Biology:Morpheein

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Short description: Model of protein allosteric regulation


Proteins that function as morpheeins are illustrated using a dice analogy where one dice can morph into two different shapes, cubic and tetrahedral. The illustrated assemblies apply a rule that the dice face with one spot must contact the dice face with four spots. To satisfy the rule for each dice in an assembly, the cubic dice can only form a tetramer and the tetrahedral dice can only assemble to a pentamer. This is analogous to two different conformations (morpheein forms) of a protein subunit each dictating assembly to a different oligomer. All dice in one assembly must be of the same shape before assembly. Thus, for example, the tetramer must come apart, and its component dice must change shape to a pyramid before they can participate in assembly into a pentamer.

Morpheeins are proteins that can form two or more different homo-oligomers (morpheein forms), but must come apart and change shape to convert between forms. The alternate shape may reassemble to a different oligomer. The shape of the subunit dictates which oligomer is formed.[1][2] Each oligomer has a finite number of subunits (stoichiometry). Morpheeins can interconvert between forms under physiological conditions and can exist as an equilibrium of different oligomers. These oligomers are physiologically relevant and are not misfolded protein; this distinguishes morpheeins from prions and amyloid. The different oligomers have distinct functionality. Interconversion of morpheein forms can be a structural basis for allosteric regulation, an idea noted many years ago,[3][4] and later revived.[1][2][5][6] A mutation that shifts the normal equilibrium of morpheein forms can serve as the basis for a conformational disease.[7] Features of morpheeins can be exploited for drug discovery.[1][5][8] The dice image (Fig 1) represents a morpheein equilibrium containing two different monomeric shapes that dictate assembly to a tetramer or a pentamer. The one protein that is established to function as a morpheein is porphobilinogen synthase,[2][9][10] though there are suggestions throughout the literature that other proteins may function as morpheeins (for more information see "Table of Putative Morpheeins" below).

Implications for drug discovery

Conformational differences between subunits of different oligomers and related functional differences of a morpheein provide a starting point for drug discovery. Protein function is dependent on the oligomeric form; therefore, the protein's function can be regulated by shifting the equilibrium of forms. A small molecule compound can shift the equilibrium either by blocking or favoring formation of one of the oligomers. The equilibrium can be shifted using a small molecule that has a preferential binding affinity for only one of the alternate morpheein forms. An inhibitor of porphobilinogen synthase with this mechanism of action has been documented.[5]


Implications for allosteric regulation

The morpheein model of allosteric regulation has similarities to and differences from other models.[1][6][11] The concerted model (the Monod, Wyman and Changeux (MWC) model) of allosteric regulation requires all subunits to be in the same conformation or state within an oligomer like the morpheein model.[12][13] However, neither this model nor the sequential model (Koshland, Nemethy, and Filmer model) takes into account that the protein may dissociate to interconvert between oligomers.[12][13][14][15] Nonetheless, shortly after these theories were described, two groups of workers[3][4] proposed what is now called the morpheein model and showed that it accounted for the regulatory behavior of glutamate dehydrogenase.[16] Kurganov and Friedrich discussed models of this kind extensively in their books.[17][18]

Implications for teaching about protein structure-function relationships

It is generally taught [citation needed] that a given amino acid sequence will have only one physiologically relevant (native) quaternary structure; morpheeins challenge this concept. The morpheein model does not require gross changes in the basic protein fold.[1] The conformational differences that accompany conversion between oligomers may be similar to the protein motions necessary for function of some proteins.[19] The morpheein model highlights the importance of conformational flexibility for protein functionality and offers a potential explanation for proteins showing non-Michaelis-Menten kinetics, hysteresis, and/or protein concentration dependent specific activity.[11]

Implications for understanding the structural basis for disease

The term "conformational disease" generally encompasses mutations that result in misfolded proteins that aggregate, such as Alzheimer's and Creutzfeldt–Jakob diseases.[20] In light of the discovery of morpheeins, however, this definition could be expanded to include mutations that shift an equilibrium of alternate oligomeric forms of a protein. An example of such a conformational disease is ALAD porphyria, which results from a mutation of porphobilinogen synthase that causes a shift in its morpheein equilibrium.[7]

Table of proteins whose published behavior is consistent with that of a morpheein

