Papers – old/do not use

2017

“Unlocking Reactivity of TrpB: A General Biocatalytic Platform for Synthesis of Tryptophan Analogues” D. K. Romney, J. Murciano-Calles, J. E. Wehrmuller, F. H. Arnold. Journal of the American Chemical Society, online publication July 14, 2017. doi:10.1021/jacs.7b05007   “Enantioselective Total Synthesis of Nigelladine A via Late-Stage C-H Oxidation Enabled by an Engineered P450 Enzyme” S. A. Loskot, D. K. Romney, F. H. Arnold, B. M. Stoltz. Journal of the American Chemical Society, online publication July 19, 2017. doi: 10.1021/jacs.7b05196   “Exploiting and Engineering Hemoproteins for Abiological Carbene and Nitrene Transfer Reactions” O. F. Brandenberg, R. Fasan, F. H. Arnold. Current Opinion in Biotechnology 47, 102-111 (2017). doi.org/10.1016/j.copbio.2017.06.005   Design and Evolution of Enzymes for Non-natural Chemistry”  S. C. Hammer, A. M. Knight, F. H. Arnold. Current Opinion in Green Sustainable Chemistry 7, 23-30 (2017). doi.org/10.1016/j.cogsc.2017.06.002
“Enantioselective, Intermolecular Benzylic C-H Amination Catalysed by an Engineered Iron-Haem Enzyme”  C. K. Prier, R. K. Zhang, A. R. Buller, S. Brinkmann-Chen, F. H. Arnold. Nature Chemistry 9, 629-634 (2017). doi:10.1038/NCHEM.278
“Chapter 1. Directed Evolution of an Allosteric Tryptophan Synthase to Create a Platform for Synthesis of Noncanonical Amino Acids”  J. Murciano-Calles, A. R. Buller, F. H. Arnold. In M. Alcalde (ed.), Directed Enzyme Evolution: Advances and Applications, pp. 1-16 (2017). Springer International Publishing AG. doi: 10.1007/978-3-319-50413-1_
“Structure-Guided SCHEMA Recombination Generates Diverse Chimeric Channelrhodopsins”  C. N. Bedbrook, A. J. Rice, K. K. Yang, X. Ding, S. Chen, E. M. LeProust, V. Gradinaru, F. H. Arnold. Proceedings of the National Academy of Sciences 114, E2624-E2633 (2017). doi/10.1073/pnas.170026911
“Directed Evolution of a Bright Near-Infrared Fluorescent Rhodopsin Using a Synthetic Chromophore”  L. Herwig, A. J. Rice, C. N. Bedbrook, R. K. Zhang, A. Lignell, J. K. B. Cahn, H. Renata, S. C. Dodani, I. Cho, L. Cai, V. Gradinaru, F. H. Arnold. Cell Chemical Biology 24, 415-425 (2017). http://dx.doi.org/10.1016/j.chembiol.2017.02.008.
“Engineering Green Biocatalysts for Chemical Reactions Not Known in Biology  K. E. Hernandez. ACS Green Chemistry: The Nexus Blog (2017).

2016

“Tryptophan Synthase Uses an Atypical Mechanism To Achieve Substrate Specificity”  A. R. Buller, P. van Roye, J. Murciano-Calles, F. H. Arnold. Biochemistry 55, 7043-7046 (2016). doi: 10.1021/acs.biochem.6b01127.
“Directed Evolution of Cytochrome c for Carbon-Silicon Bond Formation: Bringing Silicon to Life”  S.B. J. Kan, R. D. Lewis, K. Chen, F. H. Arnold. Science 354, 1048-1051 (2016). doi: 10.1126/science.aah6219.
“Highly Stereoselective Biocatalytic Synthesis of Key Cyclopropane Intermediate to Ticagrelor”   K. E. Hernandez, H. Renata, R. D. Lewis, S. B. J. Kan, C. Zhang, J. Forte, D. Rozzell, J. A. McIntosh, F. H. Arnold. ACS Catalysis 6, 7810-7813 (2016). doi: 10.1021/acscatal.6b02550.
“A General Tool for Engineering the NAD/NADP Cofactor Preference of Oxidoreductases”   J. Cahn, C. Werlang, A. Baumschlager, S. Brinkmann-Chen, S. Mayo, F. H. Arnold. ACS Synthetic Biology, online web publication September 30, 2016: doi: 10.1021/acssynbio.6b00188.
“Identification of Mechanism-Based Inactivation in P450-Catalyzed Cyclopropanation Facilitates Engineering of Improved Enzymes”   H. Renata, R. D. Lewis, M. J. Sweredoski, A. Moradian, S. Hess, Z. J. Wang, F. H. Arnold. Journal of the American Chemical Society 138, 12527-12533 (2016). doi:10.1021/jacs.6b06823
“A Panel of TrpB Biocatalysts Derived from Tryptophan Synthase through the Transfer of Mutations that Mimic Allosteric Activation”   J. Murciano-Calles, D. K. Romney, S. Brinkmann-Chen, A. R. Buller, F. H. Arnold. Angewandte Chemie 55, 11577-11581 (2016). doi:10.1002/anie.201606242R1
“Enhancement of Cellulosome-Mediated Deconstruction of Cellulose By Improving Enzyme Thermostability”   S. Moraïs, J. Stern, A. Kahn, A. P Galanopoulou, S. Yoav, M. Shamshoum, M. A. Smith, D. G. Hatzinikolaou, F. H. Arnold, E. A. Bayer.Biotechnology for Biofuels 9, 164 (2016). doi:10.1186/s13068-016-0577-z
“Synthesis of β-Branched Tryptophan Analogues Using an Engineered SubUnit of Tryptophan Synthase”   M. Herger, P. van Roye, D. K. Romney, S. Brinkmann-Chen, A. R. Buller, F. H. Arnold. Journal of the American Chemical Society, 138, 8388-8391 (2016). doi:10.1021/jacs.6b04836
“The NAI Fellow Profile: An Interview with Dr. Frances Arnold”   F. H. Arnold, K. A. Macuare Technology and Innovation 18, 79-82 (2016). doi:10.21300/18.1.2016.79
“Discovery of a Regioselectivity Switch in Nitrating P450s Guided by MD Simulations and Markov Models”   S. C. Dodani, G. Kiss, J. K. B. Cahn, Y. Su, V. S. Pande, F. H. Arnold. Nature Chemistry 8, 419-425 (2016). doi:10.1038/nchem.2474
“Asymmetric Enzymatic Synthesis of Allylic Amines: A Sigmatropic Rearrangement Strategy”   C. K. Prier, T. K. Hyster, C. C. Farwell, A. Huang, F. H. Arnold. Angewandte Chemie 55, 4711-4715 (2016). doi: 10.1002/anie.201601056
“Exploring the Mechanism Responsible for Cellulase Thermostability by Structure-Guided Recombination.”   C. J. Chang, C. C. Lee, Y. T. Chan, D. L. Trudeau, M. H. Wu, C. H. Tsai, S. M. Yu, T. H. Ho, A. H. Wang, C. D. Hsiao, F. H. Arnold, Y. C. Chao.PLoS ONE 11(3), e0147485 (2016). doi: 10.1371/journal.pone.0147485
“Mutations in Adenine Binding Pockets Enhance Catalytic Properties of NAD(P)H-Dependent Enzymes”   J. K. B. Cahn, A. Baumschlager, S. Brinkmann-Chen, F. H. Arnold. Protein Engineering, Design and Selection 29, 31-38 (2016). doi: 10.1093/protein/gzv057

