arXiv subjects

Christopher V. Kelly

Publications and source records attributed to Christopher V. Kelly.

4 recordsLinked to original sources

arXiv2025

RAPID-Net: Accurate Pocket Identification for Binding-Site-Agnostic Docking

Accurate identification of druggable pockets and their features is essential for structure-based drug design and effective downstream docking. Here, we present RAPID-Net, a deep learning-based algorithm designed for the accurate prediction of binding pockets and seamless integration with docking pipelines. On the PoseBusters benchmark, RAPID-Net-guided AutoDock Vina achieves 54.9% of Top-1 poses with RMSD < 2 A and satisfying the PoseBusters chemical-validity criterion, compared to 49.1% for DiffBindFR. On the most challenging time split of PoseBusters aiming to assess generalization ability (structures submitted after September 30, 2021), RAPID-Net-guided AutoDock Vina achieves 53.1% of Top-1 poses with RMSD < 2 A and PB-valid, versus 59.5% for AlphaFold 3. Notably, in 92.2% of cases, RAPID-Net-guided Vina samples at least one pose with RMSD < 2 A (regardless of its rank), indicating that pose ranking, rather than sampling, is the primary accuracy bottleneck. The lightweight inference, scalability, and competitive accuracy of RAPID-Net position it as a viable option for large-scale virtual screening campaigns. Across diverse benchmark datasets, RAPID-Net outperforms other pocket prediction tools, including PUResNet and Kalasanty, in both docking accuracy and pocket-ligand intersection rates. Furthermore, we demonstrate the potential of RAPID-Net to accelerate the development of novel therapeutics by highlighting its performance on pharmacologically relevant targets. RAPID-Net accurately identifies distal functional sites, offering new opportunities for allosteric inhibitor design. In the case of the RNA-dependent RNA polymerase of SARS-CoV-2, RAPID-Net uncovers a wider array of potential binding pockets than existing predictors, which typically annotate only the orthosteric pocket and overlook secondary cavities.

q-bio.BM↗

arXiv2017

Resolving the effects of nanoscale membrane curvature on lipid mobility

The biophysical consequences of nanoscale curvature have been challenging to resolve due to size-dependent membrane behavior and the experimental resolution limits imposed by optical diffraction. Recent advances in nanoengineering and super-resolution techniques have enabled new capabilities for creating and observing curvature. In particular, draping supported lipid bilayers over lithographically patterned substrates provides a model system for endocytic pits. The experiments and simulations presented below describe the possible detection of membrane curvature through fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS), single particle tracking (SPT), and polarized localization microscopy (PLM). FRAP and FCS depend on diffraction-limited illumination and detection. In particular, a simulation of FRAP shows no effects on lipids diffusion due to a 50 nm diameter membrane bud at any stage in the budding process. Simulated FCS demonstrated small effects due to a 50 nm radius membrane bud that was amplified with curvature-dependent lipid mobility changes. However, PLM and SPT achieve sub-diffraction-limited resolution of membrane budding and lipid mobility through the identification of the single-lipid positions with <15 nm spatial and <20 ms temporal resolution. By mapping the single-lipid step lengths to locations on the membrane, the effects of curvature on lipid behavior have been resolved.

physics.bio-ph↗

arXiv2017

The Detection of Nanoscale Membrane Bending with Polarized Localization Microscopy

The curvature of biological membranes at the nanometer scale is critically important for vesicle trafficking, organelle morphology, and disease propagation. This manuscript reports the development of Polarized Localization Microscopy (PLM), a pointillist optical imaging technique for the detection of nanoscale membrane curvature in correlation with single-molecule dynamics and molecular sorting. PLM combines polarized total internal reflection fluorescence microscopy (TIRFM) and single-molecule localization microscopy to reveal membrane orientation with sub-diffraction-limited resolution without reducing localization precision by point spread function (PSF) manipulation. Further, membrane curvature detection with PLM requires fewer localization events to detect curvature than 3D single-molecule localization microscopy (e.g., PALM or STORM), which enables curvature detection 10x faster via PLM than via 3D single-molecule localizations. With high sensitivity, PLM detects curvature with provides super resolution images with >10x signal-to-noise enhancement from diffraction-limited polarized TIRFM. With rotationally confined lipophilic fluorophores and the polarized incident fluorescence excitation, membrane-bending events are revealed with super-resolution. Engineered hemispherical membrane curvature with a radius >= 24 nm was detected with PLM with individual fluorophore have a localization precision of 13 +/- 5 nm. Further, deciphering molecular dynamics as a function of membrane topology was enabled. The diffusion coefficient of individual DiI molecules was 7.6x higher in planar supported lipid bilayers than within nanoscale membrane curvature.

physics.bio-ph↗

arXiv2017

Nanoscale membrane budding induced by CTxB on quasi-one component lipid bilayers detected by polarized localization microscopy

For endocytosis and exocytosis, membranes transition between planar, budding, and vesicular topographies through nanoscale reorganization of lipids, proteins, and carbohydrates. However, prior attempts to understand the initial stages of nanoscale bending have been limited by experimental resolution. Through the implementation of polarized localization microscopy (PLM), this manuscript reports the inherent membrane bending capability of cholera toxin subunit B (CTxB) in quasi-one component supported lipid bilayers. Membrane buds were first detected with <50 nm radius, grew to >200 nm radius, and extended into longer tubules with dependence on the membrane tension and CTxB concentration. Compared to the concentration of the planar supported lipid bilayers, CTxB was >10x more concentrated on the positive curvature top and >25x more concentrated on the negative Gaussian curvature neck of the nanoscale membrane buds. This finding elucidates prior observations by correlating CTxB clustering and diffusion to CTxB-induced membrane bending. CTxB is frequently used as a marker for liquid-ordered lipid phases; however, the coupling between CTxB and membrane bending provides an alternate understanding of CTxB-induced membrane reorganization. Single-particle tracking was performed on both lipids and CTxB to reveal the correlation between single-molecule diffusion, CTxB accumulation, and membrane topography. Slowed lipid and CTxB diffusion was observed at the nanoscale buds locations, suggesting a local increase in membrane viscosity or molecular crowding upon membrane bending. These results suggest inherent CTxB-induced membrane bending as a mechanism for initiating CTxB internalization in cells that is initially independent of clathrin, caveolin, actin, and lipid phase separation.

physics.bio-ph↗