The bacterial dicarboxylate transporter VcINDY uses a two-domain elevator-type mechanism

Secondary transporters use alternating-access mechanisms to couple uphill substrate movement to downhill ion flux. Most known transporters use a 'rocking bundle' motion, wherein the protein moves around an immobile substrate-binding site. However, the glutamate-transporter homolog GltPh translocates its substrate-binding site vertically across the membrane, through an 'elevator' mechanism. Here, we used the 'repeat swap' approach to computationally predict the outward-facing state of the Na(+)/succinate transporter VcINDY, from Vibrio cholerae. Our model predicts a substantial elevator-like movement of VcINDY's substrate-binding site, with a vertical translation of ~15 Å and a rotation of ~43°. Our observation that multiple disulfide cross-links completely inhibit transport provides experimental confirmation of the model and demonstrates that such movement is essential. In contrast, cross-links across the VcINDY dimer interface preserve transport, thus revealing an absence of large-scale coupling between protomers

Virtual insights on G protein inhibition and ion channel block – a computer-based study

The present work focuses on understanding the mechanisms of action of two pharmaceutically relevant inhibitor protein systems: the cyclic depsipeptides YM-254890 (YM) and FR900359 (FR) and their target protein, the alpha- (α) subunit of a heterotrimeric G protein as well as conotoxins, venoms obtainable from marine cone snails, which can act as blockers of voltage-gated ion channels. Understanding the mechanism of how drugs or drug candidates are affecting their molecular target is of vital importance in order to develop a promising drug candidate into a valuable medicine. Nowadays, such understanding is mainly gained from computational studies, better known as molecular modelling approaches, which are an essential part of every drug development campaign. Using the example of said two distinct protein ligand systems, respectively consisting of a target protein and an appropriate binding molecule, we aimed at elucidating the intrinsic subtype specificity determinants inherent in interacting biological systems by employing up-to-date computational techniques. Our explorations resulted in the successful generation of reliable data sets that are in accordance with to date published literature from laboratory experiments and might even be able to lay the foundation of learning or training data sets required for further computer-based investigations on similar systems

Virtual insights on G protein inhibition and ion channel block – a computer-based study

The present work focuses on understanding the mechanisms of action of two pharmaceutically relevant inhibitor protein systems: the cyclic depsipeptides YM-254890 (YM) and FR900359 (FR) and their target protein, the alpha- (α) subunit of a heterotrimeric G protein as well as conotoxins, venoms obtainable from marine cone snails, which can act as blockers of voltage-gated ion channels. Understanding the mechanism of how drugs or drug candidates are affecting their molecular target is of vital importance in order to develop a promising drug candidate into a valuable medicine. Nowadays, such understanding is mainly gained from computational studies, better known as molecular modelling approaches, which are an essential part of every drug development campaign. Using the example of said two distinct protein ligand systems, respectively consisting of a target protein and an appropriate binding molecule, we aimed at elucidating the intrinsic subtype specificity determinants inherent in interacting biological systems by employing up-to-date computational techniques. Our explorations resulted in the successful generation of reliable data sets that are in accordance with to date published literature from laboratory experiments and might even be able to lay the foundation of learning or training data sets required for further computer-based investigations on similar systems

In Silico Analysis of the Subtype Selective Blockage of KCNA Ion Channels through the µ-Conotoxins PIIIA, SIIIA, and GIIIA

Understanding subtype specific ion channel pore blockage by natural peptide-based toxins is crucial for developing such compounds into promising drug candidates. Herein, docking and molecular dynamics simulations were employed in order to understand the dynamics and binding states of the µ-conotoxins, PIIIA, SIIIA, and GIIIA, at the voltage-gated potassium channels of the KV1 family, and they were correlated with their experimental activities recently reported by Leipold et al. Their different activities can only adequately be understood when dynamic information about the toxin-channel systems is available. For all of the channel-bound toxins investigated herein, a certain conformational flexibility was observed during the molecular dynamic simulations, which corresponds to their bioactivity. Our data suggest a similar binding mode of µ-PIIIA at KV1.6 and KV1.1, in which a plethora of hydrogen bonds are formed by the Arg and Lys residues within the α-helical core region of µ-PIIIA, with the central pore residues of the channel. Furthermore, the contribution of the K+ channel’s outer and inner pore loops with respect to the toxin binding. and how the subtype specificity is induced, were proposed