2015

“Artificial Domain Duplication Replicates Evolutionary History of Ketol-Acid Reductoisomerases”   J. K. B. Cahn, S. Brinkmann-Chen, A. R. Buller, F. H. Arnold. Protein Science 25, 1241-1248. doi: 10.1002/pro.2852
Directed Evolution of the Tryptophan Synthase β-Subunit for Stand-Alone Function Recapitulates Allosteric Activation   A. R. Buller, S. Brinkmann-Chen, D. K. Romney, M. Herger, J. Murciano-Calles, F. H. Arnold. Proceedings of the National Academy of Sciences 112, 14599-14604 (2015). doi: 10.1073/pnas.1516401112
Chemomimetic Biocatalysis: Exploiting the Synthetic Potential of Cofactor-Dependent Enzymes to Create New Catalysts  C. K. Prier, F. H. Arnold. Journal of the American Chemical Society 137, 13992-14006 (2015). doi: 10.1021/jacs.5b09348
“Structural Adaptability Facilitates Histidine Heme Ligation in a Cytochrome P450”   J. A. McIntosh, T. Heel, A. R. Buller, L. Chio, F. H. Arnold. Journal of the American Chemical Society 137, 13861-13865 (2015) doi: 10.1021/jacs.5b07107
“The Nature of Chemical Innovation: New Enzymes by Evolution”   F. H. Arnold. Quarterly Reviews of Biophysics Discovery — The Nobel Workshop Issue 48, 404-410 (2015). doi:10.1017/S003358351500013X.
“Genetically Encoded Spy Peptide Fusion System to Detect Plasma Membrane-Localized Proteins In Vivo”   C. N. Bedbrook, M. Kato, S. R. Kumar, A. Lakshmanan, R. D. Nath, F. Sun, P. W. Sternberg, F. H. Arnold, V. Gradinaru. Chemistry and Biology 22, 1108-1121 (2015). http://dx.doi:10.1016/j.chembiol.2015.06.020
“Recent Advances in Engineering Microbial Rhodopsins for Optogenetics”   R. S. McIsaac, C. N. Bedbrook, F. H. Arnold.Current Opinion in Structural Biology 33, 8-15 (August 2015). doi:10.1016/j.sbi.2015.05.001
Enantioselective Enzyme-Catalyzed Aziridination Enabled by Active-Site Evolution of a Cytochrome P450   C. C. Farwell, R. K. Zhang, J. A. McIntosh, T. K. Hyster, F. H. Arnold. ACS Central Science 1, 89-93 (2015). doi: 10.1021/acscentsci.5b00056
Cofactor Specificity Motifs and the Induced Fit Mechanism in Class I Ketol-Acid Reductoisomerases   J. K. Cahn, S. Brinkmann-Chen, T. Spatzal, J. A. Wiig, A. R. Buller, O. Einsle, Y. Hu, M. W. Ribbe, F. H. Arnold. Biochemical Journal 468 (part 3), 475-484 (2015). doi: 10.1042/BJ20150183
Expanding the Enzyme Universe: Accessing Non-Natural Reactions by Mechanism-Guided Directed Evolution   H. Renata, Z. J. Wang, F. H. Arnold. Angewandte Chemie Int. Ed. 54, 3351-3367 (2015). doi: 10.1002/anie.201409470
P450 BM3-Axial Mutations: A Gateway to Non-Natural Reactivity   T. K. Hyster, F. H. Arnold. Israel Journal of Chemistry 55, 14-20 (2015). doi: 10.1002/ijch.201400080
Directed Evolution of Gloebacter violaceus Rhodopsin Spectral Properties  M. K. M. Engqvist, R. S. McIsaac, P. Dollinger, N. C. Flytzanis, M. Abrams, S. Schor, F. H. Arnold. Journal of Molecular Biology 427, 205-220 (2015). doi:10.1016/j.jmb.2014.06.015

2014

Enzyme-Controlled Nitrogen-Atom Transfer Enables Regiodivergent C-H Amination   T. K. Hyster, C. C. Farwell, A. R. Buller, J. A. McIntosh, F. H. Arnold. Journal of the American Chemical Society 136, 15505-15508 (2014) doi: 10.1021/ja509308v
Non-natural Olefin Cyclopropanation Catalyzed by Diverse Cytochrome P450s and Other Hemoproteins   T. Heel, J. A. McIntosh, S. C. Dodani, J. T. Meyerowitz, F. H. Arnold. ChemBioChem 15, 2556-2562 (2014). doi: 10.1002/cbic.201402286
Structural, Functional, and Spectroscopic Characterization of the Substrate Scope of the Novel Nitrating Cytochrome P450 TxtE   S. Dodani, J. K. B. Cahn, T. Heinisch, S. Brinkmann-Chen, J. A. McIntosh, F. H. Arnold. ChemBioChem 15, 2259-2267 (2014). doi: 10.1002/cbic.201402241
Uncovering Rare NADH-Preferring Ketol-Acid Reductoisomerases   S. Brinkmann-Chen, J. K .B. Cahn, F. H. Arnold. Metabolic Engineering 26, 17-22 (2014). doi: 10.1016/j.ymben.2014.08.003
Directed Evolution of a Far-Red Fluorescent Rhodopsin   R. S. McIsaac, M. K. M. Engqvist, T. Wannier, A. Z. Rosenthal, L. Herwig, N. C. Flytzanis, E. S. Imasheva, J. K. Lanyi, S. P. Balashov, V. Gradinaru, F. H. Arnold. Proceedings of the National Academy of Sciences 111, 13034-13039 (2014). doi: 10.1073/pnas.1413987111
Synthesis of Bioactive Protein Hydrogels by Genetically Encoded SpyTag-SpyCatcher Chemistry   F. Sun, W.-B. Zhang, A. Mahdavi, F. H. Arnold, D. Tirrell. Proceedings of the National Academy of Sciences 111, 11269-11274 (2014). doi: 10.1073/pnas.1401291111
Archaerhodopsin Variants with Enhanced Voltage Sensitive Fluorescence in Mammalian and C. elegans Neurons   N. C. Flytzanis, C. N. Bedbrook, H. Chiu, M. K. M. Engqvist, C. Xiao, K. Y. Chan, P. W. Sternberg, F. H. Arnold, V. Gradinaru. Nature Communications 5, 4894 (2014). doi: 10.1038/ncomms5894
P450-Catalyzed Asymmetric Cyclopropanation of Electron-Deficient Olefins Under Aerobic Conditions   H. Renata, Z. J. Wang, R. Z. Kitto, F. H. Arnold. Catalysis Science & Technology 4, 3640-3643 (2014). doi:10.1039/C4CY00633J
“Engineered Thermostable Fungal Cellulases Exhibit Efficient Synergistic Cellulose Hydrolysis at Elevated Temperatures”  D. L. Trudeau, T. M. Lee, F. H. Arnold. Biotechnology and Bioengineering 111, 2390-2397. doi: 10.1002/bit.25308
Enantioselective Imidation of Sulfides via Enzyme-Catalyzed Intermolecular Nitrogen-Atom Transfer   C. C. Farwell, J. A. McIntosh, T. K. Hyster, Z. J. Wang, F. H. Arnold. Journal of the American Chemical Society 136, 8766-8771 (2014). doi: 10.1021/ja503593n
“Synthetic Biology: Engineering Explored”   F. H. Arnold, J. T. Meyerowitz. Nature News & Views 509, 166-167 (May 8, 2014).
“Improved Cyclopropanation Activity of Histidine-Ligated Cytochrome P450 Enables Formal Synthesis of Levomilnacipran”   Z. J. Wang, H. Renata, N. E. Peck, C. C. Farwell, P. S. Coelho, F. H. Arnold. Angewandte Chemie Intl. Ed. 126, 6928-6931 (2014). doi:10.1002/ange.201402809R1
“Isobutanol Production at Elevated Temperatures in Thermophilic Geobacillus thermoglucosidasius   P. P. Lin, K. S. Rabe, J. L. Takasumi, M. Kadisch, F. H. Arnold, J. C. Liao. Metabolic Engineering 24, 1-8 (2014). http://dx.doi.org/10.1016/j.ymben.2014.03.006. Erratum to article.
“Expanding P450 Catalytic Reaction Space Through Evolution and Engineering”   J. A. McIntosh, C. C. Farwell, F. H. Arnold. Current Opinion in Chemical Biology 19, 126-134 (2014). doi:10.1016/j.cbpa.2014.02.001
“Chapter 9.15. Synthetic Biology Approaches for Organic Synthesis”   P. S Coelho, F. H. Arnold, J. C. Lewis. In Gary A. Molander and Paul Knochel (eds.), Comprehensive Organic Synthesis, 2nd edition, Vol 9, pp. 390-420 (2014). Oxford: Elsevier. doi.org/10.1016/B978-0-08-097742-3.00931-9
“Cytochrome P450-Catalyzed Insertion of Carbenoids into N-H Bonds”   Z. J. Wang, N. E. Peck, H. Renata, F. Arnold. Chemical Sciences 5, 598-601 (2014). doi:10.1039/c3sc52535j
“Expanding the Enzyme Universe Through a Marriage of Chemistry and Evolution”   F. H. Arnold. In K. Wüthrich, I.A. Wilson, D. Hilvert, D.W. Wolan, A. De Wit (eds.) New Chemistry and New Opportunities from the Expanding Protein Universe. 23rd International Solvay Conference on Chemistry, pp. 84-89 (2014), World Scientific Publishing Co. Pte. Ltd. ISBN 978-9814603829.
“Photo-Limited and Electron Transfer Reactivity of Ruthenium-Labeled Cytochrome P450”   M. E. Ener, P. S. Coelho, Z. J. Wang, F. H. Arnold, J. R. Winkler, H. B. Gray. Journal of Biological Inorganic Chemistry 19 (S1), S219 (2014). ISSN 0949-8257.

