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• Article

  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 journal › Article › peer-review

  Open Access

  • RNA splicing
  • Speckle
  • RNA Splicing
  • RNA
  • Messenger RNA

• 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 journal › Article › peer-review

  Open Access

  • Chromatophores
  • Energy Metabolism
  • Atoms
  • Energy conversion
  • Proteobacteria

• 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 journal › Article › peer-review

  • Protein
  • Cell Division
  • Transcription
  • Gene Expression
  • proteins

• 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 journal › Article › peer-review

  • Electrons
  • Tomography
  • Geometry
  • cells
  • electrons

• 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 journal › Article › peer-review

  • Single Molecule Imaging
  • cohesins
  • Mechanical stability
  • Atomic force microscopy
  • Scaffolds

• 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 journal › Article › peer-review

  Open Access

  • Electron Microscope Tomography
  • Molecular Models
  • Escherichia coli
  • Molecular Dynamics Simulation
  • Bacteria

• 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 journal › Article › peer-review

  • Biotin
  • biotin-streptavidin complex
  • biotin
  • Streptavidin
  • Direction compound

• 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., Crécy-Lagard, V. D., Haas, D., Hanson, A. D., Labhsetwar, P., Glass, J. I. & Luthey-Schulten, Z., 2019, In: eLife. 8, p. 1-75 75 p., e36842.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Metabolism
  • Genes
  • Genome
  • Mycoplasma mycoides
  • Essential Genes

• 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 journal › Article › peer-review

  • RNA
  • RNA-Binding Proteins
  • Proteins
  • proteins
  • U1A protein

• 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 journal › Article › peer-review

  • assembly
  • proteins
  • Forster resonance energy transfer
  • ribonucleic acids
  • ribosomes

• Generalized correlation-based dynamical network analysis: A new high-performance approach for identifying allosteric communications in molecular dynamics trajectories

  Melo, M. C. R., Bernardi, R. C., De La Fuente-Nunez, C. & Luthey-Schulten, Z., Oct 7 2020, In: The Journal of Chemical Physics. 153, 13, 134104.

  Research output: Contribution to journal › Article › peer-review

  • network analysis
  • Molecular dynamics
  • Electric network analysis
  • Orotidine-5'-Phosphate Decarboxylase
  • communication

• 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 journal › Article › peer-review

  • Methanosarcina
  • Half-Life
  • RNA
  • Genome
  • Gene Expression

• 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 journal › Article › peer-review

  Open Access

  • Phosphotransferases
  • Escherichia coli
  • Glycine
  • Electron Microscope Tomography
  • serine receptor

• 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 journal › Article › peer-review

  Open Access

  • Genetic Phenomena
  • Genes
  • Kinetics
  • Genome
  • Electronic Data Processing

• 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 journal › Article › peer-review

  • Single Molecule Imaging
  • Molecular Dynamics Simulation
  • Molecular dynamics
  • Spectroscopy
  • Molecules

• 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 journal › Article › peer-review

  • autotrophs
  • photosystem I
  • Prochlorococcus
  • thylakoids
  • photosystem II

• 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 journal › Article › peer-review

  • Escherichia coli
  • metabolic studies
  • geometry
  • Growth
  • 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 journal › Article › peer-review

  • Yeast
  • Phenotype
  • phenotype
  • Proteomics
  • yeast

• 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 journal › Article › peer-review

  • Ribosomes
  • Messenger RNA
  • Cells
  • Genes
  • Escherichia coli

• 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 journal › Article › peer-review

  • RNA
  • RNA-Binding Proteins
  • Electrostatics
  • Proteins
  • Binding sites

• Scalable molecular dynamics on CPU and GPU architectures with NAMD

  Phillips, J. C., Hardy, D. J., Maia, J. D. C., Stone, J. E., Ribeiro, J. V., Bernardi, R. C., Buch, R., Fiorin, G., Hénin, J., Jiang, W., McGreevy, R., Melo, M. C. R., Radak, B. K., Skeel, R. D., Singharoy, A., Wang, Y., Roux, B., Aksimentiev, A., Luthey-Schulten, Z., Kalé, L. V. & 3 others, Schulten, K., Chipot, C. & Tajkhorshid, E., Jul 28 2020, In: Journal of Chemical Physics. 153, 4, 044130.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Molecular dynamics
  • Graphics processing unit
  • Program processors
  • molecular dynamics
  • Sampling

• 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 journal › Article › peer-review

  Open Access

  • Electron Microscope Tomography
  • Histidine Kinase
  • processing chemistry
  • histidine kinase
  • tomography

• 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 journal › Article › peer-review

  • Peptide Elongation Factor Tu
  • Hydrolysis
  • Transfer RNA
  • Ribosomes
  • Conformations
• Conference contribution

  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 proceeding › Conference contribution

  • Graphics processing unit
  • Computer hardware
  • Mobile computing
  • Energy efficiency
  • Visualization

• 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 proceeding › Conference contribution

  • Kinetic parameters
  • Graphics processing unit
  • Data storage equipment
• Editorial

  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 journal › Editorial › peer-review
• Review article

  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 journal › Review article › peer-review

  • genetically engineered microorganisms
  • Archaea
  • Metabolic Networks and Pathways
  • genome
  • Genome