Erik Lindahl
Table of contents
Group Members
- Erik Lindahl, Professor, lindahl@cbr.su.se, +468164675
- Berk Hess, Senior scientist, hess@cbr.su.se
- Sander Pronk, Senior scientist, pronk@cbr.su.se
- Björn Wallner, Senior scientist, bjorn@cbr.su.se
- Peter Kasson, Senior scientist, kasson@gmail.com
- Samuel Murail, Postdoctoral scholar, samuel.murail@cbr.su.se
- Wiktor Jurkowski, Postdoctoral scholar, jurkow@cbr.su.se
- Rossen Apostolov, Postdoctoral scholar, rossen@cbr.su.se
- Teemu Murtola, Postdoctoral scholar, teemu.murtola@cbr.su.se
- Per Larsson, PhD student, per.larsson@cbr.su.se
- Aron Hennerdal, PhD student, aron.hennerdal@cbr.su.se
- Pär Bjelkmar, PhD student, bjelkmar@cbr.su.se
- Christine Sophie Schwaiger, PhD student, cschwaig@cbr.su.se
- Arjun Ray, PhD student, arjun.ray@cbr.su.se
- Szilard Pall, PhD student, szilard.pall@cbr.su.se
- Diogo Martins, project student, diogo@cbr.su.se
Alumni
- Anna Johansson, now postdoc at Uppsala University
- Jenny Falk, now teacher in Ludvika
- Yana Vereshchaga, now postdoc in Juelich
Contact Information
Research
The overall goal of our research is to better understand how proteins fold, interaction and function, in particular applied to membrane proteins and large-scale modeling. It is notoriously difficult to determine experimental structures for this important class of proteins, which makes computational methods extremely useful. Our computational tools of choice range from sequence analysis and molecular modeling through simplified models, multiscale molecular dynamics simulations, and non-equilibrium methods such as free energy calculations in the GROMACS molecular modeling & simulation toolkit we are developing. We have also been pioneers in developing extremely high performance biocomputational software through the use of single-instruction-multiple-data instructions such as SSE or Altivec. Please don't hesitate to contact us if you share our interests!
Current Projects
Molecular modeling and refinement
We have recently developed a new molecular modeling algorithm based on fragments from the Protein Data Bank to build 3D-coordinates from sequence alignments using multiple structural templates, combined with side-chain prediction and energy functions from GROMACS, and fragment libraries that are optimized separately for globular/membrane proteins. Related work involves introducing mean-field based refinement of backbone and sidechain placement.
Understanding membrane helix insertion & solvation
The structure and energetics of helix solvation in membranes is an important field that we are studying through molecular dynamics simulations. Specifically, stochastic dynamics is used to determine free energy of solvation for different residue types and positions in individual helices. The results of these calculations can e.g. be related to experimental hydrophobicity scales recently developed (Hessa 2005), and used to create better prediction models as well as aid understanding. However, somewhat surprisingly all biophysically computed scales predict significantly higher free energies of inserting hydrophilic residues into membranes compared to the in vivo cost. We still do not know why, but solving this question will be a key step towards our understanding of the translocon insertion mechanism, with important implications e.g. for membrane protein design.
Acknowledgments
The Lindahl group research is generously supported by the Swedish Foundation for Strategic Research (Ingvar Carlsson Award & Future Research Leaders III), The Swedish Research Council, The European Research Council under Framework Program 7, The Swedish Foundation for International Cooperation in Research and Higher Education (STINT), The Carl Trygger Foundation and The Sven & Ebba-Christina Hagberg Foundation.
