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.

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.

Identification of the SV2 protein receptor-binding site of botulinum neurotoxin type E

2013 ◽  
Vol 453 (1) ◽  
pp. 37-47 ◽  
Author(s):  
Stefan Mahrhold ◽  
Jasmin Strotmeier ◽  
Consuelo Garcia-Rodriguez ◽  
Jianlong Lou ◽  
James D. Marks ◽  
...  
Keyword(s):  
Binding Site ◽  
Synaptic Vesicle ◽  
Specific Binding ◽  
Cell Surface Receptor ◽  
Vesicle Membrane ◽  
Receptor Binding Site ◽  
Binding Interface ◽  
Protein Receptor ◽  
Surface Receptor ◽  
Extended Surface

The highly specific binding and uptake of BoNTs (botulinum neurotoxins; A–G) into peripheral cholinergic motoneurons turns them into the most poisonous substances known. Interaction with gangliosides accumulates the neurotoxins on the plasma membrane and binding to a synaptic vesicle membrane protein leads to neurotoxin endocytosis. SV2 (synaptic vesicle glycoprotein 2) mediates the uptake of BoNT/A and /E, whereas Syt (synaptotagmin) is responsible for the endocytosis of BoNT/B and /G. The Syt-binding site of the former was identified by co-crystallization and mutational analyses. In the present study we report the identification of the SV2-binding interface of BoNT/E. Mutations interfering with SV2 binding were located at a site that corresponds to the Syt-binding site of BoNT/B and at an extended surface area located on the back of the conserved ganglioside-binding site, comprising the N- and C-terminal half of the BoNT/E-binding domain. Mutations impairing the affinity also reduced the neurotoxicity of full-length BoNT/E at mouse phrenic nerve hemidiaphragm preparations demonstrating the crucial role of the identified binding interface. Furthermore, we show that a monoclonal antibody neutralizes BoNT/E activity because it directly interferes with the BoNT/E–SV2 interaction. The results of the present study suggest a novel mode of binding for BoNTs that exploit SV2 as a cell surface receptor.

scholarly journals Crystal structure of the DENR-MCT-1 complex revealed zinc-binding site essential for heterodimer formation

2018 ◽  
Vol 116 (2) ◽  
pp. 528-533 ◽  
Author(s):  
Ivan B. Lomakin ◽  
Sergey E. Dmitriev ◽  
Thomas A. Steitz
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Translation Initiation ◽  
Zinc Ion ◽  
Zinc Binding ◽  
Ion Binding ◽  
Binding Interface ◽  
Zinc Binding Site ◽  
Reading Frames ◽  
Zinc Ion Binding

The density-regulated protein (DENR) and the malignant T cell-amplified sequence 1 (MCT-1/MCTS1) oncoprotein support noncanonical translation initiation, promote translation reinitiation on a specific set of mRNAs with short upstream reading frames, and regulate ribosome recycling. DENR and MCT-1 form a heterodimer, which binds to the ribosome. We determined the crystal structure of the heterodimer formed by human MCT-1 and the N-terminal domain of DENR at 2.0-Å resolution. The structure of the heterodimer reveals atomic details of the mechanism of DENR and MCT-1 interaction. Four conserved cysteine residues of DENR (C34, C37, C44, C53) form a classical tetrahedral zinc ion-binding site, which preserves the structure of the DENR’s MCT-1–binding interface that is essential for the dimerization. Substitution of all four cysteines by alanine abolished a heterodimer formation. Our findings elucidate further the mechanism of regulation of DENR-MCT-1 activities in unconventional translation initiation, reinitiation, and recycling.

scholarly journals The Potential for SARS-CoV-2 to Evade Both Natural and Vaccine-induced Immunity

2020 ◽  
Author(s):  
Emily Shang ◽  
Paul Axelsen
Keyword(s):  
Human Infection ◽  
Antibody Binding ◽  
Spike Protein ◽  
Wild Type ◽  
Binding Interface ◽  
Naturally Occurring ◽  
Binding Interfaces ◽  
Induced Immunity ◽  
Wild Type Form