[6]

Protein Example species EC number CAS number Alternate oligomers Evidence
Acetyl-CoA carboxylase-1 Gallus domesticus EC 6.4.1.2 9023-93-2 inactive dimer, active dimer, larger[21] Effector molecules impact multimerization,[22] Multiple/protein moonlighting functions[21]
α-Acetylgalactosaminidase Bos taurus EC 4.3.2.2 9027-81-0 inactive monomer, active tetramer[23] Substrate binding/turnover impacts multimerization,[23] Protein concentration dependent specific activity,[24] Different assemblies have different activities,[24] Conformationally distinct oligomeric forms.[23][24]
Adenylosuccinate lyase Bacillus subtilis EC 4.3.2.2 9027-81-0 monomer, dimer, trimer, tetramer[25] Mutations shift the equilibrium of oligomers,[26] Oligomer-dependent kinetic parameters,[26] Protein concentration dependent molecular weight[26]
L-Asparaginase Leptosphaeria michotii EC 3.5.1.1 9015-68-3 dimer, tetramer, inactive octamer[27] Substrate binding/turnover impacts multimerization[28]
Aspartokinase Escherichia coli EC 2.7.2.4 & EC 1.1.1.3 9012-50-4 monomer, dimer, tetramer[29][30] Multiple/protein moonlighting functions,[31] Conformationally distinct oligomeric forms[30]
ATPase of the ABCA1 transporter Homo sapiens dimer, tetramer[32] Substrate binding/turnover impacts multimerization[32]
Biotin—(acetyl-CoA-carboxylase) ligase holoenzyme synthetase Escherichia coli EC 6.3.4.15 37340-95-7 monomer, dimer[33] Multiple/protein moonlighting functions,[33] Different assemblies have different activities[34]
Chorismate mutase Escherichia coli EC 5.4.99.5 9068-30-8 dimer, trimer, hexamer Conformationally distinct oligomeric forms[35]
Citrate synthase Escherichia coli EC 2.3.3.1 9027-96-7 monomer, dimer, trimer, tetramer, pentamer, hexamer, dodecamer[36] Substrate binding/turnover impacts multimerization,[36] Characterized equilibrium of oligomers,[36] Protein concentration dependent specific activity,[36] pH-dependent oligomeric equilibrium[36]
Cyanovirin-N Nostoc ellipsosporum 918555-82-5 monomer and domain-swapped dimer[37][38] Characterized equilibrium of oligomers,[39][40] Conformationally distinct oligomeric forms[39][40]
3-oxoacid CoA-transferase Sus scrofa domestica EC 2.8.3.5 9027-43-4 dimer, tetramer[41] Chromatographically separable oligomers,[41] Substrate might preferentially stabilize one form[41]
Cystathionine β-synthase Homo sapiens EC 4.2.1.22 9023-99-8 multiple - ranges from dimer to 16-mer[42] Effector molecules impact multimerization,[43] Mutations shift the equilibrium of oligomers,[44] Different assemblies have different activities,[43] disease-causing mutations at sites distant from active site[45]
D-amino acid oxidase EC 1.4.3.3 9000-88-8 monomers, dimers, higher-order oligomers[46][47] Oligomer-dependent kinetic parameters[46][47]
Dihydrolipoamide dehydrogenase Sus scrofa domestica EC 1.8.1.4 9001-18-7 monomer, two different dimer forms, tetramer[48] Multiple/protein moonlighting functions,[48] Different assemblies have different activities,[48] pH-dependent oligomeric equilibrium,[48] Conformationally distinct oligomeric forms[49][50][51]
Dopamine β-monooxygenase Bos taurus EC 1.14.17.1 9013-38-1 dimers, tetramers[52][53][54] Effector molecules impact multimerization,[52][53][54] Characterized equilibrium of oligomers,[52][53][54] Oligomer-dependent kinetic parameters[52][53][54]
Geranylgeranyl pyrophosphate synthase / Farnesyltranstransferase Homo sapiens EC 2.5.1.29 9032-58-0 hexamer, octamer[55][56][57] Effector molecules impact multimerization[56]
GDP-mannose 6-dehydrogenase Pseudomonas aeruginosa EC 1.1.1.132 37250-63-8 trimer, 2 tetramers, and hexamer[58][59] Protein concentration dependent specific activity,[60] Kinetic hysteresis[60]
Glutamate dehydrogenase Bos taurus EC 1.4.1.2 9001-46-1 active & inactive hexamers, higher order[61] Effector molecules impact multimerization,[62] Characterized equilibrium of oligomers[61]
Glutamate racemase Mycobacterium tuberculosis, Escherichia coli, Bacillus subtilis, Aquifex pyrophilus EC 5.1.1.3 9024-08-02 monomer, 2 dimers, tetramer[63][64][65][66][67] Multiple/protein moonlighting functions,[68][69][70] Characterized equilibrium of oligomers,[66][67] Conformationally distinct oligomeric forms[63][64][65]
Glyceraldehyde-3-phosphate dehydrogenase Oryctolagus cuniculas, Sus scrofa domestica EC 1.2.1.12 1.2.1.12 9001-50-7 monomer, dimer, tetramer[71] Characterized equilibrium of oligomers,[72] Different assemblies have different activities[73]
