Theoretical study of intramolecular interaction energies during dynamics simulations of oligopeptides by the fragment molecular orbital-Hamiltonian algorithm method

2005 ◽  
Vol 122 (9) ◽  
pp. 094905 ◽  
Author(s):  
Takayoshi Ishimoto ◽  
Hiroaki Tokiwa ◽  
Hiroyuki Teramae ◽  
Umpei Nagashima
Keyword(s):  
Molecular Orbital ◽  
Theoretical Study ◽  
Intramolecular Interaction ◽  
Interaction Energies ◽  
Fragment Molecular Orbital ◽  
Hamiltonian Algorithm ◽  
Dynamics Simulations

scholarly journals Fragment Molecular Orbital Based Interaction Analyses on Complexes Between RBD Variants and ACE2

2021 ◽  
Author(s):  
Kazuki Akisawa ◽  
Ryo Hatano ◽  
Koji Okuwaki ◽  
Shun Kitahara ◽  
Yusuke Tachino ◽  
...  
Keyword(s):  
South Africa ◽  
Angiotensin Converting Enzyme ◽  
Molecular Orbital ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
Interaction Energies ◽  
Converting Enzyme ◽  
Angiotensin Converting Enzyme 2 ◽  
Fragment Molecular Orbital ◽  
Fragment Interaction

The spike protein plays an important role in the infection of SARS-CoV-2 to human cells, and the binding affinity of receptor binding domain (RBD) to angiotensin-converting enzyme 2 (ACE2) is of special interest. In this report, we present a series of interaction analyses for the RBD - ACE2 complex (PDB ID: 6M0J) and mutated complexes of UK (B.1.1.7 lineage), South Africa (B1.3.51) and Brazil (B1.1.248) types, based on the fragment molecular orbital (FMO) calculations. The effects of mutations are investigated in terms of inter-fragment interaction energies (IFIEs), indicating the higher affinities of RBD variants with ACE2.

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