期刊
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
卷 82, 期 -, 页码 145-156出版社
ELSEVIER SCIENCE INC
DOI: 10.1016/j.jmgm.2018.04.012
关键词
Molecular dynamics; DNA aptamer; PDGF-B; PDGFR beta/PDGF-B interaction; Angiogenesis
类别
资金
- Thammasat University [1/6/2560]
- Central Scientific Instrument Center (CSIC), Faculty of Science and Technology, Thammasat University
- Asean Economics Community (AEC) scholarship from Thammasat University
PDGFR beta/PDGF-B interaction plays a role in angiogenesis, and is mandatory in wound healing and cancer treatment. It has been reported that the PDGF-B aptamer was able to bind to PDGF-B, thus regulating the angiogenesis. However, the binding interaction between the aptamer and the growth factor, including the binding sites, has not been well investigated. This study applied a molecular dynamics (MD) simulation to investigate the aptamer-growth factor interaction in the presence or absence of a receptor (PDGFR beta). Characterization of the structure of an aptamer-growth factor complex revealed binding sites from each section in the complex. Upon the complex formation, PDGF-B and its aptamer exhibited less flexibility in their molecular movement, as indicated by the minimum values of RMSD, RMSF, loop-to-loop distance, and the summation of PCA eigenvalues. Our study of residue pairwise interaction demonstrated that the binding interaction was mainly contributed by electrostatic interaction between the positively-charged amino acid and the negatively-charged phosphate backbone. The role of the PDGF-B aptamer in PDGFR beta/PDGF-B interaction was also investigated. We demonstrated that the stability of the Apt-PDGF-B complex could prevent the presence of a competitor, of PDGFR beta, interrupting the binding process. Because the aptamer was capable of binding with PDGF-B, and blocking the growth factor from the PDGFR beta, it could down regulate the consequent signaling pathway. We provide evidence that the PDGF-BB aptamer is a promising molecule for regulation of angiogenesis. The MD study provides a molecular understanding to modification of the aptamer binding interaction, which could be used in a number of medical applications. (C) 2018 Elsevier Inc. All rights reserved.
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