Role of protein interactions in defining HIV-1 viral capsid shape and stability: a coarse-grained analysis.
Coarse-grained models of the HIV-1 CA dimer are constructed based on all-atom molecular dynamics simulations. Coarse-grained representations of the capsid shell, which is composed of approximately 1500 copies of CA proteins, are constructed and their stability is examined. A key interaction between carboxyl and hexameric amino terminal domains is shown to generate the curvature of the capsid shell. It is demonstrated that variation of the strength of this interaction for different subunits in the lattice can cause formation of asymmetric, conical-shaped closed capsid shells, and it is proposed that variations, in the structure of the additional carboxyl-amino terminal binding interface during self-assembly, are important aspects of capsid cone formation. These results are in agreement with recent structural studies of the capsid hexamer subunit, which suggest that variability in the binding interface is a cause of the differences in subunit environments that exist in a conical structure.
Krishna
Vinod
V
Center for Biophysical Modeling and Simulation, and Department of Chemistry, University of Utah, Salt Lake City, Utah, USA.
Ayton
Gary S
GS
Voth
Gregory A
GA
D001665:Binding Sites; D002213:Capsid / Q000737:chemistry* / Q000648:ultrastructure*; D036022:Capsid Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D003198:Computer Simulation; D015497:HIV-1 / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D011485:Protein Binding; D025941:Protein Interaction Mapping
D036022:Capsid Proteins