scholarly journals Structural model of F 1 –ATPase and the implications for rotary catalysis

2000 ◽  
Vol 355 (1396) ◽  
pp. 465-471 ◽  
Author(s):  
A. G. W. Leslie ◽  
J. E. Walker
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Structural Model ◽  
Change Mechanism ◽  
Γ Subunit ◽  
Catalytic Sites ◽  
Mechanism Of Catalysis ◽  
Rotary Catalysis ◽  
High Degree ◽  
Binding Change Mechanism

The crystal structure of bovine mitochondrial F 1 –ATPase is described. Several features of the structure are consistent with the binding change mechanism of catalysis, in which binding of substrates induces conformational changes that result in a high degree of cooperativity between the three catalytic sites. Furthermore, the structure also suggests that catalysis is accompanied by a physical rotation of the centrally placed γ–subunit relative to the approximately spherical α 3 β 3 sub–assembly.

scholarly journals How F o –ATPase generates rotary torque

2000 ◽  
Vol 355 (1396) ◽  
pp. 523-528 ◽  
Author(s):  
George Oster ◽  
Hongyun Wang ◽  
Michael Grabe
Keyword(s):  
Electron Transport ◽  
Electron Transport Chain ◽  
Change Mechanism ◽  
Transport Chain ◽  
Catalytic Sites ◽  
Binding Change Mechanism ◽  
The Imf

The F–ATPases synthesize ATP using a transmembrane ionmotive force (IMF) established by the electron transport chain. This transduction involves first converting the IMF to a rotary torque in the transmembrane F o portion. This torque is communicated from F o to the F 1 portion where the energy is used to release the newly synthesized ATP from the catalytic sites according to Boyer's binding change mechanism. Here we explain the principle by which an IMF generates this rotary torque in the F o ion engine.

Crystal Structure of Na+, K+-ATPase in the Na+-Bound State

Science ◽  
2013 ◽  
Vol 342 (6154) ◽  
pp. 123-127 ◽  
Author(s):  
Maria Nyblom ◽  
Hanne Poulsen ◽  
Pontus Gourdon ◽  
Linda Reinhard ◽  
Magnus Andersson ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Structural Information ◽  
Bound State ◽  
Electrical Excitability ◽  
Α Subunit ◽  
Γ Subunit ◽  
Extracellular Release ◽  
Unique Site ◽  
Electrophysiological Studies

The Na+, K+–adenosine triphosphatase (ATPase) maintains the electrochemical gradients of Na+ and K+ across the plasma membrane—a prerequisite for electrical excitability and secondary transport. Hitherto, structural information has been limited to K+-bound or ouabain-blocked forms. We present the crystal structure of a Na+-bound Na+, K+-ATPase as determined at 4.3 Å resolution. Compared with the K+-bound form, large conformational changes are observed in the α subunit whereas the β and γ subunit structures are maintained. The locations of the three Na+ sites are indicated with the unique site III at the recently suggested IIIb, as further supported by electrophysiological studies on leak currents. Extracellular release of the third Na+ from IIIb through IIIa, followed by exchange of Na+ for K+ at sites I and II, is suggested.

Improved resolution crystal structure of Acanthamoeba actophorin reveals structural plasticity not induced by microgravity

2021 ◽  
Vol 77 (12) ◽  
Author(s):  
Stephen Quirk ◽  
Raquel L. Lieberman
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Actin Filaments ◽  
Space Station ◽  
Acanthamoeba Castellanii ◽  
Test Case ◽  
Molecular Replacement ◽  
International Space ◽  
Microgravity Conditions ◽  
Turn Region

Actophorin, a protein that severs actin filaments isolated from the amoeba Acanthamoeba castellanii, was employed as a test case for crystallization under microgravity. Crystals of purified actophorin were grown under microgravity conditions aboard the International Space Station (ISS) utilizing an interactive crystallization setup between the ISS crew and ground-based experimenters. Crystals grew in conditions similar to those grown on earth. The structure was solved by molecular replacement at a resolution of 1.65 Å. Surprisingly, the structure reveals conformational changes in a remote β-turn region that were previously associated with actophorin phosphorylated at the terminal residue Ser1. Although crystallization under microgravity did not yield a higher resolution than crystals grown under typical laboratory conditions, the conformation of actophorin obtained from solving the structure suggests greater flexibility in the actophorin β-turn than previously appreciated and may be beneficial for the binding of actophorin to actin filaments.

scholarly journals The Core and Holoenzyme Forms of RNA Polymerase from Mycobacterium smegmatis

2018 ◽  
Vol 201 (4) ◽  
Author(s):  
Tomáš Kouba ◽  
Jiří Pospíšil ◽  
Jarmila Hnilicová ◽  
Hana Šanderová ◽  
Ivan Barvík ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Rna Polymerase ◽  
Conformational Changes ◽  
Mycobacterium Smegmatis ◽  
Drug Target ◽  
Conformational Dynamics ◽  
Three Dimensional ◽  
Cryo Electron Microscopy ◽  
Bacterial Rna ◽  
High Degree

ABSTRACT Bacterial RNA polymerase (RNAP) is essential for gene expression and as such is a valid drug target. Hence, it is imperative to know its structure and dynamics. Here, we present two as-yet-unreported forms of Mycobacterium smegmatis RNAP: core and holoenzyme containing σA but no other factors. Each form was detected by cryo-electron microscopy in two major conformations. Comparisons of these structures with known structures of other RNAPs reveal a high degree of conformational flexibility of the mycobacterial enzyme and confirm that region 1.1 of σA is directed into the primary channel of RNAP. Taken together, we describe the conformational changes of unrestrained mycobacterial RNAP. IMPORTANCE We describe here three-dimensional structures of core and holoenzyme forms of mycobacterial RNA polymerase (RNAP) solved by cryo-electron microscopy. These structures fill the thus-far-empty spots in the gallery of the pivotal forms of mycobacterial RNAP and illuminate the extent of conformational dynamics of this enzyme. The presented findings may facilitate future designs of antimycobacterial drugs targeting RNAP.