2013

“Innovation By Homologous Recombination”   D. L. Trudeau, M. A. Smith, F. H. Arnold. Current Opinion in Chemical Biology17, 902-909 (2013). http://dx.doi.org/10.1016/j.cbpa.2013.10.007
“Controlling Macromolecular Topology with Genetically Encoded SpyTag-SpyCatcher Chemistry”   W.-B. Zhang, F. Sun, D. A. Tirrell, F. H. Arnold. Journal of the American Chemical Society 135, 13988-13997 (2013). doi:10.1021/ja4076452
“Enantioselective Intramolecular C-H Amination Catalyzed by Engineered Cytochrome P450 Enzymes in vitro and in vivo  J. A. McIntosh, P. S. Coelho, C. C. Farwell, Z. J. Wang, J. C. Lewis, T. R. Brown, F. H. Arnold. Angewandte Chemie International Edition 529309-9312 (2013). doi:10.1002/anie.201304401
“A Serine-Substituted P450 Catalyzes Highly Efficient Carbene Transfer to Olefins in vivo   P. S. Coelho, Z. J. Wang, M. E. Ener, S. A. Baril, A. Kannan, F. H. Arnold, E. M. Brustad. Nature Chemical Biology 9485- 487 (2013). doi:10.1038/nchembio.1278
Hypocrea jecorina Cellobiohydrolase I Stabilizing Mutations Identified Using Noncontiguous Recombination”   M. A. Smith, C. N. Bedbrook, T. Wu, F. H. Arnold. ACS Synthetic Biology 2, 690-696 (2013). doi: 10.1021/sb400010m
“General Approach to Reversing Ketol-Acid Reductoisomerase Cofactor Dependence from NADPH to NADH”   S. Brinkmann-Chen, T. Flock, J. K. B. Cahn, C. D. Snow, E. M. Brustad, J. A. McIntosh, P. Meinhold, L. Zhang, F. H. Arnold. Proceedings of the National Academy of Sciences 110, 10946-10951 (2013). doi:10.1073/pnas.1306073110
“Role of Cysteine Residues in Thermal Inactivation of Fungal Cel6A Cellobiohydrolases”   I. Wu, T. Heel, F. H. Arnold. Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics 1834, 1539-1544 (2013). doi: 10.1016/j.bbapap.2013.05.003
“Chapter 14. Directed Evolution of Protein-Based Neurotransmitter Sensors for MRI”   P. A. Romero, M. G. Shapiro, F. H. Arnold, A. Jasanoff. In M. R. Banghart (ed.) Chemical Neurobiology: Methods and Protocols – Methods in Molecular Biology, Vol. 995, pp. 193-205 (2013). Springer Science-Business Media, New York. doi: 10.1007/978-1-62703-345-9_14
“High-Throughput Screening for Terpene-Synthase-Cyclization Activity and Directed Evolution of a Terpene Synthase”   R. Lauchli, K. S. Rabe, K. Z. Kalbarczyk, A. Tata, T. Heel, R. Z. Kitto, F. H. Arnold. Angewandte Chemie, Intl. Ed. 52, 5571-5574 (2013). doi: 10.1002/anie.201301362
“Chapter Sixteen – Efficient Sampling of SCHEMA Chimera Families to Identify Useful Sequence Elements”   P. Heinzelman, P. A. Romero, F. H. Arnold. In A. E. Keating (ed.) Methods in Enzymology, Vol. 523, pp. 351-368 (2013). Burlington: Academic Press. ISBN: 978-0-12-394292-0.
“Engineered Thermostable Fungal Cel6A and Cel7A Cellobiohydrolases Hydrolyze Cellulose Efficiently at Elevated Temperatures   I. Wu, F. H. Arnold. Biotechnology & Bioengineering, 110, 1874-1883 (2013). doi: 10.1002/bit.24864
Chimeragenesis of Distantly-Related Proteins by Noncontiguous Recombination   M. A. Smith, P. A. Romero, T. Wu, E. M. Brustad, F. H. Arnold. Protein Science 22, 231-238 (2013). doi: 10.1002/pro.2202
“Olefin Cyclopropanation via Carbene Transfer Catalyzed by Engineered Cytochrome P450 Enzymes   P. S. Coelho, E. M. Brustad, A. Kannan, F. H. Arnold. Science 339, 307-310 (2013). doi: 10.1126/science.1231434 See Commentary by Narayan and Sherman.
“Navigating the Protein Fitness Landscape With Gaussian Processes”   P. A. Romero, A. Krause, F. H. Arnold. Proceedings of the National Academy of Sciences 110(3), E193-E201 (2013). www.pnas.org/cgi/doi/10.1073/pnas.1215251110

2012

“A Diverse Set of Family 48 Bacterial Cellulases Created By Structure-Guided Recombination”   M. A. Smith, A. Rentmeister, C. D. Snow, T. Wu, M. F. Farrow, F. Mingardon, F. H. Arnold. FEBS Journal 279, 4453-4465 (2012). doi: 10.1111/febs.12032
“Random Field Model Reveals Structure of the Protein Recombinational Landscape”   P. A. Romero, F. H. Arnold. PLoS Computational Biology 8(10), e1002713 (2012). doi:10.1371/journal.pcbi.1002713
“Highly Thermostable Fungal Cellobiohydrolase I (Cel7A) Engineered Using Predictive Methods”   R. S. Komor, P. A. Romero, C. B. Xie, F. H. Arnold. Protein Engineering, Design and Selection25, 827-833 (2012). doi: 10.1093/protein/gzs058
“Structure-Guided Engineering of Lactococcus lactis Alcohol Dehydrogenase LlAdhA for Improved Conversion of Isobutyraldehyde to Isobutanol”   X. Liu, S. Bastian, C. D. Snow, E. M. Brustad, T. E. Saleski, J-H. Xu, P. Meinhold, F. H. Arnold. Journal of Biotechnology 164, 188-195 (2012). doi: 10.1016/j.jbiotec.2012.08.008
“Structure-Guided Directed Evolution of Highly Selective P450-based Magnetic Resonance Imaging Sensors for Dopamine and Serotonin”   E. M. Brustad, V. S. Lelyveld, C. D. Snow, N. Crook, S. T. Jung, F. M. Martinez, T. J. Scholl, A. Jasanoff, F. H. Arnold. Journal of Molecular Biology 422, 245-262 (2012). doi: 10.1016/j.jmb.2012.05.029.
“SCHEMA Designed Variants of Human Arginase I & II Reveal Sequence Elements Important to Stability and Catalysis”   P. A. Romero, E. Stone, C. Lamb, L. Chantranupong, A. Krause, A. Miklos, R. A. Hughes, B. Fechtel, A. D. Ellington, F. H. Arnold, G. Georgiou. ACS Synthetic Biology 1, 221-228 (2012). doi: 10.1021/sb300014t.
“Comparison of Random Mutagenesis and Semi-Rational Designed Libraries for Improved Cytochrome P450 BM3-Catalyzed Hydroxylation of Small Alkanes”  M. M. Y. Chen, C. D. Snow, C. L. Vizcarra, S. L. Mayo, F. H. Arnold. Protein Engineering, Design & Selection 25, 171-178 (2012). doi:10.1093/protein/gzs004
“Utilizing Terminal Oxidants to Achieve P450-Catalyzed Oxidation of Methane”  M. M. Chen, P. S. Coelho, F. H. Arnold. Advanced Synthesis and Catalysis 354, 964-968 (2012). doi:10.1002/adsc.201100833
“Reversal of NAD(P)H Cofactor Dependence by Protein Engineering”  S. Bastian, F. H. Arnold, in Microbial Metabolic Engineering, Methods and Protocols,” Q. Cheng (ed.). Methods in Molecular Biology, vol. 834, p. 17-31 (2012). Humana Press, N.Y. doi:10.1007/978-1-61779-483-4_2
“Computational Thermostable Cellulase Engineering for Enhanced Biofuel Production”  T. Lee, M. Farrow, F. H. Arnold. Protein Science 21 (S1), 71-72 (2012). doi:10.1002/pro.2113
“High Resolution Models from Low Resolution Data: Recombination of Fragments by Crystallographic Structure Determination”  C. Snow, E. Brustad, F. H. Arnold. Protein Science 21 (S1), 91-92 (2012). doi:10.1002/pro.2113
“Metalloprotein-Based Contrast Sensors for Neurochemical Detection by MRI”  V. Lelyveld, E. Brustad, F. H. Arnold. Protein Science 21 (S1), 184 (2012). doi:10.1002/pro.2113

