Recent Publications


A. Ramasubramanian, R. Muckom, C. Sugnaux, C. Fuentes, B.L. Ekerdt, D.S. Clark, K.E. Healy, D.V. Schaffer, “High-Throughput Discovery of Targeted, Minimally Complex Peptide Surfaces for Human Pluripotent Stem Cell Culture,” ACS Biomaterials Science & Engineering, 7, 1344 (2021).

J. Huang, Z. Liu, B. Bloomer, D.S. Clark, A. Mukhopadhyay, J. Keasling, J. Hartwig, “Unnatural Biosynthesis by an Engineered Microorganism with Heterologously Expressed Natural Enzymes and an Artificial Metalloenzyme,”

A. J. Abel, D. S. Clark, “A comprehensive modeling analysis of formate‐mediated microbial electrosynthesis,” ChemSusChem, 14, 344 (2021).


A. Berliner, J.M. Hilzinger,  A.J. Abel, M. McNulty, G. Makrygiorgos, N.J. Averesch, S. Sen Gupta, A. Benvenuti, D. Caddell, S. Cestellos-Blanco, A. Doloman, S. Friedline, D. Ho, W. Gu, A. Hill, P. Kusuma, I. Lipsky, M. Mirkovic, J. Meraz, V. Pane, K.B. Sander, F. Shi, J.M. Skerker, A. Styer, K. Valgardson, K. Wetmore,  S. Woo, Y. Xiong, K. Yates, C. Zhang, S. Zhen, B. Bugbee, D. Coleman-Derr, A. Mesbah, S. Nandi, R.W. Waymouth, P. Yang, C.S. Criddle, K.A. McDonald, A.A. Menezes, L.C. Seefeldt, D.S. Clark, A.P. Arkin,  “Towards a Biomanufactory on Mars,” Preprints, 2020120714 (2020) DOI: 10.20944/preprints202012.0714.v1

R. Muckom, X. Bao, E. Tran, E. Chen, A. Murugappan, J. S. Dordick, D. S. Clark, D. V. Schaffer, “High-throughput 3D screening for differentiation of hPSC-derived cell therapy candidates,” Science advances, 6 (32), eaaz1457 (2020) DOI: 10.1126/sciadv.aaz1457  

D. L. Winter, H. Iranmanesh, D. S. Clark, D. J. Glover, “Design of Tunable Protein Interfaces Controlled by Post-Translational Modifications,” ACS Synthetic Biology, 9 (8), 2132-2143 (2020) DOI: 10.1021/acssynbio.0c00208

S. Lim, D. S. Clark, and D. J. Glover, “Production of Multicomponent Protein Templates for the Positioning and Stabilization of Enzymes,” Protein Nanotechnology. New York: Humana Press, 2020. 101-115.

S. Lim, J. Kim, Y.Kim, D. Xu, D.S. Clark, “CRISPR/Cas-directed programmable assembly of multi-enzyme complexes,” Chemical Communications (2020).

J.B. McCluskey, D.S. Clark, and D.J. Glover, “Functional applications of nucleic acid-protein hybrid nanostructures,” Trends in Biotechnology (2020), in press.

T.A. Whitehead, S. Banta, W.E. Bentley, M.J. Betenbaugh, C. Chan, D.S. Clark, C.A. Hoesli, M.C. Jewett, B. Junker, M. Koffas, R. Kshirsagar, A. Lewis, CT. Li, C. Maranas, E.T. Papoutsakis, K.L.J. Prather, S. Schaffer, L. Segatori, and I. Wheeldon, “The Importance and Future of Biochemical Engineering,” Biotechnology and Bioengineering (2020).

Y.X. Chen, N.L. Ing, F. Wang, D. Xu, N.B. Sloan, N.T. Lam, D.L. Winter, E.H. Egelman, A.I. Hochbaum, D.S. Clark, D.J. Glover, “Structural Determination of a Filamentous Chaperone to Fabricate Electronically Conductive Metalloprotein Nanowires,” ACS Nano (2020).


R. Muckom, S. McFarland, C. Yang, B. Perea, M. Gentes, A. Murugappan, E. Tran, J. S. Dordick, D. S. Clark, and D. V. Schaffer. “High‐Throughput Combinatorial Screening Reveals Interactions Between Signaling Molecules that Regulate Adult Neural Stem Cell Fate,” Biotechnology and Bioengineering, 116, 193 (2019).

G. J. Nierode, S. Gopal, P. Kwon, D. S. Clark, D. V. Schaffer, and J. S. Dordick. “High‐throughput identification of factors promoting neuronal differentiation of human neural progenitor cells in microscale 3D cell culture,” Biotechnology and Bioengineering, 116, 168 (2019).

S. Lim, G. A. Jung, R. J. Muckom, D. J. Glover, and D. S. Clark. “Engineering biorthogonal protein-polymer hybrid hydrogel as a functional protein immobilization platform,” Chemical Communications, 55, 806-809 (2019).

D. J. Glover, D. Xu, and D. S. Clark. “Shaping the future of protein engineering,” Biochemistry, (2019).

S. Lim, G. A. Jung, D. J. Glover, and D. S. Clark, “Enhanced enzyme activity through scaffolding on customizable self-assembling protein filaments,” Small (inside cover article), 15, 1805558 (2019).

