Zan Luthey-Schulten

Description

Address

  • 3027 Beckman Institute
  • 405 North Mathews Avenue
  • Urbana, Illinois 61801

Biography

Zaida (Zan) Luthey-Schulten is a William and Janet Lycan Professor of Chemistry in the Department of Chemistry and a part-time faculty member in the Beckman Institute Theoretical and Computational Biophysics Group. She is also affiliated with the Center for Biophysics and Computational Biology.

Professor Schulten received a B.S. in Chemistry from the University of Southern California in 1969, a M.S. in Chemistry from Harvard University in 1972, and a Ph.D. in Applied Mathematics from Harvard University in 1975. From 1975 to 1980 she was a Research Fellow at the Max-Planck Institute for Biophysical Chemistry in Goettingen, and from 1980 to 1985 a Research Fellow in the Department of Theoretical Physics at the Technical University of Munich.

Honors

Chair/Vice-Chair Biophysics Subsection of the ACS (2002-2005); Fellow of the American Physical Society (2000); Fellow-Advanced Studies Institute, Hebrew University, Israel (1998).

Research

Prof. Luthey-Schulten is Co-Director of the NSF Physics Frontier Center “Center for the Physics of Living Cells,” and since 2002 a Co-Investigator of the NIH Center for Macromolecular Modeling and Bioinformatics. Since joining the UIUC faculty, Prof. Luthey-Schulten has authored over 150 peer-reviewed articles and made profound contributions in the areas of protein folding, photosynthesis, bioinformatics, population flux balance analysis (FBA) in systems biology and stochastic simulations of cellular processes at the whole cell level. The focus on exploring emerging areas of computational biology has led to the development of new software tools and broadened the scope and userbase of the NIH Center's molecular and cellular software.

She has led the development of a bioinformatics analysis environment (MultiSeq) in VMD for investigating the sequence and structural evolution of nucleic acids and proteins, as well as novel methods for analyzing and visualizing the networks of interactions (NetworkView) arising from correlations in molecular dynamics simulations (NAMD, Anton) of protein/RNA involved in transcription and translation. More recently we have introduced an integrative QM/MM suite of programs to the Center’s MD and visualization programs NAMD and VMD,respectively, that couple them with quantum mechanical codes such as ORCA, MOPAC, TERACHEM, QCHEM, and GAUSSIAN.

 
Starting in 2011, Prof. Luthey-Schulten and co-workers introduced cell-scale modeling, developing the Lattice Microbes (LM) software for simulating complex biochemical reaction networks in physically realistic models of whole cells on biologically relevant timescales, as well as visualization tools to bring the simulations to life in VMD. LM is now running on the Blue Waters, Maverick, and Titan Supercomputers, and has been ported to the IBM POWER architecture used in the upcoming DOE Summit machine. This work required both intellectual advances, developing increasingly sophisticated and ever-more complete models of key biological processes and networks, as well as technical advances, including the rapid adoption of state-of-the-art GPU computing technologies through highly specialized work and close ties to NVIDIA developers. Much of our success in whole-cell modeling has depended on forging long-standing and fruitful collaborations with leading experimentalists from around the globe, including structural cell biologists and imaging experts in the fields of super-resolution fluorescence microscopy (TJ Ha) and cryo-electron tomography (Baumeister, Villa). A new collaboration with the J. Craig Venter Institute focuses on constructing and visualizing the first fully-detailed computational model of an entire living “minimal” cell (a synthetic organism involving the fewest number of genes possible to sustain life

 

Publications

  • 2017
    • M.C.R. Melo, R.C. Bernardi, T. Rudack, M. Scheurer, C. Riplinger, J.C. Phillips, J.D.C. Maia, G.B. Rocha, J.V. Ribeiro, J.E. Stone, F. Neese, K. Schulten, Z. Luthey-Schulten NAMD goes quantum: A new integrative suite for QM/MM simulations Nat. Methods, 2017 - Under Revision
    • T. Verdorfer, R.C. Bernardi, A. Meinhold, W. Ott, Z. Luthey-Schulten, M.A. Nash, H.E. Gaub Combining in Vitro and in Silico Single-Molecule Force Spectroscopy to Characterize and Tune Cellulosomal Scaffoldin Mechanics J. Ame. Chem. Soc., 2017 - In Print
    • S.C. Abeysirigunawardena, H. Kim, J. Lai, K. Ragunathan, M.C. Rappe, Z. Luthey-Schulten, T. Ha, S. A. Woodson Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes Nat. Commun., 2017, Sep 8, 8(1):492, doi: 10.1038/s41467-017-00536-1
    • P. Labhsetwar*, M.C.R. Melo*, J.A. Cole*, Z. Luthey-Schulten Population FBA Predicts Metabolic Phenotypes in Yeast PLOS Comput. Biol. 2017, Sep 8, 13(9):e1005728. doi: 10.1371/journal.pcbi.1005728
    • 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
  • 2016
    • 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
  • 2015
    • Guzman, I.; Ghaemi, Z.; Baranger, A.; Luthey-Schulten, Z.; Gruebele, M., Native Conformational Dynamics of the Spliceosomal U1a Protein. Journal of Physical Chemistry B 2015, 119, (9), 3651-3661, DOI: 10.1021/Jp511760m.

