Protein Interaction and Genetic Disease

Niels Gregersen, Aarhus University Hospital, Skejby, Aarhus, Denmark
Peter Bross, Aarhus University Hospital, Skejby, Aarhus, Denmark
Rikke KJ Olsen, Aarhus University Hospital, Skejby, Aarhus, Denmark
Johan Palmfeldt, Aarhus University Hospital, Skejby, Aarhus, Denmark
Thomas J Corydon, Aarhus University, Aarhus, Denmark

Published online: February 2011

DOI: 10.1002/9780470015902.a0021450

The function of proteins is dependent on other proteins. Proteins function as oligomers, complexes, super-complexes or higher order networks, in which they interact with each other, either temporarily when they exert their function or ‘permanently’ in functional units. Genetic defects in single proteins may therefore, in addition to disturbing the specific function of the defective protein, disturb other functions that are dependent on it. In this review we will discuss how the two main types of defects in genetic disease, truncating variations (stop-codon introductions and small out-of-frame deletions/insertions) and in-frame variations (missense variations and small in-frame deletions/insertions), may disturb normal interactions. Depending on the importance (location) of the missing or aberrant protein, the effect on the cellular pathway or interacting network may be severe or mild. Protein interactions and disturbances therein may be determined by protein mass spectrometry after immuno-precipitation or other fractionation and separation methods.

Key Concepts:

  • Cellular proteins interact in oligomer and complex structures as well as in higher order networks.
  • Protein interactions may be permanent in the lifetime of proteins or temporary during their function.
  • Genetic defects may disturb interactions between proteins depending on the nature of the defect and type of interaction.
  • Missing proteins due to truncation, comprising big deletions, small out-of-frame deletions/insertions and severe splice alteration, may abolish the function of oligomers, complexes, pathways and networks.
  • Aberrant proteins due to missense variations and in-frame deletions/insertions may disturb interactions with protein partners in oligomers, complexes and networks.
  • Missing and aberrant proteins in branch-points (nodes) have as a role severe consequences, resulting in genotype–phenotype association.
  • Missing and aberrant proteins in redundant pathways have variable consequences, resulting in poor genotype–phenotype association.
  • Missing and aberrant proteins in molecular machines, such as the chaperonin Hsp60, may elicit pleotropic effects due to defective processing of client proteins.
  • Protein interactions and disturbances therein may be determined experimentally by protein mass spectrometry (MS), preceded by immunoprecipitation of target proteins, either directly or after cross-linking, or indicated after mild solubilisation followed by extensive separating procedures and MS.
  • The challenge is to design experiments that can determine qualitative and quantitative disturbances of proteins interactions in cells and tissue from patients, model animals and model cells compared to interactions in normal cells and tissue.

Keywords: aberrant protein structures; disturbed protein interaction; protein complexes; protein super-complexes; protein networks; protein quality control; metabolon structures; metabolic channelling; determination of protein interaction; structural mass spectrometry

