Zaida Ann Luthey-Schulten

1977 …2019
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Research Output 1977 2019

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

Chromatophores
Energy conversion
Energy Metabolism
Phenotype
Atoms

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

biotin
Streptavidin
Biotin
Geometry
Mechanics

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

Research output: Contribution to journalArticle

Open Access
Metabolism
Genes
Genome
Mycoplasma mycoides
Essential Genes

In Situ Conformational Changes of the Escherichia coli Serine Chemoreceptor in Different Signaling States

Yang, W., Cassidy, C. K., Ames, P., Diebolder, C. A., Schulten, K., Luthey-Schulten, Z. A., Parkinson, J. S. & Briegel, A., Jul 2 2019, In : mBio. 10, 4

Research output: Contribution to journalArticle

Open Access
Serine
Phosphotransferases
Escherichia coli
Electron Microscope Tomography
Glycine

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

Molecular Dynamics Simulation
Molecular dynamics
spectroscopy
Spectroscopy
Proteins
2018

CryoEM-based hybrid modeling approaches for structure determination

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

Research output: Contribution to journalReview article

Cryoelectron Microscopy

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

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

Research output: Contribution to journalArticle

DNA Repair Enzymes
DNA Helicases
Computational Biology
Nucleic Acids
Free energy

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. A., Aug 1 2018, In : IET Systems Biology. 12, 4, p. 170-176 7 p.

Research output: Contribution to journalArticle

Master Equation
Galactose
Yeast
Switch
Yeasts

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

Mechanics
Visualization
Quantum chemistry
Molecular mechanics
Quantum theory

Simulating biological processes: Stochastic physics from whole cells to colonies

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

Research output: Contribution to journalReview article

stochastic processes
physics
cells
biological evolution
ribosomes
2017

Biography of Klaus Schulten

Amaro, R. E., Villa, E. & Luthey-Schulten, Z. A., 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. A., Jun 27 2017, In : Physical Review E. 95, 6, 062418.

Research output: Contribution to journalArticle

Cell Division
ribosomes
proteins
Protein
cell division

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

Electron Microscope Tomography
Electrons
Tomography
Geometry
cells

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

atomic force microscopy
Mechanical stability
Mechanics
Scaffolds
Computer Simulation

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

assembly
RNA
ribonucleic acids
ribosomes
proteins

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

Thor, S., Peterson, J. R. & Luthey-Schulten, Z. A., Jan 1 2017, In : Archaea. 2017, 9763848.

Research output: Contribution to journalReview article

genetically engineered microorganisms
Archaea
Metabolic Networks and Pathways
genome
Genome

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

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

Research output: Contribution to journalArticle

metabolic studies
Escherichia coli
Growth
acetates
Acetates

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

Phenotype
Yeast
yeast
proteomics
phenotype

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

RNA-Binding Proteins
Static Electricity
RNA
Electrostatics
electrostatics

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

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

Research output: Contribution to journalArticle

Peptide Elongation Factor Tu
Transfer RNA
Ribosomes
Hydrolysis
Conformations
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

RNA-Binding Proteins
RNA
proteins
Proteins
Cell signaling

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

Energy efficiency
Visualization
Hardware
Molecular modeling
Mobile computing

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. A., Nov 16 2016, In : BMC genomics. 17, 1, 924.

Research output: Contribution to journalArticle

Methanosarcina
Half-Life
Genome
RNA
Gene Expression

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

Hallock, M. J. & Luthey-Schulten, Z. A., 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

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

Kinetic parameters
Data storage equipment
Graphics processing unit

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

Ribosomes
Cells
Genes
Chromosomes
Experiments
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

Amino Acyl-tRNA Synthetases
Transfer RNA
Tyrosine
Catalytic Domain
RNA, Transfer, Leu

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

DNA Replication
Noise
Messenger RNA
Gene Expression
Gene Dosage

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

Molecular Dynamics Simulation
Tryptophan
Molecular dynamics
Fluorescence
RNA

Spatially-resolved metabolic cooperativity within dense bacterial colonies

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

Research output: Contribution to journalArticle

Metabolism
Escherichia coli
Cell
Direct analogs
Escherichia Coli

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. A., Sep 19 2015, In : Biophysical journal. 109, 6, p. 1117-1135 19 p.

