David Benson


David Benson

Education

  • B.A., Goshen College, 1990
  • Ph.D., University of Illinois, Urbana-Champaign, Inorganic Chemistry, 1997

Professional History

  • Professor of Chemistry, Calvin University, 2014-present
  • Visiting Scientist, Van Andel Research Institute, 2015-2019
  • Associate Professor of Chemistry, Calvin University (College), 2008-2014
  • Assistant Professor of Chemistry, Wayne State University, 2001-2008
  • NIH Postdoctoral Fellow, Duke University Medical Center, 1997-2001

Biography

Professor Benson came to Calvin University from a faculty position at Wayne State University with an excitement for training undergraduate research students at a Christian college. Coming from Mennonite and Non-Denominational backgrounds, he sees that a Reformed Christian perspective provides an excellent foundation for doing science while being Christian. To do chemistry and biochemistry, he has pulled together a variety of research experiences from undergraduate synthetic chemistry (through his work at Bowling Green State University), graduate bioinorganic enzymology (through his work at University of Illinois), postdoctoral metalloprotein design (through his work at Duke University Medical Center), and nutrient biosensors (through his work at Wayne State University) to integrate most of the traditional chemistry and biochemistry disciplines into unique teaching and research experiences. In addition to first year chemistry courses, he has taught upper-division inorganic and analytical courses from a biological context. His research projects integrate traditional biochemical methods (such as microbiology, protein expression & purification, gel electrophoresis) with spectroscopic and chromatographic analysis. He also serves on the committee that maintains the sizeable fleet of instrumentation in the Science Division at Calvin University to provide students with hands-on access to high-end research instrumentation. Outside of Calvin, you can find him spending time with his family, playing board games, doing home projects, or running.

Research and scholarship

  • Proteins as Antioxidants in Disease: Antioxidants are low-molecular weight molecules that sacrificially lose electrons (oxidized) rather than important biological molecules (proteins, DNA, lipids, etc.) This is why we need a mixture of water- and fat-soluble vitamins, some of which are antioxidants, in our diet. There are a few chemical modifications of the twenty amino acids that make up proteins (post-translational modifications) that also function as antioxidants that are tethered to the protein backbone, rather than freely flowing within the cell. Most of these antioxidant post-translational modifications are generated by iron or copper ions bound to proteins through binding and activation of atmospheric oxygen. The best studied antioxidant post-translational modification is where a covalent C-S bond is formed between a tyrosine (phenol) and cysteine (thiol) sidechain, called Cys-Tyr. While there are Cys-Tyr containing proteins in bacteria (sulfite reductase), fungi (galactose oxidase), and mammals (cysteine dioxygenase), we have identified Cys-Tyr in and are studying a protein of unknown function from Bacteroides fragilis named BF4112 from the encoding gene number. Although BF4112 was crystallographically characterized with Zn2+ ion bound, the Cu2+ and Fe2+/3+ ion bound forms of BF4112 have been shown by us to form Cys-Tyr with exposure to dioxygen. We are currently studying the mechanism of Cys-Tyr formation and the physiological function of Cys-Tyr BF4112 in Bacteroides fragilis. Cys-Tyr formation is likely important for the oxygen resistance of Bacteroides fragilis as this bacterium is responsible for post-operative intestinal infections. Beyond diseases associated with Bacteroides fragilis, we are interested in developing more tools to identify these difficult to detect antioxidant post-translational modifications.
  • Organic acid contributions to buffer capacity of wort: The pH of malted barley extracts is important for the taste, stability, and safety of finished beer. Two main steps in the manufacturing process require careful attention to pH; starch conversion to glucose (mashing) and conversion of glucose to alcohol (fermentation). The brewing literature states that carbonate and phosphate are the only contributors to regulating/buffering the pH during mashing, and also fermentation. While carbonate and phosphate are abundant in barley extracts (wort) the pKas are outside of the buffer region (pH 5-6 for mashing, pH 3.8-5 for fermentation). We were struct by the pKas of organic acids from metabolism, especially malate and citrate, that that have pKas in the pH ranges for mashing and fermentation. We have found correlations with malate and citrate concentrations in barley extracts before fermentation using ion chromatography and buffer capacity by titrations with strong acids and bases. We hope to better understand differences in malted barley recipe variation influences final serving pH and overall perception of beer.  

Publications

Undergraduate student names appear in bold.

