Materials and Methods
Table 1 shows the structure templates used in the modeling work. Seven templates were taken from the Brookhaven Protein Data Bank (PDB). Their PDB codes are 1AXH, 1AGG, 1EIT, 1VTX, 1OMN, 1OMG and 1GUR respectively. The structure of the Chinese bird spider toxin Huwentoxin-I (1HWT) was solved in our laboratory [Qu et al., 1997], which has not been deposited to the PDB bank. Sequence alignment was performed taking into account that three disulfide bridges are conserved among all these peptides (Fig 1).
Table 1 Structure templates used for modeling
|
Code |
Name |
Source |
Activity |
|
1AXH |
Atracotoxin-HVI |
Funnel-web spider toxin |
Insecticidal toxin |
|
1HWT |
Huwentoxin-I |
Chinese bird spider toxin |
Neuromuscular transmission blocker |
|
1AGG |
Omega-agatoxin-Ivb |
Funnel-web spider toxin |
P-type calcium channel antagonist |
|
1EIT |
mu-agatoxin-I |
Funnel-web spider toxin |
Diverse ion channel specificity |
|
1VTX |
delta-Atracotoxin-HVI |
Funnel-web spider toxin |
Sodium channel blocker |
|
1OMN |
Omega-conotoxin-MVIIc |
Magus cone |
P-type calcium channel antagonist |
|
1OMG |
Omega-conotoxin-MVIIa |
Magus cone |
P-type calcium channel antagonist |
|
1GUR |
Gurmarin |
Gymnema sylvestre |
Sweet taste repressor |
The model building was mainly carried on using the molecular modeling program Whatif [Vriend, 1998]. The NMR coordinates of 1AXH were used to build up the backbone fragments. Loops were searched against the Whatif built-in loop fragment database. The modeled structure was refined geometrically within Whatif and energy minimized with the CHARM program to reduce side chain crash.