Y. Gu, S. N. Natoli, Z. Liu, D. S. Clark, J. F. Hartwig, “Site-Selective Functionalization of (sp3) C‐H Bonds Catayzed by Artificial Metalloenzymes Containing an Iridium‐Porphyrin Cofactor,” Angewandte Chemie, 58, 13954 (2019).

X. Bao, M. M. Adil, R. Muckom, J. A. Zimmermann, A. Tran, N. Suhy, Y. Xu, R. G. Sampayo, D. S. Clark, and D. V. Schaffer, “Gene Editing to Generate Versatile Human Pluripotent Stem Cell Reporter Lines for Analysis of Differentiation and Lineage Tracing,” Stem Cells, (2019).


D. S. Clark and D. J. Glover. “Controlled Assembly of the Filamentous Chaperone Gamma-Prefoldin into Defined Nanostructures,” Protein Scaffolds. Methods in Molecular Biology. New York: Humana Press, 2018. 293-306.

L. J. Bonassar, M. P. DeLisa, D. A. Putnam, D. S Clark, C. Fischbach-Teschl, D. A. Hammer, K. H. Lee, J. B. Lucks, C. Reinhart-King, M. Saltzman, and A. Stroock. “Michael L. Shuler Tribute,” Biotechnology and Bioengineering, 115, 1642 (2018).

C. Khosla, D. S. Clark, and W. Chen. “A tribute to Professor Jay Bailey: A pioneer in biochemical engineering,” AIChE Journal (2018).

R. Muckom, S. McFarland, C. Yang, B. Perea, M. Gentes, A. Murugappan, E. Tran, J. S. Dordick, D. S. Clark, and D. V. Schaffer. “High‐Throughput Combinatorial Screening Reveals Interactions Between Signaling Molecules that Regulate Adult Neural Stem Cell Fate,” Biotechnology and Bioengineering (2018).

G. J. Nierode, S. Gopal, P. Kwon, D. S. Clark, D. V. Schaffer, and J. S. Dordick. “High‐throughput identification of factors promoting neuronal differentiation of human neural progenitor cells in microscale 3D cell culture,” Biotechnology and Bioengineering (2018).

D. J. Glover, S. Lim, D. Xu, N. B. Sloan, Y. Zhang, and D. S. Clark. “Assembly of multicomponent protein filaments using engineered subunit interfaces,” ACS Synthetic Biology, 7, 2447 (2018).

S. Lim, D. J. Glover, and D. S. Clark. “Prefoldins in Archaea,” Prefoldins: The New Chaperones, Advances in Experimental Medicine and Biology 1106. N. Djouder (ed.), Springer Nature Switzerland (2018). 11-23.


H. M. Key, P. Dydio, Z. Liu, J. Y -E Rha, A. Nazarenko, V. Seyedkazemi, D. S. Clark, J. F. Hartwig, "Beyond Iron: Iridium-Containing P450 Enzymes for Selective Cyclopropanations of Structurally Diverse Alkenes," ACS Central Science, 3, 302 (2017).

H. C. Lo, J. D. Ryan, J. B. Kerr, D. S. Clark, and R. H. Fish, "Bioorganometallic chemistry: Co-factor regeneration, enzyme recognition of biomimetric 1, 4-NADH analogs, and organic synthesis; tandem catalyzed regioselective formation of N-substituted-1, 4-dihydronicotinamide derivatives with [Cp* Rh (bpy) H]+, coupled to chiral S-alcohol formation with HLADH, and engineered cytochrome P450s, for selective CH oxidization reactions," Journal of Organometallic Chemistry, 839, 38 (2017). 

V. W. Wu, C. M. Dana, A. T. Iavarone, D. S. Clark, and N. L. Glass, "Identification of Glutaminyl Cyclase Genes Involved in Pyroglutamate Modification of Fungal Lignocellulolytic Enzymes," mBio, 8, e02231 (2017).

P. Dydio, H. M. Key, H. Hayashi. D. S. Clark, and J. F. Hartwig, "Chemoselective, Enzymatic CH Bond Amination Catalyzed by a Cytochrome P450 Containing an Ir (Me)-PIX Cofactor," Journal of the American Chemical Society, 139, 1750 (2017).

F. Dean Toste, 
Pazhamalai Anbarasan, 
Joseph B. Binder, 
Paul A. Willems, 
Douglas S. Clark, 
Zach Baer, 
Sanil Sreekumar, 
Harvey W. Blanch
"Method to Convert Fermentation Mixture into Fuels,"


P. Dydio, H. M. Key, A. Nazarenko, J. Y.-E. Rha, V. Seyedkazemi, D. S. Clark, and J. F. Hartwig, "An artificial metalloenzyme with the kinetics of native enzymes," Science, 354, 102 (2016).

