Development Project

YOUNGCHOOL CHOE, Ph. D.

** *** ***** ******, ********, CA 94030

Cell: 650-***-****, E-mail: abgfhg@r.postjobfree.com

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Youngchool Choe, Ph.D. Cell: 650-***-****; E-mail: abgfhg@r.postjobfree.com

CAREER SUMMARY: Energetic, motivated, detail-oriented protein chemist and biochemist with 7 years of

experience in the biotechnology industry and 6 years of Postdoctoral experience at UC San Francisco. Broad

background and extensive hands-on experience in a variety of protein chemistry, recombinant protein expression,

refolding, isolation and purification technologies, process and assay development, analysis methods as well as

bacterial cell culture and fermentation. Trusted and well-liked team player with strong analytical and problem-

solving skills. Performs efficiently under time-constrained and multitasking environment. Supervised RA level staff.

Interested in work opportunities in a biotech or a pharmaceutical company with a focus on developing new

biological therapeutics, diagnostics or technologies for unmet medical and scientific needs.

EXPERTISE & EXPERIENCE: Protein expression and production using E. coli, Pichia, and mammalian cells.

Recombinant protein refolding & optimization. Soluble & functional intracellular expression Purification using

AKTA/FPLC and various methods including IEX, SEC, HIC, affinity, IMAC, RP, tangential flow filtration,

ultrafiltration, ultracentrifugation, ammonium sulfate precipitation Protein characterization using PAGE

electrophoresis, Western blot, ELISA, IEF, N-terminal sequencing, UV/Fluorescence spectrophotometers Cell

culture, fermentation using bioreactors up to 50-L scale (batch, fed-batch mode) Analytical & preparative HPLC

(IEX, SEC, RP, NP) Protein modification including PEGylation & biotinylation Endotoxin removal & assays

Peptide synthesis and purification, construction of combinatorial substrate libraries MALDI-MS Purification of

antibodies and small molecules Solvent extraction Enzyme & inhibitor kinetics assays (fluorogenic/FRET,

chromogenic) Screening & assay method development Molecular cloning, site-directed mutagenesis,

expression vector design, PCR Multitasking & problem solving. Project planning & management MS Word,

Excel, Powerpoint, Softmax, Unicorn, Chemstation, EZstart softwares.

WORK EXPERIENCES

Research Scientist (Sep. 2012 – Present), Dophen Biomed. West Sacramento, CA.

Developed a method to functionally express and purify mutated microbial Transglutaminases from E. coli

(Intracellular soluble expression).

Staff Scientist (Jul. 2005 – Apr. 2012), Catalyst Biosciences Inc. Protein Sciences group, South San

Francisco, CA.

As a member of the protein production group, participated in planning of various research programs and

partnered programs. Planned and organized production to ensure sample supply was completed within

project scopes, timelines, and per success criteria.

Optimized refolding and production strategies to provide hundreds of proteins & reagents to support various

projects in a complex multi-disciplinary biotech startup R&D environment.

Lead multiple team efforts to produce low yielding Alterase TM candidates for various partnered programs.

Provided several hundred mg of high quality, low endotoxin protein in a timely manner.

Lead the SERPIN bait production effort for whole company’s selection and counter-selection processes

which comprise the core of Catalyst’s technology.

Produced hundreds of proteins of several different platforms and their modified forms including PEGylation

for better efficacy and tolerance. Produced dozens of proteins per week and hundreds per year utilizing

automated AKTATM purification systems. Consistently delivered high quality products in a timely manner.

IEX, RP, GPC/SEC, Affinity, IMAC (TALON, Ni-NTA), HIC, Tag (FLAG, HisTag) based protein purification.

Production process optimization and maximization of chromatographic separation using additives.

iFOLD refolding condition screens.

Reshuffling of disulphide bonds to improve protein folding.

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Youngchool Choe, Ph.D. Cell: 650-***-****; E-mail: abgfhg@r.postjobfree.com

Experienced with various E. coli competent cells including Rosetta2, NEBexpress Iq, or a cotransformation

approach to produce problematic proteins with rare-codons or other toxicity issues.

Protein modification including PEGylation, biotinylation, Fc Fusion, heparin binding domain, & SUMO fusion.

Experienced in endotoxin removal and assays.

