Benjamin R. Gilbert, Zane R. Thornburg, Troy A. Brier, Jan A. Stevens, Fabian Grünewald, John E. Stone, Siewert J. Marrink, Zaida Luthey-Schulten, Dynamics of chromsome organization in a minimal bacterial cell, Frontiers in Cell and Developmental Biology, 2023, https://doi.org/10.3389/fchem.2023.1214962
Jan A. Stevens, Fabian Grünewald, P.A. Marco van Tilburg, Melanie Konig, Benjamin R. Gilbert, Troy A. Brier, Zane R. Thornburg, Zaida Luthey-Schulten, and Siewert J. Marrink, Molecular dynamics simulation of an entire cell, Frontiers in Chemistry, 2023, https://doi.org/10.3389/fchem.2023.1106495
David M. Bianchi, James F. Pelletier, Clyde H. Hutchison III, John I. Glass, Zaida Luthey-Schulten, Towards the Complete Functional Characterization of a Minimal Bacterial Proteome, Journal of Physical Chemistry B, 2022, https://doi.org/10.1021/acs.jpcb.2c04188
A database of Associated AlphaFold2 Predictions for all JCVI-syn3A protein-coding genes as well as functional summary spreadsheet for the above publication is available at: Syn3A AF2 Predictions
Zaida Luthey-Schulten, Zane R. Thornburg, Benjamin R. Gilbert, Integrating Cellular and Molecular Structures and Dynamics into Whole-Cell Models, Current Opinion in Structural Biology, 2022, https://doi.org/10.1016/j.sbi.2022.102392
Zane R. Thornburg, David M. Bianchi, Troy A. Brier, Benjamin R. Gilbert, Tyler M. Earnest, Marcelo C.R. Melo, Nataliya Safronova, James P. Sáenz, András T. Cook, Kim S. Wise, Clyde A. Hutchison III, Hamilton O. Smith, John I. Glass, Zaida Luthey-Schulten, Fundamental behaviors emerge from simulations of a living minimal cell, Cell, 2022, https://doi.org/10.1016/j.cell.2021.12.025
A "News at a Glance" research highlight of our Minimal Cell Simulations "Computer mimics ‘minimal’ cell" by Science Magazine is available at the following: Computer Mimics a Minimal Cell, Take a look!.
The National Science Foundation (NSF) Public Affairs Bureau has published a research highlight of our Minimal Cell Simulations "Researchers simulate behavior of living 'minimal cell' in three dimensions" which is available at: Simulations offer insight into fundamental principles of life.
The New Yorker Magazine has published a research highlight of our Minimal Cell Simulations "A Journey to the Center of Our Cells" which is available at: Biologists are discovering the true nature of cells—and learning to build their own..
Highlight by Nature Methods: Lin Tang, Simulating a whole cell, DOI: https://doi.org/10.1038/s41592-022-01429-y
Zaida Luthey-Schulten, Integrating experiments, theory and simulations into whole-cell models, Nature Methods, 2021, https://doi.org/10.1038/s41592-021-01150-2
Benjamin R. Gilbert, Zane R. Thornburg, Vinson Lam, Fatema-Zahra M. Rashid, John I. Glass, Elizabeth Villa, Remus T. Dame, Zaida Ann Luthey-Schulten, Generating Chromosome Geometries in a Minimal Cell from Cryo-Electron Tomograms and Chromosome Conformation Capture Maps, Frontiers in Molecular Biosciences, 2021, https://doi.org/10.3389/fmolb.2021.644133
