Margot Borgel, Ph.D.

Margot Borgel, Ph.D.

Charleston, South Carolina Metropolitan Area
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    Charleston, South Carolina Metropolitan Area

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    Greater Atlanta Area

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    Greater Atlanta Area

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    Atlanta, GA

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    Atlanta, GA

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    State College, PA

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    State College, PA

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    Melbourne, FL

Education

Publications

  • Loop-loop interactions govern multiple steps in indole-3-glycerol phosphate synthase catalysis

    Protein Science

    Substrate binding, product release, and likely chemical catalysis in the tryptophan biosynthetic enzyme indole-3-glycerol phosphate synthase (IGPS) are dependent on the structural dynamics of the β1α1 active-site loop. Statistical coupling analysis/molecular dynamic simulations previously indicated that covarying residues in the β1α1 and β2α2 loops, corresponding to Arg54 and Asn90, respectively, in the Sulfolobus sulfataricus enzyme (sIGPS), are likely important for coordinating functional…

    Substrate binding, product release, and likely chemical catalysis in the tryptophan biosynthetic enzyme indole-3-glycerol phosphate synthase (IGPS) are dependent on the structural dynamics of the β1α1 active-site loop. Statistical coupling analysis/molecular dynamic simulations previously indicated that covarying residues in the β1α1 and β2α2 loops, corresponding to Arg54 and Asn90, respectively, in the Sulfolobus sulfataricus enzyme (sIGPS), are likely important for coordinating functional motions of these loops. To test this hypothesis, we characterized site mutants at these positions for changes in catalytic function, protein stability and structural dynamics for the thermophilic sIGPS enzyme. Although there were only modest changes in the overall steady-state kinetic parameters, solvent viscosity and solvent deuterium kinetic isotope effects indicated that these amino acid substitutions change the identity of the rate-determining step across multiple temperatures. Surprisingly, the N90A substitution had a dramatic effect on the general acid/base catalysis of the dehydration step, as indicated by the loss of the descending limb in the pH rate profile, which we had previously assigned to Lys53 on the β1α1 loop. These changes in enzyme function are accompanied with a quenching of ps-ns/µs-ms timescale motions in the β1α1 loop as measured by nuclear magnetic resonance studies. Altogether, our studies provide structural, dynamic and functional rationales for the coevolution of residues on the β1α1 and β2α2 loops, and highlight the multiple roles that the β1α1 loop plays in IGPS catalysis. Thus, substitution of covarying residues in the active-site β1α1 and β2α2 loops of IGPS results in functional, structural, and dynamic changes, highlighting the multiple roles that the β1α1 loop plays in enzyme catalysis and the importance of regulating the structural dynamics of this loop through noncovalent interactions with nearby structural elements.

    Other authors
    • O'Rourke, K.
    • Yezdimer, E.
    • Loggia, L.J.
    • woldt, S
    • Boehr, D.D.
    See publication

  • Functional identification of the general acid and base in the dehydration step of indole-3-glycerol phosphate synthase catalysis

    Journal of Biological Chemistry

    The tryptophan biosynthetic enzyme indole-3-glycerol phosphate synthase is a proposed target for new antimicrobials and is a favored starting framework in enzyme engineering studies. Forty years ago, Parry proposed that the enzyme mechanism proceeds through two intermediates in a series of condensation, decarboxylation, and dehydration steps. X-ray crystal structures have suggested that Lys-110 (numbering according to the Sulfolobus solfataricus enzyme) behaves as a general acid both in the…

    The tryptophan biosynthetic enzyme indole-3-glycerol phosphate synthase is a proposed target for new antimicrobials and is a favored starting framework in enzyme engineering studies. Forty years ago, Parry proposed that the enzyme mechanism proceeds through two intermediates in a series of condensation, decarboxylation, and dehydration steps. X-ray crystal structures have suggested that Lys-110 (numbering according to the Sulfolobus solfataricus enzyme) behaves as a general acid both in the condensation and dehydration steps, but did not reveal an efficient pathway for the reprotonation of this critical residue. Our mutagenesis and kinetic experiments suggest an alternative mechanism whereby Lys-110 acts as a general acid in the condensation step, but another invariant residue, Lys-53, acts as the general acid in the dehydration step. These studies also indicate that the conserved residue Glu-51 acts as the general base in the dehydration step. The revised mechanism effectively divides the active site into discrete regions where the catalytic surfaces containing Lys-110 and Lys-53/Glu-51 catalyze the ring closure (i.e. condensation and decarboxylation) and dehydration steps, respectively. These results can be leveraged toward the development of novel inhibitors against this validated antimicrobial target and toward the rational engineering of the enzyme to produce indole derivatives that are highly prized by the pharmaceutical and agricultural industries.

