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• Over 4 years of data analysis and machine learning experience
• Extensive research…

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Publications

  • Label-Free Real-Time Monitoring of Reactions Between Internalin A and Its Antibody by an Oblique-Incidence Reflectivity-Difference Method

    ACS Omega

    Using a microarray-based assay, we studied how the substitution of amino acids in the immediate vicinity of the receptor-binding domain on a peptide affects its binding to a protein. Replicates of 802 linear peptides consisting of the variants of WTHPQFAT and LQWHPQAGK, GKFPIPLGKQSG, and NGQFQVWIPGAQK, different by one amino acid, were synthesized on a glass slide with a maskless photolithography. Using a microarray-compatible label-free optical sensor, we measured the binding curves of…

    Using a microarray-based assay, we studied how the substitution of amino acids in the immediate vicinity of the receptor-binding domain on a peptide affects its binding to a protein. Replicates of 802 linear peptides consisting of the variants of WTHPQFAT and LQWHPQAGK, GKFPIPLGKQSG, and NGQFQVWIPGAQK, different by one amino acid, were synthesized on a glass slide with a maskless photolithography. Using a microarray-compatible label-free optical sensor, we measured the binding curves of streptavidin with the synthesized peptides and extracted the streptavidin–peptide affinity constants. We found that (a) the substitution of one residue in the HPQ motif reduces the affinity constant Ka from 10⁸ M–1 by at least 3–4 orders of magnitude, with an exception of HPM; (b) substitution of the immediate flanking residue on the Gln side also causes the affinity to decrease by up to 3–4 orders of magnitude, depending on the substituting residue and the second-neighboring flanking residue; (c) substitution of the flanking residues on the His side has no significant effect on the affinity, possibly due to the strong binding of streptavidin to HPQF and HPQAG motifs. We also found that some of amino acid residues located close to the C-terminus (and the solid surface) improve the yield of peptide synthesis on a glass surface and can be exploited in the fabrication of peptide microarrays.

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  • Single Amino Acid Substitution in the Vicinity of a Receptor-Binding Domain Changes Protein–Peptide Binding Affinity

    ACS Omega

    Using a microarray-based assay, we studied how the substitution of amino acids in the immediate vicinity of the receptor-binding domain on a peptide affects its binding to a protein. Replicates of 802 linear peptides consisting of the variants of WTHPQFAT and LQWHPQAGK, GKFPIPLGKQSG, and NGQFQVWIPGAQK, different by one amino acid, were synthesized on a glass slide with a maskless photolithography. Using a microarray-compatible label-free optical sensor, we measured the binding curves of…

    Using a microarray-based assay, we studied how the substitution of amino acids in the immediate vicinity of the receptor-binding domain on a peptide affects its binding to a protein. Replicates of 802 linear peptides consisting of the variants of WTHPQFAT and LQWHPQAGK, GKFPIPLGKQSG, and NGQFQVWIPGAQK, different by one amino acid, were synthesized on a glass slide with a maskless photolithography. Using a microarray-compatible label-free optical sensor, we measured the binding curves of streptavidin with the synthesized peptides and extracted the streptavidin–peptide affinity constants. We found that (a) the substitution of one residue in the HPQ motif reduces the affinity constant Ka from 10⁸ M–1 by at least 3–4 orders of magnitude, with an exception of HPM; (b) substitution of the immediate flanking residue on the Gln side also causes the affinity to decrease by up to 3–4 orders of magnitude, depending on the substituting residue and the second-neighboring flanking residue; (c) substitution of the flanking residues on the His side has no significant effect on the affinity, possibly due to the strong binding of streptavidin to HPQF and HPQAG motifs. We also found that some of amino acid residues located close to the C-terminus (and the solid surface) improve the yield of peptide synthesis on a glass surface and can be exploited in the fabrication of peptide microarrays.

    See publication
  • Zero Loop-Area Sagnac Interferometer at Oblique-Incidence for Detecting in-Plane Magneto-Optic Kerr Effect.

    AIP Advances

    We describe a zero loop-area Sagnac interferometer at oblique incidence for detecting magneto-optic Kerr effect arising from in-plane magnetization in a sample. By exploiting properties of polarization states under relevant crystal symmetry transformation, we show that contributions from longitudinal and transverse Kerr effects can be separated. In addition we can select one optical arrangement out of four that detects the longitudinal effect with the highest signal-to-noise ratio. Compared to…

    We describe a zero loop-area Sagnac interferometer at oblique incidence for detecting magneto-optic Kerr effect arising from in-plane magnetization in a sample. By exploiting properties of polarization states under relevant crystal symmetry transformation, we show that contributions from longitudinal and transverse Kerr effects can be separated. In addition we can select one optical arrangement out of four that detects the longitudinal effect with the highest signal-to-noise ratio. Compared to finite loop-area Sagnac interferometers operating at oblique incidence, the zero loop-area interferometer involves significantly fewer optical elements and is thus more stable against drifts in the optical system. For demonstration, we measured the in-plane magneto-optic Kerr effect from a 42-nm Ni film.

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  • High-Throughput Dose–Response Measurement Using a Label-Free Microarray-in-Microplate Assay Platform

    Analytical Chenistry

    Microarray-based binding assays facilitate the discovery of protein ligands from large collections of small molecules. Hundreds of ligands can be identified, yet only a small portion of them have interfering effects (competitive or noncompetitive) on a specific protein–receptor binding reaction. Further efficient screening of ligands for those with specific modifying effect is needed in order to take the full advantage of throughputs of microarray-based assays for drug discovery. We report a…

    Microarray-based binding assays facilitate the discovery of protein ligands from large collections of small molecules. Hundreds of ligands can be identified, yet only a small portion of them have interfering effects (competitive or noncompetitive) on a specific protein–receptor binding reaction. Further efficient screening of ligands for those with specific modifying effect is needed in order to take the full advantage of throughputs of microarray-based assays for drug discovery. We report a label-free “microarray-in-microplate” assay platform for simultaneous acquisition of at least 32 dose–response curves in a single experiment, each curve having 12 concentration points. When combined with ligand discovery, this makes the microarray-based platform a true high-throughout means of finding inhibitors to specific protein–receptor reactions starting from a large collection of small-molecule libraries.

    Other authors
    • James LandryZhu
    • X.D. Zhu
    See publication

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