Force-Extension and Force-Clamp AFM Spectroscopies in Investigating Mechanochemical Reactions and Mechanical Properties of Single Biomolecules

Single molecule studies of force-induced S2 site exposure in the mammalian Notch negative regulatory domain

Notch signaling in metazoans is responsible for key cellular processes related to embryonic development and tissue homeostasis. Proteolitic cleavage of the S2 site within an extracellular NRR domain of Notch is a key early event in Notch signaling. We use single molecule force-extension (FX) atomic force microscopy (AFM) to study force-induced exposure of the S2 site in the NRR domain from mouse Notch 1. Our FX AFM measurements yield a histogram of N-to-C termini lengths, which we relate to conformational transitions within the NRR domain. We detect four classes of such conformational transitions. From our steered molecular dynamics (SMD) results, we associate first three classes of such events with the S2 site exposure. AFM experiments yield their mean unfolding forces as 69 ± 42, 79 ± 45, and 90 ± 50 pN, respectively, at 400 nm/s AFM pulling speeds. These forces are matched by the SMD results recalibrated to the AFM force loading rates. Next, we provide a conditional probability analysis of the AFM data to support the hypothesis that a whole sequence of conformational transitions within those three clases is the most probable pathway for the force-induced S2 site exposure. Our results support the hypothesis that force-induced Notch activation requires ligand binding to exert mechanical force not in random but in several strokes and over a substantial period of time.

Complete noise analysis of a simple force spectroscopy AFM setup and its applications to study nanomechanics of mammalian Notch 1 protein

We describe a complete noise analysis and application of a custom made AFM force spectroscopy setup on pulling a recombinant protein with an NRR domain of mouse Notch 1. Our table top AFM setup is affordable, has an open architecture, and is easily transferable to other laboratories. Its calculated noise characteristics are dominated by the Brownian noise with 2% non-Brownian components integrated over the first thermally induced resonance of a typical cantilever. For a typical SiN cantilever with a force constant of ~15 pN nm(-1) and in water the force sensitivity and resolution are less than 10 pN, and the corresponding deflection sensitivities are less than 100 pm Hz(-1/2). Also, we obtain a sub-ms time resolution in detecting the protein length change, and only few ms cantilever response times as measured in the force clamp mode on a well-known protein standard. Using this setup we investigate force-induced conformational transitions in the NRR region of a mouse Notch 1. Notch is an important protein related to leukemia and breast cancers in humans. We demonstrate that it is feasible to develop AFM-based studies of the force-induced conformational transitions in Notch. Our results match recent steered molecular dynamics simulations of the NRR unfolding and constitute a first step towards a detailed study of Notch activation with AFM.

Comment on "Print your atomic force microscope" [Rev. Sci. Instrum. 78, 075105 (2007)]

The paper of Kühner et al. [Rev. Sci. Instrum. 78, 075105 (2007)], presents a sound realization of a very nice idea. Namely, to design and prepare (via rapid prototyping) a custom head for atomic force microscope (AFM). Custom AFM heads are essential for various applications, which include the AFM force spectroscopy modes and convenient AFM coupling with other techniques. Our comment concerns the deflection data for a thermally driven AFM cantilever obtained by Kühner et al. using their AFM setup (Figure 3 therein). The results of Kühner et al. imply that a thermally excited AFM cantilever vibrates with aberrantly large amplitudes. Namely, the deflection noise amplitudes for the MLCT-D cantilever are 60-100 times larger than what is typically observed in our lab and by others. As we argue, the author's mistake is likely attributed to an improper usage of the AFM bandwidth. We explain the necessary correction and discuss the issue of bandwidth for the AFM force spectroscopy measurements.