Protein Interaction and Genetic Disease

Abstract

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., ), 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 FAO3‐hydroxy acyl‐CoA dehydrogenases (HADs) to CI. The FAD/FADH2 systems, located in the active centres of FAOacyl‐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 α subunit containing long‐chain 3‐hydroxy acyl‐CoA dehydroganse and long‐chain enoyl‐CoA hydratase, and a β 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. ETFα (turquoise) and ETFβ (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.).

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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]