About

Stefan Franzen is a professor in the Department of Chemistry at NC State University. He holds a Ph.D. from Stanford University obtained in 1992 and a B.S. from the University of California, Berkeley, earned in 1982. His area of expertise involves the application of spectroscopy to the structure and determination of enzymatic reaction mechanisms in biology. He serves as the college liaison for STEM international programs and is based in Dabney Hall, Room 208. His research focuses on chemical biology, particularly in understanding enzymatic processes through spectroscopic methods, contributing to the fields of drug discovery, energy, green chemistry, inorganic, organic, and physical chemistry.

Research topics

• Molecular physics
• Physics
• Optics
• Materials science
• Optoelectronics
• Atomic physics
• Geometry
• Nanotechnology
• Geology
• Chemistry
• Mathematics

Selected publications

• Comparison of the Backbone Dynamics of Dehaloperoxidase-Hemoglobin Isoenzymes

  The Journal of Physical Chemistry B · 2024-04-02 · 4 citations

  articleSenior authorCorresponding

  Dehaloperoxidase (DHP) is a multifunctional hemeprotein with a functional switch generally regulated by the chemical class of the substrate. Its two isoforms, DHP-A and DHP-B, differ by only five amino acids and have an almost identical protein fold. However, the catalytic efficiency of DHP-B for oxidation by a peroxidase mechanism ranges from 2- to 6-fold greater than that of DHP-A depending on the conditions. X-ray crystallography has shown that many substrates and ligands have nearly identical binding in the two isoenzymes, suggesting that the difference in catalytic efficiency could be due to differences in the conformational dynamics. We compared the backbone dynamics of the DHP isoenzymes at pH 7 through heteronuclear relaxation dynamics at 11.75, 16.45, and 19.97 T in combination with four 300 ns MD simulations. While the overall dynamics of the isoenzymes are similar, there are specific local differences in functional regions of each protein. In DHP-A, Phe35 undergoes a slow chemical exchange between two conformational states likely coupled to a swinging motion of Tyr34. Moreover, Asn37 undergoes fast chemical exchange in DHP-A. Given that Phe35 and Asn37 are adjacent to Tyr34 and Tyr38, it is possible that their dynamics modulate the formation and migration of the active tyrosyl radicals in DHP-A at pH 7. Another significant difference is that both distal and proximal histidines have a 15–18% smaller S2 value in DHP-B, thus their greater flexibility could account for the higher catalytic activity. The distal histidine grants substrate access to the distal pocket. The greater flexibility of the proximal histidine could also accelerate H2O2 activation at the heme Fe by increased coupling of an amino acid charge relay to stabilize the ferryl Fe(IV) oxidation state in a Poulos-Kraut “push–pull”-type peroxidase mechanism.

  PublisherDOI

• A physical demonstration of the increase in global surface energy due to increasing PCO2

  Research Square · 2024-01-12 · 1 citations

  preprintOpen accessSenior author

  Abstract Although study of the effect of energy-absorbing gases in our atmosphere has a two-hundred year history and an unequivocal explanation based on scientific observation and theory, a significant fraction of the public and even a few scientists doubt the correlation between the increasing the partial pressure of atmospheric carbon dioxide ( PCO 2 ) and the observed increase in terrestrial temperature over the past 120 years. Although the basic science showing that CO 2 would absorb the infrared radiation emitted by the earth produce a surface-warming effect was first calculated by Arrhenius in 1896, the issue was neglected by the scientific community for decades. Today there are ample climate models of the climactic effects arising from the forcing term of increasing PCO 2 . In this paper we follow Arrhenius’ concept, although we use the HITRAN database as the input to prove the connection between earth’s surface temperature and atmospheric absorption of terrestrial radiation. The spectra of CO 2 are enormously complicated, broadened by Fermi Resonance, and intense because of the quantum coupling of the rotation of CO 2 to its bending. The absorption by CO 2 reduces the transmittance of the Earth’s thermal radiation through the atmosphere, which in turn results in heating of the surface. The model does not make any predictions other than that the global temperature will increase as a function of PCO 2 . A rigorous statement of that connection will hopefully foster greater appreciation of the significance of atmospheric chemistry. We hope that the presentation of a simple model will give scientists the impetus to reach out to the public with lucid explanations based on physical principles.

