Publications 2004 2018

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2018

Characterization of individual human antibodies that bind pertussis toxin stimulated by acellular immunization

Acquaye-Seedah, E., Reczek, E. E., Russell, H. H., DiVenere, A. M., Sandman, S. O., Collins, J. H., Stein, C. A., Whitehead, T. A. & Maynard, J. A. Jun 1 2018 In : Infection and Immunity. 86, 6, e00004-18

Research output: Contribution to journalArticle

Pertussis Toxin
Immunization
Antibodies
Whooping Cough
Acellular Vaccines

Pro region engineering of nerve growth factor by deep mutational scanning enables a yeast platform for conformational epitope mapping of anti-NGF monoclonal antibodies

Medina-Cucurella, A. V., Zhu, Y., Bowen, S. J., Bergeron, L. M. & Whitehead, T. A. Jan 1 2018 (Accepted/In press) In : Biotechnology and Bioengineering.

Research output: Contribution to journalArticle

Engine mountings
Hangars
Epitope Mapping
Epitopes
Monoclonal antibodies
2017
3 Citations

Fine Epitope Mapping of Two Antibodies Neutralizing the Bordetella Adenylate Cyclase Toxin

Wang, X., Stapleton, J. A., Klesmith, J. R., Hewlett, E. L., Whitehead, T. A. & Maynard, J. A. Mar 7 2017 In : Biochemistry. 56, 9, p. 1324-1336 13 p.

Research output: Contribution to journalArticle

Adenylate Cyclase Toxin
Epitope Mapping
Neutralizing Antibodies
Epitopes
Antibodies
4 Citations

Insights into cellulase-lignin non-specific binding revealed by computational redesign of the surface of green fluorescent protein

Haarmeyer, C. N., Smith, M. D., Chundawat, S. P. S., Sammond, D. & Whitehead, T. A. Apr 1 2017 In : Biotechnology and Bioengineering. 114, 4, p. 740-750 11 p.

Research output: Contribution to journalArticle

Cellulase
Lignin
Green Fluorescent Proteins
Proteins
Adsorption
1 Citations

Negatively Supercharging Cellulases Render Them Lignin-Resistant

Whitehead, T. A., Bandi, C. K., Berger, M., Park, J. & Chundawat, S. P. S. Jul 3 2017 In : ACS Sustainable Chemistry and Engineering. 5, 7, p. 6247-6252 6 p.

Research output: Contribution to journalArticle

Cellulases
Lignin
lignin
Proteins
Cellulose
6 Citations

Single-mutation fitness landscapes for an enzyme on multiple substrates reveal specificity is globally encoded

Wrenbeck, E. E., Azouz, L. R. & Whitehead, T. A. Jun 6 2017 In : Nature Communications. 8, 15695

Research output: Contribution to journalArticle

fitness
mutations
Substrate Specificity
enzymes
Mutation
6 Citations

Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning

Klesmith, J. R., Bacik, J. P., Wrenbeck, E. E., Michalczyk, R. & Whitehead, T. A. Feb 28 2017 In : Proceedings of the National Academy of Sciences of the United States of America. 114, 9, p. 2265-2270 6 p.

Research output: Contribution to journalArticle

Solubility
Enzymes
Mutation
Proteins
Phosphotransferases
2016
4 Citations
Clostridium cellulolyticum
Clostridium thermocellum
High-Throughput Nucleotide Sequencing
Clostridium
Benchmarking
5 Citations

Haplotype-phased synthetic long reads from short-read sequencing

Stapleton, J. A., Kim, J., Hamilton, J. P., Wu, M., Irber, L. C., Maddamsetti, R., Briney, B., Newton, L., Burton, D. R., Brown, C. T., Chan, C., Buell, C. R. & Whitehead, T. A. Jan 1 2016 In : PLoS One. 11, 1, e0147229

Research output: Contribution to journalArticle

Haplotypes
haplotypes
Genes
env Genes
DNA
14 Citations

Plasmid-based one-pot saturation mutagenesis

Wrenbeck, E. E., Klesmith, J. R., Stapleton, J. A., Adeniran, A., Tyo, K. E. J. & Whitehead, T. A. Nov 1 2016 In : Nature Methods. 13, 11, p. 928-930 3 p.

