Publications: 2005 - 2004

P. O'Donoghue, A. Sethi, C. R. Woese, and Z. Luthey-Schulten
The evolutionary history of Cys-tRNA(Cys) formation
Proc. Natl. Acad. Sci. U S A, 102(52):19003-19008, 2005
Supplementary Material
- Poster based on this work (PDF)
- M. jannaschii SepRS Theoretical Model (PDB).
- M. jannaschii SepCysS Theoretical Models: apo monomer (PDB), dimer with substrates (PDB).
- Parameter file for o-phosphoserine(SEP)-adenosine-5'-monophosphate and o-phosphoserine attached to cytosine from the CCA end of the tRNA (inp).
- Topology file for o-phosphoserine(SEP)-adenosine-5'-monophosphate and o-phosphoserine attached to cytosine from the CCA end of the tRNA (inp).

R.S. Meyers, R. Amaro, Z. Luthey-Schulten, and V.J. Davisson
Reaction Coupling through Interdomain Contacts in Imidazole Glycerol Phosphate Synthase
Biochemistry, 13; 44(36):11974-85, 2005

R. Amaro, R.S. Myers, Z. Luthey-Schulten, and V.J. Davisson
Structural elements in IGP synthase exclude water to optimize ammonia transfer
Biophys J., 89(1):475-87, 2005

A. Sethi, P. O'Donoghue, and Z. Luthey-Schulten
Evolutionary profiles from the QR factorization of multiple sequence alignments
Proc. Natl. Acad. Sci. USA, 102, 4045-4050, 2005.
Supplementary Material

P. O'Donoghue and Z. Luthey-Schulten
Evolutionary profiles derived from the QR factorization of multiple structural alignments gives an economy of information
J. Mol. Biol., 346, 875-894, 2005

Authenrieth F., Tajkhorshid E., Schulten K., and Luthey-Schulten Z.
Role of water in transient cytochrome c2 docking
Journal of Physical Chemistry B, 108, 20376-20387, 2004
Supplementary Material
- Behavior of water inside the hydrophobic pocket (mpg).
- Electrostatic interactions during pulling of cyt to 10A (mpg).
- Heme parameters in CHARMM27 format (inp).
- Heme topology in CHARMM27 format (inp).

Amaro R. and Luthey-Schulten Z.,
Molecular dynamics simulations of substrate channeling through an alpha-beta barrel protein,
Chemical Physics, 307, 147-155, 2004.

Authenrieth F., Tajkhorshid E., Baudry J., and Luthey-Schulten Z.,
Classical force field parameters for the heme prosthetic group of cytochrome c,
Journal of Computational Chemistry, 25: 1613-1622, 2004.
Supplementary Material
- RESP charges (pdf).
- HF generated Mulliken charges (pdf).
- Heme parameters in CHARMM27 format (inp).
- Heme topology in CHARMM27 format (inp).
- Topology and parameter zip file (zip).

Pogorelov T.V. and Luthey-Schulten Z.,
Variations in the fast folding rates of the lambda-repressor: a hybrid molecular dynamics study,
Biophysical Journal, 87: 207-214, 2004.

Papoian G. A., Ulander J., Eastwood M.P., Luthey-Schulten Z., and Wolynes P.G.
Water in protein structure prediction,
Proc. Natl. Acad. Sci. USA, 101(10):3352-3357, 2004.

Fujitsuka Y., Takada S., Luthey-Schulten Z.A., and Wolynes P.G.
Optimizing physical energy functions for protein folding,
Proteins: Structure, Function, & Bioinformatics. 54(1):88-103, 2004.