Recent advances in sensing the inter-biomolecular interactions at the nanoscale – A comprehensive review of AFM-based force spectroscopy

Biomolecular interactions underpin most processes inside the cell. Hence, a precise and quantitative understanding of molecular association and dissociation events is crucial, not only from a fundamental perspective, but also for the rational design of biomolecular platforms for state-of-the-art biomedical and industrial applications. In this context, atomic force microscopy (AFM) appears as an invaluable experimental technique, allowing the measurement of the mechanical strength of biomolecular complexes to provide a quantitative characterization of their interaction properties from a single molecule perspective. In the present review, the most recent methodological advances in this field are presented with special focus on bioconjugation, immobilization and AFM tip functionalization, dynamic force spectroscopy measurements, molecular recognition imaging and theoretical modeling. We expect this work to significantly aid in grasping the principles of AFM-based force spectroscopy (AFM-FS) technique and provide the necessary tools to acquaint the type of data that can be achieved from this type of experiments. Furthermore, a critical assessment is done with other nanotechnology techniques to better visualize the future prospects of AFM-FS

Hydrocolloids of egg white and gelatin as a platform for hydrogel-based tissue engineering

Innovative materials are needed to produce scaffolds for various tissue engineering and regenerative medicine (TERM) applications, including tissue models. Materials derived from natural sources that offer low production costs, easy availability, and high bioactivity are highly preferred. Chicken egg white (EW) is an overlooked protein-based material. Whilst its combination with the biopolymer gelatin has been investigated in the food technology industry, mixed hydrocolloids of EW and gelatin have not been reported in TERM. This paper investigates these hydrocolloids as a suitable platform for hydrogel-based tissue engineering, including 2D coating films, miniaturized 3D hydrogels in microfluidic devices, and 3D hydrogel scaffolds. Rheological assessment of the hydrocolloid solutions suggested that temperature and EW concentration can be used to fine-tune the viscosity of the ensuing gels. Fabricated thin 2D hydrocolloid films presented globular nano-topography and in vitro cell work showed that the mixed hydrocolloids had increased cell growth compared with EW films. Results showed that hydrocolloids of EW and gelatin can be used for creating a 3D hydrogel environment for cell studies inside microfluidic devices. Finally, 3D hydrogel scaffolds were fabricated by sequential temperature-dependent gelation followed by chemical cross-linking of the polymeric network of the hydrogel for added mechanical strength and stability. These 3D hydrogel scaffolds displayed pores, lamellae, globular nano-topography, tunable mechanical properties, high affinity for water, and cell proliferation and penetration properties. In conclusion, the large range of properties and characteristics of these materials provide a strong potential for a large variety of TERM applications, including cancer models, organoid growth, compatibility with bioprinting, or implantable devices

Beyond a platform protein for the degradosome assembly: the apoptosis-inducing factor as an efficient nuclease involved in chromatinolysis

The Apoptosis-Inducing Factor (AIF) is a moonlighting flavoenzyme involved in the assembly of mitochondrial respiratory complexes in healthy cells, but also able to trigger DNA cleavage and parthanatos. Upon apoptotic-stimuli, AIF redistributes from the mitochondria to the nucleus, where upon association with other proteins such as endonuclease CypA and histone H2AX, it is proposed to organize a DNA–degradosome complex. In this work, we provide evidence for the molecular assembly of this complex as well as for the cooperative effects among its protein components to degrade genomic DNA into large fragments. We have also uncovered that AIF has nuclease activity that is stimulated in the presence of either Mg2+ or Ca2+. Such activity allows AIF by itself and in cooperation with CypA to efficiently degrade genomic DNA. Finally, we have identified TopIB and DEK motifs in AIF as responsible for its nuclease activity. These new findings point, for the first time, to AIF as a nuclease able to digest nuclear dsDNA in dying cells, improving our understanding of its role in promoting apoptosis and opening paths for the development of new therapeutic strategies

Enhanced molecular spin-photon coupling at superconducting nanoconstrictions

We combine top-down and bottom-up nanolithography to optimize the coupling of small molecular spin ensembles to 1.4 GHz on-chip superconducting resonators. Nanoscopic constrictions, fabricated with a focused ion beam at the central transmission line, locally concentrate the microwave magnetic field. Drops of free-radical molecules have been deposited from solution onto the circuits. For the smallest ones, the molecules were delivered at the relevant circuit areas by means of an atomic force microscope. The number of spins Neff effectively coupled to each device was accurately determined combining Scanning Electron and Atomic Force Microscopies. The collective spin-photon coupling constant has been determined for samples with Neff ranging between 2 × 106 and 1012 spins, and for temperatures down to 44 mK. The results show the well-known collective enhancement of the coupling proportional to the square root of Neff. The average coupling of individual spins is enhanced by more than 4 orders of magnitude (from 4 mHz up to above 180 Hz), when the transmission line width is reduced from 400 μm down to 42 nm, and reaches maximum values near 1 kHz for molecules located on the smallest nanoconstrictions.The authors acknowledge funding from the EU (COST Action 15128 MOLSPIN, QUANTERA SUMO and MICROSENSE projects, FET-OPEN Grant 862893 FATMOLS), the Spanish MICINN (Grants RTI2018-096075-B-C21, PCI2018-093116, MAT2017-89993-R, MAT2017-88358-C3-1-R, EUR2019-103823), the Gobierno de Aragón Ggrants E09-17R Q-MAD, E35-20R, BE and LMP55-18, FANDEPAM) and the BBVA foundation (Leonardo Grants 2018 and 2019).Peer reviewe