Research output: Contribution to journalArticle

Mutagenesis
Plasmids
Libraries
Scanning
2015
11 Citations

Comprehensive Sequence-Flux Mapping of a Levoglucosan Utilization Pathway in E. coli

Klesmith, J. R., Bacik, J. P., Michalczyk, R. & Whitehead, T. A. Nov 20 2015 In : ACS Synthetic Biology. 4, 11, p. 1235-1243 9 p.

Research output: Contribution to journalArticle

Escherichia coli
Enzymes
Fluxes
Mutation
Gene encoding
10 Citations

Computational redesign of the lipid-facing surface of the outer membrane protein OmpA

Stapleton, J. A., Whitehead, T. A. & Nanda, V. Aug 4 2015 In : Proceedings of the National Academy of Sciences of the United States of America. 112, 31, p. 9632-9637 6 p.

Research output: Contribution to journalArticle

Membrane Proteins
Lipids
Protein Engineering
Cell Membrane
Escherichia coli
16 Citations

High-resolution sequence-function mapping of full-length proteins

Kowalsky, C. A., Klesmith, J. R., Stapleton, J. A., Kelly, V., Reichkitzer, N. & Whitehead, T. A. Mar 19 2015 In : PLoS One. 10, 3, e0118193

Research output: Contribution to journalArticle

Practice Guidelines
High-Throughput Nucleotide Sequencing
DNA libraries
Gene Library
Genes
1 Citations

Introduction to the Rosetta Special Collection

Khare, S. D. & Whitehead, T. A. Dec 1 2015 In : PLoS One. 10, 12, 0144326

Research output: Contribution to journalArticle

Library Science
Industrial research
Research
Software
4 Citations

Producing Glucose 6-phosphate from cellulosic biomass: Structural insights into levoglucosan bioconversion

Bacik, J. P., Klesmith, J. R., Whitehead, T. A., Jarboe, L. R., Unkefer, C. J., Mark, B. L. & Michalczyk, R. Oct 30 2015 In : Journal of Biological Chemistry. 290, 44, p. 26638-26648 11 p.

Research output: Contribution to journalArticle

Bioconversion
Glucose-6-Phosphate
Biomass
Phosphotransferases
Sugars
17 Citations

Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing

Kowalsky, C. A., Faber, M. S., Nath, A., Dann, H. E., Kelly, V. W., Liu, L., Shanker, P., Wagner, E. K., Maynard, J. A., Chan, C. & Whitehead, T. A. Oct 30 2015 In : Journal of Biological Chemistry. 290, 44, p. 26457-26470 14 p.

Research output: Contribution to journalArticle

Epitope Mapping
High-Throughput Nucleotide Sequencing
Mutagenesis
Epitopes
Antibodies
2 Citations

Removal and upgrading of lignocellulosic fermentation inhibitors by in situ biocatalysis and liquid-liquid extraction

Tomek, K. J., Saldarriaga, C. R. C., Velasquez, F. P. C., Liu, T., Hodge, D. B. & Whitehead, T. A. Mar 1 2015 In : Biotechnology and Bioengineering. 112, 3, p. 627-632 6 p.

Research output: Contribution to journalArticle

ferulic acid
Biocatalysis
Liquid-Liquid Extraction
Fermentation
Guaiacol
2014
47 Citations

Lignin triggers irreversible cellulase loss during pretreated lignocellulosic biomass saccharification

Gao, D., Haarmeyer, C., Balan, V., Whitehead, T. A., Dale, B. E. & Chundawat, S. P. S. Nov 27 2014 In : Biotechnology for Biofuels. 7, 1, 0175

Research output: Contribution to journalArticle

Cellulases
Saccharification
Cellulase
Lignin
Biomass
20 Citations

The interrelationship between promoter strength, gene expression, and growth rate

Bienick, M. S., Young, K. W., Klesmith, J. R., Detwiler, E. E., Tomek, K. J. & Whitehead, T. A. Oct 6 2014 In : PLoS One. 9, 10, e109105

Research output: Contribution to journalArticle

Gene expression
promoter regions
Gene Expression
gene expression
protein synthesis
2012
160 Citations

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing

Whitehead, T. A., Chevalier, A., Song, Y., Dreyfus, C., Fleishman, S. J., De Mattos, C., Myers, C. A., Kamisetty, H., Blair, P., Wilson, I. A. & Baker, D. Jun 2012 In : Nature Biotechnology. 30, 6, p. 543-548 6 p.