Figure 1. Consequences at the protein level of various types of gene defects. (a) In-frame variations may result in folding intermediates, which are rapidly degraded or are forming aggregates or unstable functional conformations with increased turnover; (b) truncating variations resulting in rapid degradation of mRNAs containing a premature termination codons (PTC) and (c) regulatory defects resulting in decreased biogenesis of normal/wild-type protein.
Figure 2. Schematic representation of the mitochondrial respiratory chain (RC) and fatty acid oxidation (FAO) metabolic network (FAO metabolon). Although the integrity of the FAO enzymes and the complexes of RC has been documented functionally (Wang et al., 2010), the precise interactions between the proteins have not been elucidated fully. The super-complex CI/CIII2/CIV is indicated, and CII and CV are shown separately. The structural interactions within the FAO metabolon are speculative, except that ETF has been shown to interact with MCAD. The metabolic interaction through NAD/NADH and FAD/FADH2 are shown. The NAD/NADH cycle transfer electrons and protons from FAO 3-hydroxy acyl-CoA dehydrogenases (HADs) to CI. The FAD/FADH2 systems, located in the active centres of FAO acyl-CoA dehydrogenases (like SCAD, MCAD and VLCAD), ETF, ETFQO and CII, transfer electrons and protons to ubiquinone (Q10), which is reduced to ubiquinol. Ubiquinol produced from FADH2 as well as from reducing equivalents of CI transfers the cargo of electrons and protons to CIII, which pass them further to CIV by cytochrome C (cytC). The enzymes of the FAO metabolon are: VLCAD: very-long-chain acyl-CoA dehydrogenase; MTP: mitochondrial trifunctional protein, comprising two subunits; an subunit containing long-chain 3-hydroxy acyl-CoA dehydroganse and long-chain enoyl-CoA hydratase, and a subunit, containing long-chain 3-keto acyl-CoA thiolase; MCAD: medium-chain acyl-CoA dehydrogenase; SCAD: short-chain acyl-CoA dehydrogenase; EH: enoyl hydratases; HAD: 3-hydroxy acyl-CoA dehydrogenases; KT: 3-keto acyl-CoA thiolases; ETF: electron transfer flavoprotein, interacting with ETFQO: electron transfer flavoprotein ubiquinone oxidoreductase.
Figure 3. Molecular structure of chaperonin GroELS (Hsp60). The structure is based on the coordinates for the closed (a) and open (b) ring of E. coli GroELS (PDB coordinates 1AON). GroEL (colored) and GroES (black and white) subunits in the closed and open ring, representing the extreme conformations of the complex, are given in surface representation. One subunit of GroEL is shown in solid ribbon representation and the bound ATP in (a) is shown as yellow stick. Position of disease-associated amino acid variations in the Hsp60 chaperonin are shown as the homologues in GroEL. Residues Asp5 and Val74, which are conserved between GroEL and Hsp60, and correspond to Asp29 and Val98 in Hsp60, respectively, are given as blue spheres and labelled. The picture was produced using Discovery Studio Visualizer 2.5.5 (Accelrys Software Inc.).
Figure 4. Schematic illustration of consequences of various gene defects. (a) Loss of ETF proteins, which abolish electron and proton transfer to ubiquinone (Q10); (b) aberrant ETF protein, disturbing/inhibiting electron and proton transfer to ubiquinone (Q10); (c) loss of MCAD protein, diminishing flux through FAO and (d) aberrant MCAD protein, which may interact negatively with other FAO enzyme proteins.
Figure 5. Position of three disease-associated amino acid variations in ETF. The structure is based on PDB coordinates 1EFV. ETF (turquoise) and ETF (pale blue) are represented by solid ribbons, FAD (yellow) and AMP (orange). Residues Cys42, Asp128 and Arg191, which have been found changed in MADD patients (see text), are given as red spheres and labelled. The recognition loop binding to a cavity in medium-chain acyl-CoA dehydrogenase is shown in a dark blue surface representation. The picture was produced using Discovery Studio Visualizer 2.5.5 (Accelrys Software Inc.).
close
 References
    Andresen BS, Bross P, Udvari S et al. (1997) The molecular basis of medium-chain acyl-CoA degydrogenase (MCAD) deficiency in compound heterozygous patients: is there correlation between genotype and phenotype? Human Molecular Genetics 6: 695–707.