Angela M. Barragan, Alexander V. Soudackov, Zaida Luthey-Schulten, Sharon Hammes-Schiffer, Klaus Schulten and Ilia A. Solov'yov, Theoretical Description of the Primary Proton-Coupled Electron Transfer Reaction in the Cytochrome bc1 Complex, J. Am. Chem. Soc., 2021, https://doi.org/10.1021/jacs.0c07799
M. Sener, S. Levy, JE Stone, AJ Christensen, B. Israelewitz, R. Patterson, K. Borkiewicz, J. Carpenter, C Neil Hunter, Zaida Luthey-Schulten, Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales, Parallel Computing, 2020, https://doi.org/10.1016/j.parco.2020.102698
David M. Bianchi, Troy A. Brier, Anustup Poddar, Muhammad S. Azam, Carin K. Vanderpool, Taekjip Ha, and Zaida Luthey-Schulten, Stochastic Analysis Demonstrates the Dual Role of Hfq in Chaperoning E. coli Sugar Shock Response, Special Issue: Experiments and Simulations: A Pas de Deux to Unravel Biological Function Frontiers in Molecular Biosciences, 2020, https://doi.org/10.3389/fmolb.2020.593826
Marcelo C.R. Melo, Rafael C. Bernardi, Cesar de la Fuente-Nunez and Zaida Luthey-Schulten, Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories, J. Chem. Phys., 2020, https://doi.org/10.1063/5.0018980
James C. Phillips, David J. Hardy, Julio D.C. Maia, John E. Stone, Joao V. Ribeiro, Rafael C. Bernardi, Ronak Buch, Giacomo Fiorin, Jerome Henin, Wei Jiang, Ryan McGreevy, Marcelo C.R. Melo, Brian K. Radak, Robert D. Skeel, Abhishek Singharoy, Yi Wang, Benoit Roux, Aleksei Aksimentiev, Zaida Luthey-Schulten, Laxmikant V. Kale, Klaus Schulten, Christophe Chipot, and Emad Tajkhorshid, Scalable molecular dynamics on CPU and GPU architectures with NAMD, J. Chem. Phys., 2020, https://doi.org/10.1063/5.0014475
Zhaleh Ghaemi, Joseph R. Peterson, Martin Gruebele, and Zaida Luthey-Schulten, An in-silico human cell model reveals the influence of organization on RNA splicing, PLOS Computational Biology, 2020, PLOS Computational Biology, 2020, doi:10.1371/journal.pcbi.1007717
To install Lattice Microbes v2.3 to build and simulate the HeLa cell model given in the publication above: please follow the HeLa Cell Model Installation Guide and the LM Linux Installation Guide. and use the LM_2.3_dependency_sources as mentioned in the Installation Guide.
C. Keith Cassidy, Benjamin A. Himes, Dapeng Sun, Jun Ma, Gongpu Chao, John S. Parkinson, Phillip J. Stansfeld, Zaida Luthey-Schulten and Peijun Zhang, Structure and dynamics of the E. coli chemotaxis core signalling complex by cryo-electron tomography and molecular simulations Communications Biology, 3 (24), 2020, https://doi.org/10.1038/s42003-019-0748-0
Z. Thornburg, Marcelo Melo, David Bianchi, Troy Brier, Cole Crotty, Marian Breuer, Hamilton Smith, Clyde Hutchison, John Glass, and Zaida Luthey-Schulten, Modelling the genetic information processes in a minimal cell, Frontiers in Molecular Biosciences, 2019 https://doi.org/10.3389/fmolb.2019.00130
