Zan Luthey-Schulten

Description

Address

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

Biography

Zaida (Zan) Luthey-Schulten received her Ph.D. from Harvard University in 1975. She 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. Her current research focuses on developing a statistical mechanical framework and computational methods to predict protein structures and on integrating evolutionary and bioinformatic data into molecular dynamics simulations of large integrated biological systems.

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

Understanding the principles of protein folding necessitates working at the interface of biophysics, chemistry and computer science. Energetically the folding and assembly of large protein complexes can be described in terms of the theory of energy landscapes, but the natural variations observed in these landscapes over protein families requires placing the protein folding and structure prediction problems in the context of evolution. Zan Luthey-Schulten's research attempts to correlate changes in protein sequence, structure, and function from the perspective of evolution. The most recent investigations have centered on the variation in structure and interactions in aminoacyl-tRNA synthetases (AARSs), key protein-enzyme components in the translation process in all forms of life that are responsible for charging their cognate tRNAs with the correct amino acid. The evolution of shape studies introduced new measures of structural homology along with a multidimensional QR algorithm to determine non-redundant representative structures and sequences. As protein structure is more conserved over longer times than protein sequence, this study has allowed us to glimpse the evolution of protein structure that pre-dates the root of the universal phylogenetic tree. Similar techniques are being applied to examine the variation in protein folding mechanisms for proteins with similar shape and dynamical interactions in larger biological assemblies.

In collaboration with the Theoretical and Computational Biophysics (TCB) group and the NIH Resource for Macromoleular Modeling and Bioinformatics, the evolutionary and bioinformatics analysis tools to correlate sequence and structure variations will be integrated into the widely distributed molecular graphics package VMD for biomedical researchers. The NIH Resource distributes both VMD and its simulation package NAMD which permits interactive molecular dynamics studies of protein folding and protein-RNA interactions. The new evolutionary analysis tools will also make use of the collaborative environment of BioCoRE to build both local and distant collaborations.

Professor Luthey-Schulten's research is supported by NSF and NIH.

Publications

  • 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.

Press

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