bioRxiv Science⌕ Search

bioRxiv · 10.1101/2022.10.31.514521

A Cochlea-Slice Model using Floquet Boundary Conditions shows Global Tuning

Abstract

A common assumption about the cochlea is that the local characteristic frequency (CF) is determined by a local resonance of basilar-membrane (BM) stiffness with the mass of the organ-of-Corti (OoC) and entrained fluid. We modeled the cochlea while avoiding such a priori assumptions by using a finite-element model of a 20-m-thick cross-sectional slice of the middle turn of a passive gerbil cochlea. The model had anatomically accurate structural details with physiologically appropriate material properties and interactions between the fluid spaces and solid OoC structures. The longitudinally-facing sides of the slice had a phase difference that mimicked the traveling-wave wavelength at the location of the slice by using Floquet boundary conditions. A paired volume-velocity drive was applied in the scalae at the top and bottom of the slice with the amplitudes adjusted to mimic experimental BM motion. The development of this computationally efficient model with detailed anatomical structures is a key innovation of this work. The resulting OoC motion was greatest in the transverse direction, stereocilia-tip deflections were greatest in the radial direction and longitudinal motion was small in OoC tissue but became large in the sulcus at high frequencies. If the source velocity and wavelength were held constant across frequency, the OoC motion was almost flat across frequency, i.e., the slice showed no local resonance. A model with the source velocity held constant and the wavelength varied realistically across frequency, produced a low-pass frequency response. These results indicate that tuning in the gerbil middle turn is not produced by a resonance due to local OoC mechanical properties, but rather is produced by the characteristics of the traveling wave, manifested in the driving pressure and wavelength. STATEMENT OF SIGNIFICANCEThe sensory epithelium of hearing, the organ of Corti, is encased in the bone of the fluid-filled cochlea and is difficult to study experimentally. We provide a new method to study the cochlea: making an anatomically-detailed finite-element model of a small transverse slice of the cochlea using Floquet boundary conditions and incorporating global cochlear properties in the slice drive and the wavelength-frequency relationship. The model shows that the slice properties do not show a mechanical resonance and therefore do not produce the frequency-response tuning of the cochlea. Instead, tuning emerges from global cochlear properties carried by the traveling wave.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Tubelli, A., Motallebzadeh, H., Guinan, J. J., Puria, S.. 2022-11-02. A Cochlea-Slice Model using Floquet Boundary Conditions shows Global Tuning. https://doi.org/10.1101/2022.10.31.514521

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

Design of colipids with controlled lateral distance of head group moieties for targeting strategies in the field of lipid-based nanoparticles

Lipid nanoparticles and liposomes are nanoparticle drug formulations which are firmly established in clinics. In order to expand their application and improve efficacy, surface modifications can be a key strategy, especially for cell specific targeting. Targeting can be achieved by integrating ligand functionalized lipids or lipidoids on the nanoparticle surface. In this case, not solely the targeting ligand itself, but also the structure of the whole targeting lipid/lipidoid can affect the interaction of the targeting ligand with the binding motive on cells. Especially, distal spacer structures between lipid anchor and ligand unit, often composed of polyethylene glycol chains, provide a certain distance of the ligand from the nanoparticle surface. A concept which is currently neglected is the control of the lateral distance between ligand structures on the nanoparticle. Herein we investigated the possibility to design lipidoids with a lateral spacer composed of polyethylene glycol units. We synthesized and characterized different lipidoids which provide a primary amine in the head group for possible ligand coupling. In our model lipidoids the head groups were functionalized with a paramagnetic probe to apply electron paramagnetic resonance (EPR) methods for the characterization of the lipidoid interaction with model nanoparticles, in our case liposomes. Continuous wave EPR was used to study the efficiency of the novel lipidoids to integrate into lipid bilayers of model liposomes, which was shown to depend on lipidoid structure and liposome composition. Furthermore, using double electron-electron resonance (DEER), we observed lipidoid conformational changes occurring upon integration into liposomes.

biophysics↗

Binding mechanisms of therapeutic antibodies to human claudin-18.2

Claudin-18.2 (CLDN18.2) is a tight junction component with highly restricted expression in the paracellular space of nonmalignant gastric epithelial cells. It becomes accessible on tumor cell surface during malignant transformation, making CLDN18.2 an attractive target for targeted therapies against gastric cancer. Recently, zolbetuximab has become the first FDA-approved monoclonal antibody that targets CLDN18.2 in advanced gastric cancer, and others like osemitamab have entered phase 3 clinical trials. However, the high-resolution structure of CLDN18.2 is lacking, and how CLDN18.2 is recognized by therapeutic antibodies remains undefined. Here, we report cryo-EM structures of human claudin-18.2 (hCLDN18.2) in complex with the Fab fragments of zolbetuximab and osemitamab, revealing the structure of hCLDN18.2 and its binding mechanism to the therapeutic antibodies. Further analyses reveal that three residues in the first extracellular loop of hCLDN18.2 that are different from human claudin-18.1 (hCLDN18.1) play a critical role in antibody binding. Our data elucidate the structural basis for selective binding of therapeutic antibodies to hCLDN18.2, which should aid rational design of next-generation immunotherapies targeting hCLDN18.2.

biophysics↗

Structural relationships between the SLC12 cotransporter C-terminal domain, universal stress proteins and adenylating enzymes

Several SLC12 cotransporters bind ATP in a cytoplasmic C-terminal domain (CTD). We analysed 16,192 CTD-containing SLC12 sequences and compared 42,845 representative structures to examine the relationship between this nucleotide site, universal stress proteins (USPs) and adenylating enzymes. In phosphorylated NKCC1, D891 and D927 lie near the ATP phosphate chain, while R801 and K889 form a basic phosphate-binding clamp. NKCC1 retains this arrangement, whereas KCC paralogs replace or lose several corresponding groups. In structural comparisons with USP and adenylating-enzyme references, both CTD lobes score between universal stress proteins and EC-annotated domains, and the two lobes form separate lineages that include bacterial transporters. Lobe-specific and nucleotide-frame comparisons place ATP in the corresponding structural region used for -phosphate chemistry by catalytic members of this fold. Published work on UspG provides a precedent for protein-bound AMP in a natural USP. In the examined SLC12 structures and USP models, candidate protein hydroxyls lack an in-line geometry for attack at ATP P. Protein adenylation would require a change in protein or nucleotide geometry, or a different acceptor. These results define a structural basis for testing conditional protein adenylation at SLC12 nucleotide sites. The required evidence is a covalent protein-AMP adduct, identification of its acceptor and measurement of the expected pyrophosphate coproduct, with soluble nucleotide analysis to distinguish accompanying ATP reactions.

biophysics↗