Biophysics (Erik Lindahl, SciLifeLab Stockholm)

Keywords: Bioinformatics, Structural biology, Membrane Proteins, Ion channels

Summary

Our research is focused on membrane proteins, in particular voltage- and ligand-gated ion channels. Both these classes of molecules are of critical importance in the central nervous systems and highly important drug targets. We are using a combination of bioinformatics, molecular simulation and voltage clamping to understand the gating of these channels with the goal of developing new generations of drugs.

Background

Membrane proteins are critically important for signaling and transport across membranes, and the number of available structures is now increasing rapidly. This is reshaping our view of membrane proteins: although the first structures were relatively ‘simple’, we now believe that membrane protein formation is at least as complex as for globular proteins, and their function possibly even more so due to their gatekeeper roles. The purpose of our work is to explain how interactions, conformational transitions, and dynamics of membrane proteins relate to their formation and function, in particular for ion channels. These are highly useful model systems, both because of the close relation to the helix insertion problem (charged segments), an exceptional interest in their activation and dynamics in the community, and not least the critical pharmaceutical importance. Our methods range from bioinformatics, modeling and virtual high-throughput screening to steered molecular dynamics and experimental collaborations (in particular electrophysiology), and the theoretical and computational biophysics lab is responsible for development of the GROMACS molecular simulation toolkit.

Research

Voltage-gated ion channels

Voltage-gated channels (VGICs) open in response to potentials across the membrane, and control functions such as nerve signals and heart beats. All VGICs are comprised of four subunits where each subunit consists of six TM helices, where the first four (S1-4) constitute the voltage-sensing domain (VSD), with the S4 helix and its four Arginines acting as the actual voltage sensor. However, despite a recent high-resolution structure of a Kv1.2/2.1 chimera, the nature of the S4 gating motion has been hotly debated. Based on the observation of 310 helix growth in our previous work, we started to believe the activation occurs by a gradual change in secondary structure as the segment moves, and have done a number of studies where we have calculated how the structural change occurs. We are doing a number of studies in collaboration with the Elinder lab in Linköping, where we have been able to use voltage-clamp electrophysiology to derive large sets of new constraints in several different states, and then used these to derive new models not only of open/closed structures of voltage sensors, but a sequence of intermediate states that for the first time has made it possible to track a complete voltage-sensor cycle.

Ligand-gated ion channels

Synaptic transmission in the nervous system is controlled by ligand-gated ion channels (LGIC) that combine ligand-binding and transmembrane units. Among the most important classes are the Cys-loop receptors that include acetylcholine (AChR), serotonin (5-HT3), glycine (GlyR) and GABA. However, due to the low sequence conservation and lack of high-resolution structures of the trans-membrane domain (TMD), surprisingly little is known about potential allosteric binding sites despite their extreme pharmacological importance. The receptors also differ in the sense that AChR & and 5HT3 are cation-selective, while GlyR and GABAR are anion-selective, i.e. they cause opposite effects! Until recently there were no high-resolution eukaroytic structures at all, but the crystal structure of the open form of the Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) has been solved at 2.9Å. These largely confirm our previous models for a twisting open/close motion, and the pH-regulation of GLIC has even made it possible for us to model the closing in microsecond-scale simulations. Here too we have successfully used combinations of voltage clamping in combination with molecular simulations, and have suggested a new dual-site model for anesthetic action where there is one inhibiting binding site (inside subunits) and a second potentiating one between subunits. In particular, we have been able to correlate experimental results for single-point-mutants with predictions from free energy calculations, and are working on designing new classes of anesthetics.

Some recent publications:

  1. Henrion, U., Renhorn, J. Börjesson, S.I., Nelson, E.M., Schwaiger, C.S., Bjelkmar, P. Wallner, B., Lindahl, E., Elinder, F., Tracking a complete voltage-sensor cycle with metal-ion bridges, Proc. Natl. Acad. Sci. 109, 8552-8557 (2012)

  2. Contreras, F., Ernst, A.M., Haberkant, P., Björkholm, P., Lindahl, E., Gönen, B., Tischer, C., Elofsson, A., von Heijne, G., Thiele, C., Pepperkok, R., Wieland, F., Brügger, B., Molecular recognition of a single sphingolipid species by a protein’s transmembrane domain, Nature 481, 525–529 (2012)

  3. Howard, R.J., Murail, S., Ondricek, K.E., Corringer, P.J., Lindahl, E., Trudell, J.R., Harris, R.A., Structural basis for alcohol modulation of a pentameric ligand-gated ion channel, Proc Natl Acad Sci U S A. 108, 12149-54 (2011)

  4. Murail, S., Wallner, B., Trudell, J.R., Bertaccini, E., Lindahl E., Microsecond simulations indicate that ethanol binds between subunits and could stabilize an open-state model of a glycine receptor, Biophys J. 100, 1642-50 (2011)

  5. Schwaiger, C.S., Bjelkmar, P., Hess, B., Lindahl, E., 3_10-helix conformation facilitates the transition of a voltage sensor S4 segment toward the down state, Biophys J. 100, 1446-54 (2011)

Acknowledgments

Research in the Lindahl lab is generously supported by the Swedish Foundation for Strategic Research, the European Research Council, the Swedish e-Science Research Center, the 7th European Framework Program, and the Swedish Research Council.

Resources

Our team is developing both the GROMACS molecular modelling toolkit (http://www.gromacs.org) as well as the new distributed computing framework Copernicus (http://copernicus-computing.org), and we have long experience of modelling membrane protein structure, function and drug interaction. For inquiries, contact erik@kth.se.

Collaborations

Swedish eScience Research Center, http://www.e-science.se

ScalaLife EU project, http://www.scalalife.eu

CRESTA EU project, http://cresta-project.eu/

EDICT EU project, http://www.edict-project.eu/

RIKEN Advanced Institute for Computational Science (AICS), http://www.aics.riken.jp/en/over/aics-history.html

SciLifeLab affiliated publications

Open in SciLifeLab PubRefDb