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

Current Opinion in Structural Biology, Journal Year: 2023, Volume and Issue: 80, P. 102591 - 102591

Published: April 17, 2023

Language: Английский

---

Structural studies of protein–nucleic acid complexes: A brief overview of the selected techniques

Computational and Structural Biotechnology Journal, Journal Year: 2023, Volume and Issue: 21, P. 2858 - 2872

Published: Jan. 1, 2023

Protein-nucleic acid complexes are involved in all vital processes, including replication, transcription, translation, regulation of gene expression and cell metabolism. Knowledge the biological functions molecular mechanisms beyond activity macromolecular can be determined from their tertiary structures. Undoubtably, performing structural studies protein-nucleic is challenging, mainly because these types often unstable. In addition, individual components may display extremely different surface charges, causing to precipitate at higher concentrations used many studies. Due variety biophysical properties, no simple universal guideline exists that helps scientists chose a method successfully determine structure specific complex. this review, we provide summary following experimental methods, which applied study structures complexes: X-ray neutron crystallography, nuclear magnetic resonance (NMR) spectroscopy, cryogenic electron microscopy (cryo-EM), atomic force (AFM), small angle scattering (SAS) circular dichroism (CD) infrared (IR) spectroscopy. Each discussed regarding its historical context, advancements over past decades recent years, weaknesses strengths. When single does not satisfactory data on selected complex, combination several methods should considered as hybrid approach; thus, problems solved when studying complexes.

Language: Английский

---

Precise Surface Profiling at the Nanoscale Enabled by Deep Learning

Nano Letters, Journal Year: 2024, Volume and Issue: 24(8), P. 2589 - 2595

Published: Jan. 22, 2024

Surface topography, or height profile, is a critical property for various micro- and nanostructured materials devices, as well biological systems. At the nanoscale, atomic force microscopy (AFM) tool of choice surface profiling due to its capability noninvasively map topography almost all types samples. However, this method suffers from one drawback: convolution nanoprobe's shape in profile samples, which especially severe sharp protrusion features. Here, we report deep learning (DL) approach overcome limit. Adopting an image-to-image translation methodology, use data sets tip-convoluted deconvoluted image pairs train encoder–decoder based convolutional neural network. The trained network successfully removes tip AFM topographic images nanocorrugated surfaces recovers true, precise 3D profiles these

Language: Английский

---

Topology of molecular deformations induces triphasic catch bonding in selectin–ligand bonds

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(6)

Published: Jan. 31, 2024

Among the long-standing efforts to elucidate physical mechanisms of protein–ligand catch bonding, particular attention has been directed at family selectin proteins. Selectins exhibit slip, catch–slip, and slip–catch–slip with minor structural modifications causing major changes in selectins’ response force. How can a single mechanism allow interconversion between these various behaviors? We present unifying theory selectin–ligand using structurally motivated free energy landscape show how topology force-induced deformations molecular system produces full range observed behaviors. find that pathway bond rupture deforms non-trivial ways, such unbinding dynamics depend sensitively on This implies severe breakdown Bell’s theory—a paradigmatic used widely modeling—raising questions about suitability modeling other bonds. Our approach be applied broadly systems.

Language: Английский

---

NanoLocz: Image Analysis Platform for AFM, High‐Speed AFM, and Localization AFM

Small Methods, Journal Year: 2024, Volume and Issue: unknown

Published: March 1, 2024

Abstract Atomic Force Microscopy (AFM), High‐Speed AFM (HS‐AFM) simulation AFM, and Localization (LAFM) enable the study of molecules surfaces with increasingly higher spatiotemporal resolution. However, effective rapid analysis images movies produced by these techniques can be challenging, often requiring use multiple image processing software applications scripts. Here, NanoLocz, an open‐source solution that offers advanced capabilities for community, is presented. Integration continued development tools essential to improve access data, increase throughput, open new opportunities. NanoLocz efficiently leverages rich data has offer incorporating combining existing newly developed methods HS‐AFM, LAFM seamlessly. It facilitates streamlines workflows from import raw through various workflows. demonstrates it enables including single‐molecule LAFM, time‐resolved LAFM.

Language: Английский

---