Research output: Contribution to journalArticle

Ribosomes
Large Ribosome Subunits
Small Ribosome Subunits
Escherichia coli
Temperature

Erratum: DNA looping increases the range of bistability in a stochastic model of the lac genetic switch (Physical Biology (2013) 10 (026002))

Earnest, T. M., Roberts, E., Assaf, M., Dahmen, K. & Luthey-Schulten, Z., Apr 2014, In : Physical Biology. 11, 2, 029501.

Research output: Contribution to journalComment/debate

Genetic Models
DNA

Protein-guided RNA dynamics during early ribosome assembly

Kim, H., Abeysirigunawarden, S. C., Chen, K., Mayerle, M., Ragunathan, K., Luthey-Schulten, Z. A., Ha, T. & Woodson, S. A., Feb 13 2014, In : Nature. 506, 7488, p. 334-338 5 p.

Research output: Contribution to journalArticle

Ribosomes
RNA
Fluorescence Resonance Energy Transfer
Proteins
16S Ribosomal RNA

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. A., May 2014, In : Parallel Computing. 40, 5-6, p. 86-99 14 p.

Research output: Contribution to journalArticle

Reaction-diffusion
Diffusion Process
Time Scales
Master Equation
Reaction-diffusion Equations

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. A., 2014, In : Archaea. 2014, 898453.

Research output: Contribution to journalArticle

Archaea
Methane
methane
Methanol
methane production
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

Adenosinetriphosphate
Quality Control
Adenosine
quality control
Quality control

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

Genetic Models
Messenger RNA
DNA
Lac Repressors
Space Simulation

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

phenotype
automatic control
genes
metastable state
gene expression

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

Escherichia coli
Population
Proteins
Glycolysis
Principal Component Analysis

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

Stochastic Simulation
Stochastic Methods
Master Equation
Reaction-diffusion Equations
Simulation Methods

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

Amino Acyl-tRNA Synthetases
Mycoplasma
Codon
Transfer RNA
Peptides

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

Biochemistry
Metabolism
Genes
Gene expression
Escherichia coli

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

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

Research output: Contribution to journalArticle

Small Ribosome Subunits
folding
Molecular dynamics
Carrier Proteins
assembly
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. A., Jun 14 2012, In : Journal of Physical Chemistry B. 116, 23, p. 6819-6831 13 p.

Research output: Contribution to journalArticle

RNA Folding
Small Ribosome Subunits
Molecular Dynamics Simulation
Bacterial Small Ribosome Subunits
Protein Binding

Exploring residue component contributions to dynamical network models of allostery

Vanwart, A. T., Eargle, J., Luthey-Schulten, Z. A. & 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

center of mass
glycerols
Glycerol
imidazoles
proteins

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

Eargle, J. & Luthey-Schulten, Z., Nov 1 2012, In : Bioinformatics. 28, 22, p. 3000-3001 2 p.

Research output: Contribution to journalArticle

Molecular Conformation
Protein Interaction Maps
3D Display
Protein Interaction Networks
Nucleic Acids
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

switches
proteins
gene expression
shift
cells
Amino Acyl-tRNA Synthetases
Mycoplasma
Parasites
Mutation
Amino Acids

Noise contributions in an inducible genetic switch: A whole-cell simulation study

Roberts, E., Magis, A., Ortiz, J. O., Baumeister, W. & Luthey-Schulten, Z., Mar 1 2011, In : PLoS computational biology. 7, 3, e1002010.

Research output: Contribution to journalArticle

Noise
Switch
Switches
Simulation Study
Escherichia coli
2010

Exit strategies for charged tRNA from GluRS

Black Pyrkosz, A., Eargle, J., Sethi, A. & Luthey-Schulten, Z. A., Apr 1 2010, In : Journal of Molecular Biology. 397, 5, p. 1350-1371 22 p.

Research output: Contribution to journalArticle

Transfer RNA
Adenosine Monophosphate
Amino Acyl-tRNA Synthetases
Aminoacylation
Ammonium Compounds