Structural biology

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

Structural biology of type VI secretion systems

Abstract: Type VI secretion systems (T6SSs) are transenvelope complexes specialized in the transport of proteins or domains directly into target cells. These systems are versatile as they can target either eukaryotic host cells and therefore modulate the bacteria-host interaction and pathogenesis or bacterial cells and therefore facilitate access to a specific niche. These molecular machines comprise at least 13 proteins. Although recent years have witnessed advances in the role and function of these secretion systems, little is known about how these complexes assemble in the cell envelope. Interestingly, the current information converges to the idea that T6SSs are composed of two subassemblies, one resembling the contractile bacteriophage tail, whereas the other subunits are embedded in the inner and outer membranes and anchor the bacteriophage-like structure to the cell envelope. In this review, we summarize recent structural information on individual T6SS components emphasizing the fact that T6SSs are composite systems, adapting subunits from various origins.

Cryo-EM structure of the adenosine A2A receptor coupled to an engineered heterotrimeric G protein

Abstract: The adenosine A2A receptor (A2AR) is a prototypical G protein-coupled receptor (GPCR) that couples to the heterotrimeric G protein GS. Here, we determine the structure by electron cryo-microscopy (cryo-EM) of A2AR at pH 7.5 bound to the small molecule agonist NECA and coupled to an engineered heterotrimeric G protein, which contains mini-GS, the βγ subunits and nanobody Nb35. Most regions of the complex have a resolution of ~3.8 A or better. Comparison with the 3.4 A resolution crystal structure shows that the receptor and mini-GS are virtually identical and that the density of the side chains and ligand are of comparable quality. However, the cryo-EM density map also indicates regions that are flexible in comparison to the crystal structures, which unexpectedly includes regions in the ligand binding pocket. In addition, an interaction between intracellular loop 1 of the receptor and the β subunit of the G protein was observed.

Structure, function, and mechanism of the Hsp90 molecular chaperone.

Abstract: Publisher Summary This chapter discusses the current knowledge of the structure and biochemistry of the Hsp90 family of molecular chaperones, with particular attention to the emerging understanding of the role of its ATPase activity and the opportunities this presents for and-chaperone drug development. It focuses on various co-chaperones that are known to interact with Hsp90, examining their roles in Hsp90 function as well as the complicated picture of dynamic and varied Hsp90/co-chaperone complexes that is emerging. In addition, the chapter also mentions the current understanding of the interaction of Hsp90 with its client proteins, the possible origins of client-protein specificity, and the change of state in the client proteins that is achieved by their involvement in the ATP-dependent chaperone cycle of Hsp90. In the eukaryotic Hsp90s, the N-terminal nucleotide-binding domain is connected to the remainder of the protein by a highly charged and proteolytically sensitive segment that is variable both in length and composition between different species and between different isoforms in the same species. However, many of the key phenomena associated with this system remain obscure. Most notably, the roles of the expanding set of co-chaperones and the nature of the interaction between Hsp90 and the client proteins are still very poorly understood.

Structural Analysis of Macromolecular Assemblies by Electron Microscopy

Abstract: 1.1. Light and Electron Microscopy and Their Impact in Biology To fully understand biological processes from the metabolism of a bacterium to the operation of a human brain, it is necessary to know the three-dimensional (3D) spatial arrangement and dynamics of the constituent molecules, how they assemble into complex molecular machines, and how they form functional organelles, cells, and tissues. The methods of X-ray crystallography and NMR spectroscopy can provide detailed information on molecular structure and dynamics. At the cellular level, optical microscopy reveals the spatial distribution and dynamics of molecules tagged with fluorophores. Electron microscopy (EM) overlaps with these approaches, covering a broad range from atomic to cellular structures. The development of cryogenic methods has enabled EM imaging to provide snapshots of biological molecules and cells trapped in a close to native, hydrated state.1,2 Because of the importance of macromolecular assemblies in the machinery of living cells and progress in the EM and image processing methods, EM has become a major tool for structural biology over the molecular to cellular size range. There have been tremendous advances in understanding the 3D spatial organization of macromolecules and their assemblies in cells and tissues, due to developments in both optical and electron microscopy. In light microscopy, super-resolution and single molecule methods have pushed the resolution of fluorescence images to ∼50 nm, using the power of molecular biology to fuse molecules of interest with fluorescent marker proteins.(3) X-ray cryo-tomography is developing as a method for 3D reconstruction of thicker (10 μm) hydrated samples, with resolution reaching the 15 nm resolution range.(4) In EM, major developments in instrumentation and methods have advanced the study of single particles (isolated macromolecular complexes) in vitrified solution as well as in 3D reconstruction by tomography of irregular objects such as cells or subcellular structures.1,5−7 Cryo-sectioning can be used to prepare vitrified sections of cells and tissues that would otherwise be too thick to image by transmission EM (TEM).8,9 In parallel, software improvements have facilitated 3D structure determination from the low contrast, low signal-to-noise ratio (SNR) images of projected densities provided by TEM of biological molecules.10−14 Alignment and classification of images in both 2D and 3D are key methods for improving SNR and detection and sorting of heterogeneity in EM data sets.(14) The resolution of single-particle reconstructions is steadily improving and has gone beyond 4 A for some icosahedral viruses and 5.5 A for asymmetric complexes such as ribosomes, giving a clear view of protein secondary structure elements and, in the best cases, resolving the protein or nucleic acid fold.15,16