Biology subjects

Knight, J. D.

Publications and source records attributed to Knight, J. D..

6 recordsLinked to original sources

bioRxiv2026

Single Molecule Diffusion Studies Reveal Rapid Translations Across Target Membrane Surfaces for both p40Phox PX domain and Class III PI3K VPS34 Complex 1, the Autophagy Lipid Kinase

Single molecule analyses are providing new insights into the molecular mechanisms by which peripheral membrane proteins approach and translate across a target bilayer surface before stable docking. Here we compare and contrast the translational movements of four diffusers on a representative supported lipid bilayer: (i) the fluorescent lipid LRB-(DO)PE, (ii) the G-protein Rab1A anchored to (DO)PE; (iii) the PI(3)P sensor p40Phox PX domain, and (iv) the autophagy lipid kinase VPS34 Complex 1. The latter enzyme is a Class III PI-3-Kinase and its unusual architecture exhibits two distinct membrane-docking "feet" unique to Class III PI3Ks. Notably, the membrane contact surfaces of the PX domain and autophagy lipid kinase each possess multiple positive charges suitable for electrostatic interactions with their anionic target membrane. The present single molecule tracking studies reveal that both the fluorescent lipid and the lipid-anchored G protein Rab1A exhibit 2-dimensional translation typical of simple lipid diffusion in the bilayer. Single molecule density measurements indicate both PX domain and autophagy lipid kinase exhibit significantly reduced membrane docking when the bilayer negative charge is decreased, confirming the importance of their protein-bilayer electrostatic interactions. Single molecule tracking studies reveal that both PX domain and autophagy lipid kinase exhibit hopping movements across the bilayer surface during their initial bilayer contacts, yielding a significantly higher frequency of long range displacements than allowed by lipid 2-D diffusion. After transitioning from hopping to a stable bilayer-docked state, both PX domain and autophagy lipid kinase exhibit 2-D diffusion slower than lipid diffusion indicating the appearance of increased frictional drag against the bilayer due to new protein-bilayer contacts. PX domain requires its target lipid for the transition from electrostatic hopping to stable bilayer docking, while autophagy lipid kinase can dock spontaneously to anionic lipid bilayers even in the absence of its substrate lipid. In principle, the slowly diffusing, bilayer-docked states of PX domain and autophagy lipid kinase could be interrupted by unbinding-hopping-rebinding events. However, such events are not detected for PX domain in the presence of target lipid (DO)PI(3)P nor for autophagy lipid kinase in the presence of substrate lipid (DO)PI. Instead, unbinding-hopping-rebinding events are only observed for autophagy lipid kinase in the absence of substrate lipid, indicating that the presence of a specific binding lipid reduces the frequency or spatial amplitude of such events. Overall, the findings provide evidence that p40Phox PX domain possesses a search mechanism involving electrostatic hopping that speeds its acquisition of target lipid, as previously observed for PH domains. The evidence indicates that the autophagy lipid kinase also exhibits electrostatic hopping/skating behavior that is proposed to play a functional role by speeding regulatory encounters with autophagy lipid kinase activators and effectors. Moreover, the ability of the lipid kinase to spontaneously dock to anionic membranes without a target lipid could facilitate its distribution across broad regions of the growing autophagosome. Finally, the autophagy lipid kinase exhibits multiple translational modes that we hypothesize are enabled by its two membrane docking feet.

biophysics↗

bioRxiv2025

Inflammatory Oxidative Stress Compounds Inhibit Insulin Secretion through Rapid Protein Carbonylation

