The molecular structure of long non-coding RNAs: emerging patterns and functional implications

I Chillón, M Marcia - Critical Reviews in Biochemistry and Molecular …, 2020 - Taylor & Francis
Long non-coding RNAs (lncRNAs) are recently-discovered transcripts that regulate vital
cellular processes and are crucially connected to diseases. Despite their unprecedented …

Protein dynamics by the combination of high-speed AFM and computational modeling

H Flechsig, T Ando - Current Opinion in Structural Biology, 2023 - Elsevier
High-speed atomic force microscopy (HS-AFM) allows direct observation of biological
molecules in dynamic action. However, HS-AFM has no atomic resolution. This article …

Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images

R Amyot, A Marchesi, CM Franz, I Casuso… - PLoS computational …, 2022 - journals.plos.org
Atomic force microscopy (AFM) can visualize the dynamics of single biomolecules under
near-physiological conditions. However, the scanning tip probes only the molecular surface …

End-to-end differentiable blind tip reconstruction for noisy atomic force microscopy images

Y Matsunaga, S Fuchigami, T Ogane, S Takada - Scientific Reports, 2023 - nature.com
Observing the structural dynamics of biomolecules is vital to deepening our understanding
of biomolecular functions. High-speed (HS) atomic force microscopy (AFM) is a powerful …

Biological and methodological complexities of beta‐amyloid peptide: Implications for Alzheimer's disease research

MM Matuszyk, CJ Garwood, L Ferraiuolo… - Journal of …, 2022 - Wiley Online Library
Although controversial, the amyloid cascade hypothesis remains central to the Alzheimer's
disease (AD) field and posits amyloid‐beta (Aβ) as the central factor initiating disease onset …

[HTML][HTML] Integrative/hybrid modeling approaches for studying biomolecules

A Srivastava, SP Tiwari, O Miyashita, F Tama - Journal of molecular biology, 2020 - Elsevier
The structural and dynamical characterization of biomolecules holds central importance in
the endeavor to understand the molecular mechanisms regulating living systems. However …

Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure

T Niina, Y Matsunaga, S Takada - PLOS Computational Biology, 2021 - journals.plos.org
Atomic force microscopy (AFM) can visualize functional biomolecules near the physiological
condition, but the observed data are limited to the surface height of specimens. Since the …

Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images

T Ogane, D Noshiro, T Ando, A Yamashita… - PLOS Computational …, 2022 - journals.plos.org
High-speed atomic force microscopy (HS-AFM) is a powerful technique for capturing the
time-resolved behavior of biomolecules. However, structural information in HS-AFM images …

Reconstruction of three-dimensional conformations of bacterial ClpB from high-speed atomic-force-microscopy images

B Dasgupta, O Miyashita, T Uchihashi… - Frontiers in Molecular …, 2021 - frontiersin.org
ClpB belongs to the cellular disaggretase machinery involved in rescuing misfolded or
aggregated proteins during heat or other cellular shocks. The function of this protein relies …

Analyzing atomic force microscopy images of virus-like particles by expectation-maximization

RA McCormick, NM Ralbovsky, W Gilbraith, JP Smith… - npj Vaccines, 2024 - nature.com
Abstract Analysis of virus-like particles (VLPs) is an essential task in optimizing their
implementation as vaccine antigens for virus-initiated diseases. Interrogating VLP …