Hromada S, Hilbrands A, Wolf EM, Ross JL, Hegg T, Roth A, Hollowell M, Anderson C, Benson DE. “Protein Oxidation Involved in Cys-Tyr Post-Translational Modification”, J. Inorganic Biochemistry, 176, 168-174. 2017. 

Benson DE, DeHaan SR, Hulderman CE, Swain MD. “Electron Transfer Semiconductor Nanoparticle Biosensors” in Quantum Dot Sensors: Technology and Commercial Applications ". CRC Press, Boca Raton, FL pp. 109-132, 2013. 

Opperwall SR, Divakaran A, Porter EG, Christians JA, DenHartigh AJ, Benson DE. “Wide Dynamic Range Sensing with Single Quantum Dot Biosensors”, ACS Nano, 6,  8078–8086. 2012

Martine RJ, Godakumbura PI, Porter EG, Divakaran A, Burkhart BJ, Wertz JT, Benson DE. “Identifying Proteins That Can Form Tyrosine-Cysteine Crosslinks”, Metallomics, 4, 2012, 1037-1042.

Shete V, Benson DE. “Linking Metalloprotein Design with Semiconductor Nanoparticles for Imaging Pb2+ Ion Speciation in Red Blood Cells”. Biochemistry, 48, 462-470. 2009. 

Swain MD, Octain J, Benson DE.  “Unimolecular, Soluble Semiconductor Nanoparticle-Based Biosensors for Thrombin Using Charge/Electron Transfer.” Bioconjugate Chem., 19, 2520-2526. 2008. 

Benson DE. “Semiconductor Nanoparticle-based Biosensors”, Biotechnology International, 12-15. Sept. 2008.

Trisler K, Looger LL, Sharma V, Baker M, Benson DE, Trauger S, Schultz PG, Smider VV, “A Metalloantibody That Irreversibly Binds a Protein Antigen”. J. Biol. Chem., 282, 26344-26353. 2007. 

Aryal BP, Benson DE. “Polyhistidine Fusion Proteins Can Nucleate the Growth of CdSe Nanoparticles”. Bioconjugate Chem., 18, 585-589. 2007. 

Aryal BP, Benson DE. “Electron Donor Solvent Effects Provide Semiconducting Nanoparticle-based Biosensors”, J. Am. Chem. Soc., 128, 15986-15987. 2006. 

Benson DE. “Reagentless Biosensors Based on Nanoparticles” in Volume 8, “Nanomaterals for Biosensing” in the Nanomaterials for Life Sciences book series, Wiley Interscience, pp. 337-367. 2006. 

Aryal BP, Sandros MG, Neupane, KP, Benson DE. “Metallothioneins Initiate Semiconducting Nanoparticle Cellular Toxicity”, Small, 2, 1159-1163. 2006.

Sandros MG, Shete V, Benson DE “Selective, Reversible, Reagentless Maltose Biosensing with Core-Shell Semiconducting Nanoparticles” Analyst 131, 229 - 235. 2006

Sandros MG, Gao D, Benson DE. “A Modular Nanoparticle-Based System for Reagentless Small Molecule Biosensing.” J. Am. Chem. Soc. 127, 12198-12199. 2005. 

Shaw JL, Yee GT, Wang G, Benson DE, Gokdemir C, Ziegler CJ  “Magneto-Structural Relationships in a Series of Dinuclear Oxalato-Bridged (Diphenyldipyrazolylmethane)copper(II) Complexes.” Inorg. Chem. 44, 5060-5067. 2005. 

Sandros MG, Gao D, Gokdemir C, Benson DE “General, High-Affinity Approach for the Synthesis of Fluorophore Appended Protein Nanoparticle Assemblies.” Chem. Commun., 2832-2834. 2005. 

Swain MD, Benson DE “Geometric preferences of crosslinked protein-derived cofactors reveal a high propensity for near-sequence pairs.” Proteins: Struct. Funct. Bioinform. 59, 2005, 64-71.

Dattelbaum JD, Looger LL, Benson DE, Sali KM, Thompson RB, Hellinga HW “Analysis of Allosteric Signal Transduction Mechanisms in an Engineered Fluorescent Maltose Biosensor.” Protein Sci. 14, 2005, 284-291. 2005. 

"Bioelectronic Sensors and Methods of Using Same in Analyte Detection". Hellinga HW, Conrad DW, Benson DE. (Duke University, USA). PCT Int. Appl., 38 pp. 2003. 

Benson DE, Haddy AE, Hellinga HW. “Converting a Maltose Receptor into a Binuclear Copper Oxygenase by Computational Design” Biochemistry 41, 3262-3269. 2002. 