2011

“A Structural Study of Hypocrea jecorina Cel5A”  T. M. Lee., M. F. Farrow, F. H. Arnold, S. L. Mayo. Protein Science 20, 1935-1940 (2011). doi:10.1002/pro.730
“High Throughput Screening of Fungal Endoglucanase Activity in Escherichia coli  M. F. Farrow, F. H. Arnold. Journal of Visualized Experiments54 (2011). http://www.jove.com/details.php?id=2942. doi:10.3791/2942
“The Library of Maynard-Smith: My Search for Meaning in the Protein Universe”  F. H. Arnold. MicrobeASM News 6, 316-318 (2011).
“Engineered Bacterial Mimics of Human Drug Metabolizing Enzyme CYP2C9”  A. Rentmeister, T. R. Brown, C. D. Snow, M. N. Carbone, F. H. Arnold. ChemCatChem 3, 1065-1071 (2011). doi:10.1002/cctc.201000452
“Engineered Ketol-Acid Reductoisomerase and Alcohol Dehydrogenase Enable Anaerobic 2-methylpropan-1-ol Production at Theoretical Yield in Escherichia coli  S. Bastian, X. Li, J. T. Meyerowitz, C. D. Snow, M. M. Y. Chen, F. H. Arnold.Metabolic Engineering 13, 345-352 (2011). doi:10.1016/j.ymben.2011.02.004
“Cytochrome P450: Taming a Wild Type Enzyme”  S. T. Jung, R. Lauchli, F. H. Arnold. Current Opinion in Biotechnology 22, 809-817. doi:10.1016/j.copbio.2011.02.008
“Optimizing Non-Natural Protein Function with Directed Evolution”  E. M. Brustad, F. H. Arnold. Current Opinion in ChemicalBiology 15, 201-210 (2011). doi: 10.1016/j.cbpa.2010.11.020
“Enzymatic Functionalization of Carbon-Hydrogen Bonds”  J. C. Lewis, P. S. Coelho, F. H. Arnold. Chemical Society Reviews40, 2003-2021 (2011). doi: 10.1039/C0CS00067A
“Self-Organization, Layered Structure, and Aggregation Enhance Persistence of a Synthetic Biofilm Consortium”  K. Brenner, F. H. Arnold. PLoS One 6(2): eprint 16791 (2011). doi:10.1371/journal.pone.0016791
“Metal-Substituted Protein MRI Contrast Agents Engineered for Enhanced Relaxivity and Ligand Sensitivity”  V. S. Lelyveld, E. Brustad, F. H. Arnold, A. Jasanoff. Journal of the American Chemical Society 133, 649-651 (2011).
“Comparison of Family 9 Cellulases from Mesophilic and Thermophilic Bacteria”   F. Mingardon, J. D. Bagert, C. Maisonnier, D. L. Trudeau, F. H. Arnold. Applied and Environmental Microbiology 77(4), 1436-1442 (2011).

2010

“Improved Product-Per-Glucose Yields in P450-Dependent Propane Biotransformations Using Engineered Escherichia coli,”   R. Fasan, N. C. Crook, M. W. Peters, P. Meinhold, T. Buelter, M. Landwehr, P. C. Cirino, F. H. Arnold. Biotechnology and Bioengineering 108(3), 500-510 (2010).
“A General Mechanism for Network-Dosage Compensation in Gene Networks”   M. Acar, B. F. Pando, F. H. Arnold, M. B. Elowitz, A. v. Oudernaarden. Science 329, 1656-1660 (2010).
“Combinatorial Alanine Substitution Enables Rapid Optimization of Cytochrome P450BM3 for Selective Hydroxylation of Large Substrates”   J. C. Lewis, S. M. Mantovani, Y. Fu, C. D. Snow, R. S. Komor, C. H. Wong, F. H. Arnold. ChemBioChem 11(18), 2502-2505 (2010). doi: 10.1002/cbic.201000565
“Efficient Screening of Fungal Cellobiohydrolase Class I Enzymes for Thermostabilizing Sequence Blocks by SCHEMA Structure-Guided Recombination”   P. Heinzelman, R. Komor, A. Kannan, P. Romero, X. Yu, S. Mohler, C. Snow, F. H. Arnold.Protein Engineering, Design and Selection 24,871-880 (2010). doi:10.1093/protein/gzq063
“Consensus Protein Design Without Phylogenetic Bias”   C. Jackel, J. D. Bloom, P. Kast, F. H. Arnold, D. Hilvert. Journal of Molecular Biology 399, 541-546 (2010).
“Directed Evolution of an MRI Contrast Agent for Noninvasive Imaging of Dopamine”  M. G. Shapiro, G. G. Westmeyer, P. A. Romero, J. O. Szablowski, B. Kuster, A. Shah, C. R. Otey, R. Langer, F. H. Arnold, A. Jasanoff. Nature Biotechnology 28 264-270 (2010).
“Combinatorial Recombination of Gene Fragments to Construct a Library of Chimeras”  M. Farrow, F. H. Arnold. Current Protocols in Protein Science (SUPPL. 61), pp. 26.2.1-26.2.20, 2010.

2009

“How Proteins Adapt: Lessons From Directed Evolution”  F. H. Arnold. Cold Spring Harbor Symposia on Quantitative Biology, Volume LXXIV. 2009 Cold Spring Harbor Laboratory Press 978-087969870-6.
“Exploring Protein Fitness Landscapes by Directed Evolution”   P. A. Romero, F. H. Arnold. Nature Reviews Molecular Cell Biology 10, 866-876 (2009).
“Directed Evolution: New Parts and Optimized Function”   M. J. Dougherty, F. H. Arnold. Current Opinion in Biotechnology20, 1-6 (2009). doi:10.1016/j.copbio.2009.08.005.
“A Panel of Cytochrome P450 BM3 Variants to Produce Drug Metabolites and Diversify Lead Compounds”   A. M. Sawayama, M. M. Chen, P. Kulanthaivel, M. S. Kuo, H. Hemmerle, F. H. Arnold. Chemistry, a European Journal 15, 11723-11729 (2009). doi:10.1002/chem.200900643
“SCHEMA Recombination of a Fungal Cellulase Uncovers a Single Mutation that Contributes Markedly to Stability”  P. Heinzelman, C. D. Snow, M. A. Smith, X. Yu, K. Arvind, K. Boulaware, A. Villalobos, S. Govindarajan, J. Minshull, F.H. Arnold. J. Biol. Chem. 284, 26229-26233 (2009). doi:10.1074/jbc.C109.034058.
“Chemoenzymatic Elaboration of Monosaccharides Using Engineered Cytochrome P450BM3 Demethylases”  J. C. Lewis, S. Bastian, C. S. Bennett, Y. Fu, Y. Mitsuda, M. M. Chen, W. A. Greenberg, C. H. Wong,  F. H. Arnold. Proc. Natl. Acad. Sci. 106 (39), 16550-16555 (2009).  doi/10.1073/pnas.0908954106.
“Catalysts On Demand: Selective Oxidations By Laboratory-Evolved Cytochrome P450 BM-3”  J. C. Lewis, F. H. Arnold. Chimia 63, 309-312 (2009).  doi:10.2533/chimia.2009.309.
“In the Light of Directed Evolution: Pathways of Adaptive Protein Evolution”  J. D. Bloom, F. H. Arnold. Proc. Natl. Acad. Sci.106, 9995-10000 (2009).  doi:10.1073/pnas.0901522106.
“Directed Enzyme Evolution: Climbing Fitness Peaks One Amino Acid at a Time”  C. A. Tracewell, F. H. Arnold. Current Opinion in Chemical Biology13(1): 3-9 (2009). doi:10.1016/j.cbpa.2009.01.017.
“A Family of Thermostable Fungal Cellulases Created by Structure-Guided Recombination”  P. Heinzelman, C. D. Snow, I. Wu, C. Nguyen, A. Villalobos, S. Govindarajan, J. Minshull, F. H. Arnold. Proc. Natl. Acad. Sci. 106, 5610-5615 (2009).  doi10.1073pnas.0901417106.
“In Vivo Evolution of Butane Oxidation by Terminal Alkane Hydroxylases AlkB and CYP153A6”  D. J. Koch, M. M. Chen, J. B. van Beilen, F. H. Arnold, Applied and Environmental Microbiology 75(2), 337–344 (2009).
“Protein Engineering by Structure-Guided SCHEMA Recombination”  G. Saab-Rincon, Y. Li, M. Meyer, M. N. Carbone, M. Landwehr, F. H. Arnold. pp. 481-492 in Protein Engineering Handbook, S. Lutz & U.T. Bornscheuer (Eds.).
“Chemo-Enzymatic Fluorination of Organic Scaffolds”  A. Rentmeister, F. H. Arnold, R. Fasan. Nature Chemical Biology 5(1): 26-28 (2009). Commentary in Nature.

2008

“The Race for New Biofuels”  F. H. Arnold. Engineering & Science 2, 12-19 (2008).
“Response to Goldman and Brown: Making Sense of Microbial Consortia Using Ecology and Evolution”  K. Brenner, L. You, F. H. Arnold. Trends in Biotechnology 27, 4 (2008).
“Engineering Microbial Consortia: A New Frontier in Synthetic Biology”  K. Brenner, L. You, F. H. Arnold. Trends in Biotechnology 26(9): 483-489 (2008). Authors response to commentary.
“Evolutionary History of a Specialized P450 Propane Monooxygenase”  R. Fasan, Y. T. Meharenna, C. D. Snow, T. L. Poulos, F. H. Arnold. Journal of Molecular Biology 383(5), 1069-1080 (2008)
“A Synthetic Escherichia coli Predator-Prey Ecosystem”  F. K. Balagadde, H. Song, J. Ozaki, C. H. Collins, M. Barnet, F. H. Arnold, S. R. Quake, L. You. Molecular Systems Biology 4, 187 (2008). doi: 10.1038/msb.2008.24
“Implications of Rewiring Bacterial Quorum Sensing”  E. L. Haseltine, F. H. Arnold. Applied and Evironmental Microbiology 74, 437-445 (2008). Supporting Information.
“A Synthetic Escherichia coli Predator-Prey Ecosystem”  F. K. Balagradde, H. Song, J. Ozaki, C. H. Collins, M. Barnet, F. H. Arnold, S. R. Quake, L. You Molecular Systems Biology 4, 187 (2008).

