BCM 496H: Lab Report 2

insect toxin alpha from Leiurus Quinquestriatus Hebraeus scorpion toxin II from Androctonus australis hector

A Structural Comparison of Scorpion Toxin II and Insect Toxin Alpha

Scorpion toxin II isolated from the scorpion Androctonus australis hector (shown above right) and insect toxin alpha isolated from the scorpion Leiurus Quinquestriatus Hebraeus (shown above left) share many similarities.(1,2) The Structural Classification of Proteins databank (SCOP) designates both toxins as small proteins dominated by disulfide bridges . The fold of both molecules is a knottin, a disulfide-bound fold (contains a beta-hairpin with two adjacent disulfides).(3) Scorpion toxin II contains 64 residues while insect toxin alpha contains 65 (the extra amino acid is a methionine in the first position). Primary structure analysis indicates that the sequences are very much alike (see below). 

	

   VAL1=LYS2=ASP3=GLY4=TYR5=ILE6=VAL7=ASP8=ASP9=VAL10=ASN11=CYS12=
 MET1=VAL2=ARG3=ASP4=ALA5=TYR6=ILE7=ALA8=LYS9=ASN10=TYR11=ASN12=CYS13= 	

     THR13=TYR14=PHE15=CYS16=GLY17=ARG18=ASN19=ALA20=TYR21=CYS22=ASN23=
     VAL14=TYR15=GLU16=CYS17=PHE18=ARG19=ASP20=ALA21=TYR22=CYS23=ASN24=

     GLU24=GLU25=CYS26=THR27=LYS28=LEU29=LYS30=GLY31=GLU32=SER33=GLY34=
     GLU25=LEU26=CYS27=THR28=LYS29=ASN30=GLY31=ALA32=SER33=SER34=GLY35=

     TYR35=CYS36=GLN37=TRP38=ALA39=SER40=PRO41=TYR42=GLY43=ASN44=ALA45=
     TYR36=CYS37=GLN38=TRP39=ALA40=GLY41=LYS42=TYR43=GLY44=ASN45=ALA46=

     CYS46=TYR47=CYS48=TYR49=LYS50=LEU51=PRO52=ASP53=HIS54=VAL55=ARG56=
     CYS47=TRP48=CYS49=TYR50=ALA51=LEU52=PRO53=ASP54=ASN55=VAL56=PRO57=

     THR57=LYS58=GLY59=PRO60=GLY61=ARG62=CYS63=HIS64
     ILE58=ARG59=VAL60=PRO61=GLY62=LYS63=CYS64=ARG65

Both structures contain one alpha-helix and three beta-sheets (see scorpion toxin II and insect toxin alpha for more information). 

			scorpion toxin II		insect toxin alpha

alpha helix	      ASN19-LYS28	              ASP20-ASN30

beta sheet 1	       LYS2-GLY4		       ALA5-LEU7

beta sheet 2	      GLU32-GLN37	              SER34-GLN38

beta sheet 3	      ALA45-LEU51		      ALA46-TYR50

ribbon: scorpion toxin II ribbon: insect toxin alpha A visual comparison of the molecules shows that both structures have a very similar overall composition. Scorpion toxin II (yellow) and insect toxin alpha (red) display an almost indistinguishable tertiary structure. In order to exactly compare the overall shape of the two proteins, their structures may be directly overlayed using the monomer fitting function in the molecular graphics program, Sybyl.

ribbon overlay The program calculates a RMS deviation for the two toxins. The RMS deviation, a measurement of the "differences"("local conformational variability") between the two molecules, is 1.7470 for the common atoms in the molecules and 1.2311 for just the backbone of the molecules. From the image (at left), one may discern the slight differences between the two stuctures (the ribbons illustrate the fit of common atoms). The alpha-helices are slightly out of line as well as many of the turns in the proteins. Because many of the residues are different and thus have different substituents, the deviation of common atoms will be greater than the deviation between backbones.

By modifying the sequence of insect toxin alpha, the primary structure of the toxin may be made to match that of scorpion toxin II. The matched structures at right show the differences between common atoms for the insect toxin alpha (modeled structure) and scorpion toxin II (x-ray structure). The RMS deviation of the common atoms has increased to 2.3196. The RMSD of the backbones remains the same at 1.2311 because these atoms have not changed. modified sequence This result might not seem to make sense considering that the primary structures are identical; however, the RMSD function measures the differences in common atoms between two sequences (i.e., sp3 gamma carbon to sp3 gamma carbon) so that an increase in the number of these common atoms increases as the sequences become more alike (i.e., as the substituent groups become more alike). If the RMSD between the original insect alpha toxin (red at right) and the modified insect alpha toxin (green at right)is examined, one will notice that the original conformations seem to be conserved (overall RMSD of 0.02637; backbone RMSD of 0.0000), though the subtituents might be different. (A decrease in common atoms might also account for this small difference.)
References

(1) http://www.pdb.bnl.gov/pdb-bin/pdbids?id=1lqh

(3) http://pdb.pdb.bnl.gov/scop/data/scop.1.007.003.006.001.004.html 


Jacqueline Campbell          Univer 5, 1998