Genvector), and expressed as a measure of molecular flexibility. Fig. 2 was prepared with PyMOL (26); “intermediate” structures are the result of Gromacs normal mode evaluation. Residueresidue maps of high amplitude correlated motions had been constructed with an in-house Python script (Fig. 3). Initially, every residue in a toxin of length n was assigned a vector that describes its motion along the slowest mode. Then and n n map of dot items was calculated to reveal the high amplitude correlated motions. Second, an averaged map for every toxin group was plotted, in accordance with the sequence alignment (Fig. 1) that relates structural components. As a result of the alignment process, each map in Fig. 3A has dimensions of 69 69 residues. Molecular Hydrophobicity Possible (MHP) Calculations– The MHP method assumes that each and every atom inside a molecule possesses its “intrinsic” value of hydrophobicity (atomic hydrophobicity continual), taking the molecular topology into account (16, 17).Levonadifloxacin These constants have been determined in the database of experimental log P values for any large quantity of organic compounds (27); MHP at any given point is calculated as a superposition of contributions made by every atom, monotonically decayJOURNAL OF BIOLOGICAL CHEMISTRYEXPERIMENTAL PROCEDURES Homology Modeling–To enrich statistics, structures of several -toxins with identified pharmacological profile have been modeled applying associated toxins as templates (see Table 1 for particulars). Alignments have been produced with all the ClustalW software program (19) (Fig. 1). Homology modeling was performed with Modeler version eight.two (20). The cis/trans configuration with the peptide bond in between residues 8 and 9 was left “as is” in experimental structures; in models, the configuration was derived from templates,JUNE 28, 2013 VOLUME 288 NUMBERModular Organization of Scorpion -ToxinsTABLE 1 Properties of -toxins involved inside the studyToxina Mammal toxins Aah1 Aah2* Aah3 BmK M8 BmK Tx11 Bot3* Lqh2* Lqq5* Insect toxins Aah2 chimera Bj IT* BmK IT1 Bot IT1 Lqh IT Lqq3 -Like toxins BmK M1 BmK M2 BmK M4 BmK M7 BmK M10 Bom3 Bom4 Bot1* Bot2* Lqh3* Lqh4* Lqh6*aPDB ID or Uniprot ID/template (italics)b P01479/1PTX 1PTX P01480/1PTX 1SNB 2KBH P01485/1PTX P59355/1PTX P01481/1PTX 1SEG Q56TT9/1SN1 1OMY P55902/1LQQ 1LQH 1LQQ 1SN1 1CHZ 1SN4 1KV0 2KBK P13488/1FH3 P59354/1SN1 P01488/1SN1 P01483/1SN1 1BMR P83644/1LQQ P59356/1FHComputed datac MHPSMd 0.027 0.109 0.017 0.239 0.190 0.138 0.138 0.148 0.096 0.087 0.068 0.030 0.003 0.049 0.071 0.020 0.033 0.071 0.022 0.013 0.033 0.112 0.033 0.071 0.053 0.022 0.283 0.315 0.266 0.273 0.311 0.279 0.294 0.185 0.020 0.025 0.016 0.024 0.MIF Protein, Human 025 0.PMID:23489613 019 0.021 0.018 0.018 0.022 0.016 0.020 0.039 0.016 0.019 0.021 0.024 0.024 MHPCored 0.029 0.010 0.044 0.015 0.023 0.036 0.013 0.012 0.017 0.013 0.015 0.015 0.020 0.017 0.017 0.015 RMSFRT e nm 0.17 0.18 0.26 0.18 0.22 0.16 0.20 0.24 0.13 0.19 0.16 0.17 0.23 0.11 0.20 0.16 0.13 0.21 0.ten 0.24 0.17 0.20 0.10 0.27 0.22 0.27 0.09 0.11 0.13 0.09 0.10 0.11 0.12 0.12 0.08 0.ten 0.10 0.12 0.12 0.09 0.09 0.08 0.06 0.11 0.08 0.12 0.12 0.ten 0.05 0.12 0.ten 0.11 RMSFCore e nm 0.07 0.08 0.08 0.12 0.12 0.06 0.09 0.20 0.07 0.ten 0.07 0.06 0.12 0.05 0.14 0.07 0.09 0.07 0.05 0.11 0.04 0.ten 0.05 0.12 0.15 0.12 0.06 0.06 0.04 0.09 0.07 0.04 0.06 0.12 0.05 0.05 0.06 0.03 0.08 0.04 0.08 0.07 0.06 0.05 0.04 0.09 0.03 0.07 0.04 0.08 0.08 0.04 Insects g/kg 1 900 6 500 10Toxicity (LD50)f Mammals 0.five (i.c.v.), 17.five (s.c.) 0.025 (i.c.v.), 12 (s.c.) 0.35 (i.c.v.), 25 (s.c.) 10,000 (i.v.
