Jan Saam smiling.

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

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

Jan Saam smiling. 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]

footer