Int. J. Mol. Sci. 2014, 15(6), 10459-10478; doi:10.3390/ijms150610459
Article

Computational Study on Substrate Specificity of a Novel Cysteine Protease 1 Precursor from Zea mays

1,2,†email, 3,†email, 4email, 1,2email and 1,2,* email
Received: 31 March 2014; in revised form: 27 May 2014 / Accepted: 28 May 2014 / Published: 11 June 2014
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract: Cysteine protease 1 precursor from Zea mays (zmCP1) is classified as a member of the C1A family of peptidases (papain-like cysteine protease) in MEROPS (the Peptidase Database). The 3D structure and substrate specificity of the zmCP1 is still unknown. This study is the first one to build the 3D structure of zmCP1 by computer-assisted homology modeling. In order to determine the substrate specificity of zmCP1, docking study is used for rapid and convenient analysis of large populations of ligand–enzyme complexes. Docking results show that zmCP1 has preference for P1 position and P2 position for Arg and a large hydrophobic residue (such as Phe). Gly147, Gly191, Cys189, and Asp190 are predicted to function as active residues at the S1 subsite, and the S2 subsite contains Leu283, Leu193, Ala259, Met194, and Ala286. SIFt results indicate that Gly144, Arg268, Trp308, and Ser311 play important roles in substrate binding. Then Molecular Mechanics-Poisson-Boltzmann Surface Area (MM-PBSA) method was used to explain the substrate specificity for P1 position of zmCp1. This study provides insights into the molecular basis of zmCP1 activity and substrate specificity.
Keywords: homology modeling; molecular dynamics; MM-PBSA; cysteine protease 1
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MDPI and ACS Style

Liu, H.; Chen, L.; Li, Q.; Zheng, M.; Liu, J. Computational Study on Substrate Specificity of a Novel Cysteine Protease 1 Precursor from Zea mays. Int. J. Mol. Sci. 2014, 15, 10459-10478.

AMA Style

Liu H, Chen L, Li Q, Zheng M, Liu J. Computational Study on Substrate Specificity of a Novel Cysteine Protease 1 Precursor from Zea mays. International Journal of Molecular Sciences. 2014; 15(6):10459-10478.

Chicago/Turabian Style

Liu, Huimin; Chen, Liangcheng; Li, Quan; Zheng, Mingzhu; Liu, Jingsheng. 2014. "Computational Study on Substrate Specificity of a Novel Cysteine Protease 1 Precursor from Zea mays." Int. J. Mol. Sci. 15, no. 6: 10459-10478.

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