SARS-CoV-2 attaches to the surface of susceptible cells through extensive interactions between the receptor binding domain (RBD) of its spike protein and angiotensin converting enzyme type 2 (ACE2) anchored in cell membranes. To investigate whether naturally occurring mutations in the spike protein are able to prevent antibody binding, yet while maintaining the ability to bind ACE2 and viral infectivity, mutations in the spike protein identified in cases of human infection were mapped to the crystallographically-determined interfaces between the spike protein and ACE2 (PDB entry 6M0J), antibody CC12.1 (PDB entry 6XC2), and antibody P2B-2F6 (PDB entry 7BWJ). Both antibody binding interfaces partially overlap with the ACE2 binding interface. Among 16 mutations that map to the RBD:CC12.1 interface, 11 are likely to disrupt CC12.1 binding but not ACE2 binding. Among 12 mutations that map to the RBD:P2B-2F6 interface, 8 are likely to disrupt P2B-2F6 binding but not ACE2 binding. As expected, none of the mutations observed to date appear likely to disrupt the RBD:ACE2 interface. We conclude that SARS-CoV-2 with mutated forms of the spike protein may retain the ability to bind ACE2 while evading recognition by antibodies that arise in response to the original wild-type form of the spike protein. It seems likely that immune evasion will be possible regardless of whether the spike protein was encountered in the form of infectious virus, or as the immunogen in a vaccine. Therefore, it also seems likely that reinfection with a variant strain of SARS-CoV-2 may occur among people who recover from Covid-19, and that vaccines with the ability to generate antibodies against multiple variant forms of the spike protein will be necessary to protect against variant forms of SARS-CoV-2 that are already circulating in the human population.

scholarly journals Mechanisms of antibody binding revealed by asymmetric Fab-virus complexes

2020 ◽  
Author(s):  
Daniel J. Goetschius ◽  
Samantha R. Hartmann ◽  
Lindsey J. Organtini ◽  
Heather Callaway ◽  
Kai Huang ◽  
...  
Keyword(s):  
High Resolution ◽  
Binding Site ◽  
Receptor Binding ◽  
Antibody Binding ◽  
Antigenic Epitope ◽  
Receptor Binding Site ◽  
Local Structures ◽  
Antigenic Sites ◽  
High Resolution Map ◽  
Feline Parvovirus

AbstractOverlap on the surface of parvovirus capsids between the antigenic epitope and the receptor binding site contributes to species jumping. Mab 14 strongly binds and neutralizes canine, but not feline parvovirus. The high resolution map of the canine parvovirus capsid complexed with Fab 14 was used to solve local structures of the Fab-bound and -unbound antigenic sites extracted from the same complex. The subsequent analysis includes a new method for using cryo EM to investigate complementarity of antibody binding.

Apolipoprotein E includes a binding site which is recognized by several amyloidogenic polypeptides

2000 ◽  
Vol 349 (1) ◽  
pp. 77-84 ◽  
Author(s):  
Marc H. BAUMANN ◽  
Jukka KALLIJÄRVI ◽  
Hilkka LANKINEN ◽  
Claudio SOTO ◽  
Matti HALTIA
Keyword(s):  
Apolipoprotein E ◽  
Binding Site ◽  
Late Onset ◽  
Specific Binding ◽  
Prion Diseases ◽  
Amyloid Β ◽  
Structural Motif ◽  
Amyloid Β Peptide ◽  
High Avidity ◽  
Amyloidogenic Protein