  PublisherOA PDFDOI

• Structural Comparison of Substrate Binding Sites in Dehaloperoxidase A and B

  Biochemistry · 2024-07-03 · 3 citations

  articleSenior authorCorresponding

  Dehalperoxidase (DHP) has diverse catalytic activities depending on the substrate binding conformation, pH, and dynamics in the distal pocket above the heme. According to our hypothesis, the molecular structure of the substrate and binding orientation in DHP guide enzymatic function. Enzyme kinetic studies have shown that the catalytic activity of DHP B is significantly higher than that of DHP A despite 96% sequence homology. There are more than 30 substrate-bound structures with DHP B, each providing insight into the nature of enzymatic binding at the active site. By contrast, the only X-ray crystallographic structures of small molecules in a complex with DHP A are phenols. This study is focused on investigating substrate binding in DHP A to compare with DHP B structures. Fifteen substrates were selected that were known to bind to DHP B in the crystal to test whether soaking substrates into DHP A would yield similar structures. Five of these substrates yielded X-ray crystal structures of substrate-bound DHP A, namely, 2,4-dichlorophenol (1.48 Å, PDB: 8EJN), 2,4-dibromophenol (1.52 Å, PDB: 8VSK), 4-nitrophenol (2.03 Å, PDB: 8VKC), 4-nitrocatechol (1.40 Å, PDB: 8VKD), and 4-bromo-o-cresol (1.64 Å, PDB: 8VZR). For the remaining substrates that bind to DHP B, such as cresols, 5-bromoindole, benzimidazole, 4,4-biphenol, 4.4-ethylidenebisphenol, 2,4-dimethoxyphenol, and guaiacol, the electron density maps in DHP A are not sufficient to determine the presence of the substrates, much less their orientation. In our hands, only phenols, 4-Br-o-cresol, and 4-nitrocatechol can be soaked into crystalline DHP A. None of the larger substrates were observed to bind. A minimum of seven hanging drops were selected for soaking with more than 50 crystals screened for each substrate. The five high-quality examples of direct comparison of modes of binding in DHP A and B for the same substrate provide further support for the hypothesis that the substrate-binding conformation determines the enzyme function of DHP.

  PublisherDOI

• The role of proton-coupled electron transfer from protein to heme in dehaloperoxidase

  Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · 2024-10-16 · 1 citations

  articleSenior authorCorresponding
  PublisherDOI

• A physical demonstration of the increase in global surface energy due to increasing P[CO2]

  2024-02-01 · 1 citations

  preprintOpen accessSenior author

  Although study of the effect of energy-absorbing gases in our atmosphere has a two-hundred year history and an unequivocal explanation based on scientific observation and theory, a significant fraction of the public and even a few scientists doubt the correlation between the increasing the partial pressure of atmospheric carbon dioxide (P[CO2]) and the observed increase in terrestrial temperature over the past 120 years. Although the basic science showing that CO2 would absorb the infrared radiation emitted by the earth produce a surface-warming effect was first calculated by Arrhenius in 1896, the issue was neglected by the scientific community for decades. Today there are ample climate models of the climactic effects arising from the forcing term of increasing P[CO2]. In this paper we follow Arrhenius’ concept, although we use the HITRAN database as the input to prove the connection between earth’s surface temperature and atmospheric absorption of terrestrial radiation in a direct manner that the reader can also implement. The spectra of CO2 are enormously complicated, broadened by Fermi Resonance, and intense because of the quantum coupling of the rotation of CO2 to its bending. Using an on-line database for the transitions of CO2 the reader will easily be able to show that CO2 reduces the transmittance of the Earth’s thermal radiation through the atmosphere, which in turn results in heating of the surface. The model does not make any predictions other than that the global temperature will increase as a function of P[CO2]. The result is at the intersection of Physics, Atmospheric Science, and Psychology since the demonstration is a powerful tool that will give scientists the impetus to reach out to the public with lucid explanations based on physical principles.

  PublisherOA PDFDOI

• The mechanism of autoreduction in Dehaloperoxidase-A

  Biochemical and Biophysical Research Communications · 2024-12-19

  articleSenior authorCorresponding
  PublisherDOI

• Comparative Study of the Binding and Activation of 2,4-Dichlorophenol by Dehaloperoxidase a and B

  SSRN Electronic Journal · 2023-01-01

  preprintOpen accessSenior author
  PublisherDOI

• Comparative study of the binding and activation of 2,4-dichlorophenol by dehaloperoxidase A and B

  Journal of Inorganic Biochemistry · 2023-07-17 · 6 citations

  articleSenior authorCorresponding
  PublisherDOI

• Do you want to stay single? Considerations on single arm trials in drug development and the post-regulatory space

  2023-12-06

  preprintOpen access

  Single arm trials (SAT), while not preferred, remain in use throughout the drug development cycle. They may be accepted by regulators in particular contexts (eg., oncology and in rare diseases) when potential effects of new treatments are very large and placebo treatment is unethical. However, in the post-regulatory space, SATs are common, and perhaps even more poorly suited to address the questions of interest. In this manuscript, we review regulator and HTA positions on SATs, further challenges posed by SATs to address research questions beyond regulators, evolving statistical methods to provide context for SATs, case studies where SATs could and could not address questions or interest, and communication strategies to influence decision making and optimize study design to address evidence needs.

