Recent Publications:
R.W. Alexander, J. Eargle, and Z. Luthey-Schulten
Experimental and computational analysis of tRNA dynamics
FEBS Letters, in press
A. Sethi, J. Eargle, A. Black, and Z. Luthey-Schulten
Dynamical Networks in tRNA:protein complexes
Proc Natl Acad Sci U S A, 106(16):6620-6625, 2009
Supplementary Material
E. Roberts, J.E. Stone, L. Sepulveda, W.W. Hwu, and Z. Luthey-Schulten
Long time-scale simulations of in vivo diffusion using GPU hardware
In The Eighth IEEE International Workshop on High-Performance Computational Biology, 2009
E. Roberts, A. Sethi, J. Montoya, C.R. Woese, and Z. Luthey-Schulten
Molecular signatures of ribosomal evolution
Proc Natl Acad Sci U S A, 105(37):13953-8, 2008
Supplementary Material
J. Eargle, A. Black, A. Sethi, L. Trabuco, and Z. Luthey-Schulten
Dynamics of recognition between tRNA and Elongation Factor Tu
J Mol Biol, 377(5):1382-405, 2008
D.C. Mathew and Z. Luthey-Schulten
On the physical basis of the amino acid polar requirement
J Mol Evol 66(5):519-28, 2008
T.V. Pogorelov, F. Autenrieth, E. Roberts, and Z. Luthey-Schulten
Cytochrome
c2 exit strategy: dissociation studies and evolutionary implications
J Phys Chem B, 111(3):618-634, 2007
R. Amaro, A. Sethi, R. Myers, Jo V
Davisson, and Z. Luthey-Schulten
A network of conserved interactions regulates the allosteric signal in a
glutamine amidotransferase
Biochemistry, 46(8):2156-2173, 2007
E.
Roberts, J. Eargle, D. Wright, and Z. Luthey-Schulten
MultiSeq: Unifying sequence and structure data for evolutionary analysis
BMC Bioinformatics, 7:382, 2006
J. Eargle and Z. Luthey-Schulten
Visualizing the dual space of biological molecules
Comput
Biol Chem,
30:219-226, 2006
J. Eargle, D. Wright, and Z. Luthey-Schulten
Multiple alignment of protein structures and sequences for VMD
Bioinformatics,
22(4):504-506, 2006
P. O'Donoghue, A. Sethi, C. R. Woese, and Z. Luthey-Schulten
The evolutionary history of Cys-tRNACys 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
Proceedings of the National Academy of Sciences 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
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
cytochromec,
Journal of Computational Chemistry, 25: 1613-1622, 2004. Supplementary
Material
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,
Proceedings of the National Academy of Sciences 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.
O'Donoghue P. and Luthey-Schulten Z.
On the Evolution of Structure in the Aminoacyl-tRNA Synthetases.
Microbiol. Mol. Biol. Rev. 67:
550-573, 2003. Supplementary
Material.
Amaro R., Tajkhorshid E., and Luthey-Schulten Z.,
Developing an energy landscape for the novel function of a (beta/alpha)(8)
barrel:
Ammonia conduction through HisF.
Proceedings of the National Academy of Sciences USA, 100(13):7599-7604, 2003.
Eastwood MP, Hardin C, Luthey-Schulten Z, and Wolynes PG.
Statistical mechanical refinement of protein structure prediction schemes
II:
Mayer cluster expansion approach. J. Chem. Phys. 118(18): 8500-8512, 2003.
Wang J., Luthey-Schulten Z., and Suslick K. Is the olfactory receptor a
metalloprotein?
Proceedings of the National Academy of Sciences USA, 100(6): 3035-3039, 2003.
Hardin C., Eastwood M.P., Prentiss M. C., Luthey-Schulten Z., and Wolynes
P.G.
Associative memory Hamiltonians for structure prediction without homology:
alpha/beta proteins,
Proceedings of the National Academy of Sciences USA, 100(4): 1679-1684, 2003.
NSF-NIH
Report 2003: Accelerating Mathematical-Biological Linkages
Eastwood MP, Hardin C, Luthey-Schulten Z, and Wolynes PG.
Statistical mechanical refinement of protein structure prediction schemes:
Cumulant expansion approach.
Journal of Chemical Physics.
117(9):4602-4615, 2002.