2007

“Engineered Bidirectional Communication Mediates a Consensus in a Microbial Biofilm Consortium”  K. Brenner, D. K. Karig, R. Weiss, F. H. Arnold. Proc. Natl. Acad. Sci. 104, 17300-17304 (2007). Commentary in Nature.
“Directed Evolution of Vibrio fischeri LuxR for Improved Response to Butanoyl-Homoserine Lactone”  A. C. Hawkins, F. H. Arnold, R. Stuermer, B. Hauer, J. R. Leadbetter. Applied and Environmental Microbiology 73, 5775-5781 (2007).
“A Diverse Family of Thermostable Cytochrome P450s Created By Recombination of Stabilizing Fragments”  Y. Li, D. A. Drummond, A. M. Sawayama, C. D. Snow, J. D. Bloom, F. Arnold. Nature Biotechnology 25, 1051-1056 (2007).
“Engineered Alkane-Hydroxylating Cytochrome P450 BM3 Exhibiting Native-like Catalytic Properties”  R. Fasan, M. M. Chen, N. C. Crook, F. H. Arnold. AngewChemie, Int. Ed. 46, 8414-8418 (2007). (Supplementary Material)
“Evolution Favors Protein Mutational Robustness in Sufficiently Large Populations”  J. D. Bloom, Z. Lu, D. Chen, A. Raval, O. S. Ventura, F. H. Arnold. BMC Biology 5, 29 (2007).
“Breaking Proteins with Mutations: Threads and Thresholds in Evolution”  J. D. Bloom, F. H. Arnold, C. O. Wilke. Molecular Systems Biology 3, 76 (2007).
“Engineering by Homologous Recombination: Exploring Sequence and Function Within a Conserved Fold”  M. N. Carbone, F. H. Arnold. Current Opinion in Structural Biology 17, 454-549 (2007).
“Neutral Genetic Drift Can Alter Promiscuous Protein Functions, Potentially Aiding Functional Evolution,”  J. D. Bloom, P. A. Romero, Z. Lu, F. H. Arnold. Biology Direct 2, 17 (2007).
“Synthetic Gene Circuits: Design with Directed Evolution”  E. L. Haseltine, F. H. Arnold. Annual Review of Biophysics and Biomolecular Structure 36, 1-19 (2007).
“Diversification of Catalytic Function in a Synthetic Family of Chimeric Cytochrome P450s”  M. Landwehr, M. Carbone, C. R. Otey, Y. Li, F. H. Arnold. Chemistry & Biology 14, 269-278 (2007).

2006

“Structure-Guided SCHEMA Recombination of Distantly Related beta-Lactamases”  M. M. Meyer, L. Hochrein, F. H. Arnold, Protein Engineering, Design and Selection 19, 563-570 (2006).
“Structural Determinants of the Rate of Protein Evolution in Yeast”  J. D. Bloom, D. A. Drummond, F. H. Arnold, C. O. Wilke. Molecular Biology and Evolution 23(9), 1751-1761 (2006).
“Dual Selection Enhances the Signaling Specificity of a Variant of the Quorum-Sensing Transcriptional Activator LuxR”  C. H. Collins, J. R. Leadbetter, F. H. Arnold. Nature Biotechnology 24, 708-712 (2006). Commentary in Nature Biotechnology.
“Enantioselective α-Hydroxylation of 2-Arylacetic Acid Derivatives and Buspirone Catalyzed by Engineered Cytochrome P450 BM-3”  M. Landwehr, L. Hochrein, C. R. Otey, A. Kasrayan, J. E. B�ckvall, F. H. Arnold. Journal of the American Chemical Society 128(18), 6058-6059 (2006).
“Structure-Guided Recombination Creates an Artificial Family of Cytochromes P450”  C. R. Otey, M. Landwehr, J.B. Endelman, K. Hiraga, J. D. Bloom, F. H. Arnold. PLoS Biology 4(5), e112 (2006). Synopsis and commentary in PLoS Biologyfeatured in Chemical & Engineering News.
“Engineering Cytochrome P450 BM3 for Terminal Alkane Hydroxylation”  P. Meinhold, M. W. Peters, A. Hartwick, A. R. Hernandez, F. H. Arnold. Advanced Synthesis & Catalysis 348, 763-772 (2006).
“Fancy Footwork in the Sequence-Space Shuffle”  F. H. Arnold. Nature Biotechnology 24(3), 328-330 (2006).
“Protein Stability Promotes Evolvability”  J. D. Bloom, S. T. Labthavikul, C. R. Otey, F. H. Arnold. Proc. Nat’l. Acad. Sci. USA 103(15), 5869-5874 (2006).
“Biosynthesis of Novel Carotenoid Families Based on Unnatural Carbon Backbones: a Model for Diversification of Natural Product Pathways”  A. V. Tobias, F. H. Arnold. BBA-Molecular and Cell Biology of Lipids 1761(2), 235-246 (2006).
“Enantioselective Epoxidation of Terminal Alkenes to (R)- and (S)-Epoxides by Engineered Cytochromes P450 BM-3”  T. Kubo, M. W. Peters, P. Meinhold, F. H. Arnold. Chemistry, a European Journal 12, 1216-1220 (2006).

2005

“Evolving Strategies for Enzyme Engineering”  J. D. Bloom, M. M. Meyer, P. Meinhold, C. R. Otey, D. MacMillan, F. H. Arnold. Curr. Opin. Struct. Biol. 15, 447-452 (2005).
“A Dual Selection Module for Directed Evolution of Genetic Circuits”  Y. Yokobayashi, F. H. Arnold. Natural Computing 4, 245-254 (2005).
“Preparation of Human Metabolites of Propranolol Using Laboratory-Evolved Bacterial Cytochromes P450”  C. R. Otey, G. Bandara, J. Lalonde, K. Takahashi, F. H. Arnold. Biotechnology and Bioengineering 93, 494-499 (2005).
“Why Highly Expressed Proteins Evolve Slowly”  D. A. Drummond, J. D. Bloom, C. Adami, C. O. Wilke, F. H. Arnold. Proc. Nat’l. Acad. Sci. USA 102(40), 14338-14343 (2005). Selected as Nature Research Highlight; commentary in Journal of Cell BiologyResearch Roundup.
“Direct Conversion of Ethane to Ethanol by Engineered Cytochrome P450 BM3”  P. Meinhold, M. W. Peters, M. M. Y. Chen, K. Takahashi, F. H. Arnold. ChemBioChem 6, 1765-1768 (2005).
“Long-Term Monitoring of Bacteria Undergoing Programmed Population Control in a Microchemostat”  F. K. Balagadd�, L. You, C. L. Hansen, F. H. Arnold, S. R. Quake. Science 309, 137-140 (2005). (Supplemental Material)
“Why High-Error-Rate Random Mutagenesis Libraries are Enriched in Functional and Improved Proteins”  D. A. Drummond, B. L. Iverson, G. Georgiou, F. H. Arnold. Journal of Molecular Biology 350, 806-816 (2005).
“Protein-Surfactant Film Voltammetry of Wild-Type and Mutant Cytochrome P450 BM3”  A. K. Udit, N. Hindoyan, M. G. Hill, F. H. Arnold, H. B. Gray. Inorganic Chemistry 44(12), 4109-4111 (2005).
“A Synthetic Multicellular System for Programmed Pattern Formation”  S. Basu, Y. Gerchman, C. H. Collins, F. H. Arnold, R. Weiss. Nature 434(7037), 1130-1134 (2005).
“Stereoselective Hydroxylation of an Achiral Cyclopentanecarboxylic Acid Derivative Using Engineered P450s BM-3”  D. F. M�nzer, P. Meinhold, M. W. Peters, S. Feichtenhoferc, H. Griengla, F. H. Arnold, A. Glieder, A. de Raadt. Chem. Commun. 20, 2597-2599 (2005).
“Diversifying Carotenoid Biosynthetic Pathways by Directed Evolution”  D. Umeno, A. V. Tobias, F. H. Arnold. Microbiology and Molecular Biology Reviews 69(1), 51-78 (2005).
“On the Conservative Nature of Intragenic Recombination”  D. A. Drummond, J. J. Silberg, M. M. Meyer, C. O. Wilke, F. H. Arnold. Proc. Natl. Acad. Sci. USA 102(15), 5380-5385 (2005).
“Directed Evolution of Vibrio fischeri LuxR for Increased Sensitivity to a Broad Spectrum of Acyl-Homoserine Lactones” C. H. Collins, F. H. Arnold, J. R. Leadbetter. Molecular Microbiology 55(3), 712-723 (2005).
“Thermodynamic Prediction of Protein Neutrality”  J. D. Bloom, J. J. Silberg, C. O. Wilke, D. A. Drummond, C. Adami, F. H. Arnold. Proc. Natl. Acad. Sci. USA 102(3), 606-611 (2005).
“Elastomeric Microfabricated Fluorescence-Activated Cell Sorters”  A. Y. Fu, Y. Yokobayashi, F. H. Arnold, S. R. Quake. Chapter 5 in Flow Cytometry for Biotechnology, L. A. Sklar (Ed.), Oxford University Press, USA (2005).