    Andresen BS, Olpin S, Poorthuis BJ et al. (1999) Clear correlation of genotype with disease phenotype in very-long-chain acyl-CoA dehydrogenase deficiency. American Journal of Human Genetics 64(2): 479–494.
    book Antonarakis SE, Krawczak M and Cooper DN (2001) "The nature and mechanisms of human gene mutations". In: Scriver CR, Beaudet AL and Valle D (eds) The Metabolic and Molecular Basis Inherited Disease, pp. 343–378. New York: McGraw-Hill.
    Barrientos A, Gouget K, Horn D et al. (2009) Suppression mechanisms of COX assembly defects in yeast and human: insights into the COX assembly process. Biochimica et Biophysica Acta 1793(1): 97–107.
    Bhuvanagiri M, Schlitter AM, Hentze MW et al. (2010) NMD: RNA biology meets human genetic medicine. Biochemical Journal 430(3): 365–377.
    Bross P, Andresen BS, Winter V et al. (1993) Co-overexpression of bacterial GroESL chaperonins partly overcomes non-productive folding and tetramer assembly of E.coli-expressed human medium-chain acyl-CoA dehydrogenase (MCAD) carrying the prevalent disease-causing K304E mutation. Biochimica et Biophysica Acta 1182: 264–274.
    Bross P, Jespersen C, Jensen TG et al. (1995) Effects of two mutations detected in medium chain acyl-CoA dehydrogenase (MCAD)-deficient patients on folding, oligomer assembly, and stability of MCAD enzyme. Journal of Biological Chemistry 270: 10284–10290.
    Bross P, Naundrup S, Hansen J et al. (2008) The Hsp60-(p.V98I) mutation associated with hereditary spastic paraplegia SPG13 compromises chaperonin function both in vitro and in vivo. Journal of Biological Chemistry 283(23): 15694–15700.
    Bross P, Palmfeldt J, Hansen J et al. (2010) Measuring consequences of protein misfolding and cellular stress using OMICS techniques. Methods in Molecular Biology 648: 119–135.
    Christensen JH, Nielsen MN, Hansen J et al. (2010) Inactivation of the hereditary spastic paraplegia-associated Hspd1 gene encoding the Hsp60 chaperone results in early embryonic lethality in mice. Cell Stress Chaperones 15(6): 851–863.
    Dunlop RA, Brunk UT and Rodgers KJ (2009) Oxidized proteins: mechanisms of removal and consequences of accumulation. IUBMB Life 61(5): 522–527.
    Eaton S (2002) Control of mitochondrial beta-oxidation flux. Progress in Lipid Research 41(3): 197–239.
    Fenton WA and Horwich AL (1997) GroEL-mediated protein folding. Protein Science 6(4): 743–760.
    Fernandez-Vizarra E, Bugiani M, Goffrini P et al. (2007) Impaired complex III assembly associated with BCS1L gene mutations in isolated mitochondrial encephalopathy. Human Molecular Genetics 16(10): 1241–1252.
    Fernandez-Vizarra E, Tiranti V and Zeviani M (2009) Assembly of the oxidative phosphorylation system in humans: what we have learned by studying its defects. Biochimica et Biophysica Acta 1793(1): 200–211.
    Figeys D (2008) Mapping the human protein interactome. Cell Research 18(7): 716–724.
    book Frerman FE and Goodman SI (2001) "Defects of electron transfer flavoprotein and electron transfer flavoprotein-ubiquinone oxidoreductase: glutaric aciduria type II". In: Scriver CR, Beaudet AL and Valle D (eds) The Metabolic and Molecular Basis of Inherited Disease, pp. 2357–2365. New York: McGraw-Hill.
    Gandhi TK, Zhong J, Mathivanan S et al. (2006) Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature Genetics 38(3): 285–293.
    Gavin AC, Bosche M, Krause R et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415(6868): 141–147.
    Gempel K, Topaloglu H, Talim B et al. (2007) The myopathic form of coenzyme Q10 deficiency is caused by mutations in the electron-transferring-flavoprotein dehydrogenase (ETFDH) gene. Brain 130(part 8): 2037–2044.
    Genova ML, Bianchi C and Lenaz G (2005) Supercomplex organization of the mitochondrial respiratory chain and the role of the coenzyme Q pool: pathophysiological implications. Biofactors 25(1–4): 5–20.
    Gradinaru R, Schowen R and Ghisla S (2007) Solvent isotope effects in reactions of human medium-chain acyl-CoA dehydrogenase active site mutants. Biochemistry 46(9): 2497–2509.
    Gregersen N, Andresen BS, Pedersen CB et al. (2008) Mitochondrial fatty acid oxidation defects – remaining challenges. Journal of Inherited Metabolic Disease 31(5): 643–657.