  PublisherOA PDFDOI

• Decomposition of 2,4-dihalophenols by dehaloperoxidase activity and spontaneous reaction with hydrogen peroxide

  Journal of Inorganic Biochemistry · 2023-12-24 · 2 citations

  articleOpen accessSenior authorCorresponding

  The enzyme dehaloperoxidase (DHP) found in the marine worm Amphitrite ornata is capable of enzymatic peroxidation of 2,4-dichlorophenol (DCP) and 2,4-dibromophenol (DBP). There is also at least one parallel oxidative pathway and the major products 2-chloro-1,4-benzoquinone (2-ClQ) and 2-bromo-1,4-benzoquinone (2-BrQ) undergo aspontaneous secondary hydroxylation reaction. The oxidation and hydroxylation reactions have been monitored by UV–visible spectroscopy, High Performance Liquid Chromatography (HPLC), and mass spectrometry . Evidence from time-resolved UV–visible spectroscopy suggests that the hydroxylations of 2-ClQ and 2-BrQ in the presence of hydrogen peroxide (H 2 O 2 ) are non-enzymatic spontaneous processes approximately ∼10 and ∼ 5 times slower, respectively, than the enzymatic oxidation of DCP or DBP by DHP in identical solvent conditions. The products 2-ClQ and 2-BrQ have λ max at 255 nm and 260 nm, respectively. Both substrates, DCP and DBP, react to form a parallel product peaked at 240 nm on the same time scale as the formation of 2-ClQ and 2-BrQ. The 240 nm band is not associated with the hydroxylation process, nor is it attributable to the catechol 3,5-dihalobenzene-1,3-diol observed by mass spectrometry. One possible explanation is that muconic acid is formed as a decomposition product, which could follow decomposition either the catechol or hydroxyquinone . These reactions give a more complete understanding of the biodegradation of xenobiotics by the multi-functional hemoglobin, DHP, in Amphitrite ornata . The decomposition of 2,4-dihalophenols catalyzed by dehaloperoxidase was studied by UV–visible spectroscopy, High Performance Liquid Chromatography and Liquid Chromatography-Mass Spectrometry. Spectroscopic evidence suggests two major products, which we propose are 2-halo-1,4-benzoquinone and 2-halomuconic acid. These complementary techniques give a high-level view of the degradation of xenobiotics in marine ecosystems. The enzyme dehaloperoxidase dehalogenates chlorinated phenols to produce chlorinated-1,4-benzoquinones in the presence of H 2 O 2 . A second step that involves hydroxylation of the 1,4-benzoquinone has also been observed. It apparently involves a spontaneous reaction of a second H 2 O 2 molecule with the quinone product. Time-resolved spectroscopic studies also show parallel reaction pathways. • Peroxidase-catalyzed oxidation of phenol to quinone in the presence of H 2 O 2 . • Spontaneous non-enzymatic hydroxylation of quinone also in the presence of H 2 O 2 . • Hydroxylation of quinone is 10 times slower than the enzymatic oxidation of phenol. • Application of Singular Value Decomposition analysis to understand complex reactions. • Reactions monitored by UV–visible spectroscopy, HPLC, mass spectrometry

  PublisherDOI

Recent grants

• Function Switching and Regulation of a Multifunctional Enzyme

  NSF · $524k · 2016–2020

• NIH Grant R01CA098194

  NIH · $1.0M · 2008

• Collaborative Research: Surface Plasmon Resonance in the Mid-infrared

  NSF · $514k · 2011–2016

• IRES: U.S.-Poland - RNA Structures that Promote Encapsidation

  NSF · $158k · 2007–2010

• Materials development for mid-infrared plasmonic applications

  NSF · $500k · 2015–2020

Frequent coauthors

• William H. Woodruff

  University of Illinois Urbana-Champaign

  99 shared

• Steven G. Boxer

  Stanford University

  85 shared

• Scott H. Brewer

  Franklin & Marshall College

  74 shared

• Jean‐Louis Martin

  63 shared

• Jennifer Belyea

  51 shared

• R. Brian Dyer

  50 shared

• Andrew P. Shreve

  University of New Mexico

  49 shared

• Jean‐Christophe Lambry

  École Polytechnique

  36 shared

Labs

• Chemistry Research Group of Stefan FranzenPI

Education

• PhD, Chemistry

  Stanford University

  1992