2004

“Laboratory Evolution of Cytochrome P450 BM-3 Monooxygenase for Organic Co-Solvents”  T. S. Wong, F. H. Arnold, U. Schwaneberg. Biotechnol. Bioengineering 85(3), 351-358 (2004).
In vitro DNA Recombination”  K. Miyazaki, F. H. Arnold. pp. 43-60 in Phage Display: A Practical Approach, T. Clackson and H. Lowman (Eds.), Oxford University Press Inc., NY (2004).
“SCHEMA-Guided Protein Recombination”  J. J. Silberg, J. B. Endelman, F. H. Arnold, Methods in Enzymology 388, 35-42 (2004).
“Site-Directed Protein Recombination as a Shortest-Path Problem”  J. B. Endelman, J. J. Silberg, Z-G. Wang, F. H. Arnold. Protein Engineering, Design, & Selection 17(7), 589-594 (2004).
“Reduction of Dioxygen Catalyzed by Pyrene-Wired Heme Domain Cytochrome P450 BM3 Electrodes”  A. K. Udit, M. G. Hill, V. G. Bittner, F. H. Arnold, H. B. Gray. Journal of the American Chemical Society 126(33), 10218-10219 (2004).
“Cobaltocene-Mediated Catalytic Monooxygenation Using Holo and Heme Domain Cytochrome P450 BM3”  A. K. Udit, F. H. Arnold, H. B. Gray. Journal of Inorganic Biochemistry 98(9), 1547-1550 (2004).
“Programmed Population Control by Cell-Cell Communication and Regulated Killing”  L. You, R. S. Cox III, R. Weiss, F. H. Arnold. Nature 428(6985), 868-871 (2004).
“Stability and the Evolvability of Function in a Model Protein”  J. D. Bloom, C. O. Wilke, F. H. Arnold, C. Adami. Biophysical Journal 86, 2758-2764 (2004).
“Evolution of a Pathway to Novel Long-Chain Carotenoids”  D. Umeno, F. H. Arnold. Journal of Bacteriology 186(5), 1531-1536 (2004).
“Functional Evolution and Structural Conservation in Chimeric Cytochromes P450: Calibrating a Structure-Guided Approach,”  C. R. Otey, J. J. Silberg, C. A. Voigt, J. B. Endelman, G. Bandara, F. H. Arnold. Chemistry and Biology 11, 309-318 (2004).
“Directing the Evolvable: Utilizing Robustness in Evolution”  C. A. Voigt, S. L. Mayo, Z.-G. Wang, F. H. Arnold. pp. 105-134 in Robust Design: A Repertoire of Biological, Ecological and Engineering Case Studies,” E. Jen (Ed.), Oxford University Press (2004).
“Colorimetric High-Throughput Assay for Alkene Epoxidation Catalyzed by Cytochrome P450 BM-3 Variant 139-3”  M. Alcalde, E. T. Farinas, F. H. Arnold. Journal of Biomolecular Screening 9(2), 141-146 (2004).
“Association of Antigens to ISCOMATRIXTM Adjuvant Using Metal Chelation Leads to Improved CTL Responses”  J. Malliaros, C. Quinn, F. H. Arnold, M. J. Pearse, D. P. Drne, T. J. Stewart, R. I. Macfarlan. Vaccine 22(29-30), 3968-3975 (2004). doi:10.1016/j.vaccine.2004.03.054

2003

“Regio- and Enantioselective Alkane Hydroxylation with Engineered Cytochromes P450 BM-3”  M. W. Peters, P. Meinhold, A. Glieder, F. H. Arnold. Journal of the American Chemical Society 125, 13442-13450 (2003).
“Thermostabilization of a Cytochrome P450 Peroxygenase”  O. Salazar, P. C. Cirino, F. H. Arnold. ChemBioChem 4, 891-893 (2003).
“Alkene Epoxidation Catalyzed by Cytochrome P450 BM-3 139-3”  E. T. Farinas, M. Alcalde, F. H. Arnold, Tetrahedron 60, 525-528 (2003).
Two volumes of Directed Evolution Protocols edited by F. H. Arnold and G. Georgiou are now available from Humana PressMethods in Molecular Biology series (2003): Directed evolution library creation and Directed Enzyme Evolution.
“Method to Protect a Targeted Amino Acid Residue During Random Mutagenesis”  D. Umeno, K. Hiraga, F. H. Arnold. Nucleic Acids Research 31(16), e91 (2003).
“Engineering Proteins that Bind, Move, Make and Break DNA”  C. H. Collins, Y. Yokobayashi, D. Umeno, F. H. Arnold. Current Opinion in Biotechnology 14, 371-378 (2003).
“General Method for Sequence-independent Site-directed Chimeragenesis”  K. Hiraga, F. H. Arnold. Journal of Molecular Biology 330, 287-296 (2003).
“Library Analysis of SCHEMA-Guided Protein Recombination”  M. M. Meyer, J. J. Silberg, C. A. Voigt, J. B. Endelman, S. L. Mayo, Z-G. Wang, F. H. Arnold. Protein Science 12(8), 1686-1693 (2003).
“A Self-Sufficient Peroxide-Driven Hydroxylation Biocatalyst”  P. C. Cirino, F. H. Arnold. Angewandte Chemie International Edition 42(28), 3299-3301 (2003).
“Global Incorporation of Norleucine in Place of Methionine in Cytochrome P450 BM-3 Heme Domain Increases Peroxygenase Activity”  P. C. Cirino, Y. Tang, K. Takahashi, D. A. Tirrell, F. H. Arnold. Biotechnology and Bioengineering 83, 729-734 (2003).
“A C35-Carotenoid Biosynthetic Pathway”  D. Umeno, F. H. Arnold, Applied and Environmental Microbiology 69, 3573-3579 (2003). Featured in ASM News, August 2003.
“Protein Dynamics in a Family of Laboratory Evolved Thermophilic Enzymes”  P. L. Wintrode, D. Zhang, N. Vaidehi. F. H. Arnold, W. A. Goddard III. Journal of Molecular Biology 327, 745-757 (2003).
“Functional Expression of a Fungal Laccase in Saccharomyces cerevisiae by Directed Evolution”  T. Bulter, M. Alcalde, P. Meinhold, C. Schlachtbauer, F. H. Arnold. Applied and Environmental Microbiology 69, 987-995 (2003).
“Evolutionary Design of Genetic Circuits and Cell-Cell Communications”  Y. Yokobayashi, C.H. Collins, J. R. Leadbetter, R.Weiss, F. H. Arnold. Advances in Complex Systems 6, 37-45 (2003).
“Chemistry and Biotechnology: A Productive Union Meets New Challenges”  F. H. Arnold, A. Glieder. Current Opinion in Biotechnology 14, 567-569 (2003).

2002

“Directed Evolution of a Genetic Circuit”  Y. Yokobayashi, R. Weiss, F. H. Arnold. Proc. Natl. Acad. Sci. USA 99, 16587-16591 (2002).
“Evolution of the C30 Carotenoid Synthase CrtM for Function in a C40 Pathway”  D. Umeno, A. V. Tobias, F. H. Arnold. Journal of Bacteriology 184, 6690-6699 (2002).
“Laboratory Evolution of a Soluble, Self-Sufficient, Highly Active Alkane Hydroxylase”  A. Glieder, E. T. Farinas, F. H. Arnold. Nature Biotechnology 20, 1135-1139 (2002).
“Regioselectivity and Activity of Cytochrome P450 BM-3 and Mutant F87A in Reactions Driven by Hydrogen Peroxide”  P. C. Cirino, F. H. Arnold. Advanced Synthesis & Catalysis 344, 932-937 (2002).
“Modification of Galactose Oxidase to Introduce Glucose 6-Oxidase Activity”  L. H. Sun, T. Bulter, M. Alcalde, I. P. Petrounia, F. H. Arnold. ChemBiochem 8, 781-783 (2002).
“An Integrated Microfabricated Cell Sorter”  A. Y. Fu, H-P. Chou, C. Spence, F. H. Arnold, S .R. Quake. Analytical Chemistry 74, 2451-2457 (2002).
“Protein Building Blocks Preserved by Recombination”  C. A. Voigt, C. Martinez, Z-G. Wang, S. L. Mayo, F. H. Arnold. Nature Structural Biology 9(7), 553-558 (2002).
“Directed Protein Evolution”  K. M. Mayer, F. H. Arnold. In Encyclopedia of Evolution, Vol. 1 (of 2), 268-271, M. Pagel (Ed.), Oxford University Press, NY, 2002
“Staggered Extension Process (StEP) in vitro Recombination”  A. M. Aguinaldo, F. Arnold. In Methods in Molecular Biology, Vol. 192, PCR Cloning Protocols, 2nd Edition, pp. 235-239 (B.-Y. Chan and H. W. Janes, Eds.), Humana Press Inc., Totowa, NJ, 2002.
“Exploring the Diversity of Heme Enzymes Through Directed Evolution”  P. C. Cirino, F. H. Arnold. In Directed Molecular Evolution of Proteins, S. Brakmann and K. Johnsson (Eds.) Wiley-VCH, Germany, pp. 215-243, 2002.
“A Colorimetric Assay to Quantify Dehydrogenase Activity in Crude Cell Lysates”  K. M. Mayer, F. H. Arnold. Journal of Biomolecular Screening 7(2), 135-140 (2002).
“Protein Engineering of Oxygenases for Biocatalysis”  P. C. Cirino, F. H. Arnold. Current Opinion in Chemical Biology 6, 130-135 (2002).
“Analysis of Shuffled Gene Libraries”  J. M. Joern, P. Meinhold, F. H. Arnold. Journal of Molecular Biology 316, 643-656 (2002).

