SearcharxivSearch

arXiv subjects

Felix Rico

Publications and source records attributed to Felix Rico.

2 recordsLinked to original sources

Determination of Calibration Parameters of Cantilevers of Arbitrary Shape by Finite Elements Analysis

The use of atomic force microscopy on nanomechanical measurements requires accurate calibration of the cantilever's spring constant ($k_c$) and the optical lever sensitivity ($OLS$). The thermal method, based on the cantilever's thermal fluctuations in fluid, allows estimating $k_c$ in a fast, non-invasive mode. However, differences in the cantilever geometry and mounting angle require the knowledge of three correction factors to get a good estimation of $k_c$: the contribution of the oscillation mode to the total amplitude, the shape difference between the free and the end-loaded configurations, and the tilt of the cantilever respect to the measured surface. While the correction factors for traditional rectangular and V-shaped cantilevers geometries have been reported, they must be determined for cantilevers with non-traditional geometries and large tips. Here, we develop a method based on finite element analysis to estimate the correction factors of cantilevers with arbitrary geometry and tip dimensions. The method relies on the numerical computation of the effective cantilever mass. The use of the correction factor for rectangular geometries on our model cantilever (PFQNM-LC) will lead to values underestimated by 16%. In contrast, experiments using pre-calibrated cantilevers revealed a maximum uncertainty below 5% in the estimation of the $OLS$, verifying our approach.

physics.app-ph

Heterogeneous and rate-dependent streptavidin-biotin unbinding revealed by high-speed force spectroscopy and atomistic simulations

Receptor-ligand interactions are essential for biological function and their binding strength is commonly explained in terms of static lock-and-key models based on molecular complementarity. However, detailed information of the full unbinding pathway is often lacking due, in part, to the static nature of atomic structures and ensemble averaging inherent to bulk biophysics approaches. Here we combine molecular dynamics and high-speed force spectroscopy on the streptavidin-biotin complex to determine the binding strength and unbinding pathways over the widest dynamic range. Experiment and simulation show excellent agreement at overlapping velocities and provided evidence of the unbinding mechanisms. During unbinding, biotin crosses multiple energy barriers and visits various intermediate states far from the binding pocket while streptavidin undergoes transient induced fits, all varying with loading rate. This multistate process slows down the transition to the unbound state and favors rebinding, thus explaining the long lifetime of the complex. We provide an atomistic, dynamic picture of the unbinding process, replacing a simple two-state picture with one that involves many routes to the lock and rate-dependent induced-fit motions for intermediates, which might be relevant for other receptor-ligand bonds.

physics.bio-ph