Single-molecule detection is the ultimate sensitivity in analytical chemistry and has been largely unavailable in electrochemical analysis. Here, we demonstrate the feasibility of detecting electrochemically inactive single biomacromolecules, such as enzymes, antibodies, and DNA, by blocking a solution redox reaction when molecules adsorb and block electrode sites. By oxidizing a large concentration of potassium ferrocyanide on an ultramicroelectrode (UME, radius ≤150 nm), time-resolved, discrete adsorption events of antibodies, enzymes, DNA, and polystyrene nanospheres can be differentiated from the background by their "footprint". Further, by assuming that the mass transport of proteins to the electrode surface is controlled mainly by diffusion, a size estimate using the Stokes-Einstein relationship shows good agreement of electrochemical data with known protein sizes.
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http://dx.doi.org/10.1021/jacs.5b04545 | DOI Listing |
Anal Chem
January 2025
Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.
Intact protein analysis using mass spectrometry (MS) is an important technique to characterize and provide a comprehensive overview of protein complexity. It is also the basis of "top-down" approaches in proteomics to describe the proteoforms of single protein's post-translational modifications (PTMs). MS-based analysis of intact proteins benefits from high-resolution separations prior to electrospray ionization.
View Article and Find Full Text PDFJ Gen Physiol
January 2025
Chemistry Department, University of Massachusetts Lowell, Lowell, MA, USA.
Titin is the third contractile filament in the sarcomere, and it plays a critical role in sarcomere integrity and both passive and active tension. Unlike the thick and thin filaments, which are polymers of myosin and actin, respectively, titin is a single protein that spans from Z-disk to M-line. The N2A region within titin has been identified as a signaling hub for the muscle and is shown to be involved in multiple interactions.
View Article and Find Full Text PDFAnal Chem
December 2024
Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States.
We are developing a unique protein identification method that consists of generating peptides proteolytically from a single protein molecule (i.e., peptide fingerprints) with peptide detection and identification carried out using nanoscale electrochromatography and label-free resistive pulse sensing (RPS).
View Article and Find Full Text PDFJ Mol Biol
December 2024
Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium; AI Lab, Vrije Universiteit Brussel, Brussels, Belgium; Chemistry Department, Vrije Universiteit Brussel, Brussels, Belgium; Biomedical Sciences, Vrije Universiteit Brussel, Brussels, Belgium. Electronic address:
The advent of accurate methods to predict the fold of proteins initiated by AlphaFold2 is rapidly changing our understanding of proteins and helping their design. However, these methods are mainly trained on protein structures determined with X-ray diffraction, where the protein is packed in crystals at often cryogenic temperatures. They can therefore only reliably cover well-folded parts of proteins that experience few, if any, conformational changes.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
November 2024
Department of Biomedical Engineering, Boston University, Boston, MA 02215.
The goal of this paper is predicting the conformational distributions of ligand binding sites using the AlphaFold2 (AF2) protein structure prediction program with stochastic subsampling of the multiple sequence alignment (MSA). We explored the opening of cryptic ligand binding sites in 16 proteins, where the closed and open conformations define the expected extreme points of the conformational variation. Due to the many structures of these proteins in the Protein Data Bank (PDB), we were able to study whether the distribution of X-ray structures affects the distribution of AF2 models.
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