Geoffrey Hoops

Implementation of a Collaborative Series of Classroom-Based Undergraduate Research Experiences Spanning Chemical Biology, Biochemistry, and Neurobiology

This paper describes the design, implementation, and assessment of three collaborative classroom undergraduate research experiences (CUREs) integrating faculty research interests across chemical biology, biochemistry, and neurobiology. Benefits of CURE participation included increased faculty productivity, generation of novel scientific data, and the expected CURE benefits for student learning.

Effects of sodium chloride on the properties of chlorophyll a submonolayer adsorbed onto hydrophobic and hydrophilic surfaces using broadband spectroscopy with single-mode integrated optical waveguides

In this work, we experimentally investigated the effects of sodium chloride on the molar absorptivity and surface density of a sub- monolayer of chlorophyll a adsorbed onto hydrophilic and hydrophobic solid/liquid interfaces. Those investigations were made possible by a broadband spectroscopic platform based on single-mode, integrated op- tical waveguides, which allows for extremely sensitive spectroscopic de- tection of analytes immobilized at submonolayer levels. Chlorophyll a with a constant bulk concentration (1.4 μM) was dissolved in phosphate buffer solutions (7 mM) of neutral pH, but with different sodium chloride concen- trations. For a buffer solution of 1 mM of sodium chloride, the measured surface density of chlorophyll a was 0.209 pmol/cm 2 for a hydrophilic and 0.125 pmol/cm 2 for a hydrophobic surface. For a phosphate buffer solution of 10 mM of sodium chloride, the measured surface density of chlorophyll a was 0.528 pmol/cm 2 for a hydrophilic and 0.337 pmol/cm 2 for a hy- drophobic surface. Additionally, a hypsochromic shift of the Soret band was observed for the adsorbed pigment in correlation with an increase in buffer ionic strength. The adsorption of chlorophyll a onto different sur- faces can play an important role to elucidate several processes found in nature and provide a rationale for bio-inspired new material technologies.

Fluorogenic structure activity library pinpoints molecular variations in substrate specificity of structurally homologous esterases

Cellular esterases catalyze many essential biological functions by performing hydrolysis reactions on diverse substrates. The promiscuity of esterases complicates assignment of their substrate preferences and biological functions. To identify universal factors controlling esterase substrate recognition, we designed a 32-member structure–activity relationship (SAR) library of fluorogenic ester substrates and used this library to systematically interrogate esterase preference for chain length, branching patterns, and polarity to differentiate common classes of esterase substrates. Two structurally homologous bacterial esterases were screened against this library, refining their previously broad overlapping substrate specificity. Vibrio cholerae esterase ybfF displayed a preference for γ-position thioethers and ethers, whereas Rv0045c from Mycobacterium tuberculosis displayed a preference for branched substrates with and without thioethers. We determined that this substrate differentiation was partially controlled by individual substrate selectivity residues Tyr-119 in ybfF and His-187 in Rv0045c; reciprocal substitution of these residues shifted each esterases substrate preference. This work demonstrates that the selectivity of esterases is tuned based on transition state stabilization, identifies thioethers as an underutilized functional group for esterase substrates, and provides a rapid method for differentiating structural isozymes. This SAR library could have multifaceted future applications, including in vivo imaging, biocatalyst screening, molecular fingerprinting, and inhibitor design.

Spectroscopic studies in protein films with highly sensitive single-mode guided-wave plataforms

In this work we report experimental results on the molar absorptivity of cytochrome c adsorbed at different submonolayer levels onto an aluminum oxide waveguide surface. The spectra was acquired using the broadband, single-mode, integrated optical waveguide spectroscopic technique, which is an extremely sensitive tool able to reach submonolayer levels of detection required for this type of studies. For a protein surface density of 2.3 pmol/cm² the molar absorptivity measured at 695 nm was 335 M⁻¹ cm⁻¹, and for a surface density of 14.6 pmol/cm² was 720 M⁻¹ cm⁻¹ which is much closer to the value of cyt c dissolved in an aqueous neutral buffer (830 M⁻¹ cm⁻¹). Our data show a clear dependence of the protein optical properties on its surface density. The modification of the protein molar absorptivity can most likely be attributed to conformational changes of the surface-adsorbed species.