Chemistry and Biochemistry

Daniel Clark

Biochemistry

Education & Employment

Staff Scientist, R&D, Stratagene, La Jolla, CA
Ph.D. Biochemistry, Utah State University
B.S. Biology (Cell & Molec), Minor Chemistry, California State University, Chico

Grants

California State University, Chico

  1. Clark DD, Edwards DJ (2018) New gel imager for biochemistry lab students. California State University- Chico, Student Learning Fee Grant, Total Award $16,000.
  2. Clark DD, Edwards DJ (2018) Essential small equipment bundle for biochemistry lab students. California State University- Chico, Student Learning Fee Grant, Total Award $10,000.
  3. Clark DD, Edwards DJ (2016) New micropipettes for the biochemistry lab. California State University- Chico, Student Learning Fee Grant, Total Award $18,000.
  4. Clark DD, Edwards DJ (2014) Enhanced learning and engagement in the biochemistry lab. California State University- Chico, Student Learning Fee Grant, Total Award $22,618.
  5. Clark DD (2007 – 2009) Proteomic and biochemical investigation of coenzyme-M biosynthesis in Nocardioides sp. strain JS614. Research Corporation, Total Award $46,318, Role: Principal Investigator.
  6. Clark DD (2005 - 2006) Microbial metabolism of propane and propylene, Faculty-Student Collaborative Research Seed Grant, California State University Program for Education and Research in Biotechnology (CSUPERB), Total Award $10,000, Role: Principal Investigator.

Publications

California State University, Chico

  1. Clark DD (2018) Characterization of the recombinant ( R)- and ( S)-hydroxypropyl-coenzyme M dehydrogenases: A case study to augment the teaching of enzyme kinetics and stereoselectivity. Biochemistry & Molecular Biology Education. Published online December 28, 2018.
  2. Clark DD (2018) Preliminary investigation of deoxyoligonucleotide binding to ribonuclease A using mass spectrometry: An attempt to develop a lab experience for undergraduates. F1000 Research. Published online March 20, 2018.
  3. Clark DD, Edwards DJ (2018) Virtual protein purification: A simple exercise to introduce pH as a parameter that effects ion exchange chromatography. Biochemistry & Molecular Biology Education 46: 91-97. Published online August 6, 2017.
  4. Broberg CA, Clark DD (2010) Shotgun proteomics of Xanthobacter autotrophicus Py2 reveals proteins specific to growth on propylene. Archives of Microbiology 192: 945-957.
  5. Boyd JM, Clark DD, Kofoed MA, Ensign SA (2010) Mechanism of inhibition of aliphatic epoxide carboxylation by the coenzyme M analog 2-bromoethanesulfonate. The Journal of Biological Chemistry 285: 25232-25242.

Utah State University

  1. Krishnakumar AM, Nocek BP, Clark DD, Ensign SA, Peters JW (2006) Structural basis for stereoselectivity in the ( R)- and ( S)-hydroxypropylthioethanesulfonate dehydrogenases. Biochemistry 45:8831-8840.
  2. Pandey AS, Nocek B, Clark DD, Ensign SA, Peters JW (2006) Mechanistic implications of the structure of the mixed-disulfide intermediate of the disulfide oxidoreductase, 2-ketopropyl-coenzyme M oxidoreductase/carboxylase. Biochemistry 45:113-120.
  3. Clark DD, Boyd JM, Ensign SA (2004) The Stereoselectivity and catalytic properties of Xanthobacter autotrophicus 2-[( R)-2-hydroxypropylthio]ethanesulfonate dehydrogenase are controlled by interactions between C-terminal arginine residues and the sulfonate of coenzyme M. Biochemistry 43: 6763-6771.
  4. Nocek B, Jang SB, Jeong MS, Clark DD, Ensign SA, Peters JW (2002) Structural basis for CO 2-fixation by a novel member of the disulfide oxidoreductase family of enzymes, 2-ketopropyl-coenzyme oxidoreductase/carboxylase. Biochemistry 41: 12907-12913.
  5. Nocek B, Clark DD, Ensign SA, Peters JW (2002) Crystallization and preliminary X-ray analysis of an ( R)-2-hydroxypropyl-coenzyme M dehydrogenase. Acta Crystallographica 58: 1470-1473.
  6. Clark DD, Ensign SA (2002) Characterization of the 2-[( R)-2 hydroxypropylthio]-ethanesulfonate dehydrogenase from Xanthobacter strain Py2: product inhibition, pH dependence of kinetic parameters, site-directed mutagenesis, rapid equilibrium inhibition, and chemical modification. Biochemistry 41:2727-2740.
  7. Jang SB, Jeong MS, Clark DD, Ensign SA, Peters JW (2001) Crystallization and preliminary X-ray analysis of a NADPH: 2-ketopropyl-coenzyme M oxidoreductase/carboxylase. Acta Crystallographica 57: 445-447.
  8. Clark DD, Allen JR, Ensign SA (2000) Characterization of five catalytic activities associated with the NADPH 2-(2-ketopropylthioethane sulfonate) oxidoreductase carboxylase of the Xanthobacter strain Py2 epoxide carboxylase system. Biochemistry 39: 1294 -1304
  9. Allen JR, Clark DD, Krum JG, Ensign SA (1999) A role for coenzyme M (2- mercaptoethanesulfonate) in a bacterial pathway of aliphatic epoxide carboxylation. Proceedings of the National Academy of Sciences USA 96: 8432-8437
  10. Clark DD, Ensign SA (1999) Evidence for an inducible nucleotide dependent acetone carboxylase in Rhodococcus rhodochrous strain B-276. The Journal of Bacteriology 181: 2752-2758.

Product Manuals & Patents

Stratagene

  1. Clark DD, Braman JC, Stratagene (2004) Thermostable protease with altered cleavage specificity. International Patent # WO/2004/011619.
  2. Clark DD, Felts K, Braman JC (2004) Prolytica phosphopeptide characterization kit (for the enrichment of phosphopeptides and the mapping of serine and threonine phosphorylation sites using mass spectrometry). Stratagene product manual.
  3. Clark DD, Felts K, Braman JC (2004) QuikTip-C 18 solid phase extraction micropipette tips (as a sample preparation tool for mass spectrometry). Stratagene product manual.
  4. Clark DD, Felts K, Braman JC (2004) Prolytica 18O-Labeling kit (for quantitative proteomics). Stratagene product manual.
  5. Clark DD, Anderson P, Bagga R, Braman JC (2003) Mass spectrometry grade trypsin. Stratagene product manual.
  6. Clark DD, Bagga, R, Allen R, Braman JC (2002) Prolytica In-gel digestion kit with thermogest Bca (for the identification of proteins in SDS-PAGE gels using mass spectrometry). Stratagene product manual.