Abstract
The VP40 protein plays a critical role in coordinating the virion assembly, budding, and replication of the Ebola virus. Efforts have been made in recent years to understand various aspects of VP40 structure, dynamics, and function such as assembly of the protein and its roles in virus replication and penetration of the protein into the plasma membrane. A major conformational transformation is necessary for VP40 to form some of its oligomeric structures and to perform various functions. This conformational change from a compact structure with the N-terminal domain (NTD) and C-terminal domain (CTD) closely associated involves a dissociation or springing-out of the CTD from the NTD. We perform investigations using computational molecular dynamics simulations as well as knowledge-based Monte Carlo simulations. We find that a sharp springing of the CTD from the NTD in a free VP40 protein cannot occur solely by random thermal fluctuations without intermediate oligomerized segments, and therefore is likely triggered by additional molecular events.
Highlights
The VP40 protein plays a critical role in coordinating the virion assembly, budding, and replication of the Ebola virus.[1,2,3,4,5,6] Enormous efforts have been made in recent years to understand various aspects of VP40 structure, dynamics, and function such as assembly of the protein[1] and its roles in virus replication[2] and penetration of the protein into the plasma membrane.[3]
We find that the springing of the C-terminal domain (CTD) from the N-terminal domain (NTD) of a free monomer without bridging via segmental oligomerization cannot occur by random thermal fluctuations alone, and is likely triggered by additional and perhaps specific molecular events as proposed by Ref. 7
In order to use the knowledge-based Monte Carlo (MC) simulations together with the MD simulations to understand the dynamics of the VP40 monomer, we first checked if both computational methods resulted in similar behavior
Summary
The VP40 protein plays a critical role in coordinating the virion assembly, budding, and replication of the Ebola virus.[1,2,3,4,5,6] Enormous efforts have been made in recent years to understand various aspects of VP40 structure, dynamics, and function such as assembly of the protein[1] and its roles in virus replication[2] and penetration of the protein into the plasma membrane.[3] These molecular investigations on VP40 may help in designing therapeutics[4] against the Ebola virus.
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