comparative thermal unfolding study of gp120 from HIV-1 isolates with different neutralization-sensitivity phenotype by molecular dynamics simulations
- release the differences of H061.14- and R2-gp120 in structural deviation, unfolding content and conformational diversity.
- find the mutations response to differences in conformational diversity.
structural models of H061.14- and R2-gp120. (A)H061.14-gp120 (B)R2-gp120 (C)superimpose
time evolution of the backbone RMSD values at four different temperatures. (A) 300K (B) 373K (C) 473K (D) 573K.
time evolution of the secondary structural elements at four different temperatures.
time evolution of the native contact content at four different temperatures. The native contact content in the overall, V1/V2 region, V3 loops, bridging sheet and core of gp120 are colored black, red, green, blue and yellow. 图4需要计算各个部分的天然接触含量，用不同的颜色标志，代码已经有了。
Cluster based on RMSD or other features and make the ordered unfolding pathway with 20 (more or less) representative structures.
C$_\alpha$ RMSF and RMSF-difference at four different temperatures. (A) 300K (B) 373K (C) 473K (D) 573K.
Mutational residue response to differences in conformational diversity (RMSF).
Sequence alignments between the target and template used for building structural models of H061.14-gp120.
Sequence alignments between the target and template used for building structural models of R2-gp120.
Ramachandran plots of the constructed structural models of H061.14- (left) and R2-gp120 (right).
Structure-based multiple sequence alignment between H061.14- and R2-gp120. 注意，这里没有模板。 TEST