    Gregersen N and Bross P (2010) Protein misfolding and cellular stress: an overview. Methods in Molecular Biology 648: 3–23.
    Gregersen N, Bross P, Vang S et al. (2006) Protein misfolding and Human disease. Annual Review of Genomics and Human Genetics 7: 103–124.
    Gregersen N and Olsen RK (2010) Disease mechanisms and protein structures in fatty acid oxidation defects. Journal of Inherited Metabolic Disease 33(5): 547–553.
    Hansen JJ, Durr A, Cournu-Rebeix I et al. (2002) Hereditary spastic paraplegia SPG13 is associated with a mutation in the gene encoding the mitochondrial chaperonin Hsp60. American Journal of Human Genetics 70(5): 1328–1332.
    Henriques BJ, Bross P and Gomes CM (2010) Mutational hotspots in electron transfer flavoprotein underlie defective folding and function in multiple acyl-CoA dehydrogenase deficiency. Biochimica et Biophysica Acta 1802(11): 1070–1077.
    Hsu WT, Pang CN, Sheetal J et al. (2007) Protein-protein interactions and disease: use of S. cerevisiae as a model system. Biochimica et Biophysica Acta 1774(7): 838–847.
    Ishikawa M, Tsuchiya D, Oyama T et al. (2004) Structural basis for channelling mechanism of a fatty acid beta-oxidation multienzyme complex. EMBO Journal 23(14): 2745–2754.
    Jin LY (2008) Mass spectrometric analysis of cross-linking sites for the structure of proteins and protein complexes. Molecular Biosystems 4(8): 816–823.
    Keyser B, Muhlhausen C, Dickmanns A et al. (2008) Disease-causing missense mutations affect enzymatic activity, stability and oligomerization of glutaryl-CoA dehydrogenase (GCDH). Human Molecular Genetics 17(24): 3854–3863.
    Maier EM, Gersting SW, Kemter KF et al. (2009) Protein misfolding is the molecular mechanism underlying MCADD identified in newborn screening. Human Molecular Genetics 18(9): 1612–1623.
    Maier EM, Liebl B, Roschinger W et al. (2005) Population spectrum of ACADM genotypes correlated to biochemical phenotypes in newborn screening for medium-chain acyl-CoA dehydrogenase deficiency. Human Mutatation 25(5): 443–452.
    Mathe E, Olivier M, Kato S et al. (2006) Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods. Nucleic Acids Research 34(5): 1317–1325.
    McKenzie M, Lazarou M, Thorburn DR et al. (2007) Analysis of mitochondrial subunit assembly into respiratory chain complexes using Blue Native polyacrylamide gel electrophoresis. Analytical Biochemistry 364(2): 128–137.
    Ng PC and Henikoff S (2003) SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Research 31(13): 3812–3814.
    Nielsen KL and Cowan NJ (1998) A single ring is sufficient for productive chaperonin-mediated folding in vivo. Molecular Cell 2(1): 93–99.
    Nouws J, Nijtmans L, Houten SM et al. (2010) Acyl-CoA dehydrogenase 9 is required for the biogenesis of oxidative phosphorylation complex I. Cell Metabolism 12(3): 283–294.
    Olsen RK, Andresen BS, Christensen E et al. (2003) Clear relationship between ETF/ETFDH genotype and phenotype in patients with multiple acyl-CoA dehydrogenation deficiency. Human Mutatation 22(1): 12–23.
    Olsen RK, Olpin SE, Andresen BS et al. (2007) ETFDH mutations as a major cause of riboflavin-responsive multiple acyl-CoA dehydrogenation deficiency. Brain 130(Pt 8): 2045–2054.
    Parnas A, Nadler M, Nisemblat S et al. (2009) The MitCHAP-60 disease is due to entropic destabilization of the human mitochondrial Hsp60 oligomer. Jounral of Biological Chemistry 284(41): 28198–28203.
    Piekutowska-Abramczuk D, Magner M, Popowska E et al. (2009) SURF1 missense mutations promote a mild Leigh phenotype. Clinical Genetics 76(2): 195–204.
    Rigaut G, Shevchenko A, Rutz B et al. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotechnology 17(10): 1030–1032.
    Selbach M and Mann M (2006) Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK). Nature Methods 3(12): 981–983.
    Smith EH, Thomas C, McHugh D et al. (2010) Allelic diversity in MCAD deficiency: the biochemical classification of 54 variants identified during 5 years of ACADM sequencing. Molecular Genetics and Metabolism 100(3): 241–250.
    Stanley KK and Tubbs PK (1975) The role of intermediates in mitochondrial fatty acid oxidation. Biochemical Journal 150(1): 77–88.