Wen Yang, C. Keith Cassidy, Peter Ames, Christoph A. Diebolder, Klaus Schulten, Zaida Luthey-Schulten, John S. Parkinson, Ariane Briegel, In Situ conformational changes of the Escherichia coli serine chemoreceptor in different signaling states, mBio, 2019 https://doi.org/10.1128/mBio.00973-19
Rafael C. Bernardi*,Ellis Durner, Constantin Schoeler, Klara H. Malinowska, Bruna G. Carvalho, Edward A. Bayer, Zaida Luthey-Schulten, Hermann E. Gaub, Michael A. Nash, Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy. J. Am. Chem. Soc.20191413714752-14763 Publication Date:August 29, 2019 https://doi.org/10.1021/jacs.9b06776
C. MacGregor-Chatwin, P. J. Jackson, M. Sener, J. W. Chidgey, A. Hitchcock, P. Qian, G. E. Mayneord , M. P. Johnson, Z. Luthey-Schulten, M. J. Dickman, D. J. Scanlan and C. N. Hunter, Membrane organisation of photosystem I complexes in the most abundant phototroph on Earth, Nature Plants 2019. doi.org/10.1038/s41477-019-0475-z
A. Singharoy, C. Maffeo, K.H. Delgado-Magnero, D. J. K. Swainsbury, M.Sener, U. Kleinekathofer, B. Isralewitz, I. Teo, D. Chandler, J. W. Vant, J. E. Stone, J. Phillips, T. V. Pogorelov, M. I. Mallus, C. Chipot, Z. Luthey-Schulten, P. Tieleman, C. N. Hunt, Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism, Cell, 2019 https://doi.org/10.1016/j.cell.2019.10.021
Steffen M. Sedlak, Leonard C. Schendel, Marcelo C. R. Melo, Diana A. Pippig, Zaida Luthey-Schulten, Hermann E. Gaub, Rafael C. Bernardi; Direction Matters: Monovalent Streptavidin/Biotin Complex under Load; Nano Letters, 19 (6), 3415-3421, 2019 (cover-article)
M. Breuer, T. M. Earnest, C. Merryman, K. S. Wise, L. Sun, M. R. Lynott, C. A. Hutchison III, H. O. Smith, J. D. Lapek Jr., D. J. Gonzalez,
V. de Crecy-Lagard, D. Haas, A. D. Hanson, P. Labhsetwar, J. I. Glass, Z. Luthey-Schulten
Essential Metabolism for a Minimal Cell eLife, e36842, 2019,doi.org/10.7554/eLife.36842.001
Commentaries:
Minimal Cell, Maximal Knowledge
Synthetic Organisms Simplify Biology
D. M. Bianchi, J. R. Peterson, T. M. Earnest, M. J. Hallock, and Z. Luthey-Schulten
Hybrid CME-ODE Method for Efficient Simulation of the Galactose Switch in Yeast
IET Systems Biology, 2018, 12 (4):170, doi:10.1049/iet-syb.2017.0070.
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, and Z. Luthey-Schulten
NAMD goes quantum: An integrative suite for hybrid simulations
Nature Methods, 2018, online, doi:10.1038/nmeth.4638.
W. Ma, K. D. Whitley, Y. R. Chemla , Z. Luthey-Schulten, K. Schulten
Free energy simulations reveal molecular mechanism for functional switch of a DNA helicase
eLife, 2018, online, doi:10.7554/eLife.34186.
T. M. Earnest, J. A. Cole, and Z. Luthey-Schulten.
Simulating Biological Processes: Stochastic Physics from Whole Cells to Colonies
Reports on Progress in Physics, 2018, doi:10.1088/1361-6633/aaae2c
Tobias Verdorfer, R. C. Bernardi, A. Meinhold, W. Ott, Z. Luthey-Schulten, M. A. Nash, and H. E. Gaub Combining in Vitro and in Silico Single-Molecule Force Spectroscopy to Characterize and Tune Cellulosomal Scaffoldin Mechanics J. Am. Chem. Soc.,2017, 139 (49), doi: 10.1021/jacs.7b07574