Research output: Contribution to journalArticle

High-Throughput Nucleotide Sequencing
Human Influenza
Proteins
H1N1 Subtype Influenza A Virus
Monoclonal antibodies
2011
92 Citations

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

Fleishman, S. J. , Whitehead, T. A. , Strauch, E. M. , Corn, J. E. , Qin, S. , Zhou, H. X. , Mitchell, J. C. , Demerdash, O. N. A. , Takeda-Shitaka, M. , Terashi, G. , Moal, I. H. , Li, X. , Bates, P. A. , Zacharias, M. , Park, H. , Ko, J. S. , Lee, H. , Seok, C. , Bourquard, T. , Bernauer, J. & 76 others Poupon, A., Azé, J., Soner, S., Ovali, Ş. K., Ozbek, P., Tal, N. B., Haliloglu, T., Hwang, H., Vreven, T., Pierce, B. G., Weng, Z., Pérez-Cano, L., Pons, C., Fernández-Recio, J., Jiang, F., Yang, F., Gong, X., Cao, L., Xu, X., Liu, B., Wang, P., Li, C., Wang, C., Robert, C. H., Guharoy, M., Liu, S., Huang, Y., Li, L., Guo, D., Chen, Y., Xiao, Y., London, N., Itzhaki, Z., Schueler-Furman, O., Inbar, Y., Potapov, V., Cohen, M., Schreiber, G., Tsuchiya, Y., Kanamori, E., Standley, D. M., Nakamura, H., Kinoshita, K., Driggers, C. M., Hall, R. G., Morgan, J. L., Hsu, V. L., Zhan, J., Yang, Y., Zhou, Y., Kastritis, P. L., Bonvin, A. M. J. J., Zhang, W., Camacho, C. J., Kilambi, K. P., Sircar, A., Gray, J. J., Ohue, M., Uchikoga, N., Matsuzaki, Y., Ishida, T., Akiyama, Y., Khashan, R., Bush, S., Fouches, D., Tropsha, A., Esquivel-Rodríguez, J., Kihara, D., Stranges, P. B., Jacak, R., Kuhlman, B., Huang, S. Y., Zou, X., Wodak, S. J., Janin, J. & Baker, D. Nov 25 2011 In : Journal of Molecular Biology. 414, 2, p. 289-302 14 p.

Research output: Contribution to journalArticle

Proteins
Physical Chemistry
Static Electricity
Thermodynamics
Protein Binding
320 Citations

Computational design of proteins targeting the conserved stem region of influenza hemagglutinin

Fleishman, S. J., Whitehead, T. A., Ekiert, D. C., Dreyfus, C., Corn, J. E., Strauch, E. M., Wilson, I. A. & Baker, D. May 13 2011 In : Science. 332, 6031, p. 816-821 6 p.

Research output: Contribution to journalArticle

Hemagglutinins
Protein Transport
Human Influenza
H1N1 Subtype Influenza A Virus
Proteins
25 Citations

Hotspot-centric de novo design of protein binders

Fleishman, S. J., Corn, J. E., Strauch, E. M., Whitehead, T. A., Karanicolas, J. & Baker, D. Nov 11 2011 In : Journal of Molecular Biology. 413, 5, p. 1047-1062 16 p.

Research output: Contribution to journalArticle

Proteins
Hemagglutinins
Computational Biology
Human Influenza
2010
15 Citations

Rosetta in CAPRI rounds 13-19

Fleishman, S. J., Corn, J. E., Strauch, E. M., Whitehead, T. A., Andre, I., Thompson, J., Havranek, J. J., Das, R., Bradley, P. & Baker, D. Nov 15 2010 In : Proteins: Structure, Function and Bioinformatics. 78, 15, p. 3212-3218 7 p.