Carly E Anderson, Nico R Cha, Alexander D Lindsay, Douglas S Clark, David B Graves, "The Role of Interfacial Reactions in Determining Plasma–Liquid Chemistry,"  Plasma Chemistry and Plasma Processing,

G. J. Nierode, B.C. Perea, S. K. McFarland, J. F. Pascoal, D.S. Clark, D. V. Schaffer, J. S. Dordick, "High-Throughput Toxicity and Phenotypic Screening of 3D Human Neural Progenitor Cell Cultures on a Microarray Chip Platform," Stem Cell Reports,

D. J. Glover, D. S. Clark, "Protein Calligraphy: A New Concept Begins To Take Shape", ACS Central Science,

PATENT: Zachary C Baer, Harvey W Blanch, Douglas S Clark, Sanil Sreekumar, Dean F Toste, Gorkem Gunbas, Konstantinos A Goulas, Amit A Gokhale, Joseph B Binder, "Methods to Produce Fuels,"

PATENT: Joel Edward Graham, Melinda E Clark, Frank Thomson Robb, Douglas S Clark, Harvey W Blanch, "Polypeptides for use in the deconstruction of cellulose,"

PATENT: H.A. Chokhawala, T.W. Kim, H.W. Blanch and D.S. Clark "Thermophilic Mutants of Trichoderma Reesei Endoglucanase I,

Paul W Wolski, Craig M Dana, Douglas S Clark, Harvey W Blanch, "Engineering ionic liquid-tolerant cellulases for biofuels production," Protein Engineering Design and Selection,

Zachary C Baer, Sebastian Bormann, Sanil Sreekumar, Adam Grippo, F Dean Toste, Harvey W Blanch, Douglas S Clark, "Co‐production of acetone and ethanol with molar ratio control enables production of improved gasoline or jet fuel blends," Biotech. Bioeng.,

M. E. Atreya, K. L. Strobel, and D. S. Clark, “Alleviating product inhibition in cellulase enzyme Cel7A,” Biotechnol. Bioeng., 113, 330 (2016).

K. L. Strobel, K. A. Pfeiffer, H. W. Blanch, and D. S. Clark, “Engineering Cel7A carbohydrate binding module and linker for reduced lignin inhibition,” Biotechnol. Bioeng.,

Z. M. Carrico, K. L. Strobel, M. E. Atreya, D. S. Clark, and M. B. Francis, “Simultaneous selection and counter-selection for the directed evolution of proteases in E. coli using a cytoplasmic anchoring strategy,” Biotechnol. Bioeng.,

H. M. Key, P. Dydio, D. S. Clark, and J. F. Hartwig, "Abiological catalysis by artificial haem proteins containing noble metals in place of iron," Nature,

D.J. Glover, L. Giger, S.S. Kim, R.R. Naik, and D.S. Clark, "Geometrical Assembly of Ultrastable Protein Templates For Nanomaterials," Nat. Commun., 


D.J. Glover, and D.S. Clark, "Oligometric Assembly Is Required for Chaperone Activity of the Filamentous γ-prefoldin," FEBS Journal, 282, 2985 (2015).

K. A. Pfeiffer, H. Sorek, C. M. Roche, K. L. Strobel, H. W. Blanch, and D. S. Clark, “Evaluating endoglucanase Cel7B-lignin interaction mechanisms and kinetics using quartz crystal microgravimetry,” Biotechnol. Bioeng., 112, 2256 (2015).

Hanna M Key, Douglas S Clark, John F Hartwig. "Generation, Characterization, and Tunable Reactivity of Organometallic Fragments Bound to a Protein Ligand.Journal of the American Chemical Society, Volume 137, Issue 25, Pages 8261-8268, 2015-07-01.

Douglas S Clark, Isao Karube, Koji Sode, et al.  "Klaus Mosbach Tribute."  Biotechnology and Bioengineering, Volume 112, Issue 4, Pages 645-647, 2015-04.

Sanil Sreekumar, Zachary C Baer, Anbarasan Pazhamalai, et al.  "Production of an acetone-butanol-ethanol mixture from Clostridium acetobutylicum and its conversion to high-value biofuels.Nature Protocols, Volume 10, Issue 3, 2015-03.

Harshal A Chokhawala, Christine M Roche, Tae-Wan Kim, Meera E Atreya, Neeraja Vegesna, Craig M Dana, Harvey W Blanch1, Douglas S Clark. "Mutagenesis of Trichoderma reesei endoglucanase I: impact of expression host on activity and stability at elevated temperatures." BMC Biotechnology (2015).

Chaeyoung Shin, Zachary C. Baer, X. Chelsea Chenc, A. Evren Ozcama, Douglas S. Clark, Nitash P. Balsara. "Block Copolymer Pervaporation Membrane for in situ Product Removal during Acetone-Butanol-Ethanol Fermentation." Journal of Membrane Science (2015).


S. J. Kwon, D. W. Lee, D. A. Shah, B. Ku, S. Y. Jeon, K. Solanki, J. D. Ryan, D. D. S. Clark, J. S. Dordick, M.Y. Lee, “High-throughput and combinatorial gene expression on a chip for metabolism-induced toxicology screening.” Nature Comm., 5, 3739 (2014).

H. Piao, J. Froula, C. Du, T-W. Kim, E. R. Hawley, S. Bauer, Z. Wang, N. Ivanova, D. S. Clark, H-P. Klenk, M. Hess, “Identification of novel biomass-degrading enzymes from genomic dark matter: Populating genomic sequence space with functional annotation.” Biotechnol. Bioeng., 8, 1550 (2014).

M. J. Pavlovich, T. Ono, C. Galleher, B. Curtis, D. S. Clark, Z. Macala, D. B. Graves, “Air spark-like plasma source for antimicrobial NOx generation.” J. Phys. D: Appl. Phys. 47 505202 (2014).

