Nanomechanics of multidomain neuronal cell adhesion protein contactin revealed by single molecule AFM and SMD

Abstract

Contactin-4 (CNTN4) is a complex cell adhesion molecule (CAM) localized at neuronal membranes, playing a key role in maintaining the mechanical integrity and signaling properties of the synapse. CNTN4 consists of six immunoglobulin C2 type (IgC2) domains and four fibronectin type III (FnIII) domains that are shared with many other CAMs. Mutations in CNTN4 gene have been linked to various psychiatric disorders. Toward elucidating the response of this modular protein to mechanical stress, we studied its force-induced unfolding using single molecule atomic force microscopy (smAFM) and steered molecular dynamics (SMD) simulations. Extensive smAFM and SMD data both indicate the distinctive mechanical behavior of the two types of modules distinguished by unique force-extension signatures. The data also reveal the heterogeneity of the response of the individual FNIII and IgC2 modules, which presumably plays a role in the adaptability of CNTN4 to maintaining cell-cell communication and adhesion properties under different conditions. Results show that extensive sampling of force spectra, facilitated by robot-enhanced AFM, can help reveal the existence of weak stabilizing interactions between the domains of multidomain proteins, and provide insights into the nanomechanics of such multidomain or heteromeric proteins.

Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members

“…We also applied mechanical stiffness (MechStiff) analysis, which calculates the resistance of all residue pairs to uniaxial tension. 48,49…”

NO● Represses the Oxygenation of Arachidonoyl PE by 15LOX/PEBP1: Mechanism and Role in Ferroptosis

“…Conventional full-atomic MD simulations [ 47 , 48 , 49 ] were performed for human 15LOX-2 (PDB id: 4NRE [ 20 ]) and 15LOX-2/PEBP1 complex (PDB ids: 4NRE and 1BEH [ 50 ]), with a bound substrate (SAPE), in the presence of randomly distributed nitric oxide and oxygen molecules with different ratios, such as 1:1 (five of each), 1:3, and 3:1. Multiple MD runs (see Supplementary Table S1 ) of 150 ns with different initial spatial distributions of NO ● and O 2 molecules were performed for each structure (15LOX-2 and its complex with PEBP1) using the NAMD [ 51 ] software with the CHARMM [ 52 ] force field and 2 fs time steps.…”

Dynamics, nanomechanics and signal transduction in reelin repeats

“…An atomic Force Microscope (AFM) in the force spectroscopy mode was used 44–47 . Experiments were made on mouse reelin samples, obtained from R&D Systems (3820-MR-025).…”

“…To increase the probability of selective binding of single molecules only, no direct tip-surface contact was made. This approach known as “fly fishing” 51 was successfully used for other systems 44,46,47 . The collected force curves were analyzed with in-lab developed software.…”