Pancreatic {beta}-cells in pre-type 1 diabetes (T1D) experience stress due to islet inflammation, which accompanies early defects in insulin secretion that precede autoimmune destruction. One product of inflammatory stress is protein carbonylation (PC), brought on by reactive oxygen species (ROS) combining with lipids to produce reactive aldehydes such as 4-hydroxynonenal (4-HNE) that irreversibly modify Cys, His, and Lys sidechains. In this study, we used proteomics to measure patterns of PC in pancreatic islets from 10-week-old pre-diabetic NOD mice and in cultured insulin-secreting cells treated with either 4-HNE or pro-inflammatory cytokines. All three stress conditions increased carbonylation of proteins central to {beta}-cell function including Rab GTPases and other proteins that are essential for vesicle trafficking. Gene ontology analysis indicates that the affected proteins and pathways in pre-diabetic NOD islets reflect a combination of those impacted by 4-HNE and cytokine treatment. Furthermore, both 4-HNE and cytokines significantly inhibited insulin secretion by [~]50% in cultured MIN6 and INS-1-GRINCH cells. In particular, exposure to 4-HNE for as little as 5 minutes suppressed insulin secretion and increased the carbonylation of over 1000 proteins. Overall, the observed PC pattern in pre-T1D islets is consistent with a model in which {beta}-cells experience multiple sources of oxidative stress, including ROS generation within {beta}-cells themselves and reactive compounds released by infiltrating immune cells. The latter exogenous source may represent a novel rapid mechanism for inhibiting insulin secretion.

biochemistry↗

bioRxiv2024

Synaptotagmin 7 C2 domains induce membrane curvature stress via electrostatic interactions and the wedge mechanism

0.Synaptotagmin 7 (Syt-7) is part of the synaptotagmin protein family that regulates exocytotic lipid membrane fusion. Among the family, Syt-7 stands out by its membrane binding strength and stabilization of long-lived membrane fusion pores. Given that Syt-7 vesicles form long-lived fusion pores, we hypothesize that its interactions with the membrane stabilize the specific curvatures, thicknesses, and lipid compositions that support a metastable fusion pore. Using all-atom molecular dynamics simulations and FRET-based assays of Syt-7s membrane-binding C2 domains (C2A and C2B), we found that Syt-7 C2 domains sequester anionic lipids, are sensitive to cholesterol, thin membranes, and generate lipid membrane curvature by two competing, but related mechanisms. First, Syt-7 forms strong electrostatic contacts with the membrane, generating negative curvature stress. Second, Syt-7s calcium binding loops embed in the membrane surface, acting as a wedge to thin the membrane and induce positive curvature stress. These curvature mechanisms are linked by the protein insertion depth as well as the resulting protein tilt. Simplified quantitative models of the curvature-generating mechanisms link simulation observables to their membrane-reshaping effectiveness.

biophysics↗

bioRxiv2023

A Conserved Electrostatic Membrane-Binding Surface in Synaptotagmin-Like Proteins Revealed Using Molecular Phylogenetic Analysis and Homology Modeling

Protein structure prediction has emerged as a core technology for understanding biomolecules and their interactions. Here, we combine homology-based structure prediction with molecular phylogenetic analysis to study the evolution of electrostatic membrane binding among vertebrate synaptotagmin-like proteins (Slps). Slp family proteins play key roles in the membrane trafficking of large dense-core secretory vesicles. Our previous experimental and computational study found that the C2A domain of Slp-4 (also called granuphilin) binds with high affinity to anionic phospholipids in the cytoplasmic leaflet of the plasma membrane through a large positively charged protein surface centered on a cluster of phosphoinositide-binding lysine residues. Because this surface contributes greatly to Slp-4 C2A domain membrane binding, we hypothesized that the net charge on the surface might be evolutionarily conserved. To test this hypothesis, the known C2A sequences of Slp-4 among vertebrates were organized by class (from mammalia to pisces) using molecular phylogenetic analysis. Consensus sequences for each class were then identified and used to generate homology structures, from which Poisson-Boltzmann electrostatic potentials were calculated. For comparison, homology structures and electrostatic potentials were also calculated for the five human Slp protein family members. The results demonstrate that the charge on the membrane-binding surface is highly conserved throughout the evolution of Slp-4, and more highly conserved than many individual residues among the human Slp family paralogs. Such molecular phylogenetic-driven computational analysis can help to describe the evolution of electrostatic interactions between proteins and membranes which are crucial for their function. Impact statementThe interior surface of eukaryotic plasma membranes is negatively charged, and many proteins that bind to it have correspondingly evolved a positively charged face. Here, we use techniques from evolutionary biology and computational biophysics to study the conservation of this positively charged surface in an important protein family. We find that the overall surface charge is highly conserved, more so than individual amino acids, consistent with its important role in electrostatic interaction with the membrane.