S. Sreekumar, Z.C. Baer, E. Gross, S. Padmanaban, K. Goulas, G. Gunbas, S. Alayoglu, H.W. Blanch, D.S. Clark, F.D. Toste, "Chemocatalytic Upgrading of Tailored Fermentation Products toward Biodiesel." ChemSusChem,

S. Bormann, Z.C. Baer, S. Sreekumar, J.M. Kuchenreuther, F.D. Toste, H.W. Blanch, D.S. Clark, "Engineering Clostridium acetobutylicum for production of kerosene and diesel blendstock precursors." Metabolic Engineering, 25 (2014) 124-130.

C.M. Roche, N.L. Glass, H.W. Blanch, D.S. Clark, "Engineering the filamentous fungus Neurospora crassa for lipid production from lignocellulosic biomass." Biotechnol. Bioeng.,

C.M. Dana, A. Dotson-Fagerstrom, C.M. Roche, S.M. Kal, H.A. Chokhawala, H.W. Blanch, D.S. Clark, "The importance of pyroglutamate in cellulase Cel7A." Biotechnol. Bioeng.,

Douglas S. Clark, 
Timothy Whitehead, 
Frank T. Robb, 
Pongpan Laksanalamai, 
Anchalee Jiemjit
Heterologous Expression of Extremophilic Heat Shock Proteins and Chaperones in Microorganisms to Increase Tolerance to Toxic Compounds,"


C. M. Roche, H.W. Blanch, D.S. Clark, N.L. Glass, "Physiological role of acyl coenzyme A synthetase homologs in lipid metabolism in Neurospora crassa." Eukaryot. Cell. 12 (2013), 1244-57.

Matt Pavlovich and Connor Galleher (Graves Lab) attend the Clinton Global Initiative University annual meeting in St. Louis, where they discussed plasma disinfection with President Clinton and demonstrated a prototype device. Learn more about the project to develop a low-cost, portable plasma disinfector.

M.J. Pavlovich, H. Chang, Y. Sakiyama, D.S. Clark, D.B. Graves, “Ozone correlates with antibacterial effects from indirect air dielectric barrier discharge treatment of water.” J. Phys. D: Appl. Phys., 46 (2013) 145202.

J.M. Fox, H.W. Blanch, D.S. Clark, “A single-molecule analysis reveals morphological targets for cellulase synergy.” Nature Chemical Biology, 9 (2013) 356-361.

In the press: Nature Chem Bio News and Views, LBNL News center

M.J. Pavlovich, Z. Chen, Y. Sakiyama, D.S. Clark, D.B. Graves, “Effect of Discharge Parameters and Surface Characteristics on Ambient-Gas Plasma Disinfection.” Plasma Processes and Polymers, 10, (2013) 69-76.


P. Anbarasan, Z.C. Baer, S. Sreekumar, E. Gross, J.B. Binder, H.W. Blanch, D.S. Clark, F.D. Toste, “Integration of chemical catalysis with extractive fermentation to produce fuels.” Nature, 491 (2012) 235-239. In the press: UC Berkeley News, ABC 7 Local News

K. Shill, K. Miller, D.S. Clark, H.W. Blanch, “A model for optimizing the enzymatic hydrolysis of ionic liquid-pretreated lignocellulose.” Bioresour. Technol., 126 (2012) 290-297.

D.J. Glover, L. Giger, J.R. Kim, D.S. Clark, “Engineering protein filaments with enhanced thermostability for nanomaterials.” Biotechnol. J., 8:2 (2012) 228-236.

S. Huffer, C.M. Roche, H.W. Blanch, D.S. Clark, “Escherichia coli for biofuel production: bridging the gap from promise to practice.” Trends Biotechnol., 30:10 (2012) 538-545.

C.M. Dana, P. Saija, S.M. Kal, M.B. Bryan, H.W. Blanch, D.S. Clark, “Biased clique shuffling reveals stabilizing mutations in cellulase Cel7A.” Biotechnol. Bioeng., 109:11, (2012) 2710-2719.

E. Schneider, D.S. Clark, “Cytochrome P450 (CYP) enzymes and the development of CYP biosensors.” Biosens. Bioelectron., 39:1 (2012) 1-13.

M.J. Liszka, M.E. Clark, E. Schneider, D.S. Clark, “Nature versus nurture: developing enzymes that function under extreme conditions.” Annu. Rev. Chem. Biomol. Eng., 3 (2012) 77-102.

J.M. Fox, S.E. Levine, H.W. Blanch, D.S. Clark, “An evaluation of cellulose saccharification and fermentation with an engineered Saccharomyces cerevisiae capable of cellobiose and xylose utilization.” Biotech J., 7:3 (2012) 361-373.

J.M. Fox, S.E. Levine, D.S. Clark, H.W. Blanch, “Initial- and processive-cut products from cellobiohydrolase-catalyzed hydrolysis of cellulose reveal rate-limiting steps and role of companion enzymes.” Biochem., 51:1 (2012) 442-452.

Q. Xin, K. Pfeiffer, J.M. Prausnitz, D.S. Clark, H.W. Blanch, “Extraction of lignins from aqueous-ionic liquid mixtures by organic solvents.” Biotechnol. Bioeng., 109:2 (2012) 346-352.

