Homology Modeling and Molecular Dynamics Simulations of the Mu Opioid Receptor in a Membrane-Aqueous System

ChemBioChem ◽  
2005 ◽  
Vol 6 (5) ◽  
pp. 853-859 ◽  
Author(s):  
Yan Zhang ◽  
Yuk Y. Sham ◽  
Ramkumar Rajamani ◽  
Jiali Gao ◽  
Philip S. Portoghese
Keyword(s):  
Molecular Dynamics ◽  
Homology Modeling ◽  
Molecular Dynamics Simulations ◽  
Opioid Receptor ◽  
Mu Opioid Receptor ◽  
Aqueous System ◽  
Mu Opioid ◽  
Dynamics Simulations

scholarly journals Homology modeling and molecular dynamics simulations of lymphotactin

2000 ◽  
Vol 9 (11) ◽  
pp. 2192-2199 ◽  
Author(s):  
Buyong Ma ◽  
Junjie Xiong ◽  
Jacek Lubkowski ◽  
Ruth Nussinov
Keyword(s):  
Molecular Dynamics ◽  
Homology Modeling ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations

scholarly journals Elucidating Interactions Between SARS-CoV-2 Trimeric Spike Protein and ACE2 Using Homology Modeling and Molecular Dynamics Simulations

2021 ◽  
Vol 8 ◽  
Author(s):  
Sugunadevi Sakkiah ◽  
Wenjing Guo ◽  
Bohu Pan ◽  
Zuowei Ji ◽  
Gokhan Yavas ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Homology Modeling ◽  
Molecular Dynamics Simulations ◽  
Host Cell ◽  
Tertiary Structure ◽  
Cell Receptor ◽  
Host Cells ◽  
Spike Protein ◽  
Receptor Protein ◽  
Dynamics Simulations

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). As of October 21, 2020, more than 41.4 million confirmed cases and 1.1 million deaths have been reported. Thus, it is immensely important to develop drugs and vaccines to combat COVID-19. The spike protein present on the outer surface of the virion plays a major role in viral infection by binding to receptor proteins present on the outer membrane of host cells, triggering membrane fusion and internalization, which enables release of viral ssRNA into the host cell. Understanding the interactions between the SARS-CoV-2 trimeric spike protein and its host cell receptor protein, angiotensin converting enzyme 2 (ACE2), is important for developing drugs and vaccines to prevent and treat COVID-19. Several crystal structures of partial and mutant SARS-CoV-2 spike proteins have been reported; however, an atomistic structure of the wild-type SARS-CoV-2 trimeric spike protein complexed with ACE2 is not yet available. Therefore, in our study, homology modeling was used to build the trimeric form of the spike protein complexed with human ACE2, followed by all-atom molecular dynamics simulations to elucidate interactions at the interface between the spike protein and ACE2. Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) and in silico alanine scanning were employed to characterize the interacting residues at the interface. Twenty interacting residues in the spike protein were identified that are likely to be responsible for tightly binding to ACE2, of which five residues (Val445, Thr478, Gly485, Phe490, and Ser494) were not reported in the crystal structure of the truncated spike protein receptor binding domain (RBD) complexed with ACE2. These data indicate that the interactions between ACE2 and the tertiary structure of the full-length spike protein trimer are different from those between ACE2 and the truncated monomer of the spike protein RBD. These findings could facilitate the development of drugs and vaccines to prevent SARS-CoV-2 infection and combat COVID-19.

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