Articles written in Journal of Chemical Sciences
Volume 121 Issue 5 September 2009 pp 589-594
Theory of coherent molecule to surface electron injection: An analytical model
S Ramakrishna T Seideman F Willig V May
Electron transfer from a molecular level to empty continuum levels of a substrate is described theoretically. Using a quasicontinuum approach to model the substrate, analytical expressions pertaining to the time-dependent probability among the various levels of the substrate is presented along with its extension to coherently excited molecular vibrational modes. Hidden time scales and dynamics are revealed in the analysis and possible experiments to observe the new results are suggested. We note the applicability of the model to the description of a variety of other phenomena that are formally similar to the electron injection problem, although pertaining to different physics.
Volume 127 Issue 12 December 2015 pp 2159-2169
Modeling the structure of SARS 3a transmembrane protein using a minimum unfavorable contact approach
S Ramakrishna Siladitya Padhi U Deva Priyakumar
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 𝛼-helices by minimizing the unfavorable contact surfaces between the different TM domains. The best model structure comprising all three 𝛼-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.
Volume 135, 2023
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