2001

“Directed Enzyme Evolution”  E. T. Farinas, T. Bulter, F. H. Arnold. Current Opinion in Biotechnology 12, 545-551 (2001).
“Directed Evolution of a Cytochrome P450 Monooxygenase for Alkane Oxidation”  E. T. Farinas, U. Schwaneberg, A. Glieder, F. H. Arnold. Advanced Synthesis & Catalysis 343, 601-606 (2001).
“Dynamic Pattern Formation in a Vesicle-Generating Microfluidic Device”  T. Thorsen, R. W. Roberts, F. H. Arnold, S. R. Quake. Physical Review Letters 86, 4163-4166 (2001).
“Laboratory Evolution of Toluene Dioxygenase to Accept 4-Picoline as a Substrate”  T. Sakamoto, J. M. Joern, A. Arisawa, F. H. Arnold. Applied and Environmental Microbiology 67, 3882-3887 (2001).
“Libraries of Hybrid Proteins from Distantly Related Sequences”  V. Sieber, C. A. Martinez, F. H. Arnold, Nature Biotechnology19, 456-460 (2001).
“Patterns of Adaptation in a Laboratory Evolved Thermophilic Enzyme”  P. L. Wintrode, K. Miyazaki, F. H. Arnold. Biochimica et Biophysica 1549, 1-8 (2001).
“Functional Expression and Stabilization of Horseradish Peroxidase by Directed Evolution in Saccharomyces Cerevisiae  B. Morawski, S. Quan, F. H. Arnold. Biotechnology & Bioengineering 76, 99-107 (2001).
“Cost-Effective Whole-Cell Assay for Laboratory Evolution of Hydroxylases in E. coli”  U. Schwaneberg, C. Otey, P. Cirino, E. Farinas, F. H. Arnold. Journal of Biomolecular Screening 6, 111-117 (2001).
“How Enzymes Adapt: Lessons from Directed Evolution”  F. H. Arnold, P. C. Wintrode, K. Miyazaki, A. Gershenson. Trends in Biochemical Sciences 26, 100-106 (2001).
“Expression and stabilization of galactose oxidase in Escherichia coli by directed evolution”  L. Sun, I.P. Petrounia, M. Yagasaki, G. Bandara and F.H. Arnold, Protein Engineering 14: 699-704 (2001).
“Computationally focusing the directed evolution of proteins”  C.A. Voigt, S.L. Mayo, F.H. Arnold, and Z-G. Wang, Journal of Cellular Biochemistry 84(S37): 58-63 (2001).
“Staggered Extension Process (StEP) in vitro Recombination”  A. M. Aguinaldo, F. H. Arnold. Chapter in PCR Cloning Protocols, Methods in Molecular Biology (2nd Edition) Eds. B. Chan and H. Janes, Humana Press (2001).
“Combinatorial and Computational Challenges for Biocatalyst Design”  F. H. Arnold, Nature 409, 253-257 (2001).
“A Versatile High-Throughput Screen for Dioxygenase Activity Using Solid-Phase Digital Imaging”  J. M. Joern, T. Sakamoto, A. Arisawa, F. H. Arnold. Journal of Biomolecular Screening 6, 219-223 (2001).
A new volume (Vol 55, 2001) of Advances in Protein Chemistry entitled “Evolutionary Protein Design” has been published by Academic Press. This volume, edited by F.H. Arnold, contains excellent contributions from top evolutionary design laboratories: Babbitt, Benkovic, Stemmer, Georgiou, Stevens, Plueckthun, Barbas, Wang, and Arnold. ISBN:0120342553. Advances in Protein Chemistry Vol. 55
“Computational Method to Reduce the Search Space for Directed Protein Evolution”  C. A.Voigt, S. L. Mayo, F. H. Arnold, Z-G. Wang. Proc. Natl. Acad. Sci. USA 98, 3778-3783 (2001).

2000

“Molecular Breeding of Carotenoid Biosynthetic Pathways”  C. Schmidt-Dannert, D. Umeno, F. H. Arnold. Nature Biotechnology 18, 750-753 (2000).
“Functional Expression of Horseradish Peroxidase in Saccharomyces cerevisiae and Pichia pastoris  B. Morawski, Z. Lin, P. Cirino, H. Joo, F. H. Arnold. Protein Engineering 13(5), 377-384 (2000).
“Cold Adaptation of a Mesophilic Subtilisin-like Protease by Laboratory Evolution”  P. L. Wintrode, K. Miyazaki, F. H. Arnold. Journal of Biological Chemistry 275 (41), 31635-31640 (2000).
“Designed Evolution of Enzymatic Properties”  I. P. Petrounia, F. H. Arnold. Current Opinion in Biotechnology 11(4), 325-330 (2000).
“Directed Evolution Study of Temperature Adaptation in a Psychrophilic Enzyme”  K. Miyazaki, P. L. Wintrode, R. A. Grayling, D. N. Rubingh, F. H. Arnold. Journal of Molecular Biology 297, 1015-1026 (2000).
“Tryptophan Phosphorescence Study of Enzyme Flexibility and Unfolding in Laboratory-Evolved Thermostable esterases”  A. Gershenson, J.A. Schauerte, L. Giver, F. H. Arnold. Biochemistry 39, 4658-4665 (2000).
“Enzyme Stabilization by Directed Evolution” A. Gershenson, F. H. Arnold. Genetic Engineering Principles and Methods, Vol. 22, pp. 55-76, Plenum Press (2000).
“Inverting Enantioselectivity by Directed Evolution of Hydantoinase for Improved Production of L-methionine”  O. May, P.T. Nguyen, F. H. Arnold. Nature Biotechnology 18, 317-320 (2000).
“Enzyme Engineering by Directed Evolution”  O. May, C. Voigt, F. H. Arnold. In Enzyme Catalysis in Organic Synthesis,” K. H. Drauz and H. Waldmann (Eds.), pp. 95-138, Vol. 1. Wiley-VCH (2000).
“Temperature Adaptation of Enzymes: Lessons from Laboratory Evolution,”  P. Wintrode, F. H. Arnold. pp. 161-226 in Advances in Protein Chemistry, Evolutionary Approaches to Protein Design,” F. H. Arnold (Ed.), Vol. 55. Academic Press (2000).
“Random Chimeragenesis by Heteroduplex Recombination”  A. A.Volkov, Z. Shao, F. H. Arnold. Methods in Enzymology 328, 447-456 (2000).
“Methods for in vitro DNA Recombination and Random Chimeragenesis”  A. A. Volkov, F. H. Arnold. Methods in Enzymology 328, 447-456 (2000).

