Biology subjects

Immadisetty, K.

Publications and source records attributed to Immadisetty, K..

3 recordsLinked to original sources

bioRxiv2019

Conformational Transition Pathways in Major Facilitator Superfamily Transporters

AbstractThe major facilitator superfamily (MFS) of transporters contains three classes of membrane transporters: symporters, uniporters, and antiporters. Despite utilizing a variety of transport methods, MFS transporters are believed to undergo similar con-formational changes within their distinct transport cycles. Although the similarities regarding conformational changes between the classes of MFS transporters are note-worthy, the differences are also valuable because they may explain the distinct functions of the classes within the MFS. Here, we have performed a variety of equilibrium and non-equilibrium all-atom molecular dynamics (MD) simulations of the bacterial proton-coupled oligopeptide transporter (GkPOT) and the human glucose transporter 1 (GluT1). To compare the similarities and differences of the conformational dynamics found within the three different classes of transporters we have also referenced previous simulations involving the glycerol-3-phosphate (GlpT) transporter. All of the proteins discussed here were simulated in the apo state in explicit membrane environments. Our results suggest a very similar conformational transition for all transporter types involving interbundle salt-bridge formation/disruption coupled with the orientation changes of transmembrane (TM) helices, specifically H1/H7 and H5/H11, resulting in an alternation in the accessibility of water at the cyto- and periplasmic gates.

biophysics↗

bioRxiv2019

Elucidating the Molecular Basis of pH Activation of an Engineered Mechanosensitive Channel

Mechanosensitive (MS) channels detect and respond to changes in the pressure profile of cellular membranes and transduce the mechanical energy into electrical and/or chemical signals. However, by re-engineering the MS channels, chemical signals such as pH change can trigger the activation of some MS channels. This paper elucidate the activation mechanism of an engineered MS channel of large conductance (MscL) at an atomic level through a combination of equilibrium, non-equilibrium, biased, and unbiased molecular dynamics (MD) simulations for the first time. Comparing the wild-type and engineered MscL activation processes at an atomic level suggests that the two systems are likely to be associated with different active states and different transition pathways. These findings indicate that (1) periplasmic loops play a key role in the activation process of MscL, (2) the loss of various hydrogen bonds and salt bridge interactions in the engineered MscL channel causes the spontaneous opening of the channel, and (3) the most significant interactions lost during the activation process are those between the transmembrane (TM) helices 1 and 2 (TM1 and TM2) in engineered MscL channel. In this research, the orientation-based biasing approach for producing and optimizing an open MscL model is a promising way to characterize unknown protein functional states and to research the activation processes in ion channels. String method with swarms of trajectories (SMwST) was used to identify the optimal transition pathway and elucidate the activation mechanism of the engineered MscL. Finally, the free energy profile of engineered MscL associated with the activation process using a novel along-the-path free energy calculation approach is constructed. This work paves the way for a computational framework for the studies aimed at designing pH-triggered channel-functionalized drug delivery liposomes.

biophysics↗

bioRxiv2019

The Role of a Crystallographically Unresolved Cytoplasmic Loop in Stabilizing the Bacterial Membrane Insertase YidC2

YidC, a bacterial member of the YidC/Alb3/Oxa1 insertase family, mediates membrane protein assembly and insertion. Cytoplasmic loops are known to have functional significance in membrane proteins such as YidC. Employing microsecond-level molecular dynamics (MD) simulations, we show that the crystallographically unresolved C2 loop plays a crucial role in the structural dynamics of Bacillus halodurans YidC2. We have modeled the C2 loop and used allatom MD simulations to investigate the structural dynamics of YidC2 in its apo form, both with and without the C2 loop. The C2 loop was found to stabilize the entire protein and particularly the C1 region. C2 was also found to stabilize the alpha-helical character of the C-terminal region. Interestingly, the highly polar or charged lipid head groups of the simulated membranes were found to interact with and stabilize the C2 loop. These findings demonstrate that the crystallographically unresolved loops of membrane proteins could be important for the stabilization of the protein despite the apparent lack of structure, which could be due to the absence of the relevant lipids to stabilize them in crystallographic conditions.

biophysics↗