Hardin C., Pogorelov TV, Luthey-Schulten Z.
Ab initio protein structure prediction.
Curr. Opin. Struct. Biol.
12(2):176-181, 2002.
Hardin C, Eastwood MP, Prentiss M, Luthey-Schulten Z, and Wolynes PG.
Folding funnels: The key to robust protein structure prediction.
J. Comp. Chem. 23(1):138-146,
2002.
M. Eastwood, C. Hardin, Z. Luthey-Schulten, and P. Wolynes.
Evaluating protein structure-prediction schemes using energy landscape
theory.
IBM J. Res. & Dev. 45:
475-497, 2001.
P. O'Donoghue, R. E. Amaro, and Z. Luthey-Schulten.
On the Structure of HisH: Protein Structure Prediction in the
Context of Structural and Functional Genomics.
J. Struct. Biol. 134: 257-268,
2001.
C. Hardin, M. Eastwood, Z. Luthey-Schulten and P. G. Wolynes,
"Associative Memory Hamiltonians for Structure Prediction without
Homology: Alpha-helical Proteins",
Proceedings of the National Academy of Sciences USA, 97, 14235, 2000.
P.O'Donoghue and Z. Luthey-Schulten, "Barriers to Forced Transitions
in Polysaccharides",
J. Phys. Chem. B, 104, 10398,
2000.
S. Takada, Z. Luthey-Schulten, and P.G. Wolynes, "Folding
Dynamics with Nonadditive Forces" A Simulation Study of a
Designed Helical Protein and a Random Heteropolymer",
J. Chem. Phys. 110,
11616-11629, 1999.
K. Koretke, Z. Luthey-Schulten, P. G. Wolynes,
"Self-Consistently Optimized Energy Functions for Protein
Structure Prediction by Molecular Dynamics",
Proceedings of the National Academy of Sciences USA, 95, 2932, 1998.
A. Panchenko, Z. Luthey-Schulten, R. Cole, P.G. Wolynes,
"The Foldon Universe: A Survey of Structural Similarity and
Self-Recognition of Independently Folding Units",
J. Mol. Biol., 272, 95-105,
1997.
J. Onuchic, Z. Luthey-Schulten, P. G. Wolynes, "Theory of
Protein Folding: The Energy Landscape Perspective",
Ann. Rev. Phys. Chem. 48,
539-600, 1997.
A. Panchenko, Z. Luthey-Schulten, P. G Wolynes, " Foldons,
Protein Structural Modules, and Exons",
Proceedings of the National Academy of Sciences USA, 93, 2008, 1996.
K. Koretke, Z. Luthey-Schulten, P. G. Wolynes,
"Self-Consistently Optimized Statistical Mechanical Energy
Functions for Sequence-Structure Alignment",
Protein Science, 5, 1043-1059,
1996.
J. Onuchic, P. G. Wolynes, Z. Luthey-Schulten, and N. Socci,
"Towards an Outline of the Topography of a Realistic Protein Folding
Funnel",
Proceedings of the National Academy of Sciences USA, 92, 3626-3630, 1995.
Z. Luthey-Schulten, B. Ramierez, and P. G. Wolynes,
"Helix-Coil, Liquid Crystal, and Spin Glass Transitions of a Collapsed
Heteropolymer,"
J. Phys. Chem. 99, 2177, 1995.
R. Goldstein, Z. Luthey-Schulten, P.G. Wolynes, " Protein
Tertiary Structure Recognition using Optimized Hamiltonians
with Local Interactions",
Proceedings of the National Academy of Sciences USA, 89, 9029-9033, 1992.
R. Goldstein, Z. Luthey-Schulten, P. G. Wolynes, "Optimal
Protein Folding Codes from Spin Glass Theory",
Proceedings of the National Academy of Sciences USA, 89, 4918-4922, 1992.
K. Schulten, A. Bruenger, W. Nadler, and Z.
Schulten,"Generalized Moment Description of Brownian
Dynamics in Biological Systems", Synergetics - From
Microscopic to Macroscopic Order, pp. 80-89, E. Frehland
(editor), Springer Verlag, 1984.
K. Schulten, Z. Schulten, and A. Szabo, "Dynamics of
Reactions Involving Diffusive Barrier Crossing",
Journal of Chemical Physics.
74, 4426-4432, 1981.
|
