Identification of energy-dissipation processes at the nanoscale is demonstrated by using amplitude-modulation atomic force microscopy. The variation of the energy dissipated on a surface by a vibrating tip as a function of its oscillation amplitude has a shape that singles out the dissipative process occurring at the surface. The method is illustrated by calculating the energy-dissipation curves for surface energy hysteresis, long-range interfacial interactions and viscoelasticity. The method remains valid with independency of the amount of dissipated energy per cycle, from 0.1 to 50 eV. The agreement obtained between theory and experiments performed on silicon and polystyrene validates the method.

The genome of measles virus is encapsidated by multiple copies of the nucleoprotein (N), forming helical nucleocapsids of molecular mass approaching 150 Megadalton. The intrinsically disordered C-terminal domain of N (N TAIL ) is essential for transcription and replication of the virus via interaction with the phosphoprotein P of the viral polymerase complex. The molecular recognition element (MoRE) of N TAIL that binds P is situated 90 amino acids from the folded RNA-binding domain (N CORE ) of N, raising questions about the functional role of this disordered chain. Here we report the first in situ structural characterization of N TAIL in the context of the entire N-RNA capsid. Using nuclear magnetic resonance spectroscopy, small angle scattering, and electron microscopy, we demonstrate that N TAIL is highly flexible in intact nucleocapsids and that the MoRE is in transient interaction with N CORE . We present a model in which the first 50 disordered amino acids of N TAIL are conformationally restricted as the chain escapes to the outside of the nucleocapsid via the interstitial space between successive N CORE helical turns. The model provides a structural framework for understanding the role of N TAIL in the initiation of viral transcription and replication, placing the flexible MoRE close to the viral RNA and, thus, positioning the polymerase complex in its functional environment.is a member of the Paramyxoviridae family of the Mononegavirales order of negative sense, single stranded RNA viruses. The viral genome is encapsidated by multiple copies of the nucleoprotein (N) forming a helical nucleocapsid. Transcription and replication of the viral RNA are initiated by an interaction between N and the polymerase complex, composed of the phosphoprotein (P) and the RNAdependent RNA polymerase (1). N consists of two domains: N CORE (residues 1-400), responsible for the interaction with the viral RNA and for maintaining the nucleocapsid structure, and a long intrinsically disordered domain, N TAIL (residues 401-525) serving as the anchor point for the polymerase complex (2, 3). The molecular recognition element (MoRE) (residues 485-502) of the disordered N TAIL interacts with the C-terminal three-helix bundle domain, XD, of P (residues 459-507) (4) and thereby recruits the polymerase complex onto the nucleocapsid template (5, 6).The realization that intrinsically disordered proteins (IDPs) are functional despite a lack of structure (7-9) has revealed entirely new paradigms that appear to redefine our understanding of the role of conformational flexibility in molecular interactions (10-12). Until now most IDPs have been studied in isolation, or in the presence of a single interaction partner, although it is evident that a real physiological environment could influence the nature and relevance of apparent intrinsic disorder. In this context resolving the question of whether the protein is actually disordered in situ is of paramount importance. In this case the mechanistic role of the extensive disorder present in N TA...

By recording the phase angle difference between the excitation force and the tip response in amplitude modulation AFM it is possible to image compositional variations in heterogeneous samples. In this contribution we address some of the experimental issues relevant to perform phase contrast imaging measurements. Specifically, we study the dependence of the phase shift on the tip-surface separation, interaction regime, cantilever parameters, free amplitude and tip-surface dissipative processes. We show that phase shift measurements can be converted into energy dissipation values. Energy dissipation curves show a maximum (∼10 eV/cycle) with the amplitude ratio. Furthermore, energy dissipation maps provide a robust method to image material properties because they do not depend directly on the tip-surface interaction regime. Compositional contrast images are illustrated by imaging conjugated molecular islands deposited on silicon surfaces.