PATENT: J.S. Dordick, D.S. Clark, M.Y. Lee, and R. A. Kumar, "Three-Dimensional Cellular Array Chip and Platform for Toxicology Assays,"


M.J. Traylor, M.J. Pavlovich, S. Karim, P. Hait, Y. Sakiyama, D.S. Clark, D.B. Graves, “Long-term antibacterial efficacy of air plasma-activated water.” J. Phys. D: Appl. Phys., 44, (2011).

P.W. Wolski, D.S. Clark, H.W. Blanch, “Green fluorescent protein as a screen for enzymatic activity in ionic liquid–aqueous systems for in situ hydrolysis of lignocellulose.” Green Chem., 13, (2011).

T.W. Kim, H.A. Chokhawala, M. Hess, C.M. Dana, Z. Baer, A. Sczyrba, E.M. Rubin, H.W. Blanch, D.S. Clark, “High-throughput in vitro glycoside hydrolase (HIGH) screening for enzyme discovery.” Angew. Chim. Int. Ed., (2011).

M.J. Traylor, J.D. Ryan, E.S. Arnon, J.S. Dordick, D.S. Clark, “Rapid and quantitative measurement of metabolic stability without chromatography or mass spectrometry.” JACS, 133(37), (2011).

S. Huffer, M.E. Clark, J.C. Ning, H.W. Blanch, D.S. Clark, “Role of alcohols in growth, lipid composition, and membrane fluidity of yeasts, bacteria, and archaea.” Appl. Environ. Microbiol. (2011).

J.E. Graham, M.E. Clark, D.C. Nadler, S. Huffer, H.A. Chokhawala, S.E. Rowland, H.W. Blanch, D.S. Clark, F.T. Robb. “Identification and characterization of a multidomain hyperthermophilic cellulase from an archaeal enrichment.” Nat. Commun., 2:375, (2011).

S.E. Levine, J.M. Fox, H.W. Blanch, D.S. Clark, “A mechanistic model for rational design of optimal cellulase mixtures.” Biotechnol. Bioeng., Epub ahead of print, (2011).

C.T. Trinh, J. Li, H.W. Blanch, D.S. Clark, “Redesigning Escherichia coli metabolism for anaerobic production of isobutanol.” Appl. Environ. Microbiol., 77(14), (2011).

M. Hess, A.Sczyrba, R. Egan, T.-W. Kim, H. Chokhawala, G. Schroth, S. Luo, D.S. Clark, F. Chen, T. Zhang, R.I. Mackie, L.A. Pennacchio, S.G. Tringe, A. Visel, T. Woyke, Z. Wang. E.M. Rubin, “Metagenomic discovery of biomass-degrading genes and genomes from cow rumen.” Science, 331, (2011).

K. Shill, S. Padmanabhan, Q. Xin, J.M. Prausnitz, D.S. Clark, H.W. Blanch, “Ionic liquid pretreatment of cellulosic biomass: Enzymatic hydrolysis and ionic liquid recycle.” Biotechnol. Bioeng., 108(3), (2011).

M.J. Traylor, J. Chai, D.S. Clark, “Simultaneous measurement of CYP1A2 activity, regioselectivity, and coupling: Implications for environmental sensitivity of enzyme-substrate binding.” Arch. Biochem. Biophys., 505(2), (2011).


P.G. Holder, D.T. Finley, N. Stephanopoulos, R. Walton, D.S. Clark, M.B. Francis, “Dramatic thermal stability of virus-polymer conjugates in hydrophobic solvents.” Langmuir, 26(22), (2010).

D.S. Clark, “Protein Melts: A new phase for protein chemistry.” Nature Chem., 2(8), (2010).

T.W. Kim, H.A. Chokhawala, D. Nadler, H.W. Blanch, D.S. Clark, “Binding modules alter the activity of ahimeric cellulases: effects of biomass pretreatment and enzyme source.” Biotechnol. Bioeng., 107(4), (2010).

S.E. Levine, J.M. Fox, H.W. Blanch, D.S. Clark, “A Mechanistic model of the enzymatic hydrolysis of cellulose.” Biotechnol. Bioeng., 107(1), (2010).

C.T. Trinh, S. Huffer, M.E. Clark, H.W. Blanch, D.S. Clark, “Elucidating mechanisms of solvent toxicity in ethanologenic Escherichia coli.” Biotechnol. Bioeng., 106(5), (2010).

M.Y. Lee, J.S. Dordick, D.S. Clark, “Metabolic enzyme microarray coupled with miniaturized cell-culture array technology for high-throughput toxicity screening.” Methods Mol. Biol., 632, (2010).

T.G. Fernandes, S.J. Kwon, S.S. Bale, M.Y. Lee, M.M. Diogo, D.S. Clark, J.M. Cabral, J.S. Dordick, “Three-dimensional cell culture microarray for high-throughput studies of stem cell fate.” Biotechnol. Bioeng., 106(1), (2010).

U. Akbar, D. Shin, E. Schneider, J.S. Dordick, D.S. Clark, “Two-step enzymatic modification of solid-supported bergenin in aqueous and organic media.” Tetrahedron Lett., 51(8), (2010).

