Applied Bioinformatics Course

Sequence analysis of spider toxin and antifungal peptide.

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

1QK6

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.

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14 September 2017, J Luo, CBI, PKU, Beijing, China