Research output: Contribution to journalArticle

Articular Range of Motion
RNA
Sampling
Macromolecules
beta-Strand Protein Conformation
2009
24 Citations

Biotemplated metal nanowires using hyperthermophilic protein filaments

Slocik, J. M., Kim, S. N., Whitehead, T. A., Clark, D. S. & Naik, R. R. Sep 18 2009 In : Small. 5, 18, p. 2038-2042 5 p.

Research output: Contribution to journalArticle

Nanowires
Metals
Nanoparticles
Proteins
Gold
62 Citations

Mechanical nanosensor based on fret within a thermosome: Damage-reporting polymeric materials

Bruns, N., Pustelny, K., Bergeron, L. M., Whitehead, T. A. & Clark, D. S. Jul 20 2009 In : Angewandte Chemie - International Edition. 48, 31, p. 5666-5669 4 p.

Research output: Contribution to journalArticle

Thermosomes
Chaperonins
Nanosensors
Polymers
Proteins
8 Citations

Rational shape engineering of the filamentous protein γ prefoldin through incremental gene truncation

Whitehead, T. A., Je, E. & Clark, D. S. 2009 In : Biopolymers. 91, 6, p. 496-503 8 p.

Research output: Contribution to journalArticle

Protein Engineering
Genes
Proteins
Quaternary Protein Structure
Methanocaldococcus
24 Citations

Self-renaturing enzymes: Design of an enzyme-chaperone chimera as a new approach to enzyme stabilization

Bergeron, L. M., Gomez, L., Whitehead, T. A. & Clark, D. S. Apr 1 2009 In : Biotechnology and Bioengineering. 102, 5, p. 1316-1322 7 p.

Research output: Contribution to journalArticle

Penicillin Amidase
Enzymes
Stabilization
Chitin
Immobilization
19 Citations

Tying up the loose ends: Circular permutation decreases the proteolytic susceptibility of recombinant proteins

Whitehead, T. A., Bergeron, L. M. & Clark, D. S. Oct 2009 In : Protein Engineering, Design and Selection. 22, 10, p. 607-613 7 p.

Research output: Contribution to journalArticle

Recombinant proteins
Recombinant Proteins
Proteolysis
Proteins
Thermosomes
2008
8 Citations

Controlling the self-assembly of a filamentous hyperthermophilic chaperone by an engineered capping protein

Whitehead, T. A., Meadows, A. L. & Clark, D. S. Jul 2008 In : Small. 4, 7, p. 956-960 5 p.

Research output: Contribution to journalArticle

Self assembly
Proteins
Nanostructures
Circular dichroism spectroscopy
Sequence Alignment
2007
19 Citations

A filamentous molecular chaperone of the prefoldin family from the deep-sea hyperthermophile Methanocaldococcus jannaschii

Whitehead, T. A., Boonyaratanakornkit, B. B., Höllrigl, V. & Clark, D. S. Apr 2007 In : Protein Science. 16, 4, p. 626-634 9 p.

Research output: Contribution to journalArticle

Methanocaldococcus
Molecular Chaperones
Oceans and Seas
Archaea
Group II Chaperonins
2005
36 Citations

Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non-lethal cold shock

Boonyaratanakornkit, B. B., Simpson, A. J., Whitehead, T. A., Fraser, C. M., El-Sayed, N. M. A. & Clark, D. S. Jun 2005 In : Environmental Microbiology. 7, 6, p. 789-797 9 p.

Research output: Contribution to journalArticle

Methanococcus
Methanocaldococcus
cold stress
lethal genes
Shock
2004
56 Citations

Minimal protein-folding systems in hyperthermophilic archaea

Laksanalamai, P., Whitehead, T. A. & Robb, F. T. Apr 2004 In : Nature Reviews Microbiology. 2, 4, p. 315-324 10 p.

Research output: Contribution to journalArticle

Archaeal Genome
Hydrothermal Vents
Hot Springs
Protein Folding
Archaea