Oxford University, Structural Bioinformatics & Computational Biochemistry Unit

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Dr. Martin Ulmschneider

Structural Bioinformatics and Computational Biochemistry Unit Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU United Kingdom Tel: +44 (0)1865 275380 Fax: +44 (0)1865 275273 E-mail: ulmschne@caspur.it

Implicit solvent model development for simulation of membrane protein folding and function Membrane proteins relate to numerous diseases and are directly targeted by the majority of current drugs (e.g. Prozac). Structural knowledge of membrane proteins is of immense biomedical importance, allowing drug design and virtual screening methods to be employed in the search for new medication. I am working on the development of methods to model the complex lipid-bilayer environment implicitly. Currently both bioinformatical as well as theoretical methods based on the Generalized Born theory of solvation are used. These methods are combined with molecular dynamics algorithms. This allows for large-scale atomic resolution protein folding and simulation studies by avoiding the extremely high computational cost of explicit lipid-bilayer membranes. My research is funded by an International Fellowship of the The Wellcome Trust

Collaborations
Prof. A. Di Nola and Dr. J. Ulmschneider, Department of Chemistry, University of Rome "La Sapienza", Rome, Italy
Dr. F. Momburg, German Cancer Research Center (DKFZ), Heidelberg, Germany
Dr. I. Daidone, Computational Molecular Biophysics Group, University of Heidelberg, Germany

Publications
J.P. Ulmschneider, M.B. Ulmschneider & A. Di Nola, Monte Carlo versus Molecular Dynamics for all atom polypeptide simulations, Submitted, J. Phys. Chem. B 2006 M.B. Ulmschneider, J.P. Ulmschneider, A. Di Nola & M.S.P. Sansom, A generalized born implicit membrane representation based on experimental insertion free energies, Accepted, Biophys. J. 2006 M.B. Ulmschneider, A. Di Nola & M.S.P. Sansom, Evaluating tilt angles of membrane-associated helices: Comparison of computational and NMR techniques. Biophys. J. 2006. 90, 1650-1660 M.B. Ulmschneider, D.P. Tieleman & M.S.P. Sansom, The role of extra-membranous inter-helical loops in helix-helix interactions. Protein Engineering, Design and Selection 2005. 18, 563-570 M.B. Ulmschneider, A. Di Nola & M.S.P. Sansom, Properties of integral membrane protein structures: Derivation of an implicit membrane potential, Proteins 2005. 59, 252-265 M.B. Ulmschneider, D.P. Tieleman & M.S.P. Sansom, Interactions of a transmembrane helix and a membrane: Comparative simulations of bacteriorhodopsin helix A. J. Phys. Chem. B 2004. 108, 10149-10159 D.P. Tieleman, I. Shrivastava, M.B. Ulmschneider & M.S.P. Sansom, Proline-induced hinges in transmembrane helices: Possible roles in ion channel gating. Proteins 2001. 44, 63-72 M.B. Ulmschneider & M.S.P. Sansom, Amino acid distributions in integral membrane protein structures. BBA 2001. 1512(1), 1-14

Last updated 27/01/2006