Localization atomic force microscopy

Understanding structural dynamics of biomolecules at the single-molecule level is vital to advancing our knowledge of molecular mechanisms. Currently, there are few techniques that can capture dynamics at the sub-nanometre scale and in physiologically relevant conditions. Atomic force microscopy (AF...

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Published inNature (London) Vol. 594; no. 7863; pp. 385 - 390
Main Authors Heath, George R., Kots, Ekaterina, Robertson, Janice L., Lansky, Shifra, Khelashvili, George, Weinstein, Harel, Scheuring, Simon
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 17.06.2021
Nature Publishing Group
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Abstract Understanding structural dynamics of biomolecules at the single-molecule level is vital to advancing our knowledge of molecular mechanisms. Currently, there are few techniques that can capture dynamics at the sub-nanometre scale and in physiologically relevant conditions. Atomic force microscopy (AFM) 1 has the advantage of analysing unlabelled single molecules in physiological buffer and at ambient temperature and pressure, but its resolution limits the assessment of conformational details of biomolecules 2 . Here we present localization AFM (LAFM), a technique developed to overcome current resolution limitations. By applying localization image reconstruction algorithms 3 to peak positions in high-speed AFM and conventional AFM data, we increase the resolution beyond the limits set by the tip radius, and resolve single amino acid residues on soft protein surfaces in native and dynamic conditions. LAFM enables the calculation of high-resolution maps from either images of many molecules or many images of a single molecule acquired over time, facilitating single-molecule structural analysis. LAFM is a post-acquisition image reconstruction method that can be applied to any biomolecular AFM dataset. A localization algorithm is applied to datasets obtained with conventional and high-speed atomic force microscopy to increase image resolution beyond the limits set by the radius of the tip used.
AbstractList Understanding structural dynamics of biomolecules at the single-molecule level is vital to advancing our knowledge of molecular mechanisms. Currently, there are few techniques that can capture dynamics at the sub-nanometre scale and in physiologically relevant conditions. Atomic force microscopy (AFM).sup.1 has the advantage of analysing unlabelled single molecules in physiological buffer and at ambient temperature and pressure, but its resolution limits the assessment of conformational details of biomolecules.sup.2. Here we present localization AFM (LAFM), a technique developed to overcome current resolution limitations. By applying localization image reconstruction algorithms.sup.3 to peak positions in high-speed AFM and conventional AFM data, we increase the resolution beyond the limits set by the tip radius, and resolve single amino acid residues on soft protein surfaces in native and dynamic conditions. LAFM enables the calculation of high-resolution maps from either images of many molecules or many images of a single molecule acquired over time, facilitating single-molecule structural analysis. LAFM is a post-acquisition image reconstruction method that can be applied to any biomolecular AFM dataset.
Understanding structural dynamics of biomolecules at the single-molecule level is vital to advancing our knowledge of molecular mechanisms. Currently, there are few techniques that can capture dynamics at the sub-nanometre scale and in physiologically relevant conditions. Atomic force microscopy (AFM)1 has the advantage of analysing unlabelled single molecules in physiological buffer and at ambient temperature and pressure, but its resolution limits the assessment of conformational details of biomolecules2. Here we present localization AFM (LAFM), a technique developed to overcome current resolution limitations. By applying localization image reconstruction algorithms3 to peak positions in high-speed AFM and conventional AFM data, we increase the resolution beyond the limits set by the tip radius, and resolve single amino acid residues on soft protein surfaces in native and dynamic conditions. LAFM enables the calculation of high-resolution maps from either images of many molecules or many images of a single molecule acquired over time, facilitating single-molecule structural analysis. LAFM is a post-acquisition image reconstruction method that can be applied to any biomolecular AFM dataset.
Understanding structural dynamics of biomolecules at the single-molecule level is vital to advancing our knowledge of molecular mechanisms. Currently, there are few techniques that can capture dynamics at the sub-nanometre scale and in physiologically relevant conditions. Atomic force microscopy (AFM) 1 has the advantage of analysing unlabelled single molecules in physiological buffer and at ambient temperature and pressure, but its resolution limits the assessment of conformational details of biomolecules 2 . Here we present localization AFM (LAFM), a technique developed to overcome current resolution limitations. By applying localization image reconstruction algorithms 3 to peak positions in high-speed AFM and conventional AFM data, we increase the resolution beyond the limits set by the tip radius, and resolve single amino acid residues on soft protein surfaces in native and dynamic conditions. LAFM enables the calculation of high-resolution maps from either images of many molecules or many images of a single molecule acquired over time, facilitating single-molecule structural analysis. LAFM is a post-acquisition image reconstruction method that can be applied to any biomolecular AFM dataset. A localization algorithm is applied to datasets obtained with conventional and high-speed atomic force microscopy to increase image resolution beyond the limits set by the radius of the tip used.
Understanding structural dynamics of biomolecules at the single-molecule level is vital to advancing our knowledge of molecular mechanisms. Currently, there are few techniques that can capture dynamics at the sub-nanometre scale and in physiologically relevant conditions. Atomic force microscopy (AFM).sup.1 has the advantage of analysing unlabelled single molecules in physiological buffer and at ambient temperature and pressure, but its resolution limits the assessment of conformational details of biomolecules.sup.2. Here we present localization AFM (LAFM), a technique developed to overcome current resolution limitations. By applying localization image reconstruction algorithms.sup.3 to peak positions in high-speed AFM and conventional AFM data, we increase the resolution beyond the limits set by the tip radius, and resolve single amino acid residues on soft protein surfaces in native and dynamic conditions. LAFM enables the calculation of high-resolution maps from either images of many molecules or many images of a single molecule acquired over time, facilitating single-molecule structural analysis. LAFM is a post-acquisition image reconstruction method that can be applied to any biomolecular AFM dataset. A localization algorithm is applied to datasets obtained with conventional and high-speed atomic force microscopy to increase image resolution beyond the limits set by the radius of the tip used.
