Structural analysis of membrane-bound hECE-1 dimer using molecular modeling techniques: insights into conformational changes and Aβ1–42 peptide binding

• Published in: Amino acids 2015-03, Vol.47 (3), p.543-559
• Main Authors: Sonawane, Kailas D., Barage, Sagar H.
• Format: Article
• Language: English
• Subjects: Amyloid beta-Peptides - chemistry; Amyloid beta-Peptides - metabolism; Analytical Chemistry; Aspartic Acid Endopeptidases - chemistry; Aspartic Acid Endopeptidases - metabolism; Biochemical Engineering; Biochemistry; Biomedical and Life Sciences; Endothelin-Converting Enzymes; Humans; Life Sciences; Metalloendopeptidases - chemistry; Metalloendopeptidases - metabolism; Models, Molecular; Neurobiology; Original Article; Peptide Fragments - chemistry; Peptide Fragments - metabolism; Protein Binding; Protein Multimerization; Protein Structure, Quaternary; Protein Structure, Secondary; Proteomics
• ISSN: 0939-4451; 1438-2199
• DOI: 10.1007/s00726-014-1887-8

The human endothelin converting enzyme-1 (hECE-1) is a homodimer linked by a single disulfide bridge and has been identified as an important target for Alzheimer’s disease. Structural analysis of hECE-1 dimer could lead to design specific and effective therapies against Alzheimer’s disease. Hence, in the present study homology model of transmembrane helix has been constructed and patched with available crystal structure of hECE-1 monomer. Then, membrane-bound whole model of hECE-1 dimer has been developed by considering biophysical properties of membrane proteins. The explicit molecular dynamics simulation revealed that the hECE-1 dimer exhibits conformational restrains and controls total central cavity by regulating the degree of fluctuations in some residues (238–226) for substrate/product entrance/exit sites. In turn, conformational rearrangements of interdomain linkers as well as helices close to the inner surface are responsible for increasing total central cavity of hECE-1 dimer. Further, the model of hECE-1 dimer was docked with Aβ 1–42 followed by MD simulation to investigate possible orientation and interactions of Aβ 1–42 in catalytic groove of hECE-1 dimer. The free energy calculations exposed the stability of complex and helped us to identify key residues of hECE-1 involved in interactions with Aβ 1–42 peptide. Hence, the present study might be useful to understand structural significance of membrane-bound dimeric hECE-1 to design therapies against Alzheimer’s disease.