Creative Commons License 2016 Volume 3 Issue 4

Structure study and predict the function of the diphtheria toxin in different pH levels (Acidic-Basic-Natural) using molecular dynamics simulations


Soheila Ghaderi, Mohammad Reza Bozorgmehr, Ali Morsali
Abstract

Conformational switching is broadly defined as an alteration in the spatial organization of a macromolecule in response to environmental change. This study was performed to establish the relationship between variable pH and structural and functional aspect of the diphtheria toxin (DT). Molecular dynamics (MD) simulations were performed at different pH levels (4, 6.5, and 10) consist of a DT structure in water at 300K and salt concentration 0.25M at 100ns timescale simulation. Results showed that fluctuations were changed in the key residues at different pH levels. Fluctuations were more profound in the fragments A and B of DT at pH4 compared with pH6.5 and pH10. Fluctuations in the fragment A of DT (DTA) were obtained at pH4 including residues Ser9, Pro25, Tyr46, Leu73, Arg173, and Ala187. The average of the radius of gyration (Rg) and the root mean square deviation (RMSD) of the DT structure showed that decreased at pH 6.5 in comparison with pH4 and pH10. Results showed conformational changes of DT structure at pH4 compared with pH6.5 and pH10.

 

Keywords: Chain B of Diphtheria Toxin; Chain A of Diphtheria Toxin; Molecular dynamics simulation; Root mean square fluctuation; Variable pH;


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Entomology and Applied Science Letters is an international double-blind peer reviewed publication which publishes scientific research & review articles related to insects that contain information of interest to a wider audience, e.g. papers bearing on the theoretical, genetic, agricultural, medical and biodiversity issues. Emphasis is also placed on the selection of comprehensive, revisionary or integrated systematics studies of broader biological or zoogeographical relevance. In addition to full-length research articles and reviews, the journal publishes interpretive articles in a Forum section, Short Communications, and Letters to the Editor. The journal publishes reports on all phases of medical entomology and medical acarology, including the systematics and biology of insects, acarines, and other arthropods of public health and veterinary significance.

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