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
J. Lai, Z. Ghaemi, Z. Luthey-Schulten
Conformational change in Elongation factor-Tu involves separation of its domains
Biochem., 2017, Accepted., doi: 10.1021/acs.biochem.7b00591
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
Abhishek Singharoy and Christophe Chipot
Methodology for the simulation of molecular motors at different scales
Journal of Physical
Chemistry B, 121:3502-3514, 2017. (PMC: PMC5518690) dio: 10.1021/acs.jpcb.6b09350
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
J.R. Peterson*, J.A. Cole*, J. Fei, T.J. Ha and Z. Luthey-Schulten
Effects of DNA Replication on mRNA Noise
Proc. Nat. Acad. Sci., 2015, Nov 11, 112(52): 15886-15891 doi:10.1073/pnas.1516246112
T. M. Earnest, J. Lai, K. Chen, M. J. Hallock, J. R. Williamson, and Z. Luthey-Schulten
Towards a whole-cell model of ribosome biogenesis: Kinetic modeling of SSU assembly
Biophysical Journal, 2015, Sep 15, 109(6): 1117-35 doi:10.1016/j.bpj.2015.07.030
Files for the simulation can be found: here
J. A. Cole, L. Kohler L, J. Hedhli, Z. Luthey-Schulten
Spatially-Resolved Metabolic Cooperativity Within Dense Bacterial Colonies
BMC Syst Biol, 2015, 9(15), doi:10.1186/s12918-015-0155-1
H. Zhao, A. Palencia, E. Seiradake, Z. Ghaemi, S. Cusack, Z. Luthey-Schulten, S. Martinis
Analysis of the Resistance Mechanism of a Benzoxaborole Inhibitor Reveals Insight into the Leucyl-tRNA Synthetase Editing Mechanism
ACS Chem. Biol., 2015, 10(10): 2277-2285, doi:10.1021/acschembio.5b00291
I. Guzman, Z. Ghaemi, A. Baranger, Z. Luthey-Schulten, M. Gruebele
Native Conformational Dynamics of the Spliceosomal U1A Protein
J. Phys. Chem. B, 2015, 119 (9): 3651-3661, doi:10.1021/jp511760m
J. Cole, Z. Luthey-Schulten
Whole Cell Modeling: From Single Cells to Colonies
Isr. J. Chem., 2014, 54(8-9): 1219--1229, doi: 10.1002/ijch.201300147
Hajin Kim, Sanjaya C. Abeysirigunawarden, Ke Chen, Megan Mayerle, Kaushik Ragunathan, Zaida Luthey-Schulten, Taekjip Ha & Sarah A. Woodson
Protein-guided RNA dynamics during early ribosome assembly
Nature, 2014, 506, 7488, 334--338, http://dx.doi.org/10.1038/nature13039
M. J. Hallock, J. E. Stone, E. Roberts, C. Fry, Z. Luthey-Schulten
Simulation of reaction diffusion processes over biologically-relevant size and time scales using multi-GPU workstations
Parallel Comput. 2014, 40, 86-99, doi: 10.1016/j.parco.2014.03.009.
J.R. Peterson, P. Labhsetwar, J.R. Ellermeier, P.R.A.Kohler, A. Jain, T. Ha, W.W. Metcalf, Z. Luthey-Schulten
Towards a Computational Model of a Methane Producing Archaeum
Archaea, Article ID 898453, 18 pages, 2014, http://dx.doi.org/10.1155/2014/898453
J. Cole, M. J. Hallock, P. Labhsetwar, J. R. Peterson, J. E. Stone, Z. Luthey-Schulten
Stochastic Simulations of Cellular Processes: From Single Cells to Colonies
in Computational Systems Biology 2nd Edition: From Molecular Mechanisms to Disease, Eds. Kriete and Eils, Elsevier, 2014.