Spin dynamics of Dy2 molecules deposited onto micro-SQUID sensors

Resumen del trabajo presentado al APS March Meeting, celebrado en Chicago (USA) del 14 al 18 de marzo de 2022.We acknowledge support from EU (FATMOLS FETOPEN-RIA-2019-01 862893, QUANTERA SUMO), Spanish MCIU/AEI/FEDER (RTI-2018-096075-B C21, PCI2018-093116) and CSIC Research Platform PTI-001N

Atomic force microscopy as versatile tool to discern the physico-chemical properties of proteins at the nanoscale

Resumen del trabajo presentado a la 65th International Conference Open Readings, celebrada virtualmente del 15 al 18 de marzo de 2022.N

Atomic Force Microscopy: Single-molecule imaging and force spectroscopy in the study of flavoproteins ligand binding and reaction mechanisms

Atomic force microscopy (AFM) is one of the most versatile tools currently used in nanoscience. AFM allows for performing nondestructive imaging of almost any sample in either air or liquid, regardless whether the specimen is insulating, conductive, transparent, or opaque. It also allows for measuring interaction forces between a sharp probe and a sample surface, therefore allowing to probe nanomechanical properties of the specimen by either applying a controlled force or pulling the sample. It can provide topography, mechanical, magnetic, and conductive maps for very different type of samples. Transferred to the field of biology, today, AFM is the only microscopy technique able to produce images from biomolecules to bacteria and cells with nanometric resolution in aqueous media. Here, we will focus on the biological applications of AFM to flavoproteins. Despite references in the literature are scarce in this particular field, here it is described how imaging with AFM can contribute to describe catalysis mechanisms of some flavoenzymes, how oxidation states or binding of relevant ligands influence the association state of molecules, the dynamics of functional quaternary assemblies, and even visualize structural differences of individual protein molecules. Furthermore, we will show how force spectroscopy can be used to obtain the kinetic parameters, the dissociation landscape and the mechanical forces that maintain flavoprotein complexes, including the possibility to specifically detect particular flavoproteins on a sample.We thank MINECO (BIO2016-75183-P) and Gobierno de Aragón (E35_17R and LMP58_18) with FEDER (2014-2020) funds for “Building Europe from Aragón” for financial support. A.L. acknowledges support from ARAID.Peer reviewe

Molecular recognition of proteins through quantitative force maps at single molecule level

This article belongs to the Special Issue Single-Molecule Protein Dynamics.Intermittent jumping force is an operational atomic-force microscopy mode that produces simultaneous topography and tip-sample maximum-adhesion images based on force spectroscopy. In this work, the operation conditions have been implemented scanning in a repulsive regime and applying very low forces, thus avoiding unspecific tip-sample forces. Remarkably, adhesion images give only specific rupture events, becoming qualitative and quantitative molecular recognition maps obtained at reasonably fast rates, which is a great advantage compared to the force–volume modes. This procedure has been used to go further in discriminating between two similar protein molecules, avidin and streptavidin, in hybrid samples. The adhesion maps generated scanning with biotinylated probes showed features identified as avidin molecules, in the range of 40–80 pN; meanwhile, streptavidin molecules rendered 120–170 pN at the selected working conditions. The gathered results evidence that repulsive jumping force mode applying very small forces allows the identification of biomolecules through the specific rupture forces of the complexes and could serve to identify receptors on membranes or samples or be applied to design ultrasensitive detection technologies.This research was funded by grant PID2019-103901GB-I00 funded by MCIN/AEI/10.13039/501100011033, grant QTP2103003 funded by CSIC, and grants E35_20R and LMP58_18 funded by the Government of Aragón-FEDER. The APC was funded by E35_20R.Peer reviewe

Detection of a quaternary organization into dimer of trimers of Corynebacterium ammoniagenes FAD synthetase at the single-molecule level and at the in cell level

Biochemical characterization of Corynebacterium ammoniagenes FADS (CaFADS) pointed to certain confusion about the stoichiometry of this bifunctional enzyme involved in the production of FMN and FAD in prokaryotes. Resolution of its crystal structure suggested that it might produce a hexameric ensemble formed by a dimer of trimers. We used atomic force microscopy (AFM) to direct imaging single CaFADS molecules bound to mica surfaces, while preserving their catalytic properties. AFM allowed solving individual CaFADS monomers, for which it was even possible to distinguish their sub-molecular individual N- and C-terminal modules in the elongated enzyme. Differences between monomers and higher stoichiometries were easily imaged, enabling us to detect formation of oligomeric species induced by ligand binding. The presence of ATP:Mg 2 + particularly induced the appearance of the hexameric assembly whose mean molecular volume resembles the crystallographic dimer of trimers. Finally, the AFM results are confirmed in cross-linking solution, and the presence of such oligomeric CaFADS species detected in cell extracts. All these results are consistent with the formation of a dimer of trimers during the enzyme catalytic cycle that might bear biological relevance. © 2012 Elsevier B.V.Peer Reviewe