics which expand our view of protein structure beyond the level of primary, secondary, tertiary and quaternary. In the study of ribonucleotide reductase as a drug target, the investigator Aye has referred to going beyond quaternary structure as “breaking the fourth wall”; in the study of Ebola virology, the investigator Ollmann-Saphire has termed it the “fifth level of protein structure” (; ). Herein, we use the term “fifth level of protein structure” to refer to equilibria of alternate assemblies comprised of alternate protomer conformations. This builds on the established concept that protein function is a consequence of an equilibrium of protein structures (). Both Aye’s and Ollmann-Saphire’s treatments highlight that normal protein structure dynamics can include architecturally distinct assemblies with alternate functions that are comprised of different protomer conformations. These assemblies exist as equilibria in the absence of chemical modification. The populations (e.g., mole fraction) of alternate morpheein forms responds to environmental factors (e.g., ionic strength, pH) and most significantly to ligand binding. These factors may govern the predominance of alternate morpheein forms in different cellular locations. Single amino acid substitutions that alter the mole fractions of alternate morpheein forms can cause disease (e.g., ). The morpheein model of protein allostery is a dissociative allosteric model most closely related to the equilibrium models of Nussinov (e.g., ) and Hilser (e.g., ), with the added dimension of quaternary structure. In the prototype morpheein described below, porphobilinogen synthase, the alternate functions are high activity (on) vs. low activity (off) (; ; , ). In the Ebola virus VP40 protein, the alternate functions are entirely separate activities, each one of which is essential for the viral life cycle (). Proteins that can moonlight (carry out unrelated functions, like VP40) were first discovered in the 1980’s (e.g., ), and often arose from cloning the gene responsible for a biological function only to discover that the cloned protein sequence was already known to have a different function. A fascinating example is the protein originally identified as the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase, which now has many documented functions, many of which can be targeted for drug discovery (e.g., ; ). The known moonlighting proteins have recently been assembled by the investigator Jeffery into a MoonProt® database, which currently has ∼400 listings (; ). In most instances it remains to be determined if alternate moonlighting functions are associated with alterations at the fifth level of protein structure. A related fifth level phenomenon is the reversible filamentation of some enzymes, recently reviewed by Horton (, ). Outstanding questions for many filament-forming proteins is whether they are morpheeins (with alternate protomer conformations), moonlighting proteins (with more than one function), or both. Two related enzymes, CTP synthase and IMP dehydrogenase are exemplars of this unknown. Each, separately and together, undergo changes in multimerization or filament formation in response to the state of the cell, but functional distinctions among these assemblies are yet unknown ().
Figure 1 illustrates the morpheein phenomenon using differently shaped dice to represent different conformations of the protomer. Monod first used dice assemblies to illustrate quaternary structures (). Figure 1 shows equilibration between two alternate conformations of the protomer, where one is represented by a cubic die and the other is represented by a pyramidal die. Although not obvious from the representative shapes, the interconversion of these conformations does not require any substantial changes in the protein fold at the level of secondary or tertiary structure. The interconversion is spontaneous; it does not require any external input of energy. It may involve small regions of order – disorder transition. For example, interconversion between the protomer conformations represented by the cube and pyramid could be a hinge motion between two folded domains of each protomer that allows the die face with five dots to associate with the die face with six dots, burying these surfaces. Hinge motions allow protomer shape change without requiring a change in protein fold. In Figure 1, the higher order multimers form by association of the die face with one dot to the die face with four dots. The cubic die forms a symmetric tetramer; the pyramidal die forms a symmetric pentamer. It is easy to imagine how these two assemblies, though made up of chemically identical components, will interact with different cellular partners and potentially have different functions. Note that the surface of the tetramer contains a multimer-specific surface cavity that can serve as a ligand binding site (dashed circle in Figure 1A). The ligand could be a natural allosteric effector molecule, a drug, or another cellular entity (protein, nucleic acid, lipid, membrane surface). The pentamer does not have this same surface cavity and will not interact with the same ligand. In Figure 1B, addition of the imagined ligand causes stabilization of the tetramer, which will draw the structural equilibrium toward the tetramer and alter the protein’s function to that of the tetramer. All of this happens in the absence of post-translational modifications or any other covalent changes to the protein. We note, however, that changes in protein sequence, post-translational modification, or the presence of purification tags can shift the position of the equilibrium (mole fraction of alternate morpheein forms) and enhance or inhibit allosteric ligand binding.