    Stenson PD, Mort M, Ball EV et al. (2009) The Human Gene Mutation Database: 2008 update. Genome Medicine 1(1): 13.
    Stiburek L, Vesela K, Hansikova H et al. (2009) Loss of function of Sco1 and its interaction with cytochrome c oxidase. American Journal of Physiology. Cell Physiology 296(5): C1218–C1226.
    Sunyaev S, Ramensky V, Koch I et al. (2001) Prediction of deleterious human alleles. Human Molecular Genetics 10(6): 591–597.
    Tang X and Bruce JE (2010) A new cross-linking strategy: protein interaction reporter (PIR) technology for protein-protein interaction studies. Molecular Biosystems 6(6): 939–947.
    Toogood HS, Leys D and Scrutton NS (2007) Dynamics driving function: new insights from electron transferring flavoproteins and partner complexes. FEBS Journal 274(21): 5481–5504.
    Walther TC and Mann M (2010) Mass spectrometry-based proteomics in cell biology. Journal of Cell Biology 190(4): 491–500.
    Wang GS and Cooper TA (2007) Splicing in disease: disruption of the splicing code and the decoding machinery. Nature Reviews. Genetics 8(10): 749–761.
    Wang Y, Mohsen AW, Mihalik SJ et al. (2010) Evidence for physical association of mitochondrial fatty acid oxidation and oxidative phosphorylation complexes. Journal of Biological Chemistry 285(39): 29834–29841.
    Wen B, Dai T, Li W et al. (2010) Riboflavin-responsive lipid-storage myopathy caused by ETFDH gene mutations. Journal of Neurology, Neurosurgery, and Psychiatry 81(2): 231–236.
    Yotsumoto Y, Hasegawa Y, Fukuda S et al. (2008) Clinical and molecular investigations of Japanese cases of glutaric acidemia type 2. Molecular Genetics and Metabolism 94(1): 61–67.
    Zara V, Conte L and Trumpower BL (2007) Identification and characterization of cytochrome bc(1) subcomplexes in mitochondria from yeast with single and double deletions of genes encoding cytochrome bc(1) subunits. FEBS Journal 274(17): 4526–4539.
    Zhong Q, Simonis N, Li QR et al. (2009) Edgetic perturbation models of human inherited disorders. Molecular Systems Biology 5: 321.
 Further Reading
    Gavin AC, Maeda K and Kuhner S (2010) Recent advances in charting protein-protein interaction: mass spectrometry-based approaches. Current Opinion in Biotechnology 22: 1–8.
    Gstaiger M and Aebersold R (2009) Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nature Reviews. Genetics 10: 617–627.
    Kocher T and Superti-Furga G (2007) Mass spectrometry-based functional proteomics: from molecular machines to protein networks. Nature Methods 4: 807–815.
    Krause F (2006) Detection and analysis of protein-protein interactions in organellar and prokaryotic proteomes by native gel electrophoresis: (Membrane) protein complexes and supercomplexes. Electrophoresis 27: 2759–2781.
    Lage K, Karlberg EO, Storling ZM et al. (2007) A human phenome-interactome network of protein complexes implicated in genetic disorders. Nature Biotechnology 25: 309–316.
    Schafer E, Dencher NA, Vonck J and Parcej DN (2007) Three-dimensional structure of the respiratory chain supercomplex I1III2IV1 from bovine heart mitochondria. Biochemistry 46: 12579–12585.
    Schuster-Bockler B and Bateman A (2008) Protein interactions in human genetic diseases. Genome Biology 9: R9.
    Veitia RA, Bottani S and Birchler JA (2008) Cellular reactions to gene dosage imbalance: genomic, transcriptomic and proteomic effects. Trends in Genetics 24: 390–397.
    Wang PI and Marcotte EM (2010) It's the machine that matters: predicting gene function and phenotype from protein networks. Journal of Proteomics 73: 2277–2289.

Related Sub-Topics:

Protein Structure | Protein Folding, Evolution and Degradation | Mutational Mechanisms of Genetic Disease | Techniques and Tools in Clinical Genetics | Proteomic Studies of Genetic Disease | Mitochondrial Diseases | Biomolecular Interactions | Proteins: Structure, Function, Metabolism
Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

Article Title: Protein Interaction and Genetic Disease
 
How to Cite close
Gregersen, Niels, Bross, Peter, Olsen, Rikke KJ, Palmfeldt, Johan, and Corydon, Thomas J(Feb 2011) Protein Interaction and Genetic Disease. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0021450]