    • Cole, J. A.; Kohler, L.; Hedhli, J.; Luthey-Schulten, Z., Spatially-Resolved Metabolic Cooperativity within Dense Bacterial Colonies. BMC Systems Biology 2015, 9, DOI:Artn 15 Doi 10.1186/S12918-015-0155-1.

    • Earnest, T. M.; Lai, J.; Chen, K.; Hallock, M. J.; Williamson, J. R.; Luthey-Schulten, Z., Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of Ssu Assembly. Biophysical Journal 2015, 109, (6), 1117-1135, DOI:10.1016/j.bpj.2015.07.030.
    • Ghaemi, Z.; Guzman, I.; Gruebele, M.; Luthey-Schulten, Z., Electrostatic Interaction Effects on the Binding of Spliceosomal U1A Protein-Sl2 RNA Hairpin. Biophysical Journal 2015, 108, (2), 15a-15a.
    • Nguyen, C. T.; Ngo, T.; Park, S.; Cox, K.; Ha, T.; Luthey-Schulten, Z. A.; Kuhlman, T. E., Spatial Organization of Ribosome Biogenesis of Escherichia Coli. Biophysical Journal 2015, 108, (2), 312a-312a.
    • Peterson, J. R.; Cole, J. A.; Fei, J. Y.; Ha, T.; Luthey-Schulten, Z. A., Effects of DNA Replication on Mrna Noise. Proceedings of the National Academy of Sciences of the United States of America 2015, 112, (52), 15886-15891, DOI:10.1073/pnas.1516246112.
    • Zhao, H. C.; Palencia, A.; Seiradake, E.; Ghaemi, Z.; Cusack, S.; Luthey-Schulten, Z.; Martinis, S., Analysis of the Resistance Mechanism of a Benzoxaborole Inhibitor Reveals Insight into the Leucyl-Trna Synthetase Editing Mechanism. ACS Chemical Biology 2015, 10, (10), 2277-2285, DOI:10.1021/acschembio.5b00291.
  • 2014
    • Peterson, J. R.; Labhsetwar, P.; Ellermeier, J. R.; Kohler, P. R. A.; Jain, A.; Ha, T.; Metcalf, W. W.; Luthey-Schulten, Z., Towards a Computational Model of a Methane Producing Archaeum. Archaea-An International Microbiological Journal 2014, DOI: 10.1155/2014/898453.

    • Cole, J. A.; Luthey-Schulten, Z., Whole Cell Modeling: From Single Cells to Colonies. Israel Journal of Chemistry 2014, 54, (8-9), 1219-1229, DOI: 10.1002/ijch.201300147.

  • 2013
    • Labhsetwar, P.; Cole, J. A.; Roberts, E.; Price, N. D.; Luthey-Schulten, Z. A., Heterogeneity in Protein Expression Induces Metabolic Variability in a Modeled Escherichia Coli Population. Proceedings of the National Academy of Sciences of the United States of America 2013, 110, (34), 14006-14011, DOI: 10.1073/pnas.1222569110.

    • Lai, J.; Chen, K.; Luthey-Schulten, Z., Structural Intermediates and Folding Events in the Early Assembly of the Ribosomal Small Subunit. Journal of Physical Chemistry B 2013, 117, (42), 13335-13345, DOI: 10.1021/jp404106r.

    • Li, L.; Martinis, S. A.; Luthey-Schulten, Z., Capture and Quality Control Mechanisms for Adenosine-5 '-Triphosphate Binding. Journal of the American Chemical Society 2013, 135, (16), 6047-6055.

    • Li, L.; Palencia, A.; Lukk, T.; Li, Z.; Luthey-Schulten, Z. A.; Cusack, S.; Martinis, S. A.; Boniecki, M. T., Leucyl-Trna Synthetase Editing Domain Functions as a Molecular Rheostat to Control Codon Ambiguity in Mycoplasma Pathogens. Proceedings of the National Academy of Sciences of the United States of America 2013, 110, (10), 3817-3822.

    • Peterson, J. R.; Hallock, M. J.; Cole, J. A.; Luthey-Schulten, Z., A Problem Solving Environment for Stochastic Biological Simulations, PyHPC2013 at Supercomputing 2013, Denver, Colorado.

    • Roberts, E.; Stone, J. E.; Luthey-Schulten, Z., Lattice Microbes: High-Performance Stochastic Simulation Method for the Reaction-Diffusion Master Equation. Journal of Computational Chemistry 2013, 34, (3), 245-255.

  • 2012
    • VanWart, A. T.; Eargle, J.; Luthey-Schulten, Z.; Amaro, R. E., Exploring Residue Component Contributions to Dynamical Network Models of Allostery. Journal of Chemical Theory and Computation 2012, 8, (8), 2949-2961.