FIGURE 1
The Prototype Morpheein – Porphobilinogen Synthase (PBGS)
PBGS Provides a Physiologic Relevance to the Morpheein Model of Allostery
The physiologic relevance of the morpheein model of allostery was first realized for the protein porphobilinogen synthase (PBGS), whose quaternary structure dynamic is illustrated in Figure 2A (
FIGURE 2

The equilibrium of alternate morpheein forms of PBGS. In all panels, octamer (or pro-octamer dimer) components are in shades of pink; hexamer (or pro-hexamer dimer) components are in shades of blue. (A) The reaction coordinate diagram for the interconversion of human PBGS morpheein forms [adapted with permission from
The PBGS catalyzed reaction is essential for all organisms that rely on methanogenesis, photosynthesis, and/or respiration, thus covering every branch of cellular life. With all this evolutionary time to adapt to the organism’s needs and to function in different cellular environments (e.g., cytoplasm, chloroplast, apicoplast), factors governing the fifth level of PBGS protein structure are not evolutionarily conserved. Additionally, the amino acid composition of the targeted surface cavities is not conserved, unlike active site residues. This makes the allosteric regulation of PBGS a potential target for the development of antimicrobials and herbicides. In some species (e.g., plants, bacteria, archaea) the equilibrium position depends upon an allosteric magnesium binding at an interface only present in the octamer (see yellow arrow in Figure 2B). In PBGS from metazoa and fungi, which lack the magnesium binding site, in its place is the guanidinium group of an arginine residue. In the human PBGS variant where a leucine is substituted for Phe12 (F12L), from which we obtained the crystal structure of the hexameric assembly (
Control of PBGS Morpheein Forms by pH and Ligand Binding
The human PBGS pH rate profile (Figure 2B) helped reveal a pH dependence to the quaternary structure equilibrium of wild type human PBGS (see the bottom panel of Figure 2B;
Although the PBGS quaternary structure equilibrium is controlled by different factors in different branches of life, there are unifying characteristics in the pH rate profiles of alternate PBGS morpheein forms. Mammalian PBGS at neutral pH (see Figure 2B, bottom), and plant/bacterial PBGS with magnesium present are predominantly octameric and are documented to have KM values in the range of ∼150 μM (
FIGURE 3

Native PAGE illustrates how allosteric ligands control the distribution of PBGS morpheein forms. (A) The distribution of morpheein forms of E. coli PBGS responds to magnesium and substrate (ALA), both of which stabilize the octamer [image adapted with permission from
An Inborn Error of Metabolism Is Linked to Perturbation of an Equilibrium of Morpheein Forms
ALAD porphyria is a rare inborn error of metabolism caused by dysfunctional PBGS and inherited as a recessive disease (
FIGURE 4

The activity vs. substrate relationship for disease-associated human PBGS proteins indicate the presence of two morpheein forms at neutral pH. The dashed lines are fitted to the hyperbolic Michaelis–Menten equations, which is an excellent fit for the WT protein. The solid lines are double hyperbolic fits (the sum of two species with different KM and VMAX values) [image adapted with permission from
We have posited that the disequilibrium of alternate assemblies contributes to the complex phylogenetic patterns seen in the most common inborn error of amino acid metabolism, phenylketonuria, which is caused by dysfunctional phenylalanine hydroxylase (
We Could Easily Have Missed the Fifth Level of Protein Structure When Studying PBGS
The four levels of protein structure are introduced in every biochemistry text. Additionally, the relationship between sequence, structure, and function is the foundation of broad applications of bioinformatics, which drive much biomedical research. For the first 20 years that we studied PBGS, we were not looking for the fifth level of protein structure. All of our data prior to ∼2003 was interpreted within the context that PBGS has one fixed quaternary architecture, which is an octamer (e.g.,
The first PBGS crystal structure, published in 1997, showed the architecture of the octamer, establishing precedent, as crystal structures often do (
Finding Proteins That Experience the Fifth Level of Protein Structure
Since the fifth level of protein structure provides an additional way to manipulate protein function, it also provides an additional approach to allosteric drug discovery. Consequently, there is value in identifying proteins that behave as morpheeins. This goal remains difficult. The initial discovery of the morpheein character of PBGS was serendipitously based on in vitro protein behavior coupled with X-ray crystal structures showing architecturally different assemblies comprised of different protomer conformations, but not different folds. This discovery was not based on a bioinformatics approach. The PBGS example presented itself because there happened to be a naturally occurring variant, F12L, that sufficiently stabilized the hexameric assembly to obtain its crystal structure. Although the wild-type human PBGS was later realized to readily equilibrate between octamer and hexamer in a pH-dependent fashion (Figure 2), to date all conditions that have yielded diffraction quality crystals of the wild-type protein favored crystals comprised of octamer. Serendipity favored our studying F12L; we could not have predicted the effect of this mutation. Well-established computational approaches (e.g., the program FoldX;