bioinformatics↗

bioRxiv2020

Multivalent lipid targeting by the calcium-independent C2A domain of Slp-4/granuphilin

Synaptotagmin-like protein 4 (Slp-4), also known as granuphilin, is a Rab effector responsible for docking secretory vesicles to the plasma membrane before exocytosis. Slp-4 binds vesicular Rab proteins via an N-terminal Slp homology (SHD) domain, interacts with plasma membrane SNARE complex proteins via a central linker region, and contains tandem C-terminal C2 domains (C2A and C2B) with affinity for phosphatidylinositol-(4,5)-bisphosphate (PIP2). The Slp-4 C2A domain binds with low nanomolar apparent affinity to PIP2 in lipid vesicles that also contain background anionic lipids such as phosphatidylserine (PS), but much weaker when either the background anionic lipids or PIP2 are removed. Through computational and experimental approaches, we show that this high affinity membrane interaction arises from concerted interaction at multiple sites on the C2A domain. In addition to a conserved PIP2-selective lysine cluster, there exists a larger cationic surface surrounding the cluster which contributes substantially to the affinity for physiologically relevant lipid compositions. While mutations at the PIP2-selective site decrease affinity for PIP2, multiple mutations are needed to decrease binding to physiologically relevant lipid compositions. Docking and molecular dynamics simulations indicate several conformationally flexible loops that contribute to the nonspecific cationic surface. We also identify and characterize a covalently modified variant in the bacterially expressed protein, which arises through reactivity of the PIP2-binding lysine cluster with endogenous bacterial compounds and has a low membrane affinity. Overall, multivalent lipid binding by the Slp-4 C2A domain provides selective recognition and high affinity docking of large dense-core secretory vesicles to the plasma membrane.

biophysics↗

bioRxiv2018

Cooperativity and Avidity in Membrane Binding by C2AB Tandem Domains of Synaptotagmins 1 and 7

Synaptotagmin-1 (Syt-1) and synaptotagmin-7 (Syt-7) contain analogous tandem C2 domains, C2A and C2B, which together serve as a Ca2+ sensor to bind membranes and promote the stabilization of exocytotic fusion pores. Functionally, Syt-1 triggers fast release of neurotransmitters, while Syt-7 is involved in lower-Ca2+ processes such as hormone secretion. Evidence suggests that Syt-1 C2 domains bind membranes cooperatively, penetrating farther into membranes as the C2AB tandem than as individual C2 domains. In contrast, we previously reported that the two C2 domains of Syt-7 bind membranes independently, based in part on measurements of their liposome dissociation kinetics. Here, we have investigated the effects of C2A-C2B interdomain cooperativity with Syt-1 and Syt-7 using directly comparable measurements. We report Ca2+ sensitivities, dissociation kinetics, and membrane insertion using liposomes approximating physiological lipid compositions. Equilibrium Ca2+ titrations confirm that the Syt-7 C2AB tandem has a greater Ca2+ sensitivity of membrane binding than either of its individual domains. Stopped-flow fluorescence kinetic measurements show that Syt-1 C2AB dissociates from liposome membranes much more slowly than either of its isolated C2 domains, suggesting that the two C2 domains of Syt-1 bind membranes cooperatively. In contrast, the dominant population of Syt-7 C2AB has a dissociation rate comparable to its C2A domain, indicating a lack of cooperativity, while only a small subpopulation dissociates at a slower rate. Measurements using an environment-sensitive fluorescent probe indicate that the Syt-7 C2B domain inserts more deeply into membranes as part of the C2AB tandem, similarly to Syt-1. Overall, these measurements are consistent with a model in which the structural linkage of C2A and C2B impacts the membrane-binding geometry of synaptotagmin C2B domains, but imparts little or no cooperativity to Syt-7 membrane binding and dissociation events that are dominated by its C2A domain.

biophysics↗