Fluorogenic and chromogenic assays utilizing FRET, ACC technologies.

Setup, operated, and maintained Hollow fibre concentrators (TFF), HPLCs, various AKTA TM systems.

Developed and conducted various HPLC assays for Hemophilia programs (FVII, FIX, and FXa). Streamlined

the sample submission and data analysis process for multiple collaborators.

In charge of the HPLC assays for the program that generated Catalyst’s 1 st IND compound(Jan 2012).

Solid phase extraction & other sample preparation approaches.

Designed the water & gas supplying systems for 3 bioreactors and supervised its setup and operation.

Successfully achieved high density bacterial cultures in 5L bioreactors (OD 600 > 153) using a Fed-Batch

culture method. Participated in developing serum-free, protein-free, lipid-free chemically defined media.

Analysis and control of pH, DO, oxygen transfer rates, and feed pump rate during fermentation process.

Participated in developing and writing various company protocols (SOPs).

Data mining and navigation of various protein and bioinformatics databases.

Recruited & Managed 3 RA or Lab technician level staff. Led weekly meetings to train & guide them. Trained

two media lab technicians using my microbiology background.

Postdoctoral fellow (Jan. 1999 - Dec. 2001) & Postgraduate researcher (Jan. 2002 - Jun. 2005), UC San

Francisco. Advisor: Professor Charles S. Craik, Ph.D.

Construction of the complete diverse positional scanning-synthetic peptide combinatorial libraries (PS-SCLs)

and assay development.

Study of serine/cysteine protease substrate specificity using PS-SCLs. Enzyme and inhibitor kinetics.

Peptide synthesis, purification and characterization.

Expression and characterization of the SARS (Severe Acute Respiratory Syndrome) related Cysteine

protease.

Cloning and expression of Falcipain-1, a malaria cysteine protease.

Postdoctoral researcher and Lecturer (Dec. 1997 - Nov. 1998), Myongji University. Yong-In, Korea. Advisor:

Professor Byoung-Chul, Jeong, Ph.D.

In situ reclamation of diesel contaminated soil by electrokinetic flushing combining with bioremediation.

Purification and structure determination of plant elicitor from fungi.

Lignin peroxidase from white-rot fungus and its inactivators.

Cr reductase purification from bacteria.

Research Associate, Seoul National University. Seoul, Korea.

1995 Institute for Molecular Biology and Genetics (IMBG).

1993 - 1998 Research Center for Microbial Molecular Biology (RCMM) .

1991 Anticancer activity of Duchesnia indicae extract on mouse sarcoma 180 cells.

1992 Discovery of Hemolysin from V. anguillarum as a new pathogen and assay development.

1996 - 1998 Development of elastase inhibitors from Actinomycetes.

1993 - 1998 Screening and development of cathepsin B inhibitors. Assay development.

Teaching Experience

2004 Advised rotation students (UCSF): Prostate Specific Membrane Antigen (PSMA) expression .

1998 Taught classes: Biology, Biotechnology experiments. Department of Biological Science, Myongji

University, Korea.

Teaching Assistant (Seoul National University, Korea) : 1991 - 1992 Microbiology, Biology, Immunology,

Pathology. 1994 - 1995 Fermentation microbiology.

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Youngchool Choe, Ph.D. Cell: 650-***-****; E-mail: abgfhg@r.postjobfree.com

EDUCATION

Postdoctoral & Postgraduate researcher (January 1999 – June 2005. Advisor: Professor Charles S. Craik,

Ph.D.). Department of Pharmaceutical Chemistry, University of California, San Francisco.

Ph.D. (February 1998. Advisor: Professor Kye Joon Lee, Ph.D.)

Thesis Title: "Production of Cathepsin B inhibitor from Streptomyces aburabiensis SMF30" The Laboratory of

Biotechnology and Fermentation, Department of Microbiology, Seoul National University, Seoul, Korea.

M.S. (February 1993. Advisor Gajin Jeong, Ph.D.)

Thesis Title: "Identification and Characterization of Hemolytic Toxin as a Virulence Factor of the Fish

Pathogen, Vibrio anguillarum V7 (Serotype JO1)"

The Laboratory of Immunology and Pathology, Department of Microbiology, Seoul National University, Seoul,

Korea.

B.S. (February 1991)

Department of Microbiology, College of Natural Sciences, Seoul National University, Seoul, Korea.

