Structural biology

About: Structural biology is a research topic. Over the lifetime, 2206 publications have been published within this topic receiving 126070 citations.

Visualizing the functional architecture of the endocytic machinery.

Abstract: Cells take up proteins and other useful material (called cargo) from their external environment through a process known as endocytosis. To start with, the cargo accumulates in a patch on the surface of the cell. On the inner side of the cell's membrane, a protein called clathrin gathers around the patch of cargo. Clathrin molecules and many other proteins bind together to make a lattice-like coat that causes the membrane to curve inwards and form a pocket that contains the cargo. This continues until the cargo is completely surrounded by membrane and eventually forms a bubble-like structure, or ‘vesicle’, that moves into the cell. More than 50 other proteins are involved in the endocytosis. These proteins arrive at the site of endocytosis in a particular order, complete their tasks and then move away to be used in further rounds of endocytosis. It is not clear how these proteins are organized to complete these steps because it is technically difficult to track the movements of many proteins at the same time. Here, Picco et al. developed a new fluorescence microscopy method that enabled them to track the positions of many of the proteins involved in endocytosis in yeast cells in real time. The experiments revealed when the proteins arrived at the site of endocytosis and how they assembled in relation to the membrane. For example, a group of proteins called N-BAR proteins formed an extended lattice covering the sides of the pocket that forms as the membrane curves inwards. To transform the flat membrane into a vesicle, a network of filaments made of a protein called actin needs to form at the site of endocytosis. The new method shows that the actin filaments grow in a small region at the base of the developing vesicle. By combining different types of microscopy data, Picco et al. were able to build a comprehensive model describing when the proteins involved in endocytosis move and assemble. The next challenge will be to understand the physics behind the molecular machine composed of these many proteins and the cell membrane.

Chemical Crosslinking Mass Spectrometry Analysis of Protein Conformations and Supercomplexes in Heart Tissue

Abstract: While modern structural biology technologies have greatly expanded the size and type of protein complexes that can now be studied, the ability to derive large-scale structural information on proteins and complexes as they exist within tissues is practically nonexistent. Here, we demonstrate the application of crosslinking mass spectrometry to identify protein structural features and interactions in tissue samples, providing systems structural biology insight into protein complexes as they exist in the mouse heart. This includes insights into multiple conformational states of sarcomere proteins, as well as interactions among OXPHOS complexes indicative of supercomplex assembly. The extension of crosslinking mass spectrometry analysis into the realm of tissues opens the door to increasing our understanding of protein structures and interactions within the context of the greater biological system.

Collisional and Coulombic Unfolding of Gas‐Phase Proteins: High Correlation to Their Domain Structures in Solution

Abstract: The three-dimensional structures adopted by proteins are predicated by their many biological functions Mass spectrometry has played a rapidly expanding role in protein structure discovery, enabling the generation of models for both proteins and their higher-order assemblies While important coursed-grained insights have been generated, relatively few examples exist where mass spectrometry has been successfully applied to the characterization of protein tertiary structure Here, we demonstrate that gas-phase unfolding can be used to determine the number of autonomously folded domains within monomeric proteins Our ion mobility-mass spectrometry data highlight a strong, positive correlation between the number of protein unfolding transitions observed in the gas phase and the number of known domains within a group of sixteen proteins ranging from 8–78 kDa This correlation and its potential uses for structural biology is discussed

SDS Micelles as a Membrane-Mimetic Environment for Transmembrane Segments

Abstract: An inherent dilemma in the study of the structural biology of membrane proteins is that it is often necessary to use detergents to mimic the native lipid bilayer environment. This situation is of particular interest because the generation of high-resolution structures (through X-ray crystallography and solution NMR) has overwhelmingly relied upon identification of detergents in which membrane proteins may be solubilized without denaturation into a nonbiological state. While sodium dodecyl sulfate (SDS) is perhaps the most widely employed micelle-forming detergent for laboratory procedures involving membrane proteins, it has generally been regarded as a “harsh” detergent synonymous with membrane protein denaturation. Here we investigate systematically the SDS-solubilized states of a series of model α-helical transmembrane (TM) segments of varying Ala and Ile content in conjunction with selected single-Asn polar substitutions. Using Lys-tagged peptides typified by KKKKK-FAIAIAIIAWAIAIIAIAIAI-KKKKK in a seri...

Probing a cell-embedded megadalton protein complex by DNP-supported solid-state NMR

Abstract: Studying biomolecules at atomic resolution in their native environment is the ultimate aim of structural biology. We investigated the bacterial type IV secretion system core complex (T4SScc) by cellular dynamic nuclear polarization–based solid-state nuclear magnetic resonance spectroscopy to validate a structural model previously generated by combining in vitro and in silico data. Our results indicate that T4SScc is well folded in the cellular setting, revealing protein regions that had been elusive when studied in vitro.