Glycerol kinase Escherichia coli EC 2.7.1.30 9030-66-4 monomer and 2 tetramers[74][75][76] Characterized equilibrium of oligomers,[74][75][76][77] Conformationally distinct oligomeric forms,[77][78] Effector functions by preventing domain motion[78]
HPr-Kinase/phosphatase Bacillus subtilis, Lactobacillus casei, Mycoplasma pneumoniae, Staphylococcus xylosus EC 2.7.1.-/ EC 3.1.3.- 9026-43-1 monomers, dimers, trimers, hexamers[79][80][81][82][83][84] Effector molecules impact multimerization,[83] Multiple/protein moonlighting functions,[83] Different assemblies have different activities,[83] pH-dependent oligomeric equilibrium[83]
Lactate dehydrogenase Bacillus stearothermophilus EC 1.1.1.27 9001-60-9 2 dimers, tetramer[85][86] Effector molecules impact multimerization,[86] Characterized equilibrium of oligomers,[86] Protein concentration dependent specific activity,[86] Mutations shift the equilibrium of oligomers,[87] Oligomer-dependent kinetic parameters,[86] Conformationally distinct oligomeric forms[88]
Lon protease Escherichia coli, Mycobacterium smegmatis EC 3.4.21.53 79818-35-2 monomer, dimer, trimer, tetramer[89][90] Effector molecules impact multimerization,[89][90] Substrate binding/turnover impacts multimerization,[89][90] Protein concentration dependent specific activity,[91] Kinetic hysteresis[91]
Mitochondrial NAD(P)+ Malic enzyme / malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) Homo sapiens EC 1.1.1.40 9028-47-1 monomer, 2 dimers, tetramer[92][93] Effector molecules impact multimerization,[92] Mutations shift the equilibrium of oligomers,[94] Kinetic hysteresis,[93]
Peroxiredoxins Salmonella typhimurium EC 1.6.4.- & EC 1.11.1.15 207137-51-7 2 dimers, decamer Conformationally distinct oligomeric forms,[95] Different assemblies have different activities[96]
Phosphoenolpyruvate carboxylase Escherichia coli, Zea mays EC [1] 9067-77-0 inactive dimer, active tetramer[97] Effector molecules impact multimerization, Characterized equilibrium of oligomers,[97] Kinetic hysteresis,[97] Conformationally distinct oligomeric forms[98]
Phosphofructokinase Bacillus stearothermophilus, Thermus thermophilus EC 2.7.1.11 9001-80-3 inactive dimer, active tetramer[97][99] Effector molecules impact multimerization,[97][99] Characterized equilibrium of oligomers[97][99]
Polyphenol oxidase Agaricus bisporus, Malus domestica, Lactuca sativa L. EC 1.10.3.1 9002-10-2 monomer, trimer, tetramer, octamer, dodecamer[100][101] Multiple/protein moonlighting functions,[102] Substrate binding/turnover impacts multimerization,[103] Different assemblies have different activities,[104] Kinetic hysteresis[103]
Porphobilinogen synthase Drosophila melanogaster, Danio rerio EC 4.2.1.24 9036-37-7 dimer, hexamer, octamer[105][106] PBGS is the prototype morpheein.[105]
Pyruvate kinase Homo sapiens EC 2.7.1.40 9001-59-6 active and inactive dimers, active tetramer, monomer, trimer, pentamer[107][108] Conformationally distinct oligomeric forms[107][108]
Ribonuclease A Bos taurus EC 3.1.27.5 3.1.27.5 9901-99-4 monomer, dimer, trimer, tetramer, hexamer, pentamer, higher order[109][110][111][112][113] Multiple/protein moonlighting functions,[114][115][116] Different assemblies have different activities,[114][115][116] Conformationally distinct oligomeric forms[110][112][113]
Ribonucleotide reductase Mus musculus EC 1.17.4.1 9047-64-7 tetramer, hexamer[117][118][119][120] Effector molecules impact multimerization[120]
S-adenosyl-L-homocysteine hydrolase Dictyostelium discoideum EC 3.3.1.1 9025-54-1 tetramer and other[121][122][123] Effector molecules impact multimerization[121]
Biodegrative threonine dehydratase / threonine ammonia-lyase Escherichia coli EC 4.3.1.19 4.3.1.19 774231-81-1 2 monomers, 2 tetramers[124][125][126] Effector molecules impact multimerization,[126] Characterized equilibrium of oligomers,[124][125] Different assemblies have different activities[124][125][126]
Tumor necrosis factor-α Homo sapiens 94948-61-5 monomer, dimer, trimer[127][128] Different assemblies have different activities[129]
Uracil phosphoribosyltransferase Escherichia coli EC 2.4.2.9 9030-24-4 trimer, pentamer[130] Effector molecules impact multimerization,[130] Substrate binding/turnover impacts multimerization,[130] Different assemblies have different activities[130]

