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Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

Simulation of a protein tertiary complex: Study of the Interaction Interface and Conformational Dynamics of Dark State Rhodopsin in complex with Transducin

Rhodopsin is the prototype member of G-protein coupled receptors (GPCRs), which are known to be the largest super family of proteins in the body. The immediate molecular response of rhodopsin activation is mediated by transducin, a heterotrimeric (αβγ) G-protein (1) that is localized at the intracellular side of the plasma membrane and interacts with the activated receptor. Despite the wealth of studies on the interactions between GPCRs and G-proteins, the structural details of their function and interactions with their main intracellular partners, the G-proteins, remains have not been characterize in atomic detail (2). We report the first all-atom Molecular Dynamics simulation of a transmembrane protein tertiary complex composed of the G-protein coupled receptor (GPCR) rhodopsin and its G-protein intracellular counterpart transducin in a DOPC membrane/water environment. Based on the analysis of our μsec-timescale simulation trajectory starting from a docked conformation of the complex (3), we characterize the dynamics present in the dark-adapted state and their influence in the properties of the interaction interface formed by the protein subunits. Analysis of interdomain interactions among Rhodopsin and the different Transducin subunits leads to a characterization of the interface in atomic detail. Our results suggest the presence of large-amplitude collective motions that span across the different protein domains and prelude the allosteric changes which take place during the activation of the complex (4). We suggest that the intracellular domains and cytosolic extensions of the transmembrane α-helices in rhodopsin participate in correlated motions that influence their interaction with key structural elements of transducin, such as the N- and C-terminal ?-helices. Despite the very transient nature of the interaction interface, persistent interdomain interactions involving hydrophobic clusters and charged groups are observed in our trajectories that are stable over the simulation timescale of 1 μsec. We propose the general structural features of the interface and relate our results with atomic site distance measurements from electronic paramagnetic resonance (EPR) experiments (5, 6). Our results further suggest novel mutagenesis experiments that can be used to investigate the stability and correlated dynamics of this model membrane protein receptor system.



Summary of intermolecular interactions: Three sites of interaction between the intracellular side of Rhodopsin (right) and the α subunit of Transducin (left) are illustrated on an open-book representation of the complex at its starting-point configuration. We observe a participation of the third intracellular loop and C-terminal domains of rhodopsin and various loop-helix and loop-strand motifs of transducin Gα. The C-terminal helix of Gα engages in interactions with an ATT motif, located on a crevice formed by the intercellular core of rhodopsin (shown in yellow). These interactions are observed with high probability along our 1 μsec MD simulation trajectories.

This work is funded by the NSF, IBM and RPI.

References and Footnotes
  1. Neer, E. J. Cell 80, 249-257 (1955).
  2. Oldham, W. M. & Hamm, H. E. Nat Rev Mol Cell Biol 9, 60-71 (2008).
  3. Dell'Orco, D., Seeber, M., & Fanelli, F. FEBS letters 581, 944-948 (2007).
  4. Gether, U., Asmar, F., Meinild, A. K., & Rasmussen, S. G. Pharmacology & toxicology 91, 304-312 (2002).
  5. Farrens, D. L., Altenbach, C., Yang, K., Hubbell, W. L., & Khorana, H. G. Science 274, 768-770 (1996).
  6. Oldham, W. M., Van Eps, N., Preininger, A. M., Hubbell, W. L., & Hamm, H. E. Proceedings of the National Academy of Sciences of the United States of America 104, 7927-7932 (2007).

Nikolaos G. Sgourakis1 and Angel E. Garcia2

Dept of Biology
Department of Physics, Applied Physics and Astronomy
Center for Biotechnology and Interdisciplinary Studies
Rensselaer Polytechnic Institute
Troy NY 12180

phone:(518)276-6310
fax: (518) 276-6680
sgouen@rpi.edu
angel@rpi.edu