J.R. Peterson, M.J. Hallock, J.A. Cole, and Z. Luthey-Schulten
A Problem Solving Environment for Stochastic Biological Simulations
PyHPC '13: Proceedings of the 3rd Workshop on Python for High-Performance and Scientific Computing, 2013, DOI: 10.13140/2.1.3207.7440
J. Lai, K. Chen, and Z. Luthey-Schulten
Structural Intermediates and Folding Events in the Early Assembly of the Ribosomal Small Subunit
J. Phys. Chem. B, 117(42): 13335--13345, 2013
P. Labhsetwar, J.A. Cole, E. Roberts, N.D. Price, Z. Luthey-Schulten
Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population
Proc. Nat. Acad. Sci., 110(34):14006-11, 2013, doi: 10.1073/pnas.1222569110
M. Hartmann
Stochastic simulation of reaction-diffusion systems
Master's Thesis LMU Munich, 2013
M. Assaf, E. Roberts, Z. Luthey-Schulten, N. Goldenfeld
Extrensic noise driven phenotype switching in a self-regulating gene
Phys. Rev. Lett., 111(5), e058102,2013
L. Li, S. A. Martinis, Z. Luthey-Schulten
Capture and quality control mechanisms for adenosine-5'-triphosphate binding
J. Am. Chem. Soc., 135(16), 6047-6055,2013
E. Roberts, J. E. Stone, and Z. Luthey-Schulten
Lattice microbes: high-performance stochastic simulation method for the reaction-diffusion master equation
J. Comput. Chem., 34(3), 245-55, 2013
T. Earnest, E. Roberts, M. Assaf, K. Dahmen, and Z. Luthey-Schulten
DNA looping increases range of bistability in a stochastic model of the lac genetic switch
Phys. Biol. 10 (2013) 026002
A. VanWart, J. Eargle, Z. Luthey-Schulten, and R. Amaro
Exploring residue component contributions to dynamical network models of allostery
J. Chem. Theory Comp. 8(8),2949-2961, 2012
J. Eargle and Z. Luthey-Schulten
NetworkView: 3D display and analysis of dynamic structure networks
Bioinformatics, 28(22), 3000-1, 2012
K. Chen, J. Eargle, J. Lai, H, Kim, T. Ha, T. Abeysirigunawardena, M. Mayerle, S. Woodson, and Z. Luthey-Schulten
Assembly of the fiveway junction in the ribosomal small subunit using hybrid MD/Go simulation
Journal of Physical Chemistry B: Harold A. Scheraga Festschrift, 116:23,6819-6831, 2012
J. Eargle and Z. A. Luthey-Schulten
Chapter 11: Simulating Dynamics in RNA-Protein Complexes
In RNA 3D Structure Analysis and Prediction
N. Leontis and E. Westhof (editors)
Nucleic Acids and Molecular Biology 27, DOI 10.1007/978-3-642-25740-7_11, Springer-Verlag Berlin Heidelberg 2012
L. Li, M. T. Boniecki, J. D. Jaffe, B. S. Imai, P. M. Yau, Z. Luthey-Schulten, and S. A. Martinis
Naturally occurring aminoacyl-tRNA synthetases editing-domain mutations that cause mistranslation in Mycoplasma parasites
Proc. Nat. Acad. Sci., 109(9),9378-9383, 2011
M. Assaf, E. Roberts, and Z. Luthey-Schulten
Determining the Stability of Genetic Switches: Explicitly Accounting for mRNA Noise
Phys. Rev. Lett., 106, 248102, 2011
E. Roberts, A. Magis, J.O. Ortiz, W. Baumeister, and Z. Luthey-Schulten
Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study
PLoS. Comput. Biol., 7(3):e1002010, 2011
K. Chen, J. Eargle, K. Sarkar, M. Gruebele, and Z. Luthey-Schulten
Functional role of ribosomal signatures
Biophys. J., 99(12):3930-3940, 2010
L. Trabuco, E. Schreiner, J. Eargle, P. Cornish, T.J. Ha, Z. Luthey-Schulten, and K. Schulten
The role of L1 stalk:tRNA interaction in the ribosome elongation cycle
J. Mol. Biol., 402:741-760, 2010
A.B. Pyrkosz, J. Eargle, A. Sethi, and Z. Luthey-Schulten
Exit strategies for charged tRNA from GluRS
J. Mol. Biol., 397:1350-1371, 2010
- Structure file for CysRS:tRNA(Cys):Glu-AMP model (pdb).
- Figure of CysRS:tRNA(Cys):Glu-AMP model (pdf).
D. Mathew, and Z. Luthey-Schulten
Influence of Montmorillonite on Nucleotide Oligomerization Reactions: A Molecular Dynamics Study
Ori. Life Evol. Biosp., 40:303-317, 2010
Animation of mononumcletide interaction with trinucleotide in montmorillonite clay (mpg).
