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Structural biology

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


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Journal ArticleDOI
TL;DR: The description of protein folding mechanisms in terms of the structures of well defined, partially folded intermediates is a major objective in structural biology as mentioned in this paper, despite the fleeting existence of intermediates and the fact that their structures are unlikely to be uniquely defined.

92 citations

Journal ArticleDOI
TL;DR: A detailed mechanism of action for counterion stabilization of proteins and their complexes in the gas-phase is presented, which indicates that anions must bind with high affinity, but must dissociate readily from the protein in order to be an effective stabilizer.
Abstract: The combination of ion mobility separation with mass spectrometry is an emergent and powerful structural biology tool, capable of simultaneously assessing the structure, topology, dynamics and composition of large protein assemblies within complex mixtures. An integral part of the ion mobility-mass spectrometry measurement is the ionization of intact multiprotein complexes and their removal from bulk solvent. This process, during which a substantial portion of protein structure and organization is likely to be preserved, imposes a foreign environment on proteins that may cause structural rearrangements to occur. Thus, a general means must be identified to stabilize protein structures in the absence of bulk solvent. Our approach to this problem involves the protection of protein complex structure through the addition of salts in solution prior to desorption/ionization. Anionic components of the added salts bind to the complex either in solution or during the electrospray process, and those that remain bound in the gas phase tend to have high gas phase acidities. The resulting ‘shell’ of counter-ions is able to carry away excess energy from the protein complex ion upon activation and can result in significant structural stabilization of the gas-phase protein assembly overall. By using ion mobility-mass spectrometry, we observe both the dissociation and unfolding transitions for four tetrameric protein complexes bound to populations of twelve different anions using collisional activation. The data presented here quantifies, for the first time, the influence of a large range of counter-ions on gas-phase protein structure and allows us to rank and classify counter-ions as structure stabilizers in the absence of bulk solvent. Our measurements indicate that tartrate, citrate, chloride and nitrate anions are amongst the strongest stabilizers of gas-phase protein structure identified in this screen. The rank order determined by our data is substantially different when compared to the known Hofmeister salt series in solution. While this is an expected outcome of our work, due to the diminished influence of anion and protein solvation by water, our data correlates well to expected anion binding in solution and highlights the fact that both hydration layer and anion-protein binding effects are critical for Hofmeister-type stabilization in solution. Finally, we present a detailed mechanism of action for counter-ion stabilization of proteins and their complexes in the gas-phase, which indicates that anions must bind with high-affinity, but must dissociate readily from the protein in order to be an effective stabilizer. Anion-resolved data acquired for smaller protein systems allows us to classify anions into three categories based on their ability to stabilize protein and protein complex structure in the absence of bulk solvent.

92 citations

Journal ArticleDOI
12 Oct 2017-eLife
TL;DR: It is demonstrated that human glucocorticoid receptor tunes this signaling in vivo by producing translational isoforms differing only in the length of the disordered region, which modulates the degree of frustration.
Abstract: Proteins carry out most of the key tasks inside cells. To perform these roles, proteins must fold up to form complex three-dimensional structures. Researchers used to think that the useful parts of proteins all had set structures. However, we now know that ‘disordered’ proteins with variable structures are common and disordered parts of proteins can have vital roles. In a process called allosteric regulation, regulator molecules can increase or decrease the activity of a protein by binding to it. This binding was thought to work by changing the structure of the protein, but it was not clear how this works in disordered proteins. To investigate, Li et al. studied a disordered protein called glucocorticoid receptor, and found that disordered regions can have opposing effects on other regions of the protein. This creates a ‘tug-of-war’ that Li et al. term “energetic frustration”, whereby the activity of the protein results from the combination of the opposing interactions. Further investigation revealed that the glucorticoid receptor produces different versions of itself that have different degrees of energetic frustration, which alters how effectively the proteins perform their tasks. This means that the protein can regulate its own activity even in the absence of binding to regulator molecules. The concept of energetic frustration could enhance our understanding of the many different proteins that contain disordered regions. Eventually, this knowledge could be used to develop drugs that alter the activity of these proteins and so could form part of treatments for a wide range of conditions including autoimmune diseases (such as rheumatoid arthritis and lupus), cancers, and organ rejection for transplant patients. The results presented by Li et al. suggest where more research is needed to achieve this goal. For example, we need to understand more about the stability of disordered protein regions, and to identify which surfaces of the proteins interact with each other.

92 citations

Journal ArticleDOI
TL;DR: This review focuses on both the advances and diversity of protein production and purification methods that have allowed this growth in structural knowledge of membrane proteins through X-ray crystallography, nuclear magnetic resonance spectroscopy, and cryo-electron microscopy (cryo-EM).
Abstract: Membrane proteins are still heavily under-represented in the protein data bank (PDB), owing to multiple bottlenecks. The typical low abundance of membrane proteins in their natural hosts makes it necessary to overexpress these proteins either in heterologous systems or through in vitro translation/cell-free expression. Heterologous expression of proteins, in turn, leads to multiple obstacles, owing to the unpredictability of compatibility of the target protein for expression in a given host. The highly hydrophobic and (or) amphipathic nature of membrane proteins also leads to challenges in producing a homogeneous, stable, and pure sample for structural studies. Circumventing these hurdles has become possible through the introduction of novel protein production protocols; efficient protein isolation and sample preparation methods; and, improvement in hardware and software for structural characterization. Combined, these advances have made the past 10-15 years very exciting and eventful for the field of membrane protein structural biology, with an exponential growth in the number of solved membrane protein structures. In this review, we focus on both the advances and diversity of protein production and purification methods that have allowed this growth in structural knowledge of membrane proteins through X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM).

92 citations

Journal ArticleDOI
12 Mar 2019-eLife
TL;DR: Cryo-EM structures of human TPC2 (HsTPC2), a phosphatidylinositol 3,5-bisphosphate-activated, Na+ selective channel, in the ligand-bound and apo states provide insights into the mechanism of PI(3,5)P2-regulated gating of T PC2, which is distinct from that of TPC1.
Abstract: Mammalian two-pore channels (TPCs) regulate the physiological functions of the endolysosome. Here we present cryo-EM structures of human TPC2 (HsTPC2), a phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2)-activated, Na+ selective channel, in the ligand-bound and apo states. The apo structure captures the closed conformation, while the ligand-bound form features the channel in both open and closed conformations. Combined with functional analysis, these structures provide insights into the mechanism of PI(3,5)P2-regulated gating of TPC2, which is distinct from that of TPC1. Specifically, the endolysosome-specific PI(3,5)P2 binds at the first 6-TM and activates the channel - independently of the membrane potential - by inducing a structural change at the pore-lining inner helix (IS6), which forms a continuous helix in the open state but breaks into two segments at Gly317 in the closed state. Additionally, structural comparison to the voltage-dependent TPC1 structure allowed us to identify Ile551 as being responsible for the loss of voltage dependence in TPC2.

92 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
202335
202272
2021149
2020154
2019152
2018140