Zaida Ann Luthey-Schulten

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Research Output

2020

An in-silico human cell model reveals the influence of spatial organization on RNA splicing

Ghaemi, Z., Peterson, J. R., Gruebele, M. & Luthey-Schulten, Z., Mar 25 2020, In : PLoS computational biology. 16, 3, e1007717.

Research output: Contribution to journalArticle

Open Access

Complete structure of the chemosensory array core signalling unit in an E. coli minicell strain

Burt, A., Cassidy, C. K., Ames, P., Bacia-Verloop, M., Baulard, M., Huard, K., Luthey-Schulten, Z., Desfosses, A., Stansfeld, P. J., Margolin, W., Parkinson, J. S. & Gutsche, I., Dec 1 2020, In : Nature communications. 11, 1, 743.

Research output: Contribution to journalArticle

Open Access

Structure and dynamics of the E. coli chemotaxis core signaling complex by cryo-electron tomography and molecular simulations

Cassidy, C. K., Himes, B. A., Sun, D., Ma, J., Zhao, G., Parkinson, J. S., Stansfeld, P. J., Luthey-Schulten, Z. & Zhang, P., Dec 1 2020, In : Communications biology. 3, 1, 24.

Research output: Contribution to journalArticle

Open Access
2019

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism

Singharoy, A., Maffeo, C., Delgado-Magnero, K. H., Swainsbury, D. J. K., Sener, M., Kleinekathöfer, U., Vant, J. W., Nguyen, J., Hitchcock, A., Isralewitz, B., Teo, I., Chandler, D. E., Stone, J. E., Phillips, J. C., Pogorelov, T. V., Mallus, M. I., Chipot, C., Luthey-Schulten, Z., Tieleman, D. P., Hunter, C. N. & 3 others, Tajkhorshid, E., Aksimentiev, A. & Schulten, K., Nov 14 2019, In : Cell. 179, 5, p. 1098-1111.e23

Research output: Contribution to journalArticle

Direction Matters: Monovalent Streptavidin/Biotin Complex under Load

Sedlak, S. M., Schendel, L. C., Melo, M. C. R., Pippig, D. A., Luthey-Schulten, Z., Gaub, H. E. & Bernardi, R. C., Jun 12 2019, In : Nano letters. 19, 6, p. 3415-3421 7 p.

Research output: Contribution to journalArticle

Essential metabolism for a minimal cell

Breuer, M., Earnest, T. M., Merryman, C., Wise, K. S., Sun, L., Lynott, M. R., Hutchison, C. A., Smith, H. O., Lapek, J. D., Gonzalez, D. J., de Crécy-Lagard, V., Haas, D., Hanson, A. D., Labhsetwar, P., Glass, J. I. & Luthey-Schulten, Z., Jan 18 2019, In : eLife. 8, e36842.

Research output: Contribution to journalArticle

Open Access

In situ conformational changes of the escherichia coli serine chemoreceptor in different signaling states

Yang, W., Keith Cassidy, C., Ames, P., Diebolder, C. A., Schulten, K., Luthey-Schulten, Z., Parkinson, J. S. & Briegel, A., Jul 1 2019, In : mBio. 10, 4, e00973-19.

Research output: Contribution to journalArticle

Open Access

Kinetic Modeling of the Genetic Information Processes in a Minimal Cell

Thornburg, Z. R., Melo, M. C. R., Bianchi, D., Brier, T. A., Crotty, C., Breuer, M., Smith, H. O., Hutchison, C. A., Glass, J. I. & Luthey-Schulten, Z., Nov 28 2019, In : Frontiers in Molecular Biosciences. 6, 130.

Research output: Contribution to journalArticle

Open Access

Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy

Bernardi, R. C., Durner, E., Schoeler, C., Malinowska, K. H., Carvalho, B. G., Bayer, E. A., Luthey-Schulten, Z., Gaub, H. E. & Nash, M. A., Sep 18 2019, In : Journal of the American Chemical Society. 141, 37, p. 14752-14763 12 p.

Research output: Contribution to journalArticle

Membrane organization of photosystem I complexes in the most abundant phototroph on Earth

MacGregor-Chatwin, C., Jackson, P. J., Sener, M., Chidgey, J. W., Hitchcock, A., Qian, P., Mayneord, G. E., Johnson, M. P., Luthey-Schulten, Z., Dickman, M. J., Scanlan, D. J. & Hunter, C. N., Aug 1 2019, In : Nature Plants. 5, 8, p. 879-889 11 p.

