Publications

P. Labhsetwar, M.C.R. Melo, J.A. Cole, Z. Luthey-Schulten
Population FBA Reveals Metabolic Phenotypes in Yeast
Revisions

S.C. Abeysirigunawardena, H. Kim, J. Lai, K. Ragunathan, M. Rappe, Z. Luthey-Schulten, T. Ha, S. A. Woodson
Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes
Nat. Commun. (Accepted), 2017, doi:10.1038/s41467-017-00536-1

J.R. Peterson, J.A. Cole, Z. Luthey-Schulten
Parametric Studies of Metabolic Cooperativity in Escherichia coli Colonies: Strain and Geometric Confinement Effects
PLoS ONE, 2017, Aug 18, 12(8):e0182570. doi: 10.1371/journal.pone.0182570

Z. Ghaemi, I. Guzman, D. Gnutt, Z. Luthey-Schulten, M. Gruebele
Role of Electrostatics in Protein-RNA binding: The Global vs. the Local Energy Landscape
J. Phys. Chem. B, 2017, Aug 14. doi: 10.1021/acs.jpcb.7b04318

J.A. Cole, Z. Luthey-Schulten
A Careful Accounting of Extrinsic Noise in Protein Expression Reveals Correlations Among its Sources
Phys. Rev. E. 2017, May 12, 95(6):062418. doi: 10.1103/PhysRevE.95.062418

T.M. Earnest, R. Watanabe, J.E. Stone, J. Mahamid, W. Baumeister, E. Villa, Z. Luthey-Schulten
Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations
J. Phys. Chem. B, 2017, Mar 14, 121(15):3871-3881 doi:10.1021/acs.jpcb.7b00672

S. Thor, J.R. Peterson, Z. Luthey-Schulten
Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function
Archaea, 2017, Jan 4, vol. 2017, Article ID: 9763848, 18 pages, doi: 10.1155/2017/9763848

J.R. Peterson, S. Thor, L. Kohler, P.R.A. Kohler, W.W. Metcalf, Z. Luthey-Schulten
Genome-Wide Gene Expression and RNA Half-Life Measurements allow Predictions of Regulation and Metabolic Behavior in Methanosarcina acetivorans
BMC Genomics, 2016, Nov 16, 17(1):924 doi: 10.1186/s12864-016-3219-8

Z. Ghaemi, I. Guzman, J.J. Baek, M. Gruebele, Z. Luthey-Schulten
Estimation of Relative Protein-RNA Binding Strengths from Fluctuations in the Bound State
J. Chem. Theory Comput., 2016, Aug 16, doi:10.1021/acs.jctc.6b00418

T.M. Earnest, J.A. Cole, J.R. Peterson, T.E. Kuhlman, Z. Luthey-Schulten
Ribosome biogenesis in replicating cells: integration of experiment and theory
Biopolymers, 2016, Jul 22, 105(10): 735-751 doi:10.1002/bip.22892

M.J. Hallock, Z. Luthey-Schulten
Improving reaction kernel performance in Lattice Microbes: particle-wise propensities and run-time generated code
2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), May 2016, 428-434 doi:10.1109/IPDPSW.2016.118

J.E. Stone, M.J. Hallock, J.C. Phillips, J.R. Peterson, Z. Luthey-Schulten, K. Schulten
Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads
2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), May 2016, 89-100 doi:10.1109/IPDPSW.2016.130

J.R. Peterson*, J.A. Cole*, J. Fei, T.J. Ha and Z. Luthey-Schulten
Effects of DNA Replication on mRNA Noise
Proc. Nat. Acad. Sci., 2015, Nov 11, 112(52): 15886-15891 doi:10.1073/pnas.1516246112

T. M. Earnest, J. Lai, K. Chen, M. J. Hallock, J. R. Williamson, and Z. Luthey-Schulten
Towards a whole-cell model of ribosome biogenesis: Kinetic modeling of SSU assembly
Biophysical Journal, 2015, Sep 15, 109(6): 1117-35 doi:10.1016/j.bpj.2015.07.030
Files for the simulation can be found: here

J. A. Cole, L. Kohler L, J. Hedhli, Z. Luthey-Schulten
Spatially-Resolved Metabolic Cooperativity Within Dense Bacterial Colonies
BMC Syst Biol, 2015, 9(15), doi:10.1186/s12918-015-0155-1

H. Zhao, A. Palencia, E. Seiradake, Z. Ghaemi, S. Cusack, Z. Luthey-Schulten, S. Martinis
Analysis of the Resistance Mechanism of a Benzoxaborole Inhibitor Reveals Insight into the Leucyl-tRNA Synthetase Editing Mechanism
ACS Chem. Biol., 2015, 10(10): 2277-2285, doi:10.1021/acschembio.5b00291

I. Guzman, Z. Ghaemi, A. Baranger, Z. Luthey-Schulten, M. Gruebele
Native Conformational Dynamics of the Spliceosomal U1A Protein
J. Phys. Chem. B, 2015, 119 (9): 3651-3661, doi:10.1021/jp511760m

J. Cole, Z. Luthey-Schulten
Whole Cell Modeling: From Single Cells to Colonies
Isr. J. Chem., 2014, 54(8-9): 1219--1229, doi: 10.1002/ijch.201300147