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Jaffe, Eileen K. (2005). "Morpheeins – a new structural paradigm for allosteric regulation". Trends in Biochemical Sciences 30 (9): 490–7. doi:10.1016/j.tibs.2005.07.003. PMID 16023348. 
  2. ↑ 2.0 2.1 2.2 Breinig, Sabine; Kervinen, Jukka; Stith, Linda; Wasson, Andrew S; Fairman, Robert; Wlodawer, Alexander; Zdanov, Alexander; Jaffe, Eileen K (2003). "Control of tetrapyrrole biosynthesis by alternate quaternary forms of porphobilinogen synthase". Nature Structural Biology 10 (9): 757–63. doi:10.1038/nsb963. PMID 12897770. 
  3. ↑ 3.0 3.1 Frieden, C (1967). "Treatment of enzyme kinetic data. II. The multisite case: comparison of allosteric models and a possible new mechanism". J. Biol. Chem. 242 (18): 4045–4052. doi:10.1016/S0021-9258(18)95776-5. PMID 6061697. 
  4. ↑ 4.0 4.1 Nichol, L W; Jackson, W J H; Winzor, D J (1967). "A theoretical study of the binding of small molecules to a polymerizing protein system: a model for allosteric effects". Biochemistry 6 (8): 2449–2456. doi:10.1021/bi00860a022. PMID 6049469. 
  5. ↑ 5.0 5.1 5.2 Lawrence, Sarah H.; Ramirez, Ursula D.; Tang, Lei; Fazliyez, Farit; Kundrat, Lenka; Markham, George D.; Jaffe, Eileen K. (2008). "Shape Shifting Leads to Small-Molecule Allosteric Drug Discovery". Chemistry & Biology 15 (6): 586–96. doi:10.1016/j.chembiol.2008.04.012. PMID 18559269. 
  6. ↑ 6.0 6.1 6.2 Selwood, Trevor; Jaffe, Eileen K. (2012). "Dynamic dissociating homo-oligomers and the control of protein function". Archives of Biochemistry and Biophysics 519 (2): 131–43. doi:10.1016/j.abb.2011.11.020. PMID 22182754. 
  7. ↑ 7.0 7.1 Jaffe, Eileen K.; Stith, Linda (2007). "ALAD Porphyria is a Conformational Disease". The American Journal of Human Genetics 80 (2): 329–37. doi:10.1086/511444. PMID 17236137. 
  8. ↑ Jaffe, Eileen K. (2010). "Morpheeins – A New Pathway For Allosteric Drug Discovery". The Open Conference Proceedings Journal 1: 1–6. doi:10.2174/2210289201001010001. PMID 21643557. 
  9. ↑ Tang, L.; Stith, L; Jaffe, EK (2005). "Substrate-induced Interconversion of Protein Quaternary Structure Isoforms". Journal of Biological Chemistry 280 (16): 15786–93. doi:10.1074/jbc.M500218200. PMID 15710608. 
  10. ↑ Jaffe, Eileen K.; Lawrence, Sarah H. (2012). "Allostery and the dynamic oligomerization of porphobilinogen synthase". Archives of Biochemistry and Biophysics 519 (2): 144–53. doi:10.1016/j.abb.2011.10.010. PMID 22037356. 
  11. ↑ 11.0 11.1 Lawrence, Sarah H.; Jaffe, Eileen K. (2008). "Expanding the concepts in protein structure-function relationships and enzyme kinetics: Teaching using morpheeins". Biochemistry and Molecular Biology Education 36 (4): 274–283. doi:10.1002/bmb.20211. PMID 19578473. 
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  13. ↑ 13.0 13.1 Monod, Jacques; Wyman, Jeffries; Changeux, Jean-Pierre (1965). "On the nature of allosteric transitions: A plausible model". Journal of Molecular Biology 12: 88–118. doi:10.1016/S0022-2836(65)80285-6. PMID 14343300. 
