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Open Access Publications from the University of California

Scholarly Works (8 results)

  • Thesis
  • Peer Reviewed
UCLA Electronic Theses and Dissertations (2021)

Non-covalent interactions pervade all matter and play essential roles in both chemical and biological systems. Each individual non-covalent interaction is relatively weak (0.5 – 3 kcal mol-1); however, the accumulation of these weak forces often produces functional materials, such as enzymes, catalysts, and supramolecular architectures, with high binding affinities that dictate their specificity and efficiency. Often, the behaviors of non-covalent interactions in solution are complex, since solvation has a dramatic impact on the magnitude of binding forces. In addition, complementarity, preorganization, cooperativity, and allosteric effects observed in supramolecular systems introduce another layer of complexity in their overall binding events. Likewise, noncovalent interactions are multiplex, sophisticated, and intriguing, more than just the simple binding between positive and negative regions of a molecule. I have dedicated my graduate career in studying the role of several non-covalent interactions in enzyme-substrate recognition, design of synthetic host-guest systems, and catalysis. In all of the projects that I participated in, computation and experiment were simultaneously employed as this combination is often synergistic and complementary to each other. Altogether, each non-covalent interaction is unique, modular, and often the key feature in producing selective and efficient biological and chemical systems. Chapter One is a perspective on the importance and challenges in studying non-covalent interactions using both computation and experiment. Chapter Two describes in-depth fundamental study on arene-perfluoroarene interactions in solution. Chapters Three details the rational design of new, strong cyclophane-perfluoroarene complexes by precisely engineering arene-perfluoroarene and hydrogen bonding interactions. These two chapters were jointly advised by Prof. Ellen Sletten and Prof. Ken Houk where X-ray crystallography, synthesis, 1H NMR/fluorescence titrations, and computational modeling were simultaneously leveraged. Chapters Four to Nine highlight my contributions (advised by Prof. Ken Houk) in assessing several non-covalent interactions in silico from collaborations with other eminent chemists and biologists. Chapter Four details the density functional theory (DFT) and implicit solvation model benchmark for reproducing experimental ΔGa‘s in anion-binding host-guest systems. Chapters Five, Six, and Seven entail collaborative projects with Waters and Brustad groups (UNC Chapel Hill) and explore the role of cation-π, amide-π, and CH-π interactions in the recognition of lysine methylation (KMe3) and crotoylation (Kcr) by native enzymes using DFT calculations. In Chapter Eight, the role of halogen bonding was explored in the reductive dehalogenation mechanism by a bacterial tetrabromopyrrol debrominase (Bmp8) in collaboration with Moore group (Scripps). Lastly, Chapter Nine highlights the discovery of the light harvesting properties in anthracene-triphenylamine-based platinum(II) metallocages in collaboration with the Stang (U of Utah) and Deria (Southern Illinois U) groups.

    Cover page: The Study of Non-covalent Interactions using the Synergistic Combination of Experiment and Computation
    • Article
    • Peer Reviewed
    UCLA Previously Published Works (2021)
    A systematic study of arene-perfluoroarene interactions in solution is presented. Using a combination of NMR titration experiments, X-ray crystallography, and computational analysis, we analyze the effects of fluorination, substituents, ring size, and solvation on the arene-perfluoroarene interaction. We find that fluorination, extension of the π systems, and enhancement of solvent polarity greatly stabilize the stacking energy up to 3 orders of magnitude (Ka = <1 to 6000 M-1), with the highest Ka achieved for the interaction of water-soluble variants of perfluoronaphthalene and anthracene in buffered D2O (pD = 12). Combining computational and experimental results, we conclude that this impressive binding energy is a result of enthalpically favorable electrostatic and dispersion interactions as well as the entropically driven hydrophobic effect. The enhanced understanding of arene-perfluoroarene interactions in aqueous solution sets the stage for the implementation of this abiotic intermolecular interaction in biology and medicine.
