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Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
Abstract
A novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that the silica primer be properly inert and bio-compatible, keeping the native structural features of the system at hand, while condensing into an amorphous, glass-like coating. In this work, we propose a molecular dynamics protocol, aimed at depicting and characterizing the earliest stages of the embedding process of small biomolecules in a solution of water and orthosilicic acid, here, taken as a precursor of the silica matrix. Overall, we observe a negligible influence of orthosilicic acid on the behavior of stable folded systems (such as ubiquitin). Conversely, intrinsically disordered and unstable peptides are affected by the coating, the latter seemingly inhibiting the fluctuations of flexible moieties. While further scrutiny is in order, our assessment offers a first mechanistic insight of the effects of orthosilicic acid, thereby validating its use in the proposed innovative application of APT to the structural resolution of protein molecules.
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Authors (5)
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Giovanni Novi Inverardi
- Department of Physics, University of Trento, Via Sommarive 14, 38123 Povo-Trento, Italy
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Francesco Carnovale
- Department of Physics, University of Trento, Via Sommarive 14, 38123 Povo-Trento, Italy
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Lorenzo Petrolli
- Department of Physics, University of Trento, Via Sommarive 14, 38123 Povo-Trento, Italy
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Gianluca Lattanzi
- Department of Physics, University of Trento, Via Sommarive 14, 38123 Povo-Trento, Italy
Cite as
Full text
- Publication version
- Accepted or Published Version
- DOI:
- Digital Object Identifier (open in new tab) 10.3390/biophysica3020018
- License
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Details
- Category:
- Articles
- Type:
- artykuły w czasopismach
- Published in:
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BIOPHYSICAL JOURNAL
no. 3,
pages 276 - 287,
ISSN: 0006-3495 - Language:
- English
- Publication year:
- 2023
- Bibliographic description:
- Novi Inverardi G., Carnovale F., Petrolli L., Taioli S., Lattanzi G.: Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography// BIOPHYSICAL JOURNAL -,iss. 2 (2023), s.276-287
- DOI:
- Digital Object Identifier (open in new tab) 10.3390/biophysica3020018
- Sources of funding:
-
- Horizon Europe Programme (grant agreement 101046651—MIMOSA)
- Verified by:
- Gdańsk University of Technology
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