Our initial approach to identifying proteins that use the fifth level of protein structure was to manually search the literature for proteins that have one or more characteristics that we had documented for PBGSs. This approach was especially challenging as most of these characteristics were not contained in the searchable abstract or keywords and much of the older literature was not yet available as text-searchable PDF documents. Some of the characteristics we focused on are listed in Table 1; the characteristics included in Table 1 are each consistent with an equilibrium of alternate assemblies, but none are strictly diagnostic. Each of these behaviors can be otherwise attributed. Trevor Selwood’s herculean efforts generated boxes of reprints and a list of putative morpheeins (
TABLE 1
| Characteristic | Comments |
| SDS-pure protein separating into alternate bands on native PAGE can indicate multimers of alternate stoichiometry (or conformation). | Native PAGE can be routinely incorporated into the final stages of protein characterization. |
| SDS-pure protein that separates into alternate forms using ion exchange chromatography | This has been used to monitor the interconversion of alternate assemblies as a function of ligand. |
| The enzyme-kinetic phenomenon known as hysteresis. | This can be observed if the transition from a low activity form to a high activity form occurs during the assay [as we have shown for the R240A variant of PBGS ( |
| Double hyperbolic kinetics (the sum of two hyperbola with different kinetic constants). | This can indicate alternate morpheein forms with different kinetic constants. Seeing this may require using a broad range of substrate concentration (see Figure 4). |
| X-ray crystal structures of multi-domain proteins that cannot be superposed without clashes. This observation is often dismissed as an artifact of crystal packing. | Many multi-domain proteins do not produce diffraction quality crystals. A common approach is to truncate one or more domains. If overlaying the common elements of such structures causes domains to clash, this could be a sign of alternate assemblies. This was observed for alternate truncated constructs of HIV integrase ( |
| Protein concentration dependent specific activity can indicate alternate activities associated with different multimeric stoichiometries. | This is seen for all PBGS that use only magnesium [e.g., ( |
| Evidence for soluble protein multimers that dissociate along a hydrophilic protein-protein interface. | This is a difficult characteristic to search for as many crystal structure files are at insufficient resolution to position water molecules. PBGS crystal structures contain phylogenetically conserved water molecules at the subunit-subunit interfaces that dissociate upon formation of the dimeric morpheein forms ( |
Protein behaviors that might indicate an equilibrium of morpheein forms.
Nevertheless, a key question remains as to how we can use what we have learned from PBGS to harness the fifth level of protein structure for drug discovery. In the PBGS example, the difference between the protomer that forms a hexamer and the protomer that forms an octamer is a hinge between two domains, without significantly altering the fold of these domains. This is also the case for alternate assemblies of the HIV integrase protein, where a hinge motion dictates formation of a core-core-dimer vs. a reaching dimer; and where it has been pointed out that small molecule stabilization of one or the other dimer, to prevent their interconversion, could yield a therapeutic (
Identifying Allosteric Regulators (E.G., Therapeutics)
Using PBGS as an example, we have demonstrated how an equilibrium of morpheein forms can be manipulated in ways related to drugs. Realistically, ALAD porphyria is such a rare disorder that finding an octamer-stabilizing allosteric effector is, at best, an academic exercise. However, stabilization of a PBGS hexamer could form the basis for an antimicrobial or herbicide. To test this hypothesis, we targeted a hexamer-specific surface cavity on the model of a plant PBGS hexamer (in silico docking/in vitro testing) and found a hexamer-stabilizing inhibitor that did not affect human PBGS (
Conclusion and Future Outlook
Proteins that can come apart, change shape, and reassemble differently with functional consequences provide expanded opportunities for understanding disease and designing therapeutics. This fifth level of protein structure provides another example where the one sequence/one structure/one function rule fails to provide the correct framework for data interpretation. Biophysical techniques that are becoming more widely available, (e.g., SEC-MALS, SEC-SAXS, cryo-EM, light scattering, to name just a few) are revealing the shape changing behavior of many disease-associated multimeric proteins. Other forms of microscopy are revealing changes in protein locations within cells. In some instances, these are associated with protein filamentation. All of these observations suggest the potential for harnessing the fifth level of protein structure for therapeutic advantage. As described, a few notable examples include ribonucleotide reductase (
Statements
Author contributions
The author confirms being the sole contributor of this work and has approved it for publication.