PATENT: D.S. Clark and J.S. Dordick, "Biocatalytic Solgel Microarrays," 


T.A. Whitehead, L.M. Bergeron, and D.S. Clark, “Tying up the loose ends: circular permutation decreases the proteolytic susceptibility of recombinant proteins.” Protein Eng. Des. Sel., 22(10), (2009).

J.M. Slocik, S.N. Kim, T.A. Whitehead, D.S. Clark, and R.R Naik, “Biotemplated metal nanowires using hyperthermophilic protein filaments.” Small, 5(18), (2009).

N. Bruns, K. Pustelny, L.M. Bergeron, T.A. Whitehead, and D.S. Clark, “Mechanical nanosensor based on FRET within a thermosome for damage-reporting polymeric materials.” Angew. Chem. Int., 48(31), (2009).

E.P. Hudson, R.K. Eppler, J.M. Beaudoin, J.S. Dordick, J.A. Reimer, D.S. Clark, “Active-site motions and polarity enhance catalytic turnover of hydrated subtilisin dissolved in organic solvents.” J. Am. Chem. Soc., 131(12), (2009).

T.A. Whitehead, E. Je, and D.S. Clark, “Rational shape engineering of the filamentous protein g prefoldin through incremental gene truncation.” Biopolymers, 91(6), (2009).

S.M. Sukumaran, B. Potsaid, M.Y. Lee, D.S. Clark, and J.S. Dordick, “Development of a fluorescence-based, ultra high-throughput screening platform for nanoliter-scale cytochrome P450 microarrays.” J. Biomol. Screen., 14(6), (2009).

T.G. Fernandes, M.M. Diogo, D.S. Clark, J.S. Dordick, and J.M.S. Cabral, “High-throughput cellular microarray platforms: Potential applications in drug discovery, toxicology, and stem cell research and therapy.” Trends in Biotechnology, 27(6) (2009).

R.A. Kumar, N. Papaïconomou, J.-M. Lee, J. Salminen, D.S. Clark, J. M. Prausnitz, “In vitro cytotoxicities of ionic liquids: effect of cation rings, functional groups and anions.” Environ. Toxicol., 24(4), (2009).

L.M. Bergeron, D.L. Shis, L. Gomez, and D.S. Clark, “Small molecule inhibition of a Group II chaperonin: pinpointing a loop region within the equatorial domain as necessary for protein refolding.” Arch. Biochem. Biophys., 481(1), (2009).

L.M.Bergeron, L. Gomez, T.A. Whitehead, D.S. Clark, “Self-Renaturing Enzymes: Design of an Enzyme-Chaperone Chimera as a New Approach to Enzyme Stability.” Biotechnol. Bioeng., 102(5), (2009).

L.M. Bergeron, T. Tokatlian, L. Gomez, D.S. Clark, “Redirecting the inactivation pathway of penicillin amidase and increasing amoxicillin production via a thermophilic molecular chaperone.” Biotechnol. Bioengin., 102(2), (2009).


J.D. Ryan, R.H. Fish, D.S. Clark, “Engineering Cytochrome P450 Enzymes for Improved Activity Towards Biomimetic 1,4-NADH Cofactors.” ChemBioChem., 9(16), (2008).

S.J. Brooks, L. Coulombel, D. Ahuja, D.S. Clark, J.S. Dordick, “Expanding the Scope of Biocatalysis: Oxidative Biotransformations on Solid-Supported Substrates.” Adv. Syn. Catal., 380(10), (2008).

R.K. Eppler, E.P. Hudson, S.D. Chase, J.S. Dordick, J.A. Reimer, D.S. Clark, “Biocatalyst Activity in Non-Aqueous Environments Correlates with Centisecond-Range Protein Motions.” Proc. Nat. Acad. Sci. USA, 105, 41 (2008).

T.G. Fernandes, S.J. Kown, M.Y. Lee, D.S. Clark, J.M.S Cabral, J.S Dordick, “On-Chip, Cell-Based Microarray Immunofluorescence Assay for High-Throughput Analysis of Target Proteins.” Anal. Chem., 80(17) (2008).

T.A. Whitehead, A.L. Meadows, and D.S. Clark, “Controlling the self-assembly of a filamentous hyperthermophilic chaperone by an engineered capping protein.” Small, 4(7) (2008).

L.M. Bergeron, C. Lee, D.S. Clark, “Identification of a critical chaperoning region on an archaeal recombinant thermosome.” Biochem Biophys. Res. Commun. 369: 707-711, (2008).

J.D. Ryan and D.S. Clark, “P450cam biocatalysis in surfactant-stabilized two-phase emulsions.” Biotechnol. Bioeng., 99(6), (2008).

A.L. Meadows, B. Kong, M. Berdichevsky, S. Roy, R. Rosiva, H.W. Blanch, D.S. Clark, “Metabolic and Morphological Differences between Rapidly Proliferating Cancerous and Normal Breast Epithelial Cells.” Biotech. Prog., 24(2), (2008).

J. Córdova, J.D. Ryan, B.B. Boonyaratanakornkit, and D.S. Clark, “Esterase Activity of Bovine Serum Albumin up to 160°C: A New Benchmark for Biocatalysis.” Enzyme Microb. Technol., 42, 278 (2008).

