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Current Opinion in Structural Biology

David Je Callaway, Zimei Bu
The most complex molecular machines are proteins found within cells. Protein dynamics, in particular dynamics on nanoscales, presents us with a novel paradigm for cell signaling: the idea that proteins and protein complexes can communicate directly within themselves to effect long-range information transfer, via coupled domains and correlated residue clusters. This idea has been little explored, in large part because of a paucity of experimental techniques that can address the necessary questions. Here we review recent progress in developing a promising new approach, neutron spin echo spectroscopy...
October 15, 2016: Current Opinion in Structural Biology
Wen Song, Zhifu Han, Jizong Wang, Guangzhong Lin, Jijie Chai
The large family of membrane-localized receptor kinases (RKs) has important roles in many aspects of plant physiology. RKs function to perceive external signals, leading to RK activation and downstream signaling. Progress has been recently made in structural elucidation of the mechanisms underlying ligand recognition and activation of RKs. These structural studies mainly on leucine-rich repeat RKs (LRR-RKs) support the idea that ligand-induced dimerization is an essential step for RK activation, though the modes for dimerization vary...
October 14, 2016: Current Opinion in Structural Biology
Sriram Neelamegham, Lara K Mahal
Glycosylation is a ubiquitous mammalian post-translational modification that both decorates a majority of expressed proteins and regulates their function. Cellular glycan biosynthesis is facilitated by a few hundred enzymes that are collectively termed 'glycoenzymes'. The expression and activity of these enzymes is controlled at the transcription, translation and post-translation levels. New wet-lab advances are providing analytical methods to collect large-scale data at these multiple levels, relational databases are starting to collate these results, and computer models are beginning to integrate this information across scales in order to gain new knowledge...
October 13, 2016: Current Opinion in Structural Biology
Hironori Suzuki, Takuo Osawa, Yuko Fujioka, Nobuo N Noda
In autophagy, which is an intracellular degradation system that is conserved among eukaryotes, degradation targets are sequestered through the de novo synthesis of a double-membrane organelle, the autophagosome, which delivers them to the lysosomes for degradation. The core autophagy machinery comprising 18 autophagy-related (Atg) proteins in yeast plays an essential role in autophagosome formation; however, the molecular role of each Atg factor and the mechanism of autophagosome formation remain elusive. Recent years have seen remarkable progress in structural biological studies on the core autophagy machinery, opening new avenues for autophagy research...
October 7, 2016: Current Opinion in Structural Biology
Dalei Wu, Fraydoon Rastinejad
The mammalian basic helix-loop-helix-PER-ARNT-SIM (bHLH-PAS) transcription factors share common architectural features that include a bHLH DNA-binding domain and tandemly positioned PAS domains. The sixteen members of this family include the hypoxia-inducible factors (HIF-1α and HIF-2α), ARNT (also known as HIF-1β), CLOCK and BMAL1. Most bHLH-PAS proteins have been genetically linked to variety of diseases in humans, including cancers, metabolic syndromes and psychiatric conditions. To function as transcription factors, the bHLH-PAS proteins must form heterodimeric complexes...
October 6, 2016: Current Opinion in Structural Biology
Idlir Liko, Timothy M Allison, Jonathan Ts Hopper, Carol V Robinson
With the convergence of breakthroughs in structural biology, specifically breaking the resolution barriers in cryo-electron microscopy and with continuing developments in crystallography, novel interfaces with other biophysical methods are emerging. Here we consider how mass spectrometry can inform these techniques by providing unambiguous definition of subunit stoichiometry. Moreover recent developments that increase mass spectral resolution enable molecular details to be ascribed to unassigned density within high-resolution maps of membrane and soluble protein complexes...
October 6, 2016: Current Opinion in Structural Biology
Brent L Nannenga, Tamir Gonen
In 2013 we unveiled the cryo-electron microscopy (CryoEM) method of MicroED, or three-dimensional (3D) electron diffraction of microscopic crystals. Here tiny 3D crystals of biological material are used in an electron microscope for diffraction data collection under cryogenic conditions. The data is indexed, integrated, merged and scaled using standard X-ray crystallography software to determine structures at atomic resolution. In this review we provide an overview of the MicroED method and compare it with other CryoEM methods...