Funding
This work has been funded by grants from the National Institutes of Health 5R01 ES003654; 5R21 AI063324; 5R01 NS100081; and in part by the National Institutes of Health NCI Cancer Center Support Grant P30 CA006927. The content is solely the responsibility of the author and does not necessarily represent the official views of the National Institutes of Health. Continuous support is acknowledged from the Fox Chase Cancer Center, now a part of the Temple University Health Systems.
Acknowledgments
The author acknowledges many who have contributed to our deciphering the quaternary structure dynamics of PBGS, most notably Drs. Sabine Breinig, Sarah H. Lawrence, Trevor Selwood, and Lei Tang, and Ms. Linda Stith. Special acknowledgment is given to Emilia Arturo who has contributed to expanding our general appreciation for the fifth level of protein structure.
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Footnotes
References
1
AndrakeM. D.SkalkaA. M. (2015). Retroviral integrase: then and now.Annu. Rev. Virol.2241–264. 10.1146/annurev-virology-100114-055043
2
BojjaR. S.AndrakeM. D.MerkelG.WeigandS.DunbrackR. L.Jr.SkalkaA. M. (2013). Architecture and assembly of HIV integrase multimers in the absence of DNA substrates.J. Biol. Chem.2887373–7386. 10.1074/jbc.m112.434431
3
BornholdtZ. A.NodaT.AbelsonD. M.HalfmannP.WoodM. R.KawaokaY.et al (2013). Structural rearrangement of ebola virus VP40 begets multiple functions in the virus life cycle.Cell154763–774. 10.1016/j.cell.2013.07.015
4
BreinigS.KervinenJ.StithL.WassonA. S.FairmanR.WlodawerA.et al (2003). Control of tetrapyrrole biosynthesis by alternate quaternary forms of porphobilinogen synthase.Nat. Struct. Biol.10757–763. 10.1038/nsb963
5
BuzonP.Ruiz-SanzJ.MartinezJ. C.LuqueI. (2020). Stability, conformational plasticity, oligomerization behaviour and equilibrium unfolding intermediates of the Ebola virus matrix protein VP40.J. Biomol. Struct. Dyn.384289–4303. 10.1080/07391102.2019.1671226
6
ChenC.ZabadS.LiuH.WangW.JefferyC. (2018). MoonProt 2.0: an expansion and update of the moonlighting proteins database.Nucleic Acids Res.46D640–D644.
7
Del VecchioK.FrickC. T.GcJ. B.OdaS. I.GerstmanB. S.SaphireE. O.et al (2018). A cationic, C-terminal patch and structural rearrangements in Ebola virus matrix VP40 protein control its interactions with phosphatidylserine.J. Biol. Chem.2933335–3349. 10.1074/jbc.m117.816280
8
DishmanA. F.VolkmanB. F. (2018). Unfolding the mysteries of protein metamorphosis.ACS Chem. Biol.131438–1446. 10.1021/acschembio.8b00276
9
ErskineP. T.SeniorN.AwanS.LambertR.LewisG.TickleL. J.et al (1997). X-ray structure of 5-aminolaevulinate dehydratase, a hybrid aldolase.Nat. Struct. Biol.41025–1031. 10.1038/nsb1297-1025
10
FrankenbergN.ErskineP. T.CooperJ. B.Shoolingin-JordanP. M.JahnD.HeinzD. W. (1999). High resolution crystal structure of a Mg2+-dependent porphobilinogen synthase.J. Mol. Biol.289591–602. 10.1006/jmbi.1999.2808
11
GuptaK.TurkkiV.Sherrill-MixS.HwangY.EilersG.TaylorL.et al (2016). Structural basis for inhibitor-induced aggregation of HIV integrase.PLoS Biol.14:e1002584. 10.1371/journal.pbio.1002584
12
GurneyM. E.HeinrichS.LeeM. R.YinH. S. (1986). Molecular cloning and expression of neuroleukin, a neurotrophic factor for spinal and sensory neurons.Science234566–574. 10.1126/science.3764429
13
JaffeE. K. (2003). An unusual phylogenetic variation in the metal ion binding sites of porphobilinogen synthase.Chem. Biol.1025–34. 10.1016/s1074-5521(02)00296-x