L.M. Bergeron, C. Lee, T. Tokatlian, V. Höllrigl, and D.S. Clark, “Chaperone Function in Organic Co-solvents: Experimental Characterization and Modeling of a Hyperthermophilic Chaperone Subunit from Methanocaldococcus jannaschii.” Biochim. Biophys. Acta, 2008 Feb; 1784(2): 368-78.

M.Y. Lee, A. Kumar, S. M. Sukamaran, M. G. Hogg, D.S. Clark, and J.S. Dordick, “Three-Dimensional Cellular Microarray for High-Throughput Screening.” Proc. Nat. Acad. Sci. USA, 105, 59 (2008).

Jonathan S. Dordick, 
Aravind Srinivasan, 
Jungbae Kim, 
David H. Sherman, 
Douglas S. Clark, "
In Vitro Metabolic Engineering on Microscale Devices," 


T.C. Logan, D.S. Clark, T.B. Stachowiak, F. Svec, and J.M.J. Frechet, “Photo-patterning Enzymes on Polymer Monoliths in Microfluidic Channels for Steady-State Kinetic Analysis and Spatially-Separated Multi-Enzyme Reactions.” Anal. Chem., 79, 6592 (2007).

A.L. Meadows, S. Roy, D.S. Clark, H.W. Blanch, “Optimal design of metabolic flux analysis experiments for anchorage-dependent mammalian cells using a cellular automaton model.” Biotech. Bioengin., 98(1), (2007).

H.R. Johnson, J.M. Hooker, M.B. Francis, and D.S. Clark, “Solubilization and Stabilization of Bacteriophage MS2 in Organic Solvents.” Biotechnol. Bioeng., 97, 224 (2007).

B.B. Boonyaratanakornkit, L.Y. Miao, and D.S. Clark, “Transcriptional Responses of the Deep-Sea Hyperthermophile Methanocaldococcus jannaschii under Shifting Extremes of Temperature and Pressure.” Extremophiles, 11, 495 (2007).

T.A. Whitehead, B.B. Boonyaratanakornkit, V. Höllrigl, and D.S. Clark, “A Filamentous Molecular Chaperone of the Prefoldin Family from the Deep-Sea HyperthermophileMethanocaldococcus jannaschii.” Protein Sci., 16, 626 (2007).

U. Akbar, C.D. Aschenbrenner, M.R. Harper, H.R. Johnson, J.S. Dordick, and D.S. Clark, “Direct Solubilization of Enzyme Aggregates with Enhanced Activity in Nonaqueous Media.”  Biotechnol. Bioeng., 96, 1030 (2007).

Douglas S. Clark,
Timothy Whitehead, 
Frank T. Robb, 
Pongpan Laksanalamai, 
Anchalee Jiemjit, "
Heterologous Expression of Extremophilic Heat Shock Proteins and Chaperones in Microorganisms to Increase Tolerance to Toxic Compounds,"


B.B. Boonyaratanakornkit, J. Córdova, C.B. Park, D.S. Clark, “Pressure affects transcription profiles of Methanocaldococcus jannaschii despite the absence of barophilic growth under gas-transfer limitation.” Environ. Microb., 8(11), (2006).

N.S. Forbes, A.L. Meadows, D.S. Clark, and H.W. Blanch, “Estradiol Stimulates the Biosynthetic Pathways of Breast Cancer Cells: Detection by Metabolic Flux Analysis.” Metabolic Eng., 8, 639 (2006).

J.B. Park and D.S. Clark, “New reaction system for hydrocarbon oxidation by chloroperoxidase.” Biotechnol. Bioengin., 94(1), (2006).

R.A. Kumar and D.S. Clark, “High-Throughput Screening of Biocatalytic Activity: Applications in Drug Discovery.” Current Opinion in Chemical Biology, 10, 162 (2006).

J.B. Park and D.S. Clark, “Deactivation Mechanisms of Chloroperoxidase During Biotransformations.” Biotech. Bioeng., 93, 1190 (2006).

R.K. Eppler, J. Huynh, R.S. Komor, J.S. Dordick, J.A. Reimer, and D.S. Clark, “Water Dynamics and Salt-Activation of Enzymes in Organic Media: Mechanistic Implications Revealed by NMR Spectroscopy.” Proc. Nat. Acad. Sci. USA, 103, 5706 (2006).


E.P Hudson, R.K. Eppler, D.S Clark, “Biocatalysis in semi-aqueous and nearly anhydrous conditions.” Current Opinion in Biotechnology, 16(6), (2005).

B.B. Boonyaratanakornkit, A.J. Simpson, T.A. Whitehead, C.M. Fraser, N.M.A. El-Sayed, and D.S. Clark, “Transcriptional Profiling of the Hyperthermophilic Methanarchaeon Methanococcus jannaschii in Response to Lethal Heat and Non-lethal Cold Shock.” Env. Microbiol., Env. Microbiol., 7(6), 789 (2005).

M.Y. Lee, J.S. Dordick, and D.S. Clark, “Metabolizing Enzyme Toxicology Assay Chip (MetaChip) for High-Throughput Microscale Toxicity Analyses.” Proc. Nat. Acad. Sci. USA, 102, 983 (2005).


D.S. Clark, “Characteristics of Nearly Dry Enzymes in Organic Solvents: Implications for Biocatalysis in the Absence of Water.” Phil. Trans. R. Soc. Lond. B, 359, 1299 (2004).