      Cover page: Arene-Perfluoroarene Interactions in Solution
      • Article
      • Peer Reviewed
      UCLA Previously Published Works (2022)
      Iodine-induced cleavage at phosphorothioate DNA (PT-DNA) is characterized by extremely high sensitivity (∼1 phosphorothioate link per 106 nucleotides), which has been used for detecting and sequencing PT-DNA in bacteria. Despite its foreseeable potential for wide applications, the cleavage mechanism at the PT-modified site has not been well established, and it remains unknown as to whether or not cleavage of the bridging P-O occurs at every PT-modified site. In this work, we conducted accurate ωB97X-D calculations and high-performance liquid chromatography-mass spectrometry to investigate the process of PT-DNA cleavage at the atomic and molecular levels. We have found that iodine chemoselectively binds to the sulfur atom of the phosphorothioate link via a strong halogen-chalcogen interaction (a type of halogen bond, with binding affinity as high as 14.9 kcal/mol) and thus triggers P-O bond cleavage via phosphotriester-like hydrolysis. Additionally, aside from cleavage of the bridging P-O bond, the downstream hydrolyses lead to unwanted P-S/P-O conversions and a loss of the phosphorothioate handle. The mechanism we outline helps to explain specific selectivity at the PT-modified site but also predicts the dynamic stoichiometry of P-S and P-O bond breaking. For instance, Tris is involved in the cascade derivation of S-iodo-phosphorothioate to S-amino-phosphorothioate, suppressing the S-iodo-phosphorothioate hydrolysis to a phosphate diester. However, hydrolysis of one-third of the Tris-O-grafting phosphotriester results in unwanted P-S/P-O conversions. Our study suggests that bacterial DNA phosphorothioation may more frequently occur than previous bioinformatic estimations have predicted from iodine-induced deep sequencing data.
        Cover page: Origin of iodine preferential attack at sulfur in phosphorothioate and subsequent P-O or P-S bond dissociation
        • Article
        • Peer Reviewed
        UCLA Previously Published Works (2019)
        Enzymatic dehalogenation is an important and well-studied biological process in both the detoxification and catabolism of small molecules, many of which are anthropogenic in origin. However, dedicated dehalogenation reactions that replace a halogen atom with a hydrogen are rare in the biosynthesis of natural products. In fact, the debrominase Bmp8 is the only known example. It catalyzes the reductive debromination of the coral settlement cue and the potential human toxin 2,3,4,5-tetrabromopyrrole as part of the biosynthesis of the antibiotic pentabromopseudilin. Using a combination of protein crystallography, mutagenesis, and computational modeling, we propose a catalytic mechanism for Bmp8 that is reminiscent of that catalyzed by human deiodinases in the maintenance of thyroid hormones. The identification of the key catalytic residues enabled us to recognize divergent functional homologues of Bmp8. Characterization of one of these homologues demonstrated its debromination activity even though it is found in a completely distinct genomic context. This observation suggests that additional enzymes outside those associated with the tetrabromopyrrole biosynthetic pathway may be able to alter the lifetime of this compound in the environment.
          Cover page: Bacterial Tetrabromopyrrole Debrominase Shares a Reductive Dehalogenation Strategy with Human Thyroid Deiodinase
          • Article
          • Peer Reviewed
          UCLA Previously Published Works (2020)
          Lysine crotonylation (Kcr) is a histone post-translational modification that is implicated in numerous epigenetic pathways and diseases. Recognition of Kcr by YEATS domains has been proposed to occur through intermolecular amide-π and alkene-π interactions, but little is known about the driving force of these key interactions. Herein, we probed the recognition of lysine crotonylation and acetylation by the AF9 YEATS domain through incorporation of noncanonical Phe analogs with distinct electrostatics at two positions. We found that amide-π interactions between AF9 and acyllysines are electrostatically tunable, with electron-rich rings providing more favorable interactions. This differs from trends in amide-heteroarene interactions and provides insightful information for therapeutic design. Additionally, we report for the first time that CH-π interactions at Phe28 directly contribute to AF9's recognition of acyllysines, illuminating differences among YEATS domains, as this residue is not highly conserved but has been shown to impart selectivity for specific post-translational modification.