14
JaffeE. K. (2004). The porphobilinogen synthase catalyzed reaction mechanism.Bioorg. Chem.32316–325. 10.1016/j.bioorg.2004.05.010
15
JaffeE. K. (2005). Morpheeins–a new structural paradigm for allosteric regulation.Trends Biochem. Sci.30490–497. 10.1016/j.tibs.2005.07.003
16
JaffeE. K. (2016). The remarkable character of porphobilinogen synthase.Acc. Chem. Res.492509–2517. 10.1021/acs.accounts.6b00414
17
JaffeE. K. (2017). New protein structures provide an updated understanding of phenylketonuria.Mol. Genet. Metab.121289–296. 10.1016/j.ymgme.2017.06.005
18
JaffeE. K. (2020). “Chapter three - porphobilinogen synthase: an equilibrium of different assemblies in human health, in progress,” in Molecular Biology and Translational Science, edsGiraldoJ.CiruelaF. (Cambridge, MA: Academic Press), 85–104. 10.1016/bs.pmbts.2019.11.003
19
JaffeE. K.AliS.MitchellL. W.TaylorK. M.VolinM.MarkhamG. D. (1995). Characterization of the role of the stimulatory magnesium of Escherichia coli porphobilinogen synthase.Biochemistry34244–251. 10.1021/bi00001a029
20
JaffeE. K.LawrenceS. H. (2014). “The dance of porphobilinogen synthase in the control of tetrapyrrole biosynthesis,” in Handbook of Porphyrin Science, ed.FerreiraG. C. (Toh Tuck: World Scientific Publishing Co. Pte. Ltd), 79–128. 10.1142/9789814407755_0002
21
JaffeE. K.MarkhamG. D. (1988). C-13 Nmr-Studies of methylene and methine carbons of substrate-bound to a 280000-Dalton protein, porphobilinogen synthase.Biochemistry274475–4481. 10.1021/bi00412a039
22
JaffeE. K.ShanmugamD.GardbergA.DieterichS.SankaranB.StewartL. J.et al (2011). Crystal structure of Toxoplasma gondii porphobilinogen synthase: insights on octameric structure and porphobilinogen formation.J. Biol. Chem.28615298–15307. 10.1074/jbc.m111.226225
23
JaffeE. K.StithL. (2007). ALAD porphyria is a conformational disease.Am. J. Hum. Genet.80329–337. 10.1086/511444
24
JaffeE. K.StithL.LawrenceS. H.AndrakeM.DunbrackR. L.Jr. (2013). A new model for allosteric regulation of phenylalanine hydroxylase: implications for disease and therapeutics.Arch. Biochem. Biophys.53073–82. 10.1016/j.abb.2012.12.017
25
KarG.KeskinO.GursoyA.NussinovR. (2010). Allostery and population shift in drug discovery.Curr. Opin. Pharmacol.10715–722. 10.1016/j.coph.2010.09.002
26
KashlanO. B.CoopermanB. S. (2003). Comprehensive model for allosteric regulation of mammalian ribonucleotide reductase: refinements and consequences.Biochemistry421696–1706. 10.1021/bi020634d
27
KervinenJ.DunbrackR. L.Jr.LitwinS.MartinsJ.ScarrowR. C.VolinM.et al (2000). Porphobilinogen synthase from pea: expression from an artificial gene, kinetic characterization, and novel implications for subunit interactions.Biochemistry399018–9029. 10.1021/bi000620c
28
KervinenJ.JaffeE. K.StaufferF.NeierR.WlodawerA.ZdanovA. (2001). Mechanistic basis for suicide inactivation of porphobilinogen synthase by 4,7-dioxosebacic acid, an inhibitor that shows dramatic species selectivity.Biochemistry408227–8236. 10.1021/bi010656k
29
KokonaB.RigottiD. J.WassonA. S.LawrenceS. H.JaffeE. K.FairmanR. (2008). Probing the oligomeric assemblies of pea porphobilinogen synthase by analytical ultracentrifugation.Biochemistry4710649–10656. 10.1021/bi801128d
30
KopeckovaM.PavkovaI.StulikJ. (2020). Diverse localization and protein binding abilities of Glyceraldehyde-3-Phosphate dehydrogenase in pathogenic bacteria: the key to its multifunctionality?Front. Cell. Infect. Microbiol.10:89.