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  18. ↑ Friedrich, P (1984). Supramolecular Enzyme Organization: Quaternary Structure and Beyond. Oxford: Pergamon Press. pp. 66–71. ISBN 0-08-026376-3. 
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  26. ↑ 26.0 26.1 26.2 Palenchar, Jennifer Brosius; Colman, Roberta F. (2003). "Characterization of a Mutant Bacillus subtilis Adenylosuccinate Lyase Equivalent to a Mutant Enzyme Found in Human Adenylosuccinate Lyase Deficiency: Asparagine 276 Plays an Important Structural Role". Biochemistry 42 (7): 1831–41. doi:10.1021/bi020640+. PMID 12590570. 
  27. ↑ Jerebzoff-Quintin, Simonne; Jerebzoff, Stephan (1985). "L-Asparaginase activity in Leptosphaeria michotii. Isolation and properties of two forms of the enzyme". Physiologia Plantarum 64: 74–80. doi:10.1111/j.1399-3054.1985.tb01215.x. 
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  33. ↑ 33.0 33.1 Eisenstein, Edward; Beckett, Dorothy (1999). "Dimerization of theEscherichiacoliBiotin Repressor: Corepressor Function in Protein Assembly". Biochemistry 38 (40): 13077–84. doi:10.1021/bi991241q. PMID 10529178. 
  34. ↑ Streaker, Emily D.; Beckett, Dorothy (1998). "Coupling of Site-Specific DNA Binding to Protein Dimerization in Assembly of the Biotin Repressor−Biotin Operator Complex". Biochemistry 37 (9): 3210–9. doi:10.1021/bi9715019. PMID 9485476. 
  35. ↑ Vamvaca, Katherina; Butz, Maren; Walter, Kai U.; Taylor, Sean V.; Hilvert, Donald (2005). "Simultaneous optimization of enzyme activity and quaternary structure by directed evolution". Protein Science 14 (8): 2103–14. doi:10.1110/ps.051431605. PMID 15987889. 
  36. ↑ 36.0 36.1 36.2 36.3 36.4 Tong, E. K.; Duckworth, Harry W. (1975). "Quaternary structure of citrate synthase from Escherichia coli K 12". Biochemistry 14 (2): 235–41. doi:10.1021/bi00673a007. PMID 1091285. 
  37. ↑ Bewley, Carole A.; Gustafson, Kirk R.; Boyd, Michael R.; Covell, David G.; Bax, Ad; Clore, G. Marius; Gronenborn, Angela M. (1998). "Solution structure of cyanovirin-N, a potent HIV-inactivating protein". Nature Structural Biology 5 (7): 571–8. doi:10.1038/828. PMID 9665171. 
  38. ↑ Yang, Fan; Bewley, Carole A; Louis, John M; Gustafson, Kirk R; Boyd, Michael R; Gronenborn, Angela M; Clore, G.Marius; Wlodawer, Alexander (1999). "Crystal structure of cyanovirin-N, a potent HIV-inactivating protein, shows unexpected domain swapping". Journal of Molecular Biology 288 (3): 403–12. doi:10.1006/jmbi.1999.2693. PMID 10329150. 
  39. ↑ 39.0 39.1 Barrientos, LG; Gronenborn, AM (2005). "The highly specific carbohydrate-binding protein cyanovirin-N: Structure, anti-HIV/Ebola activity and possibilities for therapy". Mini Reviews in Medicinal Chemistry 5 (1): 21–31. doi:10.2174/1389557053402783. PMID 15638789. 