October 1, 2016: Current Opinion in Structural Biology
Eva Nogales, Robert K Louder, Yuan He
Single particle cryo-Electron Microscopy (cryo-EM) is a technique that allows the structural characterization of macromolecules without the need for crystallization. For certain type of samples that are ideally suited for cryo-EM studies it has been possible to reach high-resolution structures following relatively standard procedures. Other biological systems remain highly challenging, even for cryo-EM. Challenges may involve the scarcity of the sample, poor stability of the complexes, and most often, the intrinsic flexibility of biological molecules...
September 30, 2016: Current Opinion in Structural Biology
Gillian E Norris, Mark L Patchett
First reported in 2011, glycocins (glycosylated bacteriocins) are bacterial toxins that constitute a subset of ribosomally synthesised and post-translationally modified peptide (RiPP) natural products. Three NMR structures (glycocin F, ASM1 and sublancin 168), two with helix-loop-helix Cs α/α folds, are deposited in the PDB. Each structure contains a monosaccharide β-S-linked to a cysteine side chain. Three more glycocins (thurandacin, and enterocins F4-9 and 96) have been biochemically characterised, and others predicted on the basis of bioinformatic analyses...
September 21, 2016: Current Opinion in Structural Biology
Jeffrey T Mindrebo, Charisse M Nartey, Yoshiya Seto, Michael D Burkart, Joseph P Noel
The alpha/beta hydrolase (ABH) superfamily is a widespread and functionally malleable protein fold recognized for its diverse biochemical activities across all three domains of life. ABH enzymes possess unexpected catalytic activity in the green plant lineage through selective alterations in active site architecture and chemistry. Furthermore, the ABH fold serves as the core structure for phytohormone and ligand receptors in the gibberellin, strigolactone, and karrikin signaling pathways in plants. Despite recent discoveries, the ABH family is sparsely characterized in plants, a sessile kingdom known to evolve complex and specialized chemical adaptations as survival responses to widely varying biotic and abiotic ecologies...
September 20, 2016: Current Opinion in Structural Biology
Vasudha Aggarwal, Taekjip Ha
Macromolecular complexes consisting of proteins, lipids, and/or nucleic acids are ubiquitous in biological processes. Their composition, stoichiometry, order of assembly, and conformations can be heterogeneous or can change dynamically, making single-molecule studies best suited to measure these properties accurately. Recent single-molecule pull-down and other related approaches have combined the principles of conventional co-immunoprecipitation assay with single-molecule fluorescence microscopy to probe native macromolecular complexes...
September 20, 2016: Current Opinion in Structural Biology
David W Christianson, Nigel S Scrutton
No abstract text is available yet for this article.
September 16, 2016: Current Opinion in Structural Biology
Tsung-Jen Liao, Chung-Jung Tsai, Hyunbum Jang, David Fushman, Ruth Nussinov
Is RASSF5 a tumor suppressor or activator? RASSF5 links K-Ras and the Hippo pathway. Hippo's signaling promotes YAP1 phosphorylation and degradation. YAP1 overexpression promotes cancer. Most reports point to RASSF5 suppressing cancer; however, some point to its promoting cancer. Our mechanistic view explains how RASSF5 can activate MST1/2 and suppress cancer in vivo; but inhibits MST1/2 in vitro. We propose that both activation and inhibition of MST1/2 can take place via SARAH heterodimerization. Our thesis in vivo, membrane-anchored Ras dimers (or nanoclusters) can promote SARAH domain heterodimerization, Raf-like MST1/2 kinase domain homodimerization and trans-autophosphorylation...