R.W. Alexander, J. Eargle, and Z. Luthey-Schulten
Experimental and computational analysis of tRNA dynamics
FEBS Letters, 584(2):376-386, 2010
T. Butler, N. Goldenfeld, D. Mathew, and Z. Luthey-Schulten
Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement
Phys. Rev. E, 79:060901, 2009
A. Sethi, J. Eargle, A. Black, and Z. Luthey-Schulten
Dynamical Networks in tRNA:protein complexes
Proc. Natl. Acad. Sci. U S A, 106(16):6620-6625, 2009
Supplementary Material
E. Roberts, J.E. Stone, L. Sepulveda, W.-M.W. Hwu, and Z. Luthey-Schulten
Long time-scale simulations of in vivo diffusion using GPU hardware
Parallel & Distributed Processing, 2009, IPDPS 2009. IEEE International Symposium on, vol., no., pp.1,8,23-29 May 2009 doi: 10.1109/IPDPS.2009.5160930
K. Chen, E. Roberts, and Z. Luthey-Schulten
Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4
BMC Evol. Biol., 9:179, 2009
E. Roberts, A. Sethi, J. Montoya, C.R. Woese, and Z. Luthey-Schulten
Molecular signatures of ribosomal evolution
Proc. Natl. Acad. Sci. U S A, 105(37):13953-8, 2008
Supplementary Material
J. Eargle, A. Black, A. Sethi, L. Trabuco, and Z. Luthey-Schulten
Dynamics of recognition between tRNA and Elongation Factor Tu
J. Mol. Biol., 377(5):1382-405, 2008
- Parameter file for modified nucleosides (inp).
- Topology file for modified nucleosides (inp).
D.C. Mathew and Z. Luthey-Schulten
On the physical basis of the amino acid polar requirement
J Mol Evol 66(5):519-28, 2008
T.V. Pogorelov, F. Autenrieth, E. Roberts, and Z. Luthey-Schulten
Cytochrome c2 exit strategy: dissociation studies and evolutionary implications
J Phys Chem B, 111(3):618-634, 2007
R. Amaro, A. Sethi, R. Myers, Jo V Davisson, and Z. Luthey-Schulten
A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase
Biochemistry, 46(8):2156-2173, 2007
E. Roberts, J. Eargle, D. Wright, and Z. Luthey-Schulten
MultiSeq: Unifying sequence and structure data for evolutionary analysis
BMC Bioinformatics, 7:382, 2006
J. Eargle and Z. Luthey-Schulten
Visualizing the dual space of biological molecules
Comput Biol Chem, 30:219-226, 2006
J. Eargle, D. Wright, and Z. Luthey-Schulten
Multiple alignment of protein structures and sequences for VMD
Bioinformatics, 22(4):504-506, 2006
P. O'Donoghue, A. Sethi, C. R. Woese, and Z. Luthey-Schulten
The evolutionary history of Cys-tRNA(Cys) formation
Proc. Natl. Acad. Sci. U S A, 102(52):19003-19008, 2005
Supplementary Material
- Poster based on this work (PDF)
- M. jannaschii SepRS Theoretical Model (PDB).
- M. jannaschii SepCysS Theoretical Models: apo monomer (PDB), dimer with substrates (PDB).
- Parameter file for o-phosphoserine(SEP)-adenosine-5'-monophosphate and o-phosphoserine attached to cytosine from the CCA end of the tRNA (inp).
- Topology file for o-phosphoserine(SEP)-adenosine-5'-monophosphate and o-phosphoserine attached to cytosine from the CCA end of the tRNA (inp).
R.S. Meyers, R. Amaro, Z. Luthey-Schulten, and V.J. Davisson
Reaction Coupling through Interdomain Contacts in Imidazole Glycerol Phosphate Synthase
Biochemistry, 13; 44(36):11974-85, 2005
R. Amaro, R.S. Myers, Z. Luthey-Schulten, and V.J. Davisson
Structural elements in IGP synthase exclude water to optimize ammonia transfer
Biophys J., 89(1):475-87, 2005
A. Sethi, P. O'Donoghue, and Z. Luthey-Schulten
Evolutionary profiles from the QR factorization of multiple sequence alignments
Proc. Natl. Acad. Sci. USA, 102, 4045-4050, 2005.
