Paper Citing NAMD - Abstract
Ramakrishna, S.; Padhi, Siladitya; Priyakumar, U. Deva
Modeling the structure of SARS 3a transmembrane protein using a minimum unfavorable contact approach
JOURNAL OF CHEMICAL SCIENCES, 127:2159-2169, DEC 2015
3a is an accessory protein from SARS coronavirus that is known to play a significant role in the proliferation of the virus by forming tetrameric ion channels. Although the monomeric units are known to consist of three transmembrane (TM) domains, there are no solved structures available for the complete monomer. The present study proposes a structural model for the transmembrane region of the monomer by employing our previously tested approach, which predicts potential orientations of TM alpha-helices by minimizing the unfavorable contact surfaces between the different TM domains. The best model structure comprising all three alpha-helices has been subjected to MD simulations to examine its quality. The TM bundle was found to form a compact and stable structure with significant intermolecular interactions. The structural features of the proposed model of 3a account for observations from previous experimental investigations on the activity of the protein. Further analysis indicates that residues from the TM2 and TM3 domains are likely to line the pore of the ion channel, which is in good agreement with a recent experimental study. In the absence of an experimental structure for the protein, the proposed structure can serve as a useful model for inferring structure-function relationships about the protein.
