RESUMO
There are two stages generally recognized in the viral capsid assembly: nucleation and elongation. This paper focuses on the nucleation stage and develops mathematical models for HIV-1 viral capsid nucleation based on six-species dynamical systems. The Particle Swarm Optimization (PSO) algorithm is used for parameter fitting to estimate the association and dissociation rates from biological experiment data. Numerical simulations of capsid protein (CA) multimer concentrations demonstrate a good agreement with experimental data. Sensitivity and elasticity analysis of CA multimer concentrations with respect to the association and dissociation rates further reveals the importance of CA trimer-of- dimers in the nucleation stage of viral capsid self- assembly.
Assuntos
HIV-1/fisiologia , Modelos Biológicos , Montagem de Vírus/fisiologia , Algoritmos , Capsídeo/química , Capsídeo/fisiologia , Proteínas do Capsídeo/química , Proteínas do Capsídeo/fisiologia , Simulação por Computador , HIV-1/química , Proteínas do Vírus da Imunodeficiência Humana/química , Proteínas do Vírus da Imunodeficiência Humana/fisiologia , Conceitos Matemáticos , Modelos Moleculares , Multimerização ProteicaRESUMO
This paper presents a modeling study for the intracellular trafficking and trimerization of the HIV-1 Gag proteins. A set of differential equations including initial and boundary conditions is used to characterize the transport, diffusion, association and dissociation of Gag monomers and trimers for the time period from the initial production of Gag protein monomers to the initial appearance of immature HIV-1 virions near the cell membrane (the time duration Ta). The existence and stability of the steady-state solution of the initial boundary value problems provide a quantitative characterization of the tendency and equilibrium of Gag protein movement. The numerical simulation results further demonstrate Gag trimerization near the cell membrane. Our calculations of Ta are in good agreement with published experimental data. Sensitivity analysis of Ta to the model parameters indicates that the timing of the initial appearance of HIV-1 virions on the cell membrane is affected by the diffusion and transport processes. These results provide important information and insight into the Gag protein transport and binding and HIV-1 virion formation.
Assuntos
HIV-1/fisiologia , Produtos do Gene gag do Vírus da Imunodeficiência Humana/metabolismo , Membrana Celular/virologia , Simulação por Computador , Humanos , Conceitos Matemáticos , Modelos Biológicos , Ligação Proteica , Multimerização Proteica , Montagem de Vírus , Produtos do Gene gag do Vírus da Imunodeficiência Humana/químicaRESUMO
A new full-length acyltransferase cDNA was obtained from Taxus chinensis by homology-based cloning strategy. The cDNA has an open-reading frame of 1,275 nucleotides, which encodes 425 amino acids with a calculated molecular weight of 47,241 Da and an estimated pI value of 5.93. The deduced amino acid sequence resembles the sequences of other cloned acyltransferases (56-61% identity; 71-75% similarity) involved directly in taxol biosynthetic pathways. This cDNA was expressed in Escherichia coli using the expression vector pET32a(+). The expression band corresponds to the calculated mass plus the N-terminal fusion protein derived from the vector.