  40. ↑ 40.0 40.1 Barrientos, LG; Louis, JM; Botos, I; Mori, T; Han, Z; O'Keefe, BR; Boyd, MR; Wlodawer, A et al. (2002). "The domain-swapped dimer of cyanovirin-N is in a metastable folded state: Reconciliation of X-ray and NMR structures". Structure 10 (5): 673–86. doi:10.1016/S0969-2126(02)00758-X. PMID 12015150. 
  41. ↑ 41.0 41.1 41.2 Rochet, Jean-Christophe; Brownie, Edward R.; Oikawa, Kim; Hicks, Leslie D.; Fraser, Marie E.; James, Michael N. G.; Kay, Cyril M.; Bridger, William A. et al. (2000). "Pig Heart CoA Transferase Exists as Two Oligomeric Forms Separated by a Large Kinetic Barrier". Biochemistry 39 (37): 11291–302. doi:10.1021/bi0003184. PMID 10985774. 
  42. ↑ Frank, Nina; Kery, Vladimir; MacLean, Kenneth N.; Kraus, Jan P. (2006). "Solvent-Accessible Cysteines in Human Cystathionine β-Synthase: Crucial Role of Cysteine 431 inS-Adenosyl-l-methionine Binding". Biochemistry 45 (36): 11021–9. doi:10.1021/bi060737m. PMID 16953589. 
  43. ↑ 43.0 43.1 Sen, Suvajit; Banerjee, Ruma (2007). "A Pathogenic Linked Mutation in the Catalytic Core of Human Cystathionine β-Synthase Disrupts Allosteric Regulation and Allows Kinetic Characterization of a Full-Length Dimer". Biochemistry 46 (13): 4110–6. doi:10.1021/bi602617f. PMID 17352495. 
  44. ↑ Kery, Vladimir; Poneleit, Loelle; Kraus, Jan P. (1998). "Trypsin Cleavage of Human Cystathionine β-Synthase into an Evolutionarily Conserved Active Core: Structural and Functional Consequences". Archives of Biochemistry and Biophysics 355 (2): 222–32. doi:10.1006/abbi.1998.0723. PMID 9675031. 
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  47. ↑ 47.0 47.1 Massey, V; Curti, B; Ganther, H (1966). "A temperature-dependent conformational change in D-amino acid oxidase and its effect on catalysis". The Journal of Biological Chemistry 241 (10): 2347–57. doi:10.1016/S0021-9258(18)96628-7. PMID 5911617. 
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  49. ↑ Muiswinkel-Voetberg, H.; Visser, Jaap; Veeger, Cornelis (1973). "Conformational Studies on Lipoamide Dehydrogenase from Pig Heart. 1. Interconversion of Dissociable and Non-Dissociable Forms". European Journal of Biochemistry 33 (2): 265–70. doi:10.1111/j.1432-1033.1973.tb02679.x. PMID 4348439. 
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  129. ↑ Hlodan, Roman; Pain, Roger H. (1995). "The Folding and Assembly Pathway of Tumour Necrosis Factor TNFalpha, a Globular Trimeric Protein". European Journal of Biochemistry 231 (2): 381–7. doi:10.1111/j.1432-1033.1995.tb20710.x. PMID 7635149. 
  130. ↑ 130.0 130.1 130.2 130.3 Jensen, Kaj Frank; Mygind, Bente (1996). "Different Oligomeric States are Involved in the Allosteric Behavior of Uracil Phosphoribosyltransferase from Escherichia Coli". European Journal of Biochemistry 240 (3): 637–45. doi:10.1111/j.1432-1033.1996.0637h.x. PMID 8856065. 



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