Jan Saam
Address:
Theoretical and Computational Biophysics Group
Beckman Institute, Room 3061
University of Illinois at Urbana-Champaign
405 N. Mathews Ave.
Urbana, IL 61801, USA.
Phone: 217-244-1928
Fax: 217-244-6078
Email: saam@ks.uiuc.edu
Education
- Oct 2002-Nov 2007 PhD, Institute of Biochemistry, Charite - Universitätsmedizin Berlin, Germany
- May 2001-April 2002 visiting scholar at the Theoretical and Computational Biophysics Group
- 1998-2001 studied biophysics (Hauptstudium) at Humboldt University Berlin, Germany.
- 1996-1998 studied biology (Grundstudium) at University of Konstanz, Germany.
Research Interests
VMD Development
I'm one of the VMD developers working on scientific tools in VMD.
Currently my efforts concentrate on developing QMtool, an interface to
quantum chemical simulations, and on ParaTool, an application that helps
developing force field parameters (mostly CHARMM).
Further I'm working on the improvement of the Implicit Ligand Sampling (ILS) method. One aim is to significantly speed up the computation and another one is to provide a graphical user interface for setting up, analyzing and vizualizing ILS simulations.
Biophysics
One of my main scientific interests are oxygen migration pathways in proteins.
The following project was done while I was working at the Charite in Berlin:
Identification of Dynamic Oxygen Access Pathways in 12/15-Lipoxygenase
Cells contain numerous enzymes utilizing molecular oxygen for their reactions. Often, their active sites are buried deeply inside the protein which raises the question whether there are specific access channels guiding oxygen to the site of catalysis. Choosing 12/15-lipoxygenase as a typical example for such oxygen dependent enzymes we determined the oxygen distribution within the protein and defined potential routes for oxygen access. For this purpose we have applied an integrated strategy of structural modeling, molecular dynamics simulations, site directed mutagenesis and kinetic measurements.
Figure 1:
Distribution of oxygen in lipoxygenase shown in terms of free energy isosurfaces
(yellow). Red arrows indicate the energetically most favorable oxygen access route
connecting a high affinity region at the protein surface with the catalytic center.
Above, the energy profile along this path is projected. The
grey line marks the level of the drawn energy isosurface.
Generally I'm interested in:
- Oxygen Diffusion in Proteins
- Force Field Parametrization
- Scientific Visualization
- Quantum Chemistry
Publications
Saam J, Ivanov I, Walther M, Holzhütter H, and Kuhn H. (2007)
Molecular dioxygen enters the active site of 12/15-lipoxygenase
via dynamic oxygen access channels.
Proc. Natl. Acad. Sci., 104(33), 13319-13324 [pdf]
Ivanov I, Saam J, Kühn H, Holzhütter H. (2005)
Dual role of oxygen during lipoxygenase reactions.
FEBS Journal 272, 2523-2535 [pdf]
Kühn, H, Saam J, Eibach S, Holzhütter H, Ivanov I, Walther M. (2005)
Structural biology of mammalian lipoxygenases: Enzymatic
consequences of targeted alterations of the protein structure
Biochem. Biophys. Res. Commun. 338, 93-101 [pdf]
Saam J, Tajkhorshid E, Hayashi S, and Schulten K. (2002)
Molecular Dynamics Investigation of Primary Photoinduced Events in the Activation of Rhodopsin.
Biophys. J. 83, 3097-3112 [pdf,
PubMed]
Ernsting NP, Kovalenko SA, Senyushkina T, Saam J and Farztdinov V. (2001)
Wave-packet-assisted decomposition of femtosecond transient ultraviolet-visible absorption spectra: Application to excited-state intramolecular proton
transfer in solution.
J. Phys. Chem. A 105, 3443-3453
[journal]