31
LawrenceS. H.RamirezU. D.TangL.FazliyezF.KundratL.MarkhamG. D.et al (2008). Shape shifting leads to small-molecule allosteric drug discovery.Chem. Biol.15586–596. 10.1016/j.chembiol.2008.04.012
32
LawrenceS. H.SelwoodT.JaffeE. K. (2011). Diverse clinical compounds alter the quaternary structure and inhibit the activity of an essential enzyme.Chem. Med. Chem.61067–1073. 10.1002/cmdc.201100009
33
LawrenceS. H.SelwoodT.JaffeE. K. (2013). Environmental contaminants perturb fragile protein assemblies and inhibit normal protein function.Curr. Chem. Biol.7196–206. 10.2174/2212796811307020011
34
LazarevV. F.GuzhovaI. V.MargulisB. A. (2020). Glyceraldehyde-3-phosphate dehydrogenase is a multifaceted therapeutic target.Pharmaceutics12:416. 10.3390/pharmaceutics12050416
35
LongM. J. C.Hall-BeauvaisA.VanAyeY. (2020). The more the merrier: how homo-oligomerization alters the interactome and function of ribonucleotide reductase.Curr. Opin. Chem. Biol.5410–18. 10.1016/j.cbpa.2019.09.003
36
LongM. J. C.HnedzkoD.KimB. K.AyeY. (2019). Breaking the fourth wall: modulating quaternary associations for protein regulation and drug discovery.Chembiochem201091–1104. 10.1002/cbic.201800716
37
Lopez-PelegrinM.Cerda-CostaN.Cintas-PedrolaA.Herranz-TrilloF.PeinadoJ. R.et al (2014). Multiple stable conformations account for reversible concentration-dependent oligomerization and autoinhibition of a metamorphic metallopeptidase.Angew. Chem. Int. Ed. Engl.5310624–10630. 10.1002/anie.201405727
38
LuS.HeX.NiD.ZhangJ. (2019a). Allosteric modulator discovery: from serendipity to structure-based design.J. Med. Chem.626405–6421. 10.1021/acs.jmedchem.8b01749
39
LuS.ShenQ.ZhangJ. (2019b). Allosteric methods and their applications: facilitating the discovery of allosteric drugs and the investigation of allosteric mechanisms.Acc. Chem. Res.52492–500. 10.1021/acs.accounts.8b00570
40
ManiM.ChenC.AmbleeV.LiuH.MathurT.ZwickeG.et al (2015). MoonProt: a database for proteins that are known to moonlight.Nucleic Acids Res.43D277–D282.
41
MarunoM.FuruyamaK.AkagiR.HorieY.MeguroK.GarbaczewskiL.et al (2001). Highly heterogeneous nature of delta-aminolevulinate dehydratase (ALAD) deficiencies in ALAD porphyria.Blood972972–2978. 10.1182/blood.v97.10.2972
42
Mills-DaviesN.ButlerD.NortonE.ThompsonD.SarwarM.GuoJ.et al (2017). Structural studies of substrate and product complexes of 5-aminolaevulinic acid dehydratase from humans, Escherichia coli and the hyperthermophile Pyrobaculum calidifontis.Acta Crystallogr. D. Struct. Biol.73(Pt 1)9–21.
43
MitchellL. W.JaffeE. K. (1992). Escherichia-Coli porphobilinogen synthase is a Zn(Ii) metalloenzyme.FASEB J.6A459–A459.
44
MitchellL. W.JaffeE. K. (1993). Porphobilinogen synthase from Escherichia-coli is a Zn(Ii) metalloenzyme stimulated by Mg(Ii).Arch. Biochem. Biophys.300169–177. 10.1006/abbi.1993.1024
45
MonodJ. (1965). [Reflections on the relationship between the structure and function of globular proteins].Annee Biol.59231–240.