Supplementary Material
P. O'Donoghue and Z. Luthey-Schulten
Evolutionary profiles derived from the QR factorization of multiple structural alignments gives an economy of information
J. Mol. Biol., 346, 875-894, 2005
Authenrieth F., Tajkhorshid E., Schulten K., and Luthey-Schulten Z.
Role of water in transient cytochrome c2 docking
Journal of Physical Chemistry B, 108, 20376-20387, 2004
Supplementary Material
- Behavior of water inside the hydrophobic pocket (mpg).
- Electrostatic interactions during pulling of cyt to 10A (mpg).
- Heme parameters in CHARMM27 format (inp).
- Heme topology in CHARMM27 format (inp).
Amaro R. and Luthey-Schulten Z.,
Molecular dynamics simulations of substrate channeling through an alpha-beta barrel protein,
Chemical Physics, 307, 147-155, 2004.
Authenrieth F., Tajkhorshid E., Baudry J., and Luthey-Schulten Z.,
Classical force field parameters for the heme prosthetic group of cytochrome c,
Journal of Computational Chemistry, 25: 1613-1622, 2004.
Supplementary Material
- RESP charges (pdf).
- HF generated Mulliken charges (pdf).
- Heme parameters in CHARMM27 format (inp).
- Heme topology in CHARMM27 format (inp).
- Topology and parameter zip file (zip).
Pogorelov T.V. and Luthey-Schulten Z.,
Variations in the fast folding rates of the lambda-repressor: a hybrid molecular dynamics study,
Biophysical Journal, 87: 207-214, 2004.
Papoian G. A., Ulander J., Eastwood M.P., Luthey-Schulten Z., and Wolynes P.G.
Water in protein structure prediction,
Proc. Natl. Acad. Sci. USA, 101(10):3352-3357, 2004.
Fujitsuka Y., Takada S., Luthey-Schulten Z.A., and Wolynes P.G.
Optimizing physical energy functions for protein folding,
Proteins: Structure, Function, & Bioinformatics. 54(1):88-103, 2004.
O'Donoghue P. and Luthey-Schulten Z.
On the Evolution of Structure in the Aminoacyl-tRNA Synthetases.
Microbiol. Mol. Biol. Rev. 67:550-573, 2003.
Supplementary Material.
Amaro R., Tajkhorshid E., and Luthey-Schulten Z.,
Developing an energy landscape for the novel function of a (beta/alpha)(8) barrel:
Ammonia conduction through HisF.
Proc. Natl. Acad. Sci. USA, 100(13):7599-7604, 2003.
Eastwood MP, Hardin C, Luthey-Schulten Z, and Wolynes PG.
Statistical mechanical refinement of protein structure prediction schemes II: Mayer cluster expansion approach.
J. Chem. Phys. 118(18): 8500-8512, 2003.
Wang J., Luthey-Schulten Z., and Suslick K.
Is the olfactory receptor a metalloprotein?
Proc. Natl. Acad. Sci. USA, 100(6): 3035-3039, 2003.
Hardin C., Eastwood M.P., Prentiss M. C., Luthey-Schulten Z., and Wolynes P.G.
Associative memory Hamiltonians for structure prediction without homology: alpha/beta proteins,
Proc. Natl. Acad. Sci. USA, 100(4): 1679-1684, 2003.
NSF-NIH Report 2003: Accelerating Mathematical-Biological Linkages
Eastwood MP, Hardin C, Luthey-Schulten Z, and Wolynes PG.
Statistical mechanical refinement of protein structure prediction schemes: Cumulant expansion approach.
Journal of Chemical Physics. 117(9):4602-4615, 2002.
Hardin C., Pogorelov TV, Luthey-Schulten Z.
Ab initio protein structure prediction.
Curr. Opin. Struct. Biol. 12(2):176-181, 2002.