            Cover page: More Than π–π–π Stacking: Contribution of Amide−π and CH−π Interactions to Crotonyllysine Binding by the AF9 YEATS Domain
            • Article
            • Peer Reviewed
            UCLA Previously Published Works (2022)
            The 4-anilino-6,7-ethylenedioxy-5-fluoroquinazoline scaffold is presented as a novel model system for the characterization of the weak NH⋅⋅⋅F hydrogen bonding (HB) interaction. In this scaffold, the aniline NH proton is forced into close proximity with the nearby fluorine (dH,F ∼2.0 Å, ∠∼138°), and a through-space interaction is observed by NMR spectroscopy with couplings (1h JNH,F ) of 19±1 Hz. A combination of experimental (NMR spectroscopy and X-ray crystallography) and theoretical methods (DFT calculations) were used for the characterization of this weak interaction. In particular, the effects of conformational rigidity and steric compression on coupling were investigated. This scaffold was used for the direct comparison of fluoride with methoxy as HB acceptors, and the susceptibility of the NH⋅⋅⋅F interaction to changes in electron distribution and resonance was probed by preparing a series of molecules with different electron-donating or -withdrawing groups in the positions para to the NH and F. The results support the idea that fluorine can act as a weak HB acceptor, and the HB strength can be modulated through additive and linear electronic substituent effects.
              Cover page: Intramolecular N−H⋅⋅⋅F Hydrogen Bonding Interaction in a Series of 4‐Anilino‐5‐Fluoroquinazolines: Experimental and Theoretical Characterization of Electronic and Conformational Effects
              • Article
              • Peer Reviewed
              UCLA Previously Published Works (2017)
              Trimethyllysine (Kme3) reader proteins are targets for inhibition due to their role in mediating gene expression. Although all such reader proteins bind Kme3 in an aromatic cage, the driving force for binding may differ; some readers exhibit evidence for cation-π interactions whereas others do not. We report a general unnatural amino acid mutagenesis approach to quantify the contribution of individual tyrosines to cation binding using the HP1 chromodomain as a model system. We demonstrate that two tyrosines (Y24 and Y48) bind to a Kme3-histone tail peptide via cation-π interactions, but linear free energy trends suggest they do not contribute equally to binding. X-ray structures and computational analysis suggest that the distance and degree of contact between Tyr residues and Kme3 plays an important role in tuning cation-π-mediated Kme3 recognition. Although cation-π interactions have been studied in a number of proteins, this work is the first to utilize direct binding assays, X-ray crystallography, and modeling, to pinpoint factors that influence the magnitude of the individual cation-π interactions.
                Cover page: Investigation of Trimethyllysine Binding by the HP1 Chromodomain via Unnatural Amino Acid Mutagenesis
                • Article
                • Peer Reviewed
                UCLA Previously Published Works (2020)
                Evolution has converged on cation-π interactions for recognition of quaternary alkyl ammonium groups such as trimethyllysine (Kme3). While computational modelling indicates that Trp provides the strongest cation-π interaction of the native aromatic amino acids, there is limited corroborative data from measurements within proteins. Herein we investigate a Tyr to Trp mutation in the binding pocket of the HP1 chromodomain, a reader protein that recognizes Kme3. Binding studies demonstrate that the Trp-mediated cation-π interaction is about -5 kcal mol-1 stronger, and the Y24W crystal structure shows that the mutation is not perturbing. Quantum mechanical calculations indicate that greater enthalpic binding is predominantly due to increased cation-π interactions. NMR studies indicate that differences in the unbound state of the Y24W mutation lead to enthalpy-entropy compensation. These results provide direct experimental quantification of Trp versus Tyr in a cation-π interaction and afford insight into the conservation of aromatic cage residues in Kme3 reader domains.
                  Cover page: Thermodynamic consequences of Tyr to Trp mutations in the cation–π-mediated binding of trimethyllysine by the HP1 chromodomain
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