Recent developments in electron-transparent materials have paved the way for liquid-phase electron microscopy (LPEM) leading to an unprecedented understanding of the structure and dynamics of specimens in their liquid environment. Image reconstruction in liquid-state poses several challenges, and most importantly, it undermines the single-particle analysis assumption that the three-dimensional objects captured on the image sensor are identical. We propose the combination of all-atom simulations with LPEM to complement structural studies with dynamic
investigations. In this work, we exploited LPEM to image the dynamics of particles undergoing Brownian motion, using their natural rotation to access the particle structural landscape for reconstructing its architecture in 3D using tomographic techniques. We have selected two test cases for our approach according to prior data accessibility and physiological environment factors: apoferritin and archaeal RNA polymerase. We show that the adopted approach allows to achieve sub-nanometer spatial resolutions of protein structures, either imaging proteins one by one and assessing different conformational states or combining several proteins into one statistical conformational ensemble.