Removal of a Conserved Disulfide Bond Does Not Compromise Mechanical Stability of a VHH Antibody Complex

Liu, Haipei; Schittny, Valentin; Nash, Michael A.

doi:10.1021/acs.nanolett.9b02062

Cited by 32 publications

(32 citation statements)

References 62 publications

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“…Atomic force microscopy (AFM) has allowed the imaging of biomolecules under physiological conditions [15][16][17][18][19] , which provides an alternative route to probe Ab-Ag interactions [20][21][22][23] . Previous studies have demonstrated the potential of AFM for imaging Abs with near-atomistic resolution [24][25][26] and its ability for quantitatively mapping nanomechanical forces of Ab-Ag interactions at the single-molecule level [27][28][29] . Recently, high-speed (HS) AFM offers up to video-rate temporal resolution, revealing certain types of dynamic processes of IgGs, e.g., walking on the viral surface, oligomerization, and complement activation upon antigen recognition 24,30,31 .…”

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confidence: 99%

Capturing transient antibody conformations with DNA origami epitopes

Zhang

Liu²,

et al. 2020

Nat Commun

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Revealing antibody-antigen interactions at the single-molecule level will deepen our understanding of immunology. However, structural determination under crystal or cryogenic conditions does not provide temporal resolution for resolving transient, physiologically or pathologically relevant functional antibody-antigen complexes. Here, we develop a triangular DNA origami framework with site-specifically anchored and spatially organized artificial epitopes to capture transient conformations of immunoglobulin Gs (IgGs) at room temperature. The DNA origami epitopes (DOEs) allows programmed spatial distribution of epitope spikes, which enables direct imaging of functional complexes with atomic force microscopy (AFM). We establish the critical dependence of the IgG avidity on the lateral distance of epitopes within 3-20 nm at the single-molecule level. High-speed AFM imaging of transient conformations further provides structural and dynamic evidence for the IgG avidity from monovalent to bivalent in a single event, which sheds light on various applications including virus neutralization, diagnostic detection and cancer immunotherapy.

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confidence: 99%

Capturing transient antibody conformations with DNA origami epitopes

Zhang

Liu²,

et al. 2020

Nat Commun

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“…pathways [28][29][30] and receptor-ligand interactions [31][32][33][34] . Singlemolecule FRET (smFRET) is capable of measuring distances at the molecular scale 35 , and has been used to study protein dynamics 36,37 and to characterize structures of receptor-ligand complexes 38,39 .…”

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confidence: 99%

High force catch bond mechanism of bacterial adhesion in the human gut

Liu

Vera

et al. 2020

Nat Commun

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Bacterial colonization of the human intestine requires firm adhesion of bacteria to insoluble substrates under hydrodynamic flow. Here we report the molecular mechanism behind an ultrastable protein complex responsible for resisting shear forces and adhering bacteria to cellulose fibers in the human gut. Using single-molecule force spectroscopy (SMFS), singlemolecule FRET (smFRET), and molecular dynamics (MD) simulations, we resolve two binding modes and three unbinding reaction pathways of a mechanically ultrastable R. champanellensis (Rc) Dockerin:Cohesin (Doc:Coh) complex. The complex assembles in two discrete binding modes with significantly different mechanical properties, with one breaking at 500 pN and the other at~200 pN at loading rates from 1-100 nN s −1. A neighboring X-module domain allosterically regulates the binding interaction and inhibits one of the lowforce pathways at high loading rates, giving rise to a catch bonding mechanism that manifests under force ramp protocols. Multi-state Monte Carlo simulations show strong agreement with experimental results, validating the proposed kinetic scheme. These results explain mechanistically how gut microbes regulate cell adhesion strength at high shear stress through intricate molecular mechanisms including dual-binding modes, mechanical allostery and catch bonds.

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“…For example, high-affinity non-covalent interactions including Ni:His-tag and Biotin:Avidin have both been used as immobilization tags onto surfaces or as the object of study in AFM-SMFS (Fritz et al, 1998;Berquand et al, 2005;Dupres et al, 2005;Li et al, 2019), as shown in Figure 1B. Many different classes of receptor-ligands have been probed by AFM (Milles et al, 2017;Liu et al, 2019), including antibody-antigen interactions (Dammer et al, 1996;Hinterdorfer et al, 1996Hinterdorfer et al, , 1998Allen et al, 1997;Ros et al, 1998;Schwesinger et al, 2000;Kienberger et al, 2005;Sulchek et al, 2005Sulchek et al, , 2006Neuert et al, 2006;Odorico et al, 2007;Morfill et al, 2008;Roy et al, 2010;Bizzarri and Cannistraro, 2014;Klamecka et al, 2015;Tsai et al, 2016;Liu et al, 2019Liu et al, , 2020, avidin systems (see below), bacterial adhesion systems (Herman et al, 2014;Schoeler et al, 2014;Jobst et al, 2015;Nash et al, 2016;Alonso-Caballero et al, 2018;Herman-Bausier et al, 2018;Milles et al, 2018;Viela et al, 2019), and others (Sletmoen et al, 2004;Farrance et al, 2013).…”

Section: Measurement Configurations For Afm-smfsmentioning

confidence: 99%

Next Generation Methods for Single-Molecule Force Spectroscopy on Polyproteins and Receptor-Ligand Complexes

Yang

Liu

et al. 2020

Front. Mol. Biosci.

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Single-molecule force spectroscopy with the atomic force microscope provides molecular level insights into protein function, allowing researchers to reconstruct energy landscapes and understand functional mechanisms in biology. With steadily advancing methods, this technique has greatly accelerated our understanding of force transduction, mechanical deformation, and mechanostability within single-and multi-domain polyproteins, and receptor-ligand complexes. In this focused review, we summarize the state of the art in terms of methodology and highlight recent methodological improvements for AFM-SMFS experiments, including developments in surface chemistry, considerations for protein engineering, as well as theory and algorithms for data analysis. We hope that by condensing and disseminating these methods, they can assist the community in improving data yield, reliability, and throughput and thereby enhance the information that researchers can extract from such experiments. These leading edge methods for AFM-SMFS will serve as a groundwork for researchers cognizant of its current limitations who seek to improve the technique in the future for in-depth studies of molecular biomechanics.

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Removal of a Conserved Disulfide Bond Does Not Compromise Mechanical Stability of a VHH Antibody Complex

Cited by 32 publications

References 62 publications

Capturing transient antibody conformations with DNA origami epitopes

Capturing transient antibody conformations with DNA origami epitopes

High force catch bond mechanism of bacterial adhesion in the human gut

Next Generation Methods for Single-Molecule Force Spectroscopy on Polyproteins and Receptor-Ligand Complexes

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