Inheritance of the apolipoprotein E (apoE) ϵ4 allele is a risk factor for late-onset Alzheimer's disease (AD). Biochemically apoE is present in AD plaques and neurofibrillary tangles of the AD brain. There is a high avidity and specific binding of apoE and the amyloid β-peptide (Aβ). In addition to AD apoE is also present in many other cerebral and systemic amyloidoses, Down's syndrome and prion diseases but the pathophysiological basis for its presence is still unknown. In the present study we have compared the interaction of apoE with Aβ, the gelsolin-derived amyloid fragment AGel183-210 and the amyloidogenic prion fragments PrP109-122 and PrP109-141. We show that, similar to Aβ, also AGel and PrP fragments can form a complex with apoE, and that the interaction between apoE and the amyloidogenic protein fragments is mediated through the same binding site on apoE. We also show that apoE increases the thioflavin-T fluorescence of PrP and AGel and that apoE influences the content of β-sheet conformation of these amyloidogenic fragments. Our results indicate that amyloids and amyloidogenic prion fragments share a similar structural motif, which is recognized by apoE, possibly through a single binding site, and that this motif is also responsible for the amyloidogenicity of these fragments.

Fine tuning of an anti-testosterone antibody binding site by stepwise optimisation of the CDRs

1998 ◽  
Vol 4 (1) ◽  
pp. 59-69 ◽  
Author(s):  
Ari Hemminki ◽  
Seija Niemi ◽  
Lasse Hautoniemi ◽  
Hans Söderlund ◽  
Kristiina Takkinen
Keyword(s):  
Binding Site ◽  
Antibody Binding ◽  
Fine Tuning ◽  
Antibody Binding Site

scholarly journals FcαRI binding at the IgA1 CH2–CH3 interface induces long-range conformational changes that are transmitted to the hinge region

2018 ◽  
Vol 115 (38) ◽  
pp. E8882-E8891 ◽  
Author(s):  
Monica T. Posgai ◽  
Sam Tonddast-Navaei ◽  
Manori Jayasinghe ◽  
George M. Ibrahim ◽  
George Stan ◽  
...  
Keyword(s):  
Binding Site ◽  
Long Range ◽  
Conformational Changes ◽  
Lectin Binding ◽  
Coarse Grained ◽  
Alanine Scanning Mutagenesis ◽  
Long Distance ◽  
Receptor Binding Site ◽  
Binding Interface ◽  
Functional Dynamics

IgA effector functions include proinflammatory immune responses triggered upon clustering of the IgA-specific receptor, FcαRI, by IgA immune complexes. FcαRI binds to the IgA1–Fc domain (Fcα) at the CH2–CH3 junction and, except for CH2 L257 and L258, all side-chain contacts are contributed by the CH3 domain. In this study, we used experimental and computational approaches to elucidate energetic and conformational aspects of FcαRI binding to IgA. The energetic contribution of each IgA residue in the binding interface was assessed by alanine-scanning mutagenesis and equilibrium surface plasmon resonance (SPR). As expected, hydrophobic residues central to the binding site have strong energetic contributions to the FcαRI:Fcα interaction. Surprisingly, individual mutation of CH2 residues L257 and L258, found at the periphery of the FcαRI binding site, dramatically reduced binding affinity. Comparison of antibody:receptor complexes involving IgA or its precursor IgY revealed a conserved receptor binding site at the CH2–CH3 junction (or its equivalent). Given the importance of residues near the CH2–CH3 junction, we used coarse-grained Langevin dynamics simulations to understand the functional dynamics in Fcα. Our simulations indicate that FcαRI binding, either in an asymmetric (1:1) or symmetric (2:1) complex with Fcα, propagated long-range conformational changes across the Fc domains, potentially impacting the hinge and Fab regions. Subsequent SPR experiments confirmed that FcαRI binding to the Fcα CH2–CH3 junction altered the kinetics of HAA lectin binding at the IgA1 hinge. Receptor-induced long-distance conformational transitions have important implications for the interaction of aberrantly glycosylated IgA1 with anti-glycan autoantibodies in IgA nephropathy.

Sign in / Sign up

Export Citation Format

Share Document