Hardin C, Eastwood MP, Prentiss M, Luthey-Schulten Z, and Wolynes PG.
Folding funnels: The key to robust protein structure prediction.
J. Comp. Chem. 23(1):138-146, 2002.
M. Eastwood, C. Hardin, Z. Luthey-Schulten, and P. Wolynes.
Evaluating protein structure-prediction schemes using energy landscape theory.
IBM J. Res. & Dev. 45: 475-497, 2001.
P. O'Donoghue, R. E. Amaro, and Z. Luthey-Schulten
On the Structure of HisH: Protein Structure Prediction in the Context of Structural and Functional Genomics
J. Struct. Biol. 134: 257-268, 2001.
C. Hardin, M. Eastwood, Z. Luthey-Schulten and P. G. Wolynes
"Associative Memory Hamiltonians for Structure Prediction Homology: Alpha-helical Proteins"
Proc. Natl. Acad. Sci. USA, 97, 14235, 2000.
P.O'Donoghue and Z. Luthey-Schulten
"Barriers to Forced Transitions in Polysaccharides"
J. Phys. Chem. B, 104, 10398, 2000.
S. Takada, Z. Luthey-Schulten, and P.G. Wolynes
"Folding Dynamics with Nonadditive Forces: A Simulation Study of a Designed Helical Protein and a Random Heteropolyme"
J. Chem. Phys. 110, 11616-11629, 1999.
K. Koretke, Z. Luthey-Schulten, P. G. Wolynes
"Self-Consistently Optimized Energy Functions for Protein Structure Prediction by Molecular Dynamics"
Proc. Natl. Acad. Sci. USA, 95, 2932, 1998.
A. Panchenko, Z. Luthey-Schulten, R. Cole, P.G. Wolynes
"The Foldon Universe: A Survey of Structural Similarity and Self-Recognition of Independently Folding Units"
J. Mol. Biol., 272, 95-105, 1997.
J. Onuchic, Z. Luthey-Schulten, P. G. Wolynes
"Theory of Protein Folding: The Energy Landscape Perspective"
Ann. Rev. Phys. Chem. 48, 539-600, 1997.
A. Panchenko, Z. Luthey-Schulten, P. G Wolynes
"Foldons, Protein Structural Modules, and Exons",
Proc. Natl. Acad. Sci. USA, 93, 2008, 1996.
K. Koretke, Z. Luthey-Schulten, P. G. Wolynes
"Self-Consistently Optimized Statistical Mechanical Energy Functions for Sequence-Structure Alignment"
Protein Science, 5, 1043-1059, 1996.
J. Onuchic, P. G. Wolynes, Z. Luthey-Schulten, and N. Socci
"Towards an Outline of the Topography of a Realistic Protein Folding Funnel"
Proc. Natl. Acad. Sci. USA, 92, 3626-3630, 1995.
Z. Luthey-Schulten, B. Ramierez, and P. G. Wolynes
"Helix-Coil, Liquid Crystal, and Spin Glass Transitions of a Collapsed Heteropolymer"
J. Phys. Chem. 99, 2177, 1995.
R. Goldstein, Z. Luthey-Schulten, P.G. Wolynes
"Protein Tertiary Structure Recognition using Optimized Hamiltonians with Local Interactions"
Proc. Natl. Acad. Sci. USA, 89, 9029-9033, 1992.
R. Goldstein, Z. Luthey-Schulten, P. G. Wolynes
"Optimal Protein Folding Codes from Spin Glass Theory"
Proc. Natl. Acad. Sci. USA, 89, 4918-4922, 1992.
K. Schulten, A. Bruenger, W. Nadler, and Z. Schulten
"Generalized Moment Description of Brownian Dynamics in Biological Systems"
Synergetics - From Microscopic to Macroscopic Order, pp. 80-89, E. Frehland (editor), Springer Verlag, 1984.
K. Schulten, Z. Schulten, and A. Szabo
"Dynamics of Reactions Involving Diffusive Barrier Crossing"
Journal of Chemical Physics. 74, 4426-4432, 1981.