Research output: Contribution to journalArticle

2018

CryoEM-based hybrid modeling approaches for structure determination

Cassidy, C. K., Himes, B. A., Luthey-Schulten, Z. & Zhang, P., Jun 2018, In : Current Opinion in Microbiology. 43, p. 14-23 10 p.

Research output: Contribution to journalReview article

Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase

Ma, W., Whitley, K. D., Chemla, Y. R., Luthey-Schulten, Z. & Schulten, K., Apr 17 2018, In : eLife. 7, e34186.

Research output: Contribution to journalArticle

Hybrid CME-ODE method for efficient simulation of the galactose switch in yeast

Bianchi, D. M., Peterson, J. R., Earnest, T. M., Hallock, M. J. & Luthey-Schulten, Z., Aug 1 2018, In : IET Systems Biology. 12, 4, p. 170-176 7 p.

Research output: Contribution to journalArticle

NAMD goes quantum: An integrative suite for hybrid simulations

Melo, M. C. R., Bernardi, R. C., Rudack, T., Scheurer, M., Riplinger, C., Phillips, J. C., Maia, J. D. C., Rocha, G. B., Ribeiro, J. V., Stone, J. E., Neese, F., Schulten, K. & Luthey-Schulten, Z. A., Apr 27 2018, In : Nature Methods. 15, 5, p. 351-354 4 p.

Research output: Contribution to journalArticle

Simulating biological processes: Stochastic physics from whole cells to colonies

Earnest, T. M., Cole, J. A. & Luthey-Schulten, Z., Apr 5 2018, In : Reports on Progress in Physics. 81, 5, 052601.

Research output: Contribution to journalReview article

2017

Biography of Klaus Schulten

Amaro, R. E., Villa, E. & Luthey-Schulten, Z., Apr 20 2017, In : Journal of Physical Chemistry B. 121, 15, 1 p.

Research output: Contribution to journalEditorial

Careful accounting of extrinsic noise in protein expression reveals correlations among its sources

Cole, J. A. & Luthey-Schulten, Z., Jun 27 2017, In : Physical Review E. 95, 6, 062418.

Research output: Contribution to journalArticle

Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations

Earnest, T. M., Watanabe, R., Stone, J. E., Mahamid, J., Baumeister, W., Villa, E. & Luthey-Schulten, Z., Apr 20 2017, In : Journal of Physical Chemistry B. 121, 15, p. 3871-3881 11 p.

Research output: Contribution to journalArticle

Combining in Vitro and in Silico Single-Molecule Force Spectroscopy to Characterize and Tune Cellulosomal Scaffoldin Mechanics

Verdorfer, T., Bernardi, R. C., Meinhold, A., Ott, W., Luthey-Schulten, Z., Nash, M. A. & Gaub, H. E., Dec 13 2017, In : Journal of the American Chemical Society. 139, 49, p. 17841-17852 12 p.

Research output: Contribution to journalArticle

Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes

Abeysirigunawardena, S. C., Kim, H., Lai, J., Ragunathan, K., Rappé, M. C., Luthey-Schulten, Z., Ha, T. & Woodson, S. A., Dec 1 2017, In : Nature communications. 8, 1, 492.

Research output: Contribution to journalArticle

Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function

Thor, S., Peterson, J. R. & Luthey-Schulten, Z., 2017, In : Archaea. 2017, 9763848.

Research output: Contribution to journalReview article

Parametric studies of metabolic cooperativity in Escherichia coli colonies: Strain and geometric confinement effects

Peterson, J. R., Cole, J. A. & Luthey-Schulten, Z., Aug 2017, In : PloS one. 12, 8, e0182570.

Research output: Contribution to journalArticle

Population FBA predicts metabolic phenotypes in yeast

Labhsetwar, P., Melo, M. C. R., Cole, J. A. & Luthey-Schulten, Z., Sep 2017, In : PLoS computational biology. 13, 9, e1005728.

Research output: Contribution to journalArticle

Role of Electrostatics in Protein-RNA Binding: The Global vs the Local Energy Landscape

Ghaemi, Z., Guzman, I., Gnutt, D., Luthey-Schulten, Z. & Gruebele, M., Sep 14 2017, In : Journal of Physical Chemistry B. 121, 36, p. 8437-8446 10 p.

