title: Toward Allosterically Increased Catalytic Activity of Insulin-Degrading Enzyme against Amyloid Peptides.
abstract: The physiological role of insulin-degrading enzyme (IDE) in the intracytosolic clearance of amyloid β (Aβ) and other amyloid-like peptides supports a hypothesis that human IDE hyperactivation could be therapeutically beneficial for the treatment of late-onset Alzheimer's disease (AD). The major challenge standing in the way of this goal is increasing the specific catalytic activity of IDE against the Aβ substrate. There were previous indications that the allosteric mode of IDE activity regulation could potentially provide a highly specific path toward degradation of amyloid-like peptides, while not dramatically affecting activity against other substrates. Recently developed theoretical concepts are used here to explore potential allosteric modulation of the IDE activity as a result of single-residue mutations. Five candidates are selected for experimental follow-up and allosteric free energy calculations: Ser137Ala, Lys396Ala, Asp426Ala, Phe807Ala, and Lys898Ala. Our experiments show that three mutations (Ser137Ala, Phe807Ala, and Lys898Ala) decrease the Kmof the Aβ substrate. Mutation Lys898Ala results in increased catalytic activity of IDE; on the other hand, Lys364Ala does not change the activity and Asp426Ala diminishes it. Quantifying effects of mutations in terms of allosteric free energy, we show that favorable mutations lead to stabilization of the catalytic sites and other function-relevant distal sites as well as increased dynamics of the IDE-N and IDE-C halves that allow efficient substrate entrance and cleavage. A possibility for intramolecular upregulation of IDE activity against amyloid peptides via allosteric mutations calls for further investigations in this direction. Ultimately, we are hopeful it will lead to the development of IDE-based drugs for the treatment of the late-onset form of AD characterized by an overall impairment of Aβ clearance.
authors.affiliation: Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , 30 Biopolis Street, #07-01, Matrix, Singapore 138671.
authors.forename: Igor V
authors.initials: IV
authors.lastname: Kurochkin
authors.affiliation: Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , 30 Biopolis Street, #07-01, Matrix, Singapore 138671.
authors.forename: Enrico
authors.initials: E
authors.lastname: Guarnera
authors.affiliation: Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , 30 Biopolis Street, #07-01, Matrix, Singapore 138671.
authors.forename: Jin H
authors.initials: JH
authors.lastname: Wong
authors.affiliation: Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , 30 Biopolis Street, #07-01, Matrix, Singapore 138671.|Department of Biological Sciences (DBS), National University of Singapore (NUS) , 8 Medical Drive, Singapore 117579.|School of Computer Engineering (SCE), Nanyang Technological University (NTU) , 50 Nanyang Drive, Singapore 637553.
authors.forename: Frank
authors.initials: F
authors.lastname: Eisenhaber
authors.affiliation: Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR) , 30 Biopolis Street, #07-01, Matrix, Singapore 138671.|Department of Biological Sciences (DBS), National University of Singapore (NUS) , 8 Medical Drive, Singapore 117579.
authors.forename: Igor N
authors.identifier: http://orcid.org/0000-0002-3315-8483
authors.initials: IN
authors.lastname: Berezovsky
mesh_terms: D000465:Algorithms; D000494:Allosteric Regulation; D000544:Alzheimer Disease / Q000201:enzymology / Q000235:genetics / Q000378:metabolism; D016229:Amyloid beta-Peptides / Q000737:chemistry / Q000378:metabolism*; D058227:Amyloidogenic Proteins / Q000737:chemistry / Q000378:metabolism*; D055162:Biocatalysis; D020134:Catalytic Domain; D019295:Computational Biology / Q000379:methods; D057075:Enzyme Assays / Q000379:methods; D006801:Humans; D007339:Insulysin / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D007700:Kinetics; D008958:Models, Molecular; D020125:Mutation, Missense; D000072417:Protein Domains; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: D016229:Amyloid beta-Peptides; D058227:Amyloidogenic Proteins; D007339:Insulysin