Biology subjects

Azzaz, F.

Publications and source records attributed to Azzaz, F..

5 recordsLinked to original sources

bioRxiv2026

Leucine-rich glioma inactivated 1 is a ganglioside-binding protein

In LGI1-linked animal models of inherited autosomal dominant lateral temporal lobe epilepsy, increased neuronal excitability is accompanied by modifications in the AMPA/NMDA receptor ratio and a large decrease in Kv1 type potassium channels. However, the mechanism which links the absence of LGI1 to reduced expression of key neuronal ion channels is unknown. We observed multiple conserved canonical ganglioside-binding domains (GBDs) within human LGI1, mainly located in the EPTP domain. We show that GT1b is co-captured from native rat brain extracts by human LGI1 antibodies and, using SPR analysis, that recombinant full length LGI1 interacted with liposomes containing GT1b and GM1, but not GM3, lyso-lactosylceramide, phosphatidylserine or phosphatidylcholine. The ganglioside binding capacity of GBD peptide sequences exposed at the surface of LGI1 were confirmed using SPR and Langmuir film balance. Our data suggest that LGI1 interacts with gangliosides and may be involved in organizing lipid membrane platforms accommodating functional protein complexes. The loss of LGI1 could destabilize these platforms and contribute to reduced expression of key ion channels in Lgi1-/- mice.

neuroscience↗

bioRxiv2025

Temporal Perturbation Scanning: AI-Driven Deconstruction of Universal Biomolecular Recognition Mechanisms

Understanding molecular interactions at the atomic level remains a central challenge across biology, medicine, and engineering. We introduce Perturbation Scanning (PS), an interrogative AI framework that actively deconstructs molecular interfaces. PS integrates graph-based representations of structures derived from molecular dynamics trajectories or Protein Data Bank files to systematically probe the electrostatic, hydrophobic, and steric contributions of each residue. To translate these insights into actionable design, we introduce the Intelligent Interface Optimization Scanner (IIOS), a standalone tool that generates energy-scored mutation proposals from interface maps. Together, PS and IIOS provide an integrated platform for dissecting and rationally engineering molecular interactions by resolving force-specific and stage-dependent contributions that are not directly accessible with existing computational approaches. Unlike traditional alanine scanning or free-energy methods such as MMPBSA--which provide only static or ensemble-averaged measures--PS delivers stage-resolved, force-wise decomposition of binding interfaces via a suite of targeted physicochemical perturbations applied to its AI model, directly quantifying each residues mechanistic role.

bioinformatics↗

bioRxiv2025

In Silico Study of Membrane-Inserted Synaptotagmin Conformational Changes in Complex with Botulinum Toxin B1

Synaptotagmins 1 and 2 (SYT1 and SYT2) are essential Ca2+ sensors in neurotransmission and the functional receptors of botulinum neurotoxin B1 (BoNT/B1). While crystallographic models have defined key contacts, they neglect membrane constraints. Using molecular dynamics simulations in lipid rafts, we uncover how the membrane environment reshaped synaptotagmin conformation and enables critical contacts with BoNT/B1s lipid-binding loop (LBL). Notably, ganglioside GT1b bridges BoNT/B1 and SYT1, stabilizing their interface through lipid-mediated interactions. This mechanism escapes AlphaFold prediction, which generates non-physiological complexes with steric clashed, revealing a fundamental limitation of current AI methods for membrane-constrained interfaces. Our study demonstrates that lipid rafts create functional binding modes through synergistic protein-lipid interactions, highlighting the epigenetic dimension of protein structure where environment dictates conformation.

biochemistry↗

bioRxiv2022

All-atom Molecular Dynamics Simulation of botulinum neurotoxin serotype A1 in complex with human SV2A or SV2C receptors in a lipid raft environment

Botulinum neurotoxin A1 (BoNT/A1) is the most potent serotype in humans with the highest clinical duration. BoNT/A1 interacts with synaptic vesicle glycoprotein 2 (SV2) and gangliosides to be taken up by neurons. In this study, we present three molecular dynamics simulations in which BoNT/A1 is in complex with singly or doubly glycosylated SV2C or singly glycosylated SV2A, in a ganglioside rich (lipid raft) context. Our computational data suggest that the N-glycan at position 480 (N480g) in the luminal domain of SV2C (LD-SV2C) indirectly enhanced the contacts of the neurotoxin surface with the second N-glycan at position 559 (N559g) by acting as a shield to prevent N559g to interact with residues of LD-SV2C. The N-glycosylation at the position N573 (N573g) in the luminal domain of SV2A has a slightly lower affinity for the surface of BoNT/A1 compared to 559g because of possible intermolecular contacts between N573g and residues of the luminal domain of SV2A (LD-SV2A). In addition to the ganglioside binding site (GBS) conserved across serotypes B, E, F and G, the lipid-raft associated GT1b interacted with a structure we coined the ganglioside binding loop (GBL) which is homologous to the lipid binding loop (LBL) in serotypes B, C, D, D/C and G. Finally, we proposed a global model in which BoNT/A1 interacts with its glycosylated protein receptor, one molecule of GT1b interacting in the GBS and five molecules of GT1b interacting with the GBL and residue Y1133. These data solved the puzzle generated by mutational studies that could be only partially understood with crystallographic data that lack both a biologically relevant membrane environment and a full glycosylation of SV2. Brief statementWe propose a full molecular description of the initial binding of a microbial toxin (Botulinum neurotoxin A1) to the surface of neural cells. Our model includes a protein receptor (SV2) in its native environment, i.e. the periphery of a cluster of gangliosides belonging to a membrane microdomain (lipid raft). A major outcome of our study is the elucidation of the role of the full length glycans (previously resolved by MS spectroscopy) covalently attached to the protein receptor. These data solved the puzzle generated by mutational studies that could be only partially understood with crystallographic data that lack both a biologically relevant membrane environment and a full glycosylation of SV2.

neuroscience↗

bioRxiv2021

The protein-binding pocket of Botulinum neurotoxin B accommodates a preassembled synaptotagmin / ganglioside complex

Botulinum neurotoxin serotype B (BoNT/B) uses two separate protein and polysialoglycolipid-binding pockets to interact with synaptotagmin 1/2 and gangliosides. However, an integrated model of BoNT/B bound to its neuronal receptors in a native membrane topology is still lacking. Using a panel of in silico and experimental approaches, we present here a new model for BoNT/B binding to neuronal membranes, in which the toxin binds to a preassembled synaptotagmin-ganglioside GT1b complex and a free ganglioside allowing a lipid-binding loop of BoNT/B to interact with the glycone part of the synaptotagmin-associated GT1b. Furthermore, our data provide molecular support for the decrease in BoNT/B sensitivity in Felidae that harbor the natural variant synaptotagmin2-N59Q. These results reveal multiple interactions of BoNT/B with gangliosides and support a novel paradigm in which a toxin recognizes a protein/ganglioside complex.

pharmacology and toxicology↗