    Other authors
    • Eric M. Yezdimer
    • David D. Boehr
    See publication

  • Differences in the catalytic mechanism of mesophilic and thermophilic indole-3-glycerol phosphate synthase enzymes at their adaptive temperatures

    Biochemical and biophysical research communications

    Thermophilic enzymes tend to be less catalytically-active at lower temperatures relative to their mesophilic counterparts, despite having very similar crystal structures. An often cited hypothesis for this general observation is that thermostable enzymes have evolved a more rigid tertiary structure in order to cope with their more extreme, natural environment, but they are also less flexible at lower temperatures, leading to their lower catalytic activity under mesophilic conditions. An…

    Thermophilic enzymes tend to be less catalytically-active at lower temperatures relative to their mesophilic counterparts, despite having very similar crystal structures. An often cited hypothesis for this general observation is that thermostable enzymes have evolved a more rigid tertiary structure in order to cope with their more extreme, natural environment, but they are also less flexible at lower temperatures, leading to their lower catalytic activity under mesophilic conditions. An alternative hypothesis, however,
    is that complementary thermophilic–mesophilic enzyme pairs simply operate through different
    evolutionary-optimized catalytic mechanisms. In this communication, we present evidence that while the steps of the catalytic mechanisms for mesophilic and thermophilic indole-3-glycerol phosphate synthase (IGPS) enzymes are fundamentally similar, the identity of the rate-determining step changes as a
    function of temperature. Our findings indicate that while product release is rate-determining at 25 C for thermophilic IGPS, near its adaptive temperature (75 C), a proton transfer event, involving a general acid, becomes rate-determining. The rate-determining steps for thermophilic and mesophilic IGPS
    enzymes are also different at their respective, adaptive temperatures with the mesophilic IGPS-catalyzed reaction being rate-limited before irreversible CO2 release, and the thermophilic IGPS-catalyzed reaction being rate limited afterwards.

    Other authors
    • Olga Manweiller
    • David D. Boehr

  • Preparation of Electrochemically Etched Tips for Ambient Instructional Scanning Tunneling Microscopy

    Journal of Chemical Education

    A first-year laboratory experiment that utilizes concepts of electrochemical tip etching for scanning tunneling microscopy (STM) is described. This experiment can be used in conjunction with any STM experiment. Students electrochemically etch gold STM tips using a time-efficient method, which can then be used in an instructional grade STM that operates under ambient conditions. Electrochemical etching is one method used by researchers to prepare tips for high-quality STM imaging. Whereas the…

    A first-year laboratory experiment that utilizes concepts of electrochemical tip etching for scanning tunneling microscopy (STM) is described. This experiment can be used in conjunction with any STM experiment. Students electrochemically etch gold STM tips using a time-efficient method, which can then be used in an instructional grade STM that operates under ambient conditions. Electrochemical etching is one method used by researchers to prepare tips for high-quality STM imaging. Whereas the most common materials used to fabricate electrochemically etched tips cannot be used in ambient STMs, this experiment is a way to integrate the importance of tip etching (as opposed to mechanically prepared tips) into an STM laboratory experiment. The students are able to make Au tips with a reasonably small radius of curvature (<100 nm). First-year undergraduate students with almost no previous experience using an STM instrument were routinely able to achieve atomic resolution on a graphite surface.

    Other authors
    • Kurt Winkelman
    • Joel A. Olson

Courses

  • Advanced Analytical Chemistry

    CHM 4304

  • Advanced Laboratory Techniques

    CHM 4611

  • Advanced Organic Chemistry

    CHM 4500

  • Advanced Physical Chemistry

    CHM 4111

  • Analytical Biochemistry

    Chem 474

  • Biological Chemistry

    Chem 476

  • Calculus I, II, III

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  • Differential Equations/Linear Algebra

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  • Electrochemistry

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  • NMR Spectroscopy

    Chem 597c

  • Quantum Chemistry I

    Chem 565

Organizations

  • Graduate Women in Science

    Treasurer

    - Present

  • American Chemical Society

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    - Present

  • Alpha Phi International Fraternity

    Chapter Advisor, Chapter President, Director of Finance

    - Present

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