Ab initio molecular orbital calculations on specific interactions between urokinase-type plasminogen activator and its receptor

• Published in: Journal of molecular graphics & modelling 2009-08, Vol.28 (1), p.46-53
• Main Authors: Nagase, Keisuke, Kobayashi, Hiroshi, Yoshikawa, Eri, Kurita, Noriyuki
• Format: Article
• Language: English
• Subjects: Binding Sites; Cancer invasion; Cancer metastasis; Fragment molecular orbital method; Humans; Models, Molecular; Molecular mechanics simulation; Molecular orbital calculation; Protein Binding; Protein Structure, Secondary; Protein–protein interaction; Receptors, Urokinase Plasminogen Activator - chemistry; Receptors, Urokinase Plasminogen Activator - metabolism; Specific interaction; Structure-Activity Relationship; uPAR; Urokinase-type plasminogen activator; Urokinase-Type Plasminogen Activator - chemistry; Urokinase-Type Plasminogen Activator - metabolism
• ISSN: 1093-3263; 1873-4243
• DOI: 10.1016/j.jmgm.2009.04.001

Cancer invasions and metastases are controlled by various proteases. In particular, the binding of urokinase-type plasminogen activator (uPA) to the uPA receptor (uPAR) existing on the surface of cancer cell is considered to be a trigger for cancer invasions. In the present study, we determined the structure of uPA and uPAR complex in water and investigated the specific interactions between uPA and uPAR by ab initio molecular orbital (MO) calculations based on fragment MO method. The result indicates that the 20–26 amino acid residues of uPA are important for the binding between uPA and uPAR, and that the electrostatic interactions between the charged amino acid residues existing in both uPA and uPAR have large contribution to the binding. The influence of crystal water molecules existing between uPA and uPAR was also investigated to be significant on the specific interactions between uPA and uPAR. These results are expected to be informative for developing new medicines blocking the binding of uPA and uPAR.