PUBLICATIONS

Norbury LJ, Hung A, Beckham S, Pike RN, Spithill TW, Craik CS, Choe Y, Fecondo JV, Smooker PM.

1.

Analysis of Fasciola cathepsin L5 by S(2) subsite substitutions and determination of the P(1)-P(4) specificity

reveals an unusual preference. Biochimie. 2012 May;94(5):1119-27.

Na BK, Bae YA, Zo YG, Choe Y, Kim SH, Desai PV, Avery MA, Craik CS, Kim TS, Rosenthal PJ, Kong Y.

2.

Biochemical properties of a novel cysteine protease of Plasmodium vivax, vivapain-4. PLoS Negl Trop Dis.

2010 Oct 12;4(10):e849.

Subramanian S, Hardt M, Choe Y, Niles RK, Johansen EB, Legac J, Gut J, Kerr ID, Craik CS, Rosenthal

3.

PJ. Hemoglobin cleavage site-specificity of the Plasmodium falciparum cysteine proteases falcipain-2 and

falcipain-3. PLoS One. 2009;4(4):e5156.

Liz MA, Fleming CE, Nunes AF, Almeida MR, Mar FM, Choe Y, Craik CS, Powers JC, Bogyo M, Sousa

4.

MM. Substrate specificity of transthyretin: identification of natural substrates in the nervous system. Biochem

J. 2009 Apr 15;419(2):467-74.

O'Brien TC, Mackey ZB, Fetter RD, Choe Y, O'Donoghue AJ, Zhou M, Craik CS, Caffrey CR, McKerrow

5.

JH. A parasite cysteine protease is key to host protein degradation and iron acquisition. J Biol Chem. 2008

Oct 24;283(43):28934-43.

Lucas JJ, Hayes GR, Kalsi HK, Gilbert RO, Choe Y, Craik CS, Singh BN. Characterization of a cysteine

6.

protease from Tritrichomonas foetus that induces host-cell apoptosis. Arch Biochem Biophys. 2008 Sep

15;477(2):239-43.

Goetz, DH., Choe, Y., Hansell, E., Chen, YT., McDowell, M., Jonsson, CB., Roush, WR., McKerrow, J.,

7.

Craik, CS. Substrate Specificity Profiling and Identification of a New Class of Inhibitor for the Major Protease

of the SARS Coronavirus. Biochemistry. 2007 Jul 31;46(30):8744-8752.

Samuel G. Meléndez-López, Scott Herdman, Ken Hirata, Min-Ho Choi, Youngchool Choe, Charles Craik,

8.

Conor Caffrey, Bibiana Chávez-Munguía, William R. Roush, James McKerrow, Samuel L. Stanley, Jr ., and

Sharon L. Reed. EhCP1 is a Unique, Released Cysteine Proteinase of Invasive Entamoeba

histolytica.Eukaryotic Cell. 2007 Jul;6(7):1130-6.

Park, K, Kuechle M. K., Choe, Y., Craik, C. S., Lawrence O.T., Presland, R. B. Expression and

9.

characterization of constitutively active human caspase-14. Biochem Biophys Res Commun. 2006 Sep

8;347(4):941-8.

Debela M., Magdolen V., Schechter N., Valachova M., Lottspeich F., Craik C.S., Choe Y., Bode W.,

10.

Goettig P. Specificity profiling of seven human tissue kallikreins reveals individual subsite preferences. J Biol

Chem. 2006 Sep 1;281(35):25678-88.

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Youngchool Choe, Ph.D. Cell: 650-***-****; E-mail: abgfhg@r.postjobfree.com

Choe Y., Leonetti F., Greenbaum D.C., Lecaille F., Bogyo M., Bromme D., Ellman J.A., Craik C.S.

11.

Substrate profiling of cysteine proteases using a combinatorial peptide library identifies functionally unique

specificities. J Biol Chem. 2006 May 5;281(18):12824-32.

Herter S., Piper D.E., Aaron W., Gabriele T., Cutler G., Cao P., Bhatt A.S., Choe Y., Craik C.S., Walker

12.

N., Meininger D., Hoey T., Austin R.J. Hepatocyte growth factor is a preferred in vitro substrate for human

hepsin, a membrane-anchored serine protease implicated in prostate and ovarian cancers. Biochem J. 2005

Aug 15;390(Pt 1):125-36.