1999

“Formation of Indigo by Recombinant Mammalian Cytochrome P450”  E. M. J. Gillam, A. M. A. Aguinaldo, L. M. Notley, D. Kim, R. G. Mundkowski, A. A. Volkov, F. H. Arnold, P. Soucek, J. J. DeVoss, F. P. Guengerich. Biochem. Biophys. Res. Comm. 265, 469-472 (1999).
“A Microfabricated Fluorescence-Activated Cell Sorter”  A. Y. Fu, C. Spence, A. Scherer, F. H. Arnold, S. Quake. Nature Biotechnology 17, 1109-1111 (1999).
“A High Throughput Digital Imaging Screen for the Discovery and Directed Evolution of Oxygenases”  H. Joo, A. Arisawa, Z. Lin, F. H. Arnold. Chemistry & Biology 6(10), 699-706 (1999).
“Unnatural Selection: Molecular Sex for Fun and Profit”  F. H. Arnold. Engineering & Science (Caltech), No. 1/2, pp. 40-50, 1999.
“Exploring Nonnatural Evolutionary Pathways by Saturation Mutagenesis: Rapid Improvement of Protein Function”  K. Miyazaki, F. H. Arnold. Journal of Molecular Evolution 49, 716-720 (1999).
“Engineering a Revolution”  J. Affholter, F. H. Arnold. CHEMTECH 29(9), 34-39 (1999).
“Recombination by in vitro Heteroduplex Formation and in vivo Repair”  A. Volkov, Z. Shao, F. H. Arnold. Nucleic Acids Research 27, e18 (1999).
“A Structural View of Evolutionary Divergence”  B. Spiller, A. Gershenson, F. H. Arnold, R. C. Stevens. Proc. Natl. Acad. Sci. USA96, 12305-12310 (1999).
“Laboratory Evolution of Peroxide-Mediated Cytochrome P450 Hydroxylation”  H. Joo, Z. Lin, F. H. Arnold. Nature 399, 670-673 (1999).
“Directed Evolution of Industrial Enzymes”  C. Schmidt-Dannert, F. H. Arnold. Trends in Biotechnology 17, 135-136 (1999).
“Itching for New Strategies in Protein Engineering”  S. W. Michnick, F. H. Arnold. Nature Biotechnology 17(12), 1159-60 (1999).
“Directed Evolution of Biocatalysts”  F. H. Arnold, A. A. Volkov. Current Opinion in Chemical Biology 3, 54-59 (1999).
Directed Enzyme Evolution” F. H. Arnold, P. L. Wintrode. Chapter for the Encyclopedia of Bioprocess Technology,   M. C. Flickinger and S. W. Drew (Eds.), Wiley, 1999.
“Directed Evolution of Mesophilic Enzymes Into Their Thermophilic Counterparts”  F. H. Arnold, L. Giver, A. Gershenson, H. Zhao, K. Miyazaki. Annals of the New York Academy of Sciences 870, 400-403 (1999).
“Directed Evolution Converts Subtilisin E Into a Functional Equivalent of Thermitase”  H. Zhao, F. H. Arnold, Protein Engineering 12, 47-53 (1999).
“Methods for Optimizing Industrial Enzymes by Directed Evolution” H. Zhao, J. C. Moore, A. A.Volkov, F. H. Arnold. In Manual of Industrial Microbiology and Biotechnology, 2nd Ed. A. L. Demain and J. E. Davies (Eds.) Chapter 49, pp. 597-604, ASM Press, Washington, DC, 1999.

1998

“When Blind is Better: Protein Design by Evolution”  F. H. Arnold. Commentary in Nature Biotechnology 16, 617-618 (1998).
“Directed Evolution of a Thermostable esterase”  L. Giver, A. Gershenson, P. O. Freskgard, F. H. Arnold. Proc. Natl. Acad. Sci. USA 95, 12809-12813 (1998).
“Design by Directed Evolution”  F. H. Arnold. Accounts of Chemical Research 31, 125-131 (1998).
“Combinatorial Protein Design by In vitro DNA Recombination”  L. Giver, F. H. Arnold. Current Opinion in Chemical Biology 2, 335-338 (1998).
“Enzyme Engineering Reaches the Boiling Point”  F. H. Arnold, Commentary in Proc. Natl. Acad. Sci. USA 95, 2035-2036 (1998).
“Molecular Evolution by Staggered Extension Process (StEP) in vitro Recombination”  H. Zhao, L. Giver, Z. Shao, J. A. Affholter, F. H. Arnold. Nature Biotechnology 16, 258-261 (1998).
“Random Priming in vitro Recombination: an Effective Tool for Directed Evolution”  Z. Shao, H. Zhao, L. Giver, F. H. Arnold. Nucleic Acids Research 26, 681-683 (1998).

1997

“Directed Evolution of Enzyme Catalysts”  O. Kuchner, F. H. Arnold. Trends in Biotechnology 15, 523-530 (1997).
“Combinatorial Protein Design: Strategies for Screening Protein Libraries”  H. Zhao, F. H. Arnold. Current Opinion in Structural Biology 7, 480-485 (1997).
“Strategies for the in vitro Evolution of Protein Function: Enzyme Evolution by Random Recombination of Improved Sequences”  J. C. Moore. H.-M. Jin, O. Kuchner, F. H. Arnold. Journal of Molecular Biology 272, 336-347 (1997).
“Functional and Non-Functional Mutations Distinguished by Random Recombination of Homologous Genes”  H. Zhao, F. H. Arnold. Proc. Natl. Acad. Sci. USA 94, 7997-8000 (1997).
“Optimization of DNA Shuffling for High Fidelity Recombination”  H. Zhao, F. H. Arnold. Nucleic Acids Research 25,1307-1308 (1997).
“Optimizing Industrial Enzymes by Directed Evolution”  F. H. Arnold, J. C. Moore. Advances in Biochemical Engineering 58, 1-14 (1997).
“Langmuir Monolayer Characterization of Metal Chelating Lipids for Protein Targeting to Membranes”  D. W. Pack, F. H. Arnold. Chemistry and Physics of Lipids 86(2), 135-152 (1997).

1996

Engineering New Functions and Altering Existing Functions”  Z. Shao, F. H. Arnold. Current Opinion in Structural Biology 6, 513-518 (1996).
“Directed Evolution: Creating Biocatalysts for the Future”  F. H. Arnold. Chemical Engineering Science 51, 5091-5102 (1996).
“Strategy for the Directed Evolution of a Peptide Ligase”  H. Zhao, L. You, F. H. Arnold. Proceedings of the 13th Enzyme Engineering ConferenceAnnals of the New York Academy of Sciences 799, 1-6 (1996).
Directed Evolution of a para-Nitrobenzyl Esterase for Aqueous-Organic Solvents”  J. Moore, F. H. Arnold. Nature Biotechnology 14, 458-467 (1996).
“Two-Dimensional Protein Crystallization via Metal-Ion Coordination by Naturally Occurring Surface Histidines”  W. Frey, W. R. Schief, D. W. Pack, C. Chen, A. Chilkoti, P. Stayton, V. Vogel, F. H. Arnold. Proc. Natl. Acad. Sci. USA 93(10), 4937—4941 (1996).
“Directed Evolution of Subtilisin E in Bacillus subtilis to Enhance Total Activity in Aqueous Dimethylformamide”  L. You and F.H. Arnold. Protein Engineering 9, 77-83 (1996).

1994

“Metal-Mediated Protein Stabilization”  J.-H. Zhang and F.H. Arnold, Trends in Biotechnology 12: 189-192 (1994).

1993

“Tuning the Activity of an Enzyme for Unusual Environments: Sequential Random Mutagenesis of Subtilisin E for Catalysis in Dimethylformamide”  K. Chen, F. H. Arnold. Proc. Natl. Acad. Sci. USA 90, 5618-5622 (1993).
“Protein Engineering for Unusual Environments”  F. H. Arnold. Current Opinion in Biotechnology 4, 450-455 (1993).
“Engineering Proteins for Nonnatural Environments”  F. H. Arnold. FASEB Journal 7, 744-749 (1993).
“Ruthenium-Mediated Protein Cross-Linking and Stabilization”   A. Muheim, R .J. Todd, D. R. Casimiro, H. R. Gray, F. H. Arnold. Journal of the American Chemical Society 115, 5312-5313 (1993).

1991

“Enzyme Engineering for Nonaqueous Solvents. II. Additive Effects of Mutations on the Stability and Activity of Subtilisin E in Polar Organic Media”  K. Q. Chen, A .C. Robinson, M. E. Van Dam, P. Martinez, C. Economou, F. H. Arnold. Biotechnology Progress 7(2), 125-129 (1991).
“Enzyme Engineering for Nonaqueous Solvents: Random Mutagenesis to Enhance Activity of Subtilisin E in Polar Organic Media”  K. Chen, F. H. Arnold. Biotechnology (NY) 9, 1073-1077 (1991).
“Protein Stabilization by Engineered Metal Chelation”   J. Kellis, Jr., R. J. Todd, F. H. Arnold. Biotechnology (NY) 9, 994-995 (1991).
“Engineered Metal-Binding Proteins: Purification to Protein Folding”  F. H. Arnold, B. L. Haymore. Science 252, 1796-1797 (1991).
“Cu(II)-Binding Properties of a Synthetic Metal-Binding Cytochrome c: His-X3-His in an a-Helix”  R. Todd, M. Van Dam, D. Casimiro, B. L. Haymore, F. H. Arnold. Proteins: Struct. Funct. Genet. 10, 156-161 (1991).
“Characterization of His-X3-His Sites in alpha-Helices of Synthetic Metal-Binding Bovine Somatotropin”  S. S. Suh, B. L. Haymore, F. H. Arnold. Protein Engineering 4, 301-305 (1991).

1990

“Engineering Enzymes for Non-Aqueous Solvents”  F. H. Arnold. Trends in Biotechnology 8(9), 244-249 (1990).

1988

“Protein Design for Non-Aqueous Solvents”  F. H. Arnold. Protein Engineering 2(1), 21-25 (1988).