  • 2011
    • Roberts, E.; Magis, A.; Ortiz, J. O.; Baumeister, W.; Luthey-Schulten, Z., Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study. PLOS Computational Biology 2011, 7, (3).

  • 2010
    • Trabuco, L. G.; Schreiner, E.; Eargle, J.; Cornish, P.; Ha, T.; Luthey-Schulten, Z.; Schulten, K., The Role of L1 Stalk-tRNA Interaction in the Ribosome Elongation Cycle. Journal of Molecular Biology 2010, 402, (4), 741-760. 

    • Mathew, D. C.; Luthey-Schulten, Z., Influence of Montmorillonite on Nucleotide Oligomerization Reactions: A Molecular Dynamics Study. Origins of Life and Evolution of Biospheres 2010, 40, (3), 303-317.

    • Pyrkosz, A. B.; Eargle, J.; Sethi, A.; Luthey-Schulten, Z., Exit Strategies for Charged tRNA from GluRS. Journal of Molecular Biology 2010, 397, (5), 1350-1371.

    • Chen, K.; Eargle, J.; Sarkar, K.; Gruebele, M.; Luthey-Schulten, Z., Functional Role of Ribosomal Signatures. Biophysical Journal 2010, 99, (12), 3930-3940. 

    • Alexander, R. W.; Eargle, J.; Luthey-Schulten, Z., Experimental and computational determination of tRNA dynamics. FEBS Letters 2010, 584, (2), 376-386.

  • 2009
    • Butler, T.; Goldenfeld, N.; Mathew, D.; Luthey-Schulten, Z., Extreme Genetic code optimality from a molecular dynamics calculation of amino acid polar. Physical Review E 2009, 79, (6), 060901.

    • Chen, K.; Roberts, E.; Luthey-Schulten, Z., Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4. BMC Evolutionary Biology 2009, 9.

    • Sethi, A.; Eargle, J.; Black, A. A.; Luthey-Schulten, Z., Dynamical networks in tRNA: protein complexes. Proceedings of the National Academy of Sciences of the United States of America 2009, 106, (16), 6620-6625.

  • 2008
    • Eargle, J.; Black, A. A.; Sethi, A.; Trabuco, L. G.; Luthey-Schulten, Z., Dynamics of recognition between tRNA and elongation factor Tu. Journal of Molecular Biology 2008, 377, (5), 1382-1405.

    • Mathew, D. C.; Luthey-Schulten, Z., On the physical basis of the amino acid polar requirement. Journal of Molecular Evolution 2008, 66, (5), 519-528.

    • Roberts, E.; Sethi, A.; Montoya, J.; Woese, C. R.; Luthey-Schulten, Z., Molecular signatures of ribosomal evolution. Proceedings of the National Academy of Sciences of the United States of America 2008, 105, (37), 13953-13958.

  • 2007
    • Amaro, R. E.; Sethi, A.; Myers, R. S.; Davisson, V. J.; Luthey-Schulten, Z. A., A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase. Biochemistry 2007, 46, (8), 2156-2173.

    • Pogorelov, T. V.; Autenrieth, F.; Roberts, E.; Luthey-Schulten, Z. A., Cytochrome c(2) exit strategy: Dissociation studies and evolutionary implications. Journal of Physical Chemistry B 2007, 111, (3), 618-634.

  • 2006
    • Eargle, J.; Luthey-Schulten, Z., Visualizing the dual space of biological molecules. Computational Biology and Chemistry 2006, 30, (3), 219-226.

    • Roberts, E.; Eargle, J.; Wright, D.; Luthey-Schulten, Z., MultiSeq: unifying sequence and structure data for evolutionary analysis. Bmc Bioinformatics 2006, 7.

  • 2003
    • O'Donoghue, P. and Luthey-Schulten, Z. (2003), "Evolution of Structure in the Aminoacyl-tRNA Synthetases," Microbiology and Molecular Biology Reviews, 67, pp. 550.

    • Hardin, C., Eastwood, M. P., Prentiss, M., Luthey-Schulten, Z. and Wolynes, P. G. (2003), "Associative Memory Hamiltonians for Structure Prediction without Homology: Alpha/Beta Proteins," Proceedings of the National Academy of Sciences, USA, 100, pp. 1679.

    • Wang, J., Luthey-Schulten, Z. and Suslick, K. (2003), "Is the Olfactory Receptor a Metalloprotein," Proceedings of the National Academy of Sciences, USA, 100, pp. 3035.

    • Eastwood, M., Hardin, C., Luthey-Schulten, Z. and Wolynes, P. (2003), "Statistical Mechanical Refinement of Protein Structure Prediction Schemes II: Mayer Cluster Expansion Approach," Journal of Chemical Physics, 118, pp. 8500.

    • Amaro, R., Tajkhorshid, E. and Luthey-Schulten, Z. (2003), "Developing an Energy Landscape for the Novel Function of a (/)8 Barrel: Ammonia Conduction Through HisF," Proceedings of the National Academy of Sciences, USA, 100, pp. 7599.

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