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

Lostao, Anabel; Lim, Keesiang; Pallarés, María Carmen; Ptak, Arkadiusz; Marcuello, Carlos

doi:10.1016/j.ijbiomac.2023.124089

Cited by 36 publications

(24 citation statements)

References 239 publications

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“…Single-molecule FRET stands out as a precise tool for detecting conformational transitions and kinetics within the 10-nanometer range, which has provided rich knowledge about the nucleosome dual function in compacting the genome and regulating the DNA accessibility. ,− At the same time, single-molecule manipulation techniques, such as optical tweezers, magnetic tweezers, and AFM, offer dynamic methods to trap, stretch, or twist biomolecules by applying specific tensions or torques (Figure ). These techniques enable tracking of conformational transitions with high temporal and spatial resolution.…”

Section: Single-molecule Manipulation Approachesmentioning

confidence: 99%

Nucleosome Dynamics Derived at the Single-Molecule Level Bridges Its Structures and Functions

Chen,

Li,

2024

JACS Au

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Nucleosome, the building block of chromatin, plays pivotal roles in all DNA-related processes. While cryogenic-electron microscopy (cryo-EM) has significantly advanced our understanding of nucleosome structures, the emerging field of single-molecule force spectroscopy is illuminating their dynamic properties. This technique is crucial for revealing how nucleosome behavior is influenced by chaperones, remodelers, histone variants, and posttranslational modifications, particularly in their folding and unfolding mechanisms under tension. Such insights are vital for deciphering the complex interplay in nucleosome assembly and structural regulation, highlighting the nucleosome's versatility in response to DNA activities. In this Perspective, we aim to consolidate the latest advancements in nucleosome dynamics, with a special focus on the revelations brought forth by single-molecule manipulation. Our objective is to highlight the insights gained from studying nucleosome dynamics through this innovative approach, emphasizing the transformative impact of single-molecule manipulation techniques in the field of chromatin research.

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Section: Single-molecule Manipulation Approachesmentioning

confidence: 99%

Nucleosome Dynamics Derived at the Single-Molecule Level Bridges Its Structures and Functions

Chen,

Li,

2024

JACS Au

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“…The experiments performed on prefoldin action deliver highly valuable information concerning its dependence on external conditions (temperature, ionic strength, and osmotic stress) ( Blanco-Touriñán et al, 2021 ). Experimental approaches to study the biomolecular interactions driven under force, such as single-molecule force spectroscopy ( Lostao et al, 2023 ) or optical tweezers ( Bustamanta et al, 2020 ), highlight the potential limitations to these techniques as the complexity of calibration steps prior the data acquisition.…”

Section: Introductionmentioning

confidence: 99%

Model of the external force field for the protein folding process—the role of prefoldin

Roterman,

Stapor,

Konieczny

2024

Front. Chem.

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Introduction: The protein folding process is very sensitive to environmental conditions. Many possibilities in the form of numerous pathways for this process can—if an incorrect one is chosen—lead to the creation of forms described as misfolded. The aqueous environment is the natural one for the protein folding process. Nonetheless, other factors such as the cell membrane and the presence of specific molecules (chaperones) affect this process, ensuring the correct expected structural form to guarantee biological activity. All these factors can be considered components of the external force field for this process.Methods: The fuzzy oil drop-modified (FOD-M) model makes possible the quantitative evaluation of the modification of the external field, treating the aqueous environment as a reference. The FOD-M model (tested on membrane proteins) includes the component modifying the water environment, allowing the assessment of the external force field generated by prefoldin.Results: In this work, prefoldin was treated as the provider of a specific external force field for actin and tubulin. The discussed model can be applied to any folding process simulation, taking into account the changed external conditions. Hence, it can help simulate the in silico protein folding process under defined external conditions determined by the respective external force field. In this work, the structures of prefoldin and protein folded with the participation of prefoldin were analyzed.Discussion: Thus, the role of prefoldin can be treated as a provider of an external field comparable to other environmental factors affecting the protein folding process.

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“…Systems involving transmembrane or peripheral membrane proteins can be even more challenging, as protein dynamics in a lipid bilayer environment can be slowed down, coupled to membrane fluctuations, and possibly dependent on lipid composition 8,9 . AA approaches are also heavily challenged by the interpretation of experimental data such as single-molecule force spectroscopy by atomic force microscopy (AFM-SMFS) profiles generated in nanomechanical studies, where it is critical to accumulate enough sampling of non-equilibrium pulling processes 10–12 . Similarly, in the case of disordered proteins or domains, integrating small-angle x-ray scattering (SAXS) with MD data requires the determination of whole ensembles of conformations which can be difficult to obtain with AA methods 13,14 .…”

Section: Introductionmentioning

confidence: 99%

GōMartini 3: From large conformational changes in proteins to environmental bias corrections

Souza,

Borges-Araújo,

Brasnett

et al. 2024

Preprint

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Coarse-grained modeling has become an important tool to supplement experimental measurements, allowing access to spatio-temporal scales beyond all-atom based approaches. The GōMartini model combines structure- and physics-based coarse-grained approaches, balancing computational efficiency and accurate representation of protein dynamics with the capabilities of studying proteins in different biological environments. This paper introduces an enhanced GōMartini model, which combines a virtual-site implementation of Gō models with Martini 3. The implementation has been extensively tested by the community since the release of the new version of Martini. This work demonstrates the capabilities of the model in diverse case studies, ranging from protein-membrane binding to protein-ligand interactions and AFM force profile calculations. The model is also versatile, as it can address recent inaccuracies reported in the Martini protein model. Lastly, the paper discusses the advantages, limitations, and future perspectives of the Martini 3 protein model and its combination with Gō models.

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

Cited by 36 publications

References 239 publications

Nucleosome Dynamics Derived at the Single-Molecule Level Bridges Its Structures and Functions

Nucleosome Dynamics Derived at the Single-Molecule Level Bridges Its Structures and Functions

Model of the external force field for the protein folding process—the role of prefoldin

GōMartini 3: From large conformational changes in proteins to environmental bias corrections

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