Interaction models of substrate peptides and beta-secretase studied by NMR spectroscopy and molecular dynamics simulation.
The formation of beta-amyloid peptide (Abeta) is initiated from cleavage of amyloid precursor protein (APP) by a family of protease, alpha-, beta-, and gamma-secretase. Sub W, a substrate peptide, consists of 10 amino acids, which are adjacent to the beta-cleavage site of wild-type APP, and Sub M is Swedish mutant with double mutations on the left side of the beta-cleavage site of APP. Sub W is a normal product of the metabolism of APP in the secretary pathway. Sub M is known to increase the efficiency of beta-secretase activity, resulting in a more specific binding model compared to Sub W. Three-dimensional structures of Sub W and Sub M were studied by CD and NMR spectroscopy in water solution. On the basis of these structures, interaction models of beta-secretase and substrate peptides were determined by molecular dynamics simulation. Four hydrogen bonds and one water-mediated interaction were formed in the docking models. In particular, the hydrogen bonding network of Sub M-BACE formed spread over the broad region of the active site of beta-secretase (P5-P3'), and the side chain of P2-Asn formed a hydrogen bond specifically with the side chain of Arg235. These are more favorable to the cleavage of Sub M by beta-secretase than Sub W. The two substrate peptides showed different tendency to bind to beta-secretase and this information may useful for drug development to treat and prevent Alzheimer's disease.
Lee
Jee-Young
JY
Bio/Molecular Informatics Center, Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Korea.
Lee
Sung-Ah
SA
Kim
Jin-Kyoung
JK
Chae
Chi-Bom
CB
Kim
Yangmee
Y
D000595:Amino Acid Sequence; D053829:Amyloid Precursor Protein Secretases / Q000737:chemistry / Q000378:metabolism*; D016564:Amyloid beta-Protein Precursor / Q000737:chemistry / Q000378:metabolism; D002942:Circular Dichroism; D003198:Computer Simulation; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D017433:Protein Structure, Secondary; D013379:Substrate Specificity; D013816:Thermodynamics
D016564:Amyloid beta-Protein Precursor; D010455:Peptides; D053829:Amyloid Precursor Protein Secretases