Research output: Contribution to journalArticle

The Conformational Change in Elongation Factor Tu Involves Separation of Its Domains

Lai, J., Ghaemi, Z. & Luthey-Schulten, Z., Nov 14 2017, In : Biochemistry. 56, 45, p. 5972-5979 8 p.

Research output: Contribution to journalArticle

2016

Estimation of Relative Protein-RNA Binding Strengths from Fluctuations in the Bound State

Ghaemi, Z., Guzman, I., Baek, J. U. J., Gruebele, M. & Luthey-Schulten, Z., Sep 13 2016, In : Journal of Chemical Theory and Computation. 12, 9, p. 4593-4599 7 p.

Research output: Contribution to journalArticle

Evaluation of emerging energy-efficient heterogeneous computing platforms for biomolecular and cellular simulation workloads

Stone, J. E., Hallock, M. J., Phillips, J. C., Peterson, J. R., Luthey-Schulten, Z. A. & Schulten, K. J., Jul 18 2016, Proceedings - 2016 IEEE 30th International Parallel and Distributed Processing Symposium, IPDPS 2016. Institute of Electrical and Electronics Engineers Inc., p. 89-100 12 p. 7529854. (Proceedings - 2016 IEEE 30th International Parallel and Distributed Processing Symposium, IPDPS 2016).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans

Peterson, J. R., Thor, S. S., Kohler, L., Kohler, P. R. A., Metcalf, W. W. & Luthey-Schulten, Z., Nov 16 2016, In : BMC genomics. 17, 1, 924.

Research output: Contribution to journalArticle

Improving reaction kernel performance in lattice microbes: Particle-wise propensities and run-time generated code

Hallock, M. J. & Luthey-Schulten, Z., Jul 18 2016, Proceedings - 2016 IEEE 30th International Parallel and Distributed Processing Symposium, IPDPS 2016. Institute of Electrical and Electronics Engineers Inc., p. 428-434 7 p. 7529899. (Proceedings - 2016 IEEE 30th International Parallel and Distributed Processing Symposium, IPDPS 2016).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Ribosome biogenesis in replicating cells: Integration of experiment and theory

Earnest, T. M., Cole, J. A., Peterson, J. R., Hallock, M. J., Kuhlman, T. E. & Luthey-Schulten, Z., Oct 1 2016, In : Biopolymers. p. 735-751 17 p.

Research output: Contribution to journalArticle

2015

Analysis of the Resistance Mechanism of a Benzoxaborole Inhibitor Reveals Insight into the Leucyl-tRNA Synthetase Editing Mechanism

Zhao, H., Palencia, A., Seiradake, E., Ghaemi, Z., Cusack, S., Luthey-Schulten, Z. & Martinis, S., Oct 16 2015, In : ACS chemical biology. 10, 10, p. 2277-2285 9 p.

Research output: Contribution to journalArticle

Effects of DNA replication on mRNA noise

Peterson, J. R., Cole, J. A., Fei, J., Ha, T. & Luthey-Schulten, Z. A., Dec 29 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 52, p. 15886-15891 6 p.

Research output: Contribution to journalArticle

Native conformational dynamics of the spliceosomal U1A protein

Guzman, I., Ghaemi, Z., Baranger, A., Luthey-Schulten, Z. & Gruebele, M., Mar 5 2015, In : Journal of Physical Chemistry B. 119, 9, p. 3651-3661 11 p.

Research output: Contribution to journalArticle

Spatially-resolved metabolic cooperativity within dense bacterial colonies

Cole, J. A., Kohler, L., Hedhli, J. & Luthey-Schulten, Z., Mar 18 2015, In : BMC Systems Biology. 9, 1, p. 1-17 17 p., 15.

Research output: Contribution to journalArticle

Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly

Earnest, T. M., Lai, J., Chen, K., Hallock, M. J., Williamson, J. R. & Luthey-Schulten, Z., Sep 19 2015, In : Biophysical journal. 109, 6, p. 1117-1135 19 p.

Research output: Contribution to journalArticle

2014

Protein-guided RNA dynamics during early ribosome assembly

Kim, H., Abeysirigunawarden, S. C., Chen, K., Mayerle, M., Ragunathan, K., Luthey-Schulten, Z., Ha, T. & Woodson, S. A., 2014, In : Nature. 506, 7488, p. 334-338 5 p.

