Daniel D. Clark

Dr. Dan Clark  

Biochemistry
Phone: 530-898-5251
Campus ZIP: 210
Department Phone: 530-898-5259
Building: PHSC 306
E-mail: ddclark@csuchico.edu 

 Teaching 

CHEM 111 General Chemistry
CHEM 350 Introductory Biochemistry
CHEM 350L Introductory Biochemistry Lab
CHEM 451 Biochemistry
CHEM 452 Biochemistry
CHEM 453M Biochemistry Lab

Education & Employment
Staff Scientist, R&D, Stratagene, La Jolla, Ca
Ph.D. Utah State University, Logan, UT
B.Sc. California State University Chico, Chico, Ca

Research Interests
Dr. Clark’s research interests span a broad array of topics in biochemical education.  A few specifics include mechanistic enzymology, proteomics, metabolomics, and the application of mass spectrometry to biological problems.

Grants
2014, Enhanced learning and engagement in the biochemistry lab. California State University- Chico Student Learning Fee Grant, Total Award $22,618.                 

2007 – 2009, Proteomic and biochemical investigation of coenzyme-M biosynthesis in Nocardioides sp. strain JS614. Research Corporation, Total Award $46,318, Role: Principal Investigator.

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
12. Broberg CA, Clark DD (2010) Shotgun proteomics of Xanthobacter autotrophicus Py2 reveals proteins specific to growth on propylene. Archives of Microbiology 192: 945-957.

11. 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.

10. 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.

9. 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.

8. 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.

7. Nocek B, Jang SB, Jeong MS, Clark DD, Ensign SA, Peters JW (2002) Structural basis for CO2-fixation by a novel member of the disulfide oxidoreductase family of enzymes, 2-ketopropyl-coenzyme oxidoreductase/carboxylase. Biochemistry 41: 12907-12913.

6. 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.

5. 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.

4. 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.

3. 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

2. 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

1. 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.

Patents & Product Manuals
6. Clark DD, Braman JR, Stratagene (2004) Thermostable protease with altered cleavage specificity. International Patent # WO/2004/011619.

5. Clark DD, Felts K, Braman JR (2004) Prolytica phosphopeptide characterization kit: Enrichment of phosphopeptides and the mapping of serine and threonine phosphorylation sites. Stratagene product manual.

4. Clark DD, Felts K, Braman JR (2004) QuikTip-C18 solid phase extraction micropipette tips. Stratagene product manual.

3. Clark DD, Felts K, Braman JR (2004) Prolytica 18O-Labeling kit. Stratagene product manual.

2. Clark DD, Anderson P, Bagga R, Braman JR (2003) Mass spectrometry grade trypsin. Stratagene product manual.

1. Clark DD, Bagga, R, Allen R, Braman JR (2002) Prolytica In-gel digestion kit with thermogest Bca.  Stratagene product manual.