Effect of cofactor-binding on the specific interactions between androgen receptor and its ligand: Ab initio molecular simulations

2016 ◽  
Author(s):  
Ittetsu Kobayashi ◽  
Kanako Shimamura ◽  
Hiromi Ishimura ◽  
Ryushi Kadoya ◽  
Noriyuki Kurita ◽  
...  
Keyword(s):  
Androgen Receptor ◽  
Ab Initio ◽  
Molecular Simulations ◽  
Specific Interactions ◽  
Cofactor Binding

Specific interactions between mycobacterial FtsZ protein and curcumin derivatives: Molecular docking and ab initio molecular simulations

2018 ◽  
Vol 692 ◽  
pp. 166-173 ◽  
Author(s):  
Mitsuki Fujimori ◽  
Haruki Sogawa ◽  
Shintaro Ota ◽  
Pavel Karpov ◽  
Sergey Shulga ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Ab Initio ◽  
Molecular Simulations ◽  
Specific Interactions ◽  
Curcumin Derivatives ◽  
Ftsz Protein

Ab initio molecular simulations on specific interactions between amyloid beta and monosaccharides

2012 ◽  
Vol 547 ◽  
pp. 89-96 ◽  
Author(s):  
Kazuya Nomura ◽  
Akisumi Okamoto ◽  
Atsushi Yano ◽  
Shin’ichi Higai ◽  
Takashi Kondo ◽  
...  
Keyword(s):  
Ab Initio ◽  
Amyloid Beta ◽  
Molecular Simulations ◽  
Specific Interactions

Specific interactions between androgen receptor and its ligand: ab initio molecular orbital calculations in water

2017 ◽  
Vol 75 ◽  
pp. 383-389 ◽  
Author(s):  
Ittetsu Kobayashi ◽  
Ryosuke Takeda ◽  
Rie Suzuki ◽  
Kanako Shimamura ◽  
Hiromi Ishimura ◽  
...  
Keyword(s):  
Androgen Receptor ◽  
Ab Initio ◽  
Molecular Orbital ◽  
Molecular Orbital Calculations ◽  
Specific Interactions

scholarly journals Specific Interactions Between The Alkaline Protease of P. Aeruginosa And Its Natural Peptide Inhibitor: Ab Initio Molecular Simulations

2021 ◽  
Author(s):  
Ryosuke Saito ◽  
Kyohei Imai ◽  
Shohei Yamamoto ◽  
Takuya Ezawa ◽  
Satoshi Sugiyama ◽  
...  
Keyword(s):  
Ab Initio ◽  
Alkaline Protease ◽  
Molecular Simulations ◽  
Significant Inhibition ◽  
Peptide Inhibitor ◽  
Orbital Method ◽  
Specific Interactions ◽  
Amino Acid Residues ◽  
Important Virulence Factor ◽  
Natural Peptide

Abstract Alkaline protease aeruginolysin (APR) is an important virulence factor in the evasion of the immune system by Pseudomonas aeruginosa (P. aeruginosa). The P. aeruginosa genome also encodes the highly potent and specific APR peptide inhibitor (APRin). However, the structural reason for the significant inhibition has not been revealed. Using ab initio molecular simulations, we here investigated the specific interactions between APR and APRin to elucidate which amino acid residues of APRin and APR contribute strongest to the inhibition. Since APR has a Zn ion at the ligand-binding site, and histidine and glutamic acid residues are coordinated with Zn, it is essential to precisely describe these coordination bonds to elucidate the specific interactions between APR and APRin. Therefore, we employed the ab initio fragment molecular orbital method to investigate the specific interactions at an electronic level. The results revealed that Ser1 and Ser2 at the N-terminal of APRin significantly contribute to the binding between APRin and APR. In particular, Ser1 binds strongly to Zn as well as to the sidechains of Hid176, Hid180, and Hid186 in APR. This is the main reason for the strong interaction between APR and APRin. The results also elucidated significant contributions of the positively charged Arg83 and Arg90 residues of APRin to the binding with APR. These findings may provide information useful for the design of novel small agents as potent APR inhibitors.

Specific interactions between amyloid-β peptide and curcumin derivatives: Ab initio molecular simulations

2015 ◽  
Vol 633 ◽  
pp. 139-145 ◽  
Author(s):  
Hiromi Ishimura ◽  
Ryushi Kadoya ◽  
Tomoya Suzuki ◽  
Takeru Murakawa ◽  
Sergiy Shulga ◽  
...  
Keyword(s):  
Ab Initio ◽  
Molecular Simulations ◽  
Amyloid Β ◽  
Amyloid Β Peptide ◽  
Specific Interactions ◽  
Curcumin Derivatives
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