Research output: Contribution to journalArticle

Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations

Hallock, M. J., Stone, J. E., Roberts, E., Fry, C. & Luthey-Schulten, Z., May 2014, In : Parallel Computing. 40, 5-6, p. 86-99 14 p.

Research output: Contribution to journalArticle

Towards a computational model of a methane producing archaeum

Peterson, J. R., Labhsetwar, P., Ellermeier, J. R., Kohler, P. R. A., Jain, A., Ha, T., Metcalf, W. W. & Luthey-Schulten, Z., 2014, In : Archaea. 2014, 898453.

Research output: Contribution to journalArticle

2013

Capture and quality control mechanisms for adenosine-5′-triphosphate binding

Li, L., Martinis, S. A. & Luthey-Schulten, Z., Apr 24 2013, In : Journal of the American Chemical Society. 135, 16, p. 6047-6055 9 p.

Research output: Contribution to journalArticle

DNA looping increases the range of bistability in a stochastic model of the lac genetic switch

Earnest, T. M., Roberts, E., Assaf, M., Dahmen, K. & Luthey-Schulten, Z., Apr 1 2013, In : Physical Biology. 10, 2, 026002.

Research output: Contribution to journalArticle

Extrinsic noise driven phenotype switching in a self-regulating gene

Assaf, M., Roberts, E., Luthey-Schulten, Z. & Goldenfeld, N., Aug 2 2013, In : Physical review letters. 111, 5, p. 58102 1 p., 058102.

Research output: Contribution to journalArticle

Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population

Labhsetwar, P., Cole, J. A., Roberts, E., Price, N. D. & Luthey-Schulten, Z. A., Jan 1 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 34, p. 14006-14011 6 p.

Research output: Contribution to journalArticle

Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation

Roberts, E., Stone, J. E. & Luthey-Schulten, Z., Jan 30 2013, In : Journal of Computational Chemistry. 34, 3, p. 245-255 11 p.

Research output: Contribution to journalArticle

Leucyl-tRNA synthetase editing domain functions as a molecular rheostat to control codon ambiguity in mycoplasma pathogens

Li, L., Palencia, A., Lukk, T., Li, Z., Luthey-Schulten, Z. A., Cusack, S., Martinis, S. A. & Boniecki, M. T., Mar 5 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 10, p. 3817-3822 6 p.

Research output: Contribution to journalArticle

Stochastic Simulations of Cellular Processes: From Single Cells to Colonies

Cole, J., Hallock, M. J., Labhsetwar, P., Peterson, J. R., Stone, J. E. & Luthey-Schulten, Z. A., Dec 1 2013, Computational Systems Biology: From Molecular Mechanisms to Disease: Second Edition. Elsevier Inc., p. 277-293 17 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Structural intermediates and folding events in the early assembly of the ribosomal small subunit

Lai, J., Chen, K. & Luthey-Schulten, Z., Nov 4 2013, In : Journal of Physical Chemistry B. 117, 42, p. 13335-13345 11 p.

Research output: Contribution to journalArticle

2012

Assembly of the five-way junction in the ribosomal small subunit using hybrid MD-Gō simulations

Chen, K., Eargle, J., Lai, J., Kim, H., Abeysirigunawardena, S., Mayerle, M., Woodson, S., Ha, T. & Luthey-Schulten, Z., Jun 14 2012, In : Journal of Physical Chemistry B. 116, 23, p. 6819-6831 13 p.

Research output: Contribution to journalArticle

Exploring residue component contributions to dynamical network models of allostery

Vanwart, A. T., Eargle, J., Luthey-Schulten, Z. & Amaro, R. E., Aug 14 2012, In : Journal of Chemical Theory and Computation. 8, 8, p. 2949-2961 13 p.

Research output: Contribution to journalArticle

Network view: 3D display and analysis of protein ·rNA interaction networks

Eargle, J. & Luthey-Schulten, Z., Nov 2012, In : Bioinformatics. 28, 22, p. 3000-3001 2 p.

Research output: Contribution to journalArticle

2011

Determining the stability of genetic switches: Explicitly accounting for mRNA noise

Assaf, M., Roberts, E. & Luthey-Schulten, Z., Jun 14 2011, In : Physical review letters. 106, 24, 248102.

Research output: Contribution to journalArticle