scholarly journals Binding site localization on non-homogeneous cell surfaces using topological image averaging

2020 ◽  
Author(s):  
Vibha Kumra Ahnlide ◽  
Johannes Kumra Ahnlide ◽  
Jason P. Beech ◽  
Pontus Nordenfelt
Keyword(s):  
Cell Surface ◽  
Binding Site ◽  
Antibody Binding ◽  
Surface Proteins ◽  
High Throughput Analysis ◽  
Native Cell ◽  
Site Localization ◽  
Homogeneous Cell ◽  
Image Averaging ◽  
Therapeutic Monoclonal Antibodies

Antibody binding to cell surface proteins plays a crucial role in immunity and the location of an epitope can altogether determine the immunological outcome of a host-target interaction. Techniques available today for epitope identification are costly, time-consuming, and unsuited for high-throughput analysis. Fast and efficient screening of epitope location can be useful for the development of therapeutic monoclonal antibodies and vaccines. In the present work, we have developed a method for imaging-based localization of binding sites on cellular surface proteins. The cellular morphology typically varies, and antibodies often bind in a non-homogenous manner, making traditional particle-averaging strategies challenging for accurate native antibody localization. Nanometer-scale resolution is achieved through localization in one dimension, namely the distance from a bound ligand to a reference surface, by using topological image averaging. Our results show that this method is well suited for antibody binding site measurements on native cell surface morphology.

scholarly journals Mechanical reinforcement of protein L from Finegoldia magna points to a new bind-and-search mechanism

2019 ◽  
Author(s):  
Narayan R. Dahal ◽  
Joel Nowitzke ◽  
Annie Eis ◽  
Ionel Popa
Keyword(s):  
Binding Site ◽  
Mechanical Stability ◽  
Magnetic Tweezers ◽  
Antibody Binding ◽  
Surface Proteins ◽  
Covalent Attachment ◽  
Molecular Response ◽  
High Avidity ◽  
Protein L ◽  
Binding Interface

AbstractSeveral significant bacterial pathogens in humans secrete surface proteins that bind antibodies in order to protect themselves from the adaptive immune response and have evolved to operate under the mechanical sheer generated by mucus flow, coughing or urination. Protein L is secreted by Finegoldia magna and has several antibody-binding domains. These domains have two antibody-binding sites with vastly different avidity and the function of the second weaker binding interface is currently unknown. Here we use magnetic tweezers and covalent attachment via HaloTag and SpyTag to expose Protein L to unfolding forces in the absence and presence of antibody-ligands. We find that antibody binding increases the mechanical stability of protein L. Using the change in mechanical stability as a binding reporter, we determined that the low-avidity binding site is acting as a mechano-sensor. We propose a novel mechanism where the high-avidity binding site engages the tether, while the low-avidity binding site acts as a mechano-sensor, allowing bacteria to sample the antibody surface concentration and localize its search during successful binding under strain.SignificanceIt is well known that bacteria have an arsenal of tools to invade and to avoid dislocation. Based on the molecular response of a protein used by anaerobic bacteria to attach to antibodies and disrupt the immune system, here we report on a force-sensor-like behavior, triggered by antibody clusters and force. This pseudo-catch bond between bacteria and antibodies is activated through a second binding site which has lower avidity to antibodies, and which acts as a mechanical sensor, potentially regulating the search radii of the bacterium. Understanding of the bacteria attachment mechanism is of great importance toward developing new antibiotics and mechano-active drugs.

What do nanometer molecular trajectories tell us about heterogeneous cell surface domaines?

1995 ◽  
Vol 53 ◽  
pp. 786-787
Author(s):  
Watt W. Webb
Keyword(s):  
Cell Surface ◽  
Lipid Membranes ◽  
Surface Proteins ◽  
Protein Diffusion ◽  
Coated Pits ◽  
Cell Surface Proteins ◽  
Membrane Heterogeneity ◽  
Fluorescence Photobleaching Recovery ◽  
Photobleaching Recovery ◽  
Plasma Membrane Heterogeneity

Plasma membrane heterogeneity is implicit in the existence of specialized cell surface organelles which are necessary for cellular function; coated pits, post and pre-synaptic terminals, microvillae, caveolae, tight junctions, focal contacts and endothelial polarization are examples. The persistence of these discrete molecular aggregates depends on localized restraint of the constituent molecules within specific domaines in the cell surface by strong intermolecular bonds and/or anchorage to extended cytoskeleton. The observed plasticity of many of organelles and the dynamical modulation of domaines induced by cellular signaling evidence evanescent intermolecular interactions even in conspicuous aggregates. There is also strong evidence that universal restraints on the mobility of cell surface proteins persist virtually everywhere in cell surfaces, not only in the discrete organelles. Diffusion of cell surface proteins is slowed by several orders of magnitude relative to corresponding protein diffusion coefficients in isolated lipid membranes as has been determined by various ensemble average methods of measurement such as fluorescence photobleaching recovery(FPR).

Genomic insights from Monoglobus pectinilyticus: a pectin-degrading specialist bacterium in the human colon

2020 ◽  
Author(s):  
CC Kim ◽  
GR Healey ◽  
WJ Kelly ◽  
ML Patchett ◽  
Z Jordens ◽  
...  
Keyword(s):  
Cell Surface ◽  
Degradation Products ◽  
Model Organism ◽  
Human Colon ◽  
Surface Proteins ◽  
Human Gut ◽  
Pectate Lyases ◽  
Unusual Distribution ◽  
Degrading Bacteria ◽  
Acetyl Esterases

© 2019, International Society for Microbial Ecology. Pectin is abundant in modern day diets, as it comprises the middle lamellae and one-third of the dry carbohydrate weight of fruit and vegetable cell walls. Currently there is no specialized model organism for studying pectin fermentation in the human colon, as our collective understanding is informed by versatile glycan-degrading bacteria rather than by specialist pectin degraders. Here we show that the genome of Monoglobus pectinilyticus possesses a highly specialized glycobiome for pectin degradation, unique amongst Firmicutes known to be in the human gut. Its genome encodes a simple set of metabolic pathways relevant to pectin sugar utilization, and its predicted glycobiome comprises an unusual distribution of carbohydrate-active enzymes (CAZymes) with numerous extracellular methyl/acetyl esterases and pectate lyases. We predict the M. pectinilyticus degradative process is facilitated by cell-surface S-layer homology (SLH) domain-containing proteins, which proteomics analysis shows are differentially expressed in response to pectin. Some of these abundant cell surface proteins of M. pectinilyticus share unique modular organizations rarely observed in human gut bacteria, featuring pectin-specific CAZyme domains and the cell wall-anchoring SLH motifs. We observed M. pectinilyticus degrades various pectins, RG-I, and galactan to produce polysaccharide degradation products (PDPs) which are presumably shared with other inhabitants of the human gut microbiome (HGM). This strain occupies a new ecological niche for a primary degrader specialized in foraging a habitually consumed plant glycan, thereby enriching our understanding of the diverse community profile of the HGM.

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