September 16, 2016: Current Opinion in Structural Biology
Austin Wt Chiang, Shangzhong Li, Philipp N Spahn, Anne Richelle, Chih-Chung Kuo, Mojtaba Samoudi, Nathan E Lewis
Diverse glycans on proteins impact cell and organism physiology, along with drug activity. Since many protein-based biotherapeutics are glycosylated and these glycans have biological activity, there is a desire to engineer glycosylation for recombinant protein-based biotherapeutics. Engineered glycosylation can impact the recombinant protein efficacy and also influence many cell pathways by first changing glycan-protein interactions and consequently modulating disease physiologies. However, its complexity is enormous...
September 14, 2016: Current Opinion in Structural Biology
Andrew G McDonald, Jerrard M Hayes, Gavin P Davey
Glycosylation is a common post-translational protein modification, in which glycans are built onto proteins through the sequential addition of monosaccharide units, in reactions catalysed by glycosyltransferases. Glycosylation influences the physicochemical and biological properties of proteins, with subsequent effects on subcellular and extracellular protein trafficking, cell-cell recognition, and ligand-receptor interactions. Glycan structures can be complex, as is the regulation of their biosynthesis, and it is only recently that the systems biology of metabolic flux control and glycosyltransferase networks has become a study in its own right...
September 9, 2016: Current Opinion in Structural Biology
James H Hurley, Eva Nogales
Autophagy is the process whereby cytosol, organelles, and inclusions are taken up in a double-membrane vesicle known as the autophagosome, and transported to the lysosome for destruction and recycling. Electron microscopy (EM) led to the discovery of autophagy in the 1950s and has been a central part of its characterization ever since. New capabilities in single particle EM studies of the autophagy machinery are beginning to provide exciting insights into the mechanisms of autophagosome initiation, growth, and substrate targeting...
September 7, 2016: Current Opinion in Structural Biology
Brian Tenner, Sohum Mehta, Jin Zhang
Protein complexes play a major role in transducing information from outside the cell into instructions for growth and survival, and understanding how these complexes relay and shape intracellular signals has been a central question in signaling biology. Fluorescent proteins have proven paramount in opening windows for researchers to peer into the architecture and inner workings of signaling assemblies within the living cell and in real-time. In this review, we will provide readers with a current perspective on the development and use of genetically encoded optical probes to dissect the function of signaling complexes...
September 6, 2016: Current Opinion in Structural Biology
Ora Schueler-Furman, Shoshana J Wodak
Allosteric regulation plays a key role in many biological processes, such as signal transduction, transcriptional regulation, and many more. It is rooted in fundamental thermodynamic and dynamic properties of macromolecular systems that are still poorly understood and are moreover modulated by the cellular context. Here we review the computational approaches used in the investigation of allosteric processes in protein systems. We outline how the models of allostery have evolved from their initial formulation in the sixties to the current views, which more fully account for the roles of the thermodynamic and dynamic properties of the system...
September 5, 2016: Current Opinion in Structural Biology
Michael A Nash, Steven P Smith, Carlos Mga Fontes, Edward A Bayer
Cohesins and dockerins are complementary interacting protein modules that form stable and highly specific receptor-ligand complexes. They play a crucial role in the assembly of cellulose-degrading multi-enzyme complexes called cellulosomes and have potential applicability in several technology areas, including biomass conversion processes. Here, we describe several exceptional properties of cohesin-dockerin complexes, including their tenacious biochemical affinity, remarkably high mechanostability and a dual-binding mode of recognition that is contrary to the conventional lock-and-key model of receptor-ligand interactions...
August 27, 2016: Current Opinion in Structural Biology
Sriram Subramaniam, Lesley A Earl, Veronica Falconieri, Jacqueline Ls Milne, Edward H Egelman
The prospect that the structures of protein assemblies, small and large, can be determined using cryo-electron microscopy (cryo-EM) is beginning to transform the landscape of structural biology and cell biology. Great progress is being made in determining 3D structures of biological assemblies ranging from icosahedral viruses and helical arrays to small membrane proteins and protein complexes. Here, we review recent advances in this field, focusing especially on the emerging use of cryo-EM in mapping the binding of drugs and inhibitors to protein targets, an application that requires structure determination at the highest possible resolutions...
August 20, 2016: Current Opinion in Structural Biology
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