Youngchool Choe, Linda S. Brinen, Mark S. Price, Juan C. Engel, Meinolf Lange, Scott G. Weston,

13.

Hong Cheng, Marsha Cullinane, Matora M. Fiorey, Corinna Grisostomi, Larry W. Hardy, David S. Hartsough,

Peter V. Pallai, Robert F. Tilton, Carmen M. Baldino, and Charles S. Craik . Development of alpha-keto-based

inhibitors of cruzain, a cysteine protease implicated in Chagas disease. Bioorg Med Chem. 2005 Mar

15;13(6):2141-56.

Williamson AL, Lecchi P, Turk BE, Choe Y, Hotez PJ, McKerrow JH, Cantley LC, Sajid M, Craik CS,

14.

Loukas A. A multi-enzyme cascade of hemoglobin proteolysis in the intestine of blood-feeding hookworms. J

Biol Chem. 2004 Aug 20;279(34):35950-7.

Na BK, Shenai BR, Sijwali PS, Choe Y, Pandey KC, Singh A, Craik CS, Rosenthal PJ.Identification and

15.

biochemical characterization of vivapains, cysteine proteases of the malaria parasite Plasmodium vivax.

Biochem J. 2004 Mar 1;378(Pt 2):529-38.

Singh A, Shenai BR, Choe Y, Gut J, Sijwali PS, Craik CS, Rosenthal PJ. Critical role of amino acid 23 in

16.

mediating activity and specificity of vinckepain-2, a papain-family cysteine protease of rodent malaria

parasites. Biochem J. 2002 Nov 15;368(Pt 1):273-81.

Wang X, Choe Y, Craik CS, Ellman JA. Design and synthesis of novel inhibitors of gelatinase B. Bioorg

17.

Med Chem Lett. 2002 Aug 19;12(16):2201-4.

Lecaille F, Choe Y, Brandt W, Li Z, Craik CS, Bromme D. Selective inhibition of the collagenolytic activity

18.

of human cathepsin K by altering its S2 subsite specificity. Biochemistry. 2002 Jul 2;41(26):8447-54.

Salter JP, Choe Y, Albrecht H, Franklin C, Lim KC, Craik CS, McKerrow JH. Cercarial elastase is

19.

encoded by a functionally conserved gene family across multiple species of schistosomes. J Biol Chem.

2002 Jul 5;277(27):24618-24.

Mathieu MA, Bogyo M, Caffrey CR, Choe Y, Lee J, Chapman H, Sajid M, Craik CS, McKerrow JH.

20.

Substrate specificity of schistosome versus human legumain determined by P1-P3 peptide libraries. Mol

Biochem Parasitol. 2002 Apr 30;121(1):99-105.

Choe, Youngchool, In S. Kim, Sang J. Park, Sung J. Yoon, and Kye Joon Lee. 1995. Production and

21.

physico-chemical properties of cathepsin B inhibitor from Streptomyces aburabiensis SMF30. J. Pharm. Soc.

Kor. 39 (3): 306-313.

Choe, Youngchool, and Gajin. Jeong. 1995. Physiological chracterization of kinetics and action

22.

mechanism of hemolysin. J. Microbiol. 33 (4): 289-294

Choe, Youngchool, and Gajin Jeong. 1995. Identification of hemolysin as one of the important virulent

23.

factors in Vibrio anguillarum. J. Microbiol. 33 (4): 283-288

Choe, Youngchool, and Gajin Jeong. 1994. Virulence evaluation of Vibrio anguillarum in accordance

24.

with hemolytic activity on human red blood cells. Kor. J. Microbiol. 32 (6): 539-544

HONORS AND AWARDS

1987-1992 Daesan Foundation Scholarship, Korea.

1998 The Best Lecturer of the Year award honored by the student council. Myongji University, Korea.

1992 Awarded an exemption from the Ph.D. course entrance exam as a reward for the excellent research I

had conducted during the mandatory Master degree course. Seoul National University, Korea .

Two-time award winning employee at Catalyst Biosciences Inc. South San Francisco, CA.

REFERENCES : Available upon request.

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Youngchool Choe, Ph.D. Cell: 650-***-****; E-mail: abgfhg@r.postjobfree.com

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