M. Assaf, E. Roberts, and Z. Luthey-Schulten
Determining the Stability of Genetic Switches: Explicitly Accounting for mRNA Noise
Phys. Rev. Lett., 106, 248102, 2011
E. Roberts, A. Magis, J.O. Ortiz, W. Baumeister, and Z. Luthey-Schulten
Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study
PLoS. Comput. Biol., 7(3):e1002010, 2011
K. Chen, J. Eargle, K. Sarkar, M. Gruebele, and Z. Luthey-Schulten
Functional role of ribosomal signatures
Biophys. J., 99(12):3930-3940, 2010
L. Trabuco, E. Schreiner, J. Eargle, P. Cornish, T.J. Ha, Z. Luthey-Schulten, and K. Schulten
The role of L1 stalk:tRNA interaction in the ribosome elongation cycle
J. Mol. Biol., 402:741-760, 2010
A.B. Pyrkosz, J. Eargle, A. Sethi, and Z. Luthey-Schulten
Exit strategies for charged tRNA from GluRS
J. Mol. Biol., 397:1350-1371, 2010
- Structure file for CysRS:tRNA(Cys):Glu-AMP model (pdb).
- Figure of CysRS:tRNA(Cys):Glu-AMP model (pdf).
D. Mathew, and Z. Luthey-Schulten
Influence of Montmorillonite on Nucleotide Oligomerization Reactions: A Molecular Dynamics Study
Ori. Life Evol. Biosp., 40:303-317, 2010
Animation of mononumcletide interaction with trinucleotide in montmorillonite clay (mpg).
R.W. Alexander, J. Eargle, and Z. Luthey-Schulten
Experimental and computational analysis of tRNA dynamics
FEBS Letters, 584(2):376-386, 2010
T. Butler, N. Goldenfeld, D. Mathew, and Z. Luthey-Schulten
Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement
Phys. Rev. E, 79:060901, 2009
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 Proceedings of the 2009 IEEE International Symposium on Parallel & Distributed Processing, 2009
K. Chen, E. Roberts, and Z. Luthey-Schulten
Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4
BMC Evol. Biol., 9:179, 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
- Parameter file for modified nucleosides (inp).
- Topology file for modified nucleosides (inp).
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-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).
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.
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.
Proc. Natl. Acad. Sci. 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?
Proc. Natl. Acad. Sci. 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,
Proc. Natl. Acad. Sci. 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 Homology: Alpha-helical Proteins"
Proc. Natl. Acad. Sci. 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 Heteropolyme"
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"
Proc. Natl. Acad. Sci. 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",
Proc. Natl. Acad. Sci. 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"
Proc. Natl. Acad. Sci. 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"
Proc. Natl. Acad. Sci. USA, 89, 9029-9033, 1992.
R. Goldstein, Z. Luthey-Schulten, P. G. Wolynes
"Optimal Protein Folding Codes from Spin Glass Theory"
Proc. Natl. Acad. Sci. 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.
