Membrane proteins are essential components of cellular organisms, allowing them to communicate with their surroundings by bridging the barrier formed by the lipid membrane. Our group is interested in understanding the mechanisms of membrane proteins during their various functions using computational and theoretical approaches. Of particular interest are transporter proteins, which capture the chemical potential energy of ionic gradients (across the membrane) in order to facilitate movement of essential chemicals, or unwelcome toxic compounds, into and out of the cell. A fundamental question in the case of the transporters is how these proteins achieve the required levels of substrate specificity, and how the protein-substrate interaction is coupled to transport of ions. A further puzzle is how the transporters undergo the requisite conformational changes, in order to allow access of the substrate binding sites to either side of the membrane, while also preventing leakage (see Figure 1).
An essential characteristic of our work is that the hypotheses and interpretations we provide be supported by direct experimental evidence. Indeed, through a close and ongoing collaboration with the Rudnick group at Yale University, we have very recently obtained new insights into the neurotransmitter:sodium symporters (see second figure for a homology model of serotonin transporter, SERT) in two important areas: first, regarding the mechanism by which they couple to chloride ions; and second, the formation of alternate conformations. Similar methodologies were used for developing models of glutamate transport, in collaboration with the Kanner group at Hebrew University, Jerusalem. We are also keen to collaborate with other experimentalists here in the MPI, in part supported by the collaborative research grant, SFB807. For example, with Christine Ziegler, we are combining computational, structural and biochemical studies on the betaine glycine transporter, BetP, which is providing key insights on the mechanisms of transport and regulation.
We apply a range of computational tools to attempt to understand these processes at atomic detail. To date, specific techniques include sequence analysis and continuum electrostatics, as well as protein structure prediction and molecular dynamics simulation. This work builds on previous studies carried out in the Honig and Woolf labs, in which we identified effective methods for predicting the structures of membrane proteins.
Khafizov K, Perez C, Koshy C, Quick M, Fendler K, Ziegler C, *Forrest LR. Investigation of the sodium binding sites in the betaine transporter BetP. Proc Natl Acad Sci (in press) (2012)
Perez C, Khafizov KF, Kraemer R, *Forrest LR, Ziegler C. Role of trimerization in the osmoregulated betaine transporter BetP. EMBO Reports 12:804-810 (2011)
Radestock S, *Forrest LR. The alternating-access mechanism of MFS transporters arises from inverted-topology repeats. J Mol Biol 407:698-715 (2011)
Crisman, T.C., Qu, S., Kanner, B.I. and Forrest, L.R., Inward-facing conformation of glutamate transporters as revealed by their inverted-topology structural repeats. Proc. Natl. Acad. Sci. USA, 106:20752-20757 (2009)
Forrest, L.R., Y.-W. Zhang, M.T. Jacobs, J. Gesmonde, L. Xie, B. Honig, and G. Rudnick, A mechanism for alternating access in neurotransmitter transporters. Proc. Natl. Acad. Sci. USA, 105:10338-10343 (2008)
Forrest, L.R., S. Tavoulari, Y.-W. Zhang, G. Rudnick, and B. Honig, Identification of a chloride ion binding site in Na+/Cl--dependent transporters. Proc. Natl. Acad. Sci. USA, 104:12761-12766 (2007)
Forrest, L.R., C.L. Tang and B. Honig. On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins. Biophysical Journal 91:508-517 (2006)
Dr. Lucy Forrest
Max Planck Research Group,
Computational Structural Biology
Phone: +49 (0) 69 6303 1600
Fax: +49 (0) 69 6303 1502