Related papers: Better results with homogeneous biological macromo…
We describe a new generation of algorithms capable of mapping the structure and conformations of macromolecules and their complexes from large ensembles of heterogeneous snapshots, and demonstrate the feasibility of determining both…
Mapping conformational heterogeneity of macromolecules presents a formidable challenge to X-ray crystallography and cryo-electron microscopy, which often presume its absence. This has severely limited our knowledge of the conformations…
Cryo-electron microscopy (cryo-EM), the subject of the 2017 Nobel Prize in Chemistry, is a technology for determining the 3-D structure of macromolecules from many noisy 2-D projections of instances of these macromolecules, whose…
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM),…
The full understanding of cellular functions requires information about protein numbers for various biomolecular assemblies and their dynamics, which can be partly accessed by super-resolution fluorescence microscopy. Yet, many protein…
Macromolecules change their shape (conformation) in the process of carrying out their functions. The imaging by cryo-electron microscopy of rapidly-frozen, individual copies of macromolecules (single particles) is a powerful and general…
Single particle cryo-electron microscopy (EM) is an increasingly popular method for determining the 3-D structure of macromolecules from noisy 2-D images of single macromolecules whose orientations and positions are random and unknown. One…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
Resolving the structural variability of proteins is often key to understanding the structure-function relationship of those macromolecular machines. Single particle analysis using Cryogenic electron microscopy (CryoEM), combined with…
Modern microscopy techniques are developing towards high-resolution imaging, and tremendous progress has been made in past decades; however, the imaging of individual biological macromolecules at atomic resolution using short-wavelength…
Cryogenic electron microscopy (cryo-EM) has transformed structural biology by allowing to reconstruct 3D biomolecular structures up to near-atomic resolution. However, the 3D reconstruction process remains challenging, as the 3D structures…
Modern microscopy techniques are aimed at imaging an individual molecule at atomic resolution. Here we show that low-energy electrons with kinetic energies of 50-250 eV offer a possibility of overcome the problem of radiation damage, and…
Cryogenic electron microscopy is widely used in structural biology, but its resolution is often limited by the dynamics of the macromolecule. Here, we developed a refinement protocol based on Gaussian mixture models that integrates particle…
Non-invasive light scattering methods provide data on biological macromolecules (i.e. proteins, nucleic acids, as well as assemblies and larger entities composed of them) that are complementary with those of size exclusion chromatography,…
Structural dynamics of macromolecules is critical to their structural-function relationship. Cryogenic electron microscopy (CryoEM) provides snapshots of vitrified protein at different compositional and conformational states, and the…
Biological cells are built up from many different constituents of varying size and stiffness which all contribute to the cell's mechanical properties. Despite this heterogeneity, in the analysis of experimental measurements such as atomic…
One of the important challenges facing high resolution molecular dynamics calculations is to reproduce biological functions that occur in the macroscopic world and involve macroscopic variables. Some of these functions can be well described…
Evidently, physical experiments are practically reproducible even though the fully identical preparation of initial state wave functions is often far beyond experimental possibilities. It is thus natural to explore if and in which sense…
Understanding complex biological macromolecules, especially proteins, is vital for grasping their diverse chemical functions with direct impact in biology and pharmacology. While techniques like X-ray crystallography and cryo-electron…
Equilibrium sampling of biomolecules remains an unmet challenge after more than 30 years of atomistic simulation. Efforts to enhance sampling capability, which are reviewed here, range from the development of new algorithms to…