Understanding structural dynamics of biomolecules at the single molecule level is vital to advancing our knowledge of molecular mechanisms. Currently, there are few techniques that can capture dynamics at the sub-nanometer scale and in physiologically relevant conditions. Atomic force microscopy (AFM 1 ) has the notable advantage of analyzing unlabeled single molecules in physiological buffer and at ambient temperature and pressure, yet its resolution has been limiting to assess conformational details of biomolecules. 2 To move beyond current resolution limitations, we developed Localization AFM (LAFM). By applying localization image reconstruction algorithms 3 to peak positions in high-speed AFM and conventional AFM data, we increase the resolution beyond the limits set by the tip radius and resolve single amino acid residues on soft protein surfaces in native and dynamic conditions. The LAFM method allows the calculation of high-resolution maps from either images of many molecules or many images of a single molecule acquired over time, opening new avenues for single molecule structural analysis. LAFM is a post-acquisition image reconstruction method that can be applied to any biomolecular AFM dataset.
Understanding structural dynamics of biomolecules at the single-molecule level is vital to advancing our knowledge of molecular mechanisms. Currently, there are few techniques that can capture dynamics at the sub-nanometre scale and in physiologically relevant conditions. Atomic force microscopy (AFM) has the advantage of analysing unlabelled single molecules in physiological buffer and at ambient temperature and pressure, but its resolution limits the assessment of conformational details of biomolecules . Here we present localization AFM (LAFM), a technique developed to overcome current resolution limitations. By applying localization image reconstruction algorithms to peak positions in high-speed AFM and conventional AFM data, we increase the resolution beyond the limits set by the tip radius, and resolve single amino acid residues on soft protein surfaces in native and dynamic conditions. LAFM enables the calculation of high-resolution maps from either images of many molecules or many images of a single molecule acquired over time, facilitating single-molecule structural analysis. LAFM is a post-acquisition image reconstruction method that can be applied to any biomolecular AFM dataset.
Audience Academic
Author Kots, Ekaterina
Weinstein, Harel
Scheuring, Simon
Robertson, Janice L.
Khelashvili, George
Lansky, Shifra
Heath, George R.
AuthorAffiliation 3 Washington University, Department of Biochemistry and Molecular Biophysics, 660 South Euclid Avenue, St. Louis, MO-63110, USA
2 Weill Cornell Medicine, Department of Physiology and Biophysics, 1300 York Avenue, New York, NY-10065, USA
1 Weill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY-10065, USA
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– name: 3 Washington University, Department of Biochemistry and Molecular Biophysics, 660 South Euclid Avenue, St. Louis, MO-63110, USA
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  fullname: Kots, Ekaterina
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  givenname: Janice L.
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  surname: Robertson
  fullname: Robertson, Janice L.
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  surname: Scheuring
  fullname: Scheuring, Simon
  email: sis2019@med.cornell.edu
  organization: Department of Anesthesiology, Weill Cornell Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine
BackLink https://www.ncbi.nlm.nih.gov/pubmed/34135520$$D View this record in MEDLINE/PubMed
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Detailed Author Contribution Statement
G.R.H. and S.S. designed the study and developed the LAFM algorithm; J.L.R purified and reconstituted the CLC-ec1. G.R.H. and S.L. performed HS-AFM experiments. E.K. and G.K. performed CLC MD simulations. S.L. performed A5 P13W-G14W cloning, expression, purification and MD simulations. G.R.H., E.K., G.K., H.W. and S.S. analyzed the data. G.R.H., E.K., J.L.R, G.K., H.W. and S.S. wrote the paper.
Current address: School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK.
ORCID 0000-0002-5499-9943
0000-0003-3534-069X
0000-0003-3473-9818
0000-0001-6431-2191
0000-0002-7139-7098
0000-0001-7235-8579
OpenAccessLink https://www.nature.com/articles/s41586-021-03551-x.pdf
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Snippet Understanding structural dynamics of biomolecules at the single-molecule level is vital to advancing our knowledge of molecular mechanisms. Currently, there...
Understanding structural dynamics of biomolecules at the single molecule level is vital to advancing our knowledge of molecular mechanisms. Currently, there...
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SubjectTerms 631/1647/2204/1262
631/57/2265
631/57/2282
639/766/930/328/1262
639/925/930/2735
Algorithms
Ambient temperature
Amino acids
Amino Acids - chemistry
Annexin A5 - chemistry
Annexin A5 - ultrastructure
Aquaporins - chemistry
Aquaporins - ultrastructure
Atomic force microscopy
Biomolecules
Chloride Channels - chemistry
Chloride Channels - ultrastructure
Datasets as Topic
Escherichia coli Proteins - chemistry
Escherichia coli Proteins - ultrastructure
Humanities and Social Sciences
Humans
Hydrogen-Ion Concentration
Image acquisition
Image processing
Image reconstruction
Image resolution
Localization
Methods
Microscopy
Microscopy, Atomic Force - methods
Microscopy, Atomic Force - standards
Molecular Dynamics Simulation
Molecular modelling
multidisciplinary
Noise
Physiology
Proteins
Science
Science (multidisciplinary)
Simulation
Structural analysis
Structure
Topography
Title Localization atomic force microscopy
URI https://link.springer.com/article/10.1038/s41586-021-03551-x
https://www.ncbi.nlm.nih.gov/pubmed/34135520
https://www.proquest.com/docview/2542759381
https://search.proquest.com/docview/2542362725
https://pubmed.ncbi.nlm.nih.gov/PMC8697813
Volume 594
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