Biology subjects

DeJong, M. P.

Publications and source records attributed to DeJong, M. P..

3 recordsLinked to original sources

bioRxiv2026

Engineering the mechanosensitivity of single DNA molecules via high-throughput microfluidic force spectroscopy

Single-molecule force spectroscopy (SMFS) is a powerful tool to measure how biomolecules respond to mechanical force, but limited sequence throughput constrains its potential. Here, we present a single-molecule, multiplexed, microfluidic force spectroscopy (SM3FS) assay that uses parallelized microfluidics to measure up to 80 sequence variants per experiment. Using SM3FS, we stretched, overstretched, or unzipped 241 different DNA structures and generated 131,847 single-molecule traces from a quarter-million observations. High sequence throughput allowed us to identify DNA structures that are kinetically stable yet mechanically fragile (Frupture < 3 pN at 0.5 pN s-1), revealing how mechanosensitivity can arise as an intrinsic property of multivalent systems. By enabling systematic sequence-function mapping under force, SM3FS opens a path to high-throughput nonequilibrium studies of biomolecules.

biophysics↗

bioRxiv2023

PDZ Domains from the Junctional Proteins Afadin and ZO-1 Act as Mechanosensors

Intercellular adhesion complexes must withstand mechanical forces to maintain tissue cohesion while also retaining the capacity for dynamic remodeling during tissue morphogenesis and repair. Many cell-cell adhesion complexes contain at least one PSD95/Dlg/ZO-1 (PDZ) domain situated between the adhesion molecule and the actin cytoskeleton. However, PDZ-mediated interactions are characteristically nonspecific, weak, and transient, with multiple binding partners per PDZ domain, micromolar dissociation constants, and bond lifetimes of seconds or less. Here, we demonstrate that the bonds between the PDZ domain of the cytoskeletal adaptor protein afadin and the intracellular domains of the adhesion molecules nectin-1 and JAM-A form molecular catch bonds that reinforce in response to mechanical load. In contrast, the bond between the PDZ3-SH3-GUK (PSG) domain of the cytoskeletal adaptor ZO-1 and the JAM-A intracellular domain becomes dramatically weaker in response to [~]2 pN of load, the amount generated by single molecules of the cytoskeletal motor protein myosin II. Thus, physiologically relevant forces can exert dramatic and opposite effects on the stability of two of the major linkages between cell-cell adhesion proteins and the F-actin cytoskeleton. Our data demonstrate that that PDZ domains can serve as force-responsive mechanical anchors at cell-cell adhesion complexes. More broadly, our findings suggest that mechanical force may serve as a previously unsuspected regulator of the hundreds of PDZ-ligand interactions present in animal cells.

biophysics↗

bioRxiv2021

A platform for deep sequence-activity mapping and engineering antimicrobial peptides

Developing potent antimicrobials, and platforms for their study and engineering, is critical as antibiotic resistance grows. A high-throughput method to quantify antimicrobial peptide and protein (AMP) activity across a broad continuum can elucidate sequence-activity landscapes and identify potent mutants. We developed a platform to perform sequence-activity mapping of AMPs via depletion (SAMP-Dep): a bacterial host culture is transformed with an AMP mutant library, induced to express AMPs, grown, and deep sequenced to quantify mutant frequency. The slope of mutant growth rate versus induction level indicates potency. Using SAMP-Dep, we screened 170,000 mutants of oncocin, a proline-rich AMP, for intracellular activity against Escherichia coli. Clonal validation of 36 mutants supported SAMP-Dep sensitivity and accuracy. The efficiency and accuracy of SAMP-Dep enabled mapping the oncocin sequence-activity space with remarkable detail and scale and guided focused, successful synthetic peptide library design, yielding a mutant with two-fold enhancement in both intracellular and extracellular activity.

bioengineering↗