Hajin Kim, Sanjaya C. Abeysirigunawarden, Ke Chen, Megan Mayerle, Kaushik Ragunathan, Zaida Luthey-Schulten, Taekjip Ha & Sarah A. Woodson
Protein-guided RNA dynamics during early ribosome assembly
Nature, 2014, 506, 7488, 334--338, http://dx.doi.org/10.1038/nature13039

M. J. Hallock, J. E. Stone, E. Roberts, C. Fry, Z. Luthey-Schulten
Simulation of reaction diffusion processes over biologically-relevant size and time scales using multi-GPU workstations
Parallel Comput. 2014, 40, 86-99, doi: 10.1016/j.parco.2014.03.009.

J.R. Peterson, P. Labhsetwar, J.R. Ellermeier, P.R.A.Kohler, A. Jain, T. Ha, W.W. Metcalf, Z. Luthey-Schulten
Towards a Computational Model of a Methane Producing Archaeum
Archaea, Article ID 898453, 18 pages, 2014, http://dx.doi.org/10.1155/2014/898453

J. Cole, M. J. Hallock, P. Labhsetwar, J. R. Peterson, J. E. Stone, Z. Luthey-Schulten
Stochastic Simulations of Cellular Processes: From Single Cells to Colonies
in Computational Systems Biology 2nd Edition: From Molecular Mechanisms to Disease, Eds. Kriete and Eils, Elsevier, 2014.

J.R. Peterson, M.J. Hallock, J.A. Cole, and Z. Luthey-Schulten
A Problem Solving Environment for Stochastic Biological Simulations
PyHPC '13: Proceedings of the 3rd Workshop on Python for High-Performance and Scientific Computing, 2013, DOI: 10.13140/2.1.3207.7440

J. Lai, K. Chen, and Z. Luthey-Schulten
Structural Intermediates and Folding Events in the Early Assembly of the Ribosomal Small Subunit
J. Phys. Chem. B, 117(42): 13335--13345, 2013

P. Labhsetwar, J.A. Cole, E. Roberts, N.D. Price, Z. Luthey-Schulten
Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population
Proc. Nat. Acad. Sci., 110(34):14006-11, 2013, doi: 10.1073/pnas.1222569110

M. Hartmann
Stochastic simulation of reaction-diffusion systems
Master's Thesis LMU Munich, 2013

M. Assaf, E. Roberts, Z. Luthey-Schulten, N. Goldenfeld
Extrensic noise driven phenotype switching in a self-regulating gene
Phys. Rev. Lett., 111(5), e058102,2013

L. Li, S. A. Martinis, Z. Luthey-Schulten
Capture and quality control mechanisms for adenosine-5'-triphosphate binding
J. Am. Chem. Soc., 135(16), 6047-6055,2013

E. Roberts, J. E. Stone, and Z. Luthey-Schulten
Lattice microbes: high-performance stochastic simulation method for the reaction-diffusion master equation
J. Comput. Chem., 34(3), 245-55, 2013

T. Earnest, E. Roberts, M. Assaf, K. Dahmen, and Z. Luthey-Schulten
DNA looping increases range of bistability in a stochastic model of the lac genetic switch
Phys. Biol. 10 (2013) 026002

A. VanWart, J. Eargle, Z. Luthey-Schulten, and R. Amaro
Exploring residue component contributions to dynamical network models of allostery
J. Chem. Theory Comp. 8(8),2949-2961, 2012

J. Eargle and Z. Luthey-Schulten
NetworkView: 3D display and analysis of dynamic structure networks
Bioinformatics, 28(22), 3000-1, 2012

K. Chen, J. Eargle, J. Lai, H, Kim, T. Ha, T. Abeysirigunawardena, M. Mayerle, S. Woodson, and Z. Luthey-Schulten
Assembly of the fiveway junction in the ribosomal small subunit using hybrid MD/Go simulation
Journal of Physical Chemistry B: Harold A. Scheraga Festschrift, 116:23,6819-6831, 2012

J. Eargle and Z. A. Luthey-Schulten
Chapter 11: Simulating Dynamics in RNA-Protein Complexes
In RNA 3D Structure Analysis and Prediction N. Leontis and E. Westhof (editors)
Nucleic Acids and Molecular Biology 27, DOI 10.1007/978-3-642-25740-7_11, Springer-Verlag Berlin Heidelberg 2012

L. Li, M. T. Boniecki, J. D. Jaffe, B. S. Imai, P. M. Yau, Z. Luthey-Schulten, and S. A. Martinis
Naturally occurring aminoacyl-tRNA synthetases editing-domain mutations that cause mistranslation in Mycoplasma parasites
Proc. Nat. Acad. Sci., 109(9),9378-9383, 2011

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.-M.W. Hwu, and Z. Luthey-Schulten
Long time-scale simulations of in vivo diffusion using GPU hardware
Parallel & Distributed Processing, 2009, IPDPS 2009. IEEE International Symposium on, vol., no., pp.1,8,23-29 May 2009 doi: 10.1109/IPDPS.2009.5160930

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).
- 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.

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.