Structure-based design of carbon nanotubes as HIV-1 protease inhibitors: Atomistic and coarse-grained simulations

2010 ◽  
Vol 29 (2) ◽  
pp. 171-177 ◽  
Author(s):  
Yuan Cheng ◽  
Dechang Li ◽  
Baohua Ji ◽  
Xinghua Shi ◽  
Huajian Gao
2009 ◽  
Vol 130 (21) ◽  
pp. 215102 ◽  
Author(s):  
Dechang Li ◽  
Ming S. Liu ◽  
Baohua Ji ◽  
Kehchih Hwang ◽  
Yonggang Huang

2016 ◽  
Author(s):  
John M A Grime ◽  
James F Dama ◽  
Barbie K Ganser-Pornillos ◽  
Cora L Woodward ◽  
Grant J Jensen ◽  
...  

The maturation of HIV-1 viral particles is essential for viral infectivity. During maturation, many copies of the capsid protein (CA) self-assemble into a capsid shell to enclose the viral RNA. The mechanistic details of the initiation and early stages of capsid assembly remain to be delineated. We present coarse-grained simulations of capsid assembly under various conditions, considering not only capsid lattice self-assembly but also the potential disassembly of capsid upon delivery to the cytoplasm of a target cell. The effects of CA concentration, molecular crowding, and the conformational variability of CA are described, with results indicating that capsid nucleation and growth is a multi-stage process requiring well-defined metastable intermediates. Generation of the mature capsid lattice is sensitive to local conditions, with relatively subtle changes in CA concentration and molecular crowding influencing self-assembly and the ensemble of structural morphologies.


2014 ◽  
Vol 106 (3) ◽  
pp. 577-585 ◽  
Author(s):  
Landry Charlier ◽  
Maxime Louet ◽  
Laurent Chaloin ◽  
Patrick Fuchs ◽  
Jean Martinez ◽  
...  

2020 ◽  
Author(s):  
Thomas G. Flower ◽  
Yoshinori Takahashi ◽  
Arpa Hudait ◽  
Kevin Rose ◽  
Nicholas Tjahjono ◽  
...  

AbstractThe ESCRT complexes drive membrane scission in HIV-1 release, autophagosome closure, MVB biogenesis, cytokinesis, and other cell processes. ESCRT-I is the most upstream complex and bridges the system to HIV-1 Gag in virus release. The crystal structure of the headpiece of human ESCRT-I comprising TSG101:VPS28:VPS37B:MVB12A was determined, revealing an ESCRT-I helical assembly with a 12 molecule repeat. Electron microscopy confirmed that ESCRT-I subcomplexes form helical filaments in solution. Mutation of VPS28 helical interface residues blocks filament formation in vitro and autophagosome closure and HIV-1 release in human cells. Coarse grained simulations of ESCRT assembly at HIV-1 budding sites suggest that formation of a 12-membered ring of ESCRT-I molecules is a geometry-dependent checkpoint during late stages of Gag assembly and HIV-1 budding, and templates ESCRT-III assembly for membrane scission. These data show that ESCRT-I is not merely a bridging adaptor, but has an essential scaffolding and mechanical role in its own right.


2015 ◽  
Author(s):  
Jessica Pepe ◽  
Ivano Mezzaroma ◽  
Alessandra Fantauzzi ◽  
Mario Falciano ◽  
Alessandra Salotti ◽  
...  

2019 ◽  
Author(s):  
Jonas Landsgesell ◽  
Oleg Rud ◽  
Pascal Hebbeker ◽  
Raju Lunkad ◽  
Peter Košovan ◽  
...  

We introduce the grand-reaction method for coarse-grained simulations of acid-base equilibria in a system coupled to a reservoir at a given pH and concentration of added salt. It can be viewed as an extension of the constant-pH method and the reaction ensemble, combining explicit simulations of reactions within the system, and grand-canonical exchange of particles with the reservoir. Unlike the previously introduced methods, the grand-reaction method is applicable to acid-base equilibria in the whole pH range because it avoids known artifacts. However, the method is more general, and can be used for simulations of any reactive system coupled to a reservoir of a known composition. To demonstrate the advantages of the grand-reaction method, we simulated a model system: A solution of weak polyelectrolytes in equilibrium with a buffer solution. By carefully accounting for the exchange of all constituents, the method ensures that all chemical potentials are equal in the system and in the multi-component reservoir. Thus, the grand-reaction method is able to predict non-monotonic swelling of weak polyelectrolytes as a function of pH, that has been known from mean-field predictions and from experiments but has never been observed in coarse-grained simulations. Finally, we outline possible extensions and further generalizations of the method, and provide a set of guidelines to enable safe usage of the method by a broad community of users.<br><br>


Tetrahedron ◽  
2002 ◽  
Vol 58 (9) ◽  
pp. 1697-1708 ◽  
Author(s):  
Yan Xing Jia ◽  
Xin Li ◽  
Bin Wu ◽  
Xue Zhi Zhao ◽  
Yong Qiang Tu

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