Por favor, use este identificador para citar o enlazar este ítem: https://hdl.handle.net/10495/29739
Título : A path collective variable for extracting free energy profiles from cryo-electron microscopy
Autor : Giraldo Barreto, Julian David
metadata.dc.contributor.advisor: Cossio Tejada, Pilar
Restrepo Cárdenas, Johans Steeven
metadata.dc.subject.*: Biomolecules
Cryoelectron microscopy
Bayes theorem
Signal-to-noise ratio
Microscopía por crioelectrón
Teorema de Bayes
Relación señal-ruido
Free energy profile
Cryo-EM bayesian inference of free energy profiles (cryo-BIFE)
Bayesian inference of electron microscopy (BioEM)
Fecha de publicación : 2021
Resumen : ABSTRACT: Cryo-electron microscopy (or cryo-EM) is an experimental technique to obtain structures of biomolecules. Although single-particle cryo-EM is widely used for 3D reconstruction, it has the potential to provide information about a biomolecule’s conformational variability, which leads to the underlying free-energy landscape of the system. However, cryo-EM as a single-molecule technique uses the 2D projections of individual particles with low signal-to-noise ratio (SNR), making it difficult to work directly with the raw cryo-EM data. Even though there are some methods that overcome the SNR issue, those normally need a big image data bank or are difficult to reproduce. This work proposes a new method called cryo-BIFE (cryo-EM Bayesian Inference of Free-Energy profiles), which uses a path collective variable to extract free-energy profiles and their uncertainties from cryo-EM images. The method is tested for different realistic experimental conditions, leading to a very good performance of extracting free energy profiles for different benchmark systems using different sets of synthetic images. The results show that, to recover the underlying free energy, the SNR in the cryoEM images and the accuracy in estimating the orientation of biomolecule’s projection, are crucial factors. Then, the method is used to study the conformational transitions of a calcium-activated channel with real cryo-EM particles. Interestingly, we recover not only the most probable conformation (used to generate a high-resolution reconstruction of the calcium-bound state) but also a metastable state that corresponds to the calcium-unbound conformation. As expected for turnover transitions within the same sample, the activation barriers are on the order of kBT. We expect our tool for extracting free-energy profiles from cryo-EM images will enable more complete characterization of the thermodynamic ensemble of biomolecules.
Aparece en las colecciones: Maestrías de la Facultad de Ciencias Exactas y Naturales

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