46
MotlaghH. N.WrablJ. O.LiJ.HilserV. J. (2014). The ensemble nature of allostery.Nature508331–339. 10.1038/nature13001
47
MurzinA. G. (2008). Metamorphic proteins.3201725–1726. 10.1126/science.1158868
48
ParisiG.ZeaD. J.MonzonA. M.Marino-BusljeC. (2015). Conformational diversity and the emergence of sequence signatures during evolution.Curr. Opin. Struct. Biol.3258–65. 10.1016/j.sbi.2015.02.005
49
ParkC. K.HortonN. C. (2019). Structures, functions, and mechanisms of filament forming enzymes: a renaissance of enzyme filamentation.Biophys. Rev.11927–994. 10.1007/s12551-019-00602-6
50
ParkC. K.HortonN. C. (2020). Novel insights into filament-forming enzymes.Nat. Rev. Mol. Cell Biol.211–2. 10.1038/s41580-019-0188-1
51
PetrovichR. M.LitwinS.JaffeE. K. (1996). Bradyrhizobium japonicum porphobilinogen synthase uses two Mg(II) and monovalent cations.J. Biol. Chem.2718692–8699. 10.1074/jbc.271.15.8692
52
SchymkowitzJ.BorgJ.StricherF.NysR.RousseauF.SerranoL. (2005). The FoldX web server: an online force field.Nucleic Acids Res.33W382–W388.
53
SelwoodT.JaffeE. K. (2012). Dynamic dissociating homo-oligomers and the control of protein function.Arch Biochem. Biophys.519131–143. 10.1016/j.abb.2011.11.020
54
SelwoodT.TangL.LawrenceS. H.AnokhinaY.JaffeE. K. (2008). Kinetics and thermodynamics of the interchange of the morpheein forms of human porphobilinogen synthase.Biochemistry473245–3257. 10.1021/bi702113z
55
ShanmugamD.WuB.RamirezU.JaffeE. K.RoosD. S. (2010). Plastid-associated porphobilinogen synthase from Toxoplasma gondii: kinetic and structural properties validate therapeutic potential.J. Biol. Chem.28522122–22131. 10.1074/jbc.m110.107243
56
SimonetJ. C.BurrellA. L.KollmanJ. M.PetersonJ. R. (2020). Freedom of assembly: metabolic enzymes come together.Mol. Biol. Cell311201–1205. 10.1091/mbc.e18-10-0675
57
StolzM.DornemannD. (1996). Purification, metal cofactor, N-terminal sequence and subunit composition of a 5-aminolevulinic acid dehydratase from the unicellular green alga Scenedesmus obliquus, mutant C-2A’.Eur. J. Biochem.236600–608. 10.1111/j.1432-1033.1996.00600.x
58
TangL.BreinigS.StithL.MischelA.TannirJ.KokonaB.et al (2006). Single amino acid mutations alter the distribution of human porphobilinogen synthase quaternary structure isoforms (morpheeins).J. Biol. Chem.2816682–6690. 10.1074/jbc.m511134200
59
ThomasW. C.BrooksF.IIIBurnimA. A.BacikJ.StubbeJ.KaelberJ. T.et al (2019). Convergent allostery in ribonucleotide reductase.Nat. Commun.10:2653.
60
WassermanH.SaphireE. O. (2016). More than meets the eye: hidden structures in the proteome.Annu. Rev. Virol.3373–386. 10.1146/annurev-virology-100114-054923
61
WuW. H.SheminD.RichardsK. E.WilliamsR. C. (1974). The quaternary structure of delta-aminolevulinic acid dehydratase from bovine liver.Proc. Natl. Acad. Sci. U.S.A.711767–1770. 10.1073/pnas.71.5.1767
Summary
Keywords
protein structure dynamics, allostery, morpheein, fifth level of protein structure, drug discovery
Citation
Jaffe EK (2020) Wrangling Shape-Shifting Morpheeins to Tackle Disease and Approach Drug Discovery. Front. Mol. Biosci. 7:582966. doi: 10.3389/fmolb.2020.582966
Received
13 July 2020
Accepted
26 October 2020
Published
27 November 2020
Volume
7 - 2020
Edited by
Guang Hu, Soochow University, China
Reviewed by
Jian Zhang, Shanghai Jiao Tong University, China; Claire Lesieur, UMR 5005 Laboratoire Ampère (Ampère), France; Athi N. Naganathan, Indian Institute of Technology Madras, India
Updates

Check for updates
Copyright
© 2020 Jaffe.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Eileen K. Jaffe, Eileen.Jaffe@fccc.edu
This article was submitted to Biological Modeling and Simulation, a section of the journal Frontiers in Molecular Biosciences
Disclaimer
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.