The Structural And Dynamics Studies Of An Ompa Protein From Shigella Flexneri
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Date
2015-07
Authors
Lee, Yung – Hung, Roy
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Abstract
Shigellosis, also known as bacillus dysentery, is caused by Shigellaflexneri. Specifically, S. flexneri serotype 2a is the major public health concern as it contributes to endemic shigellosis and the majority of shigellosis mortality in the developing and under-developed countries. Thus, early diagnosis is important for effective disease management and therapy. A 35 kDa antigenic protein from S. flexneri has been shown to be a potential biomarker in an earlier study. However, the structural and functionality of this protein has yet to be explored. Therefore, this study was conducted to predict the structure and to explore the dynamics of this 35 kDa protein. The structure of the 35 kDa protein was constructed via comparative modeling. The three dimensional structure showed that this 35 kDa protein has an OmpA domain and OmpA-like domain. The OmpA domain might act as a porin while the OmpA-like domain could be involved in peptidoglycan binding and stabilisation of Shigella outer membrane. A total of 30 nanoseconds of molecular dynamics simulationwas conducted to further explore and understand the intrinsic dynamics as well as to obtain the average structure of the 35 kDa protein. The trajectories showed thatthe 35 kDa protein secondary structure is retained and the protein integrity is not impaired. The flexibility of the extracellular loops and linker also indicated that these loops might be required for interactions with benovalent partners during bacterial conjugation while allowing variations in the membrane-peptidoglycan exact distance.In conclusion, the structure and dynamics elucidation
of the 35 kDa antigenic protein of S. flexnerithrough in silico approach have provided the insights of possible development of theshigellosis antigen detection test should the specific binders for the predicted epitope are designed. The results from this work could also be used for inhibitor design or vaccine development against shigellosis.
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Keywords
Ompa Protein , Shigella Flexneri