Unno M, Christian JF, Sjodin T, Benson DE, Macdonald IDG, Sligar SG, Champion PM.  “Complex Formation of Cytochrome P450(cam) with Putidaredoxin - Evidence for Protein-Specific Interactions Involving the Proximal Thiolate Ligand” J. Biol. Chem.,  277, 2547-2553. 2002. 

Benson DE, Conrad DW, de Lorimier RM, Trammell SA, Hellinga HW. “Design of Bioelectronic Interfaces by Exploiting
Hinge-Bending Motions in Proteins”. Science 293, 1641-1644. 2001. 

Trammell SA, Goldston, HM, Tran PT, Tender LM, Conrad DW, Benson DE, Hellinga HW. “Synthesis and Characterization of a Ruthenium(II)-Based Redox Conjugate for Reagentless Biosensing” Bioconjugate Chem. 12, 643-647, 2001.

Benson DE, Wisz MS, Hellinga HW. “Rational Design of Nascent Metalloenzymes” Proc. Natl. Acad. Sci. 97, 6292-6297. 2000.

Schlichting I, Berendzen J, Chu K, Stock AM, Maves SA, Benson DE, Sweet BM, Ringe D, Petsko GA, Sligar SG. “The Catalytic Pathway of Cytochrome P450cam at Atomic Resolution”. Science 287, 1615-1622. 2000.

Benson DE, Wisz MS, Hellinga HW. “The Development of New Biotechnologies Using Metalloprotein Design”. Curr. Opin. Biotech. 9, 370-376. 1998

Benson DE, Wisz MS, Liu WT, Hellinga HW. “Construction of A Novel Redox Protein by Rational Design: Conversion of A Disulfide Bridge into a Mononuclear Iron-Sulfur Center”. Biochemistry 37, 7070-7076. 1998. 

Unno M, Christian JF, Benson DE, Gerber NC, Sligar SG, Champion PM. “Resonance Raman Investigations of Cytochrome P450(cam) Complexed with Putidaredoxin” J. Am. Chem. Soc. 119, 6614-6620. 1997. 

Benson DE, Suslick KS, Sligar SG. “Reduced Oxy Intermediate Observed in D251N Cytochrome P450cam”. Biochemistry 36, 5104-5107. 1997. 

Awards

  • VIPEr Fellow- Cohort 2 for Pedagogy in Inorganic Chemistry - 2020
  • National Science Foundation - RUI: Protein Tyrosine Oxidations to Maintain Cellular Redox State (Award 1709787) - 2017-2020
  • National Science Foundation - MRI: Acquisition of a Circular Dichroism Spectrometer for Research and Training of Undergraduate Students (Award 1623941) - 2016-2019
  • Calvin University- Sabbatical - 2015
  • National Science Foundation- RUI: Role and Formation of Tyrosine-Cysteine Protein Cofactors (Award 1058391) - 2011-2015
  • National Science Foundation- ARI-R2 : Integrated Science Research Experimental Laboratory (Award 0963433) - 2010-2013 
  • American Chemical Society- Project SEED Summer Award - 2012
  • National Science Foundation- S-STEM: Expanding Computation for Interdisciplinary Science (Award 1154472)- 2012-2015 
  • American Chemical Society- Project SEED Summer Award - 2011
  • National Science Foundation- MRI-R2: Acquisition of Biophysical Instruments for Interdisciplinary Faculty and Student Research (Award 0959681) - 2010-2013
  •  American Chemical Society- Project SEED Summer Award - 2010
  • National Science Foundation- MRI: MALDI Acquisition for Collaborative Species and Biomolecule Identification (Award 0923167) - 2009-2012
  • National Science Foundation- MRI: Acquisition of a 500 MHz NMR Spectrometer to Enhance Faculty and Student Research (Award 0922973) - 2009-2012
  • Office of Naval Research- Semiconductor Nanoparticle-based Biosensors for Stochastic Analyte Detection - 2006-2009
  • National Science Foundation- NER: Protein-Based Nanobiosensors for Environmental Monitoring (Award 0508134) - 2005-2006
  • National Science Foundation- Conference on Metalloprotein and Protein Design (Award 0837310) - 2005-2006
  • Invited to "Emerging Investigators Issue" of The Analyst - 2006
  • Research Corporation - Research Innovation Award - 2002
  • National Institutes of Health (Duke University) - National Research Service Award - 1998-2000
  • University of Illinois - Urbana-Champaign- Lubrizol Fellowship - 1992

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