Computational modeling of substrate specificity and catalysis of the β-secretase (BACE1) enzyme

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Abstract

In this combined MD simulation and DFT study, interactions of the wild-type (WT) amyloid precursor protein (APP) and its Swedish variant (SW), Lys670 → Asn and Met671 → Leu, with the beta-secretase (BACE1) enzyme and their cleavage mechanisms have been investigated. BACE1 catalyzes the rate-limiting step in the generation of 40-42 amino acid long Alzheimer amyloid beta (Aβ) peptides. All key structural parameters such as position of the flap, volume of the active site, electrostatic binding energy, structures, and positions of the inserts A, D, and F and 10s loop obtained from the MD simulations show that, in comparison to the WT-substrate, BACE1 exhibits greater affinity for the SW-substrate and orients it in a more reactive conformation. The enzyme-substrate models derived from the MD simulations were further utilized to investigate the general acid/base mechanism used by BACE1 to hydrolytically cleave these substrates. This mechanism proceeds through the following two steps: (1) formation of the gem-diol intermediate and (2) cleavage of the peptide bond. For the WT-substrate, the overall barrier of 22.4 kcal/mol for formation of the gem-diol intermediate is 3.3 kcal/mol higher than for the SW-substrate (19.1 kcal/mol). This process is found to be the rate-limiting in the entire mechanism. The computed barrier is in agreement with the measured barrier of ca. 18.00 kcal/mol for the WT-substrate and supports the experimental observation that the cleavage of the SW-substrate is 60 times more efficient than the WT-substrate.

Original languageEnglish
Pages (from-to)4337-4349
Number of pages13
JournalBiochemistry
Volume50
Issue number20
DOIs
StatePublished - May 24 2011

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Amyloid Precursor Protein Secretases
Substrate Specificity
Catalysis
Amyloid beta-Protein Precursor
Amyloid beta-Peptides
Substrates
Enzymes
Static Electricity
Catalytic Domain
Amino Acids
Peptides
Gems
Acids
Binding energy
Amyloid
Discrete Fourier transforms
Conformations
Electrostatics

ASJC Scopus subject areas

  • Biochemistry

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Computational modeling of substrate specificity and catalysis of the β-secretase (BACE1) enzyme. / Barman, Arghya; Schuerer, Stephan C; Prabhakar, Rajeev.

In: Biochemistry, Vol. 50, No. 20, 24.05.2011, p. 4337-4349.

Research output: Contribution to journalArticle

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