CROTAMINE 3D STRUCTURE - HOMOLOGY BUILDING SIMULATION AND CIRCULAR DICHROISM

Martins, N.F.(1), Siqueira, A.(2), Cartier, A.(2), Brown, D.(3), Maigret, B.(2,3)

(1)Laboratório de Bioinformática - Embrapa - Recursos Genéticos e Biotecnologia, Brasília, Brasil. (2)Laboratory of Theoretical Chemistry, UMR CNRS/UHP 756, Université Henri Poincaré, France, (3)Laboratory of Organic Materials, Université Savoie, France and Instituto de Química, UnB, Brasil.

Snake venoms contain proteins that are responsible for their neurotoxic, cardiotoxic, hemorrhagic and myotoxic activities. The myotoxin family comprises several subclasses  involved in citolysis, myofibril clumping and hypercontraction. The general biological action of crotamine is the depolarization of cell membranes on the voltage sensitive sodium channels. The toxin also seems to alter calcium ion influx by opening the ryanocine receptor. Crotamine isolated from the venom of Crotalus durissus terrificus is a strongly basic 42-aminoacid polypeptide belonging to the small basic myotoxin family. As no three-dimensional structure is available for this myotoxin subfamily, despite the considerable amount of work, there is no clear understanding on the structure-function relationship. The common patterns for this myotoxin family provides a myotoxin signature consisting of three disulfide bridges which are important to the protein fold. FASTA and BLAST searches revealed 36% identity with beta-defensin family. The 1BNB structure was used as a template to the model. The 3D coordinates of the crotamine model was obtained by homology modeling and several rounds of molecular dynamics calculations were carried out. The analysis of the RMSD map for each structure during the 1 ns MD simulation in vacuum showed that the structure was very stable along the calculations. After procheck verification the model was analyzed for its interactions. Mainly H-bonds were detected between Asp29 side chain and Lys7 and Arg33 respectively.  In conclusion, crotamine appears to have a stable core organized around  the loops and maintained by a beta-strand. A weak helical tendency is visible in the model and which can be correlated to the CD results.

CORRESPONDENCE TO:

Bernard Maigret, R. 9 Norte Bloco 4 ap. 1202, Aguas Claras, Brasília, DF, 70000-000, Brasil, Email: maigret@unb.br