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Comparative modeling and QM/MM studies of cysteine protease mutant of Theobroma cacao
Author(s) -
Andrade Deyse Valverde Gomes de,
GóesNeto Aristóteles,
Junior Moacyr Comar,
Taranto Alex Gutterres
Publication year - 2012
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.24102
Subject(s) - theobroma , protease , mutant , cysteine , proteases , biology , cysteine protease , biochemistry , peptide sequence , genetics , computational biology , gene , enzyme , botany
The culture of cacao in Brazil was highly harmed by Moniliophthora perniciosa , the fungus that causes witches' broom disease of cocoa. This disease decreases significantly the cocoa production. An important strategy for control of the witches' broom is the molecular study of the interaction between cacao– M. perniciosa . However, there is little information about of the mechanism of molecular interaction involved in resistance/vulnerability of cacoa tree. To address this problem, the Genome Project showed genes of cysteine protease involved in the mechanism of resistance/vulnerability. Cysteine protease is expressed during the process of the maturation of the seed and it is present in necrofitics period of the disease. Furthermore, proteases have a wide application in feed products, detergents, and pharmaceutical industries. This work constructed the three‐dimensional structure of the cysteine protease of Theobroma cacao by comparative modeling. Thus, the primary sequence of the cysteine protease of T. cacao was submitted to BLASTp obtaining the protein 1PCI with 36% of structural similarity. The model was refined and validated by AMBER 11.0; and evaluated by PROCHECK and ANOLEA software, respectively. This model consists of 171 amino acids, formed by 2693 atoms linked by 2719 chemical bonds. The 3D structure of this enzyme has seven α‐helix, 23 turns, and two β‐sheets. The region of the conserved active site is represented by residues Cys25 and His159. From this model, a mutant model was then generated by replacing His159/Gly. This also was evaluated showing similar characteristics. Studies of the interaction between the mutant structure with the metal ions such as Zn +2 , Cu +1 , Cu +2 , and Cd +2 were performed by Quantum Mechanical/Molecular Mechanical (QM/MM) approach implemented in Gaussian 09W. As a result, the mutant protein is able to complex with all of them, principally with Cd +2 by −3.04 Kcal/mol. This is potentially toxic element present in the environment. Therefore this study suggests that changes in the sequence of the cysteine protease of T. Cacao can lead to development new products of commercial interest. © 2012 Wiley Periodicals, Inc.