R. Gerber, J.D. Ryan, and D.S. Clark, “Cell-based Screen of HMG-CoA Reductase Inhibitors and Expression Regulators Using LC-MS Spectrometry.” Anal. Biochem., 329, 28 (2004).

J.P. Lindsay, D.S. Clark, and J.S. Dordick, “Combinatorial Formulation of Biocatalyst Preparations for Increased Activity in Organic Solvents: Salt Activation of Penicillin Amidase.” Biotechnol. Bioeng., 85, 553 (2004).

J.A. Morgan and D.S. Clark, “Salt-Activation of Non-hydrolase Enzymes for Use in Organic Solvents.” Biotechnol. Bioeng., 85, 456 (2004).

B.P. Manquin, J.A. Morgan, J. Ju, and D.S. Clark, “Production of C35 Isoprenoids Depends on H2 Availability During Cultivation of the Hyperthermophilic Methanarchaeon Methanococcus jannaschii.” Extremophiles, 8, 13 (2004).


R.J. Frankenberg, M. Andersson, and D.S. Clark, “Effect of Temperature and Pressure on the Proteolytic Specificity of the Recombinant 20S Proteasome from Methanococcus jannaschii.” Extremophiles, 7, 353 (2003).

D.H. Altreuter, J.S. Dordick, and D.S. Clark, “Solid-phase peptide synthesis by ion-paired alpha-chymotrypsin in nonaqueous media.” Biotechnol. Bioeng., 81(7) (2003).

David H. Altreuter, 
Douglas S. Clark, 
Peter C. Michels, 
Joseph O. Rich, 
Harold Meckler, 
Jonathan S. Dordick, "
Methods for Preparing Doxorubicin Derivatives," 

Michael A. Markowitz, 
Paul E. Schoen, 
Bruce P. Gaber, 
Banahalli R. Ratna, 
Paul R. Kust, 
David C. Turner, 
Douglas S. Clark, 
Jonathan S. Dordick, "
Molecularly-Imprinted Material Made by Template-Directed Synthesis,"


C.B. Park and D.S. Clark, “Rupture of the Cell Envelope by Decompression of the Deep-Sea Methanogen Methanococcus jannaschii.” Appl. Environ. Microbiol., 68, 1458 (2002).

C.B. Park and D.S. Clark, “Sol-Gel Encapsulated Enzyme Arrays for High Throughput Screening of Biocatalytic Activity.” Biotechnol. Bioeng., 78, 229 (2002).

D.H. Altreuter, J.S. Dordick, and D.S. Clark, “Nonaqueous Biocatalytic Synthesis of New Cytotoxic Doxorubicin Derivatives: Exploiting Unexpected Differences in the Regioselectivity of Salt-Activated and Solubilized Subtilisin.” J. Am. Chem. Soc., 124, 1871 (2002).

Jonathan S. Dordick, 
Douglas S. Clark, 
Peter C. Michels, 
Yuri L. Khmelnitsky, "
Taxol Derivatives,"


R.J. Frankenberg, T. S.Hsu, H. Yakota, R. Kim, and D.S. Clark, “Chemical Denaturation and Elevated Folding Temperatures are Required for Wild-Type Activity and Stability of Recombinant Methanococcus jannaschii 20S Proteasome.” Protein Sci., 10, 1887 (2001).

Y.D. Kim, C.B. Park, and D.S. Clark, “Stable Sol-Gel Microstructured and Microfluidic Networks for Protein Patterning.” Biotechnol. Bioeng., 73, 331 (2001).

N.S. Forbes, D.S. Clark, and H.W. Blanch, “Using Isotopomer Path Tracing to Quantify Metabolic Fluxes in Pathway Models Containing Reversible Reactions.” Biotechnol. Bioeng., 74, 196 (2001).

M.T. Ru, K.C. Wu, J.P. Linday, J.S. Dordick, J.A. Reimer, and D.S. Clark, “Towards More Active Biocatalysts in Organic Media: Achieving Aqueous-Like Activity of Salt-Activated Enzymes.” Biotechnol. Bioeng., 75, 187 (2001).

R.J. Frankenberg, T.S. Hsu, H. Yakota, R. Kim, and D.S. Clark, “Chemical Denaturation and Elevated Folding Temperatures are Required for Wild-Type Activity and Stability of Recombinant Methanococcus jannaschii 20S Proteasome.” Protein Sci., 10, 1887 (2001).

M.M.C. Sun, R. Caillot, G. Mak, F.T. Robb, and D.S. Clark, “Mechanism of Pressure-Induced Thermostabilization of Proteins: Studies of Glutamate Dehydrogenases from the Hyperthermophile Thermococcus litoralis.” Protein Sci., 10, 1750 (2001).

W.B. Jang, H. Hu, M.M. Lieberman, J.A. Morgan, I.A. Stergiades, D.S. Clark, and M.A. Tius, “Parallel Synthesis and Biocatalytic Amplification of a Cross-Conjugated Cyclopentenone Library.” J. Combi. Chem., 3, 346 (2001).

PATENT: Yuri L. Khmelnitsky, Cheryl L. Budde, John M. Arnold, Joseph O. Rich, Sharon S. Chen, Alexander Ya. Usyatinsky, Douglas S. Clark, Jonathan S. Dordick, "Two-Step Enzymatic Acylation,"