scholarly journals Periprotein lipidomes of Saccharomyces cerevisiae provide a flexible environment for conformational changes of membrane proteins

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Joury S van 't Klooster ◽  
Tan-Yun Cheng ◽  
Hendrik R Sikkema ◽  
Aike Jeucken ◽  
Branch Moody ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Membrane Proteins ◽  
Small Molecules ◽  
Conformational Changes ◽  
Direct Detection ◽  
Protein Complexes ◽  
Lateral Diffusion ◽  
Low Ph ◽  
Lipid Particles ◽  
High Degree

Yeast tolerates a low pH and high solvent concentrations. The permeability of the plasma membrane (PM) for small molecules is low and lateral diffusion of proteins is slow. These findings suggest a high degree of lipid order, which raises the question of how membrane proteins function in such an environment. The yeast PM is segregated into the Micro-Compartment-of-Can1 (MCC) and Pma1 (MCP), which have different lipid compositions. We extracted proteins from these microdomains via stoichiometric capture of lipids and proteins in styrene-maleic-acid-lipid-particles (SMALPs). We purified SMALP-lipid-protein complexes by chromatography and quantitatively analyzed periprotein lipids located within the diameter defined by one SMALP. Phospholipid and sterol concentrations are similar for MCC and MCP, but sphingolipids are enriched in MCP. Ergosterol is depleted from this periprotein lipidome, whereas phosphatidylserine is enriched relative to the bulk of the plasma membrane. Direct detection of PM lipids in the 'periprotein space' supports the conclusion that proteins function in the presence of a locally disordered lipid state.

scholarly journals Crystal structure of SARS-CoV-2 main protease in complex with a Chinese herb inhibitor shikonin

2020 ◽  
Author(s):  
Jian Li ◽  
Xuelan Zhou ◽  
Yan Zhang ◽  
Fanglin Zhong ◽  
Cheng Lin ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Drug Targets ◽  
Chinese Herb ◽  
Binding Modes ◽  
High Potency ◽  
Main Protease ◽  
Covalent Inhibitors ◽  
Catalytic Dyad ◽  
Important Drug

AbstractMain protease (Mpro, also known as 3CLpro) has a major role in the replication of coronavirus life cycle and is one of the most important drug targets for anticoronavirus agents. Here we report the crystal structure of main protease of SARS-CoV-2 bound to a previously identified Chinese herb inhibitor shikonin at 2.45 angstrom resolution. Although the structure revealed here shares similar overall structure with other published structures, there are several key differences which highlight potential features that could be exploited. The catalytic dyad His41-Cys145 undergoes dramatic conformational changes, and the structure reveals an unusual arrangement of oxyanion loop stabilized by the substrate. Binding to shikonin and binding of covalent inhibitors show different binding modes, suggesting a diversity in inhibitor binding. As we learn more about different binding modes and their structure-function relationships, it is probable that we can design more effective and specific drugs with high potency that can serve as effect SARS-CoV-2 anti-viral agents.

Crystal structure of the stromelysin catalytic domain at 2.0 Å resolution: inhibitor-induced conformational changes 1 1Edited by R. Huber

1999 ◽  
Vol 293 (3) ◽  
pp. 545-557 ◽  
Author(s):  
Longyin Chen ◽  
Timothy J Rydel ◽  
Fei Gu ◽  
C.Michelle Dunaway ◽  
Stanislaw Pikul ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Catalytic Domain

scholarly journals Preferred ion diffusion pathways and activation energies for Ag in the crystal structure of stephanite, Ag5SbS4

2009 ◽  
Vol 73 (1) ◽  
pp. 17-26 ◽  
Author(s):  
M. Leitl ◽  
A. Pfitzner ◽  
L. Bindi
Keyword(s):  
Crystal Structure ◽  
Electron Density ◽  
Structural Model ◽  
Careful Analysis ◽  
Type Locality ◽  
Two Dimensional ◽  
Ionic Conductors ◽  
Ion Diffusion ◽  
Unit Cell Parameters ◽  
Cell Parameters

The crystal structure of stephanite fromthe type locality, Freiberg District, Saxony, Germany, was refined in the space group Cmc21, up to a final R index of 0.0427. Unit-cell parameters are: a 7.8329(6) Å, b 12.458(1) Å, c 8.5272(7) Å, V 832.1(1) Å3; Z = 4. The previously reported structural model is confirmed, but a higher-precision refinement was achieved herein by the introduction of thirdorder non-harmonic Gram-Charlier tensors for one Ag atom. In the structure of stephanite, Sb forms isolated SbS3 pyramids, which typically occur in sulphosalts, and Ag occupies sites with coordination ranging fromtriangular to almost tetrahedral. Both the Sb–S and Ag–S bond distances closely match the values commonly observed in the structures of other Ag sulphosalts and sulphides.The use of non-harmonic parameters for Ag allowed a better description of the electron density related to Ag, which is usually difficult to refine in good ionic conductors. A careful analysis of the energy barriers between the Ag sites defines preferred ion-diffusion pathways within the crystal structure of stephanite. The diffusion of Ag ions occurs preferentially along the sites Ag1 and Ag2, giving rise to two-dimensional nets of Ag atoms in which the ion conduction probably takes place.

scholarly journals Binding of cardiotonic steroids to Na+,K+-ATPase in the E2P state

2020 ◽  
Vol 118 (1) ◽  
pp. e2020438118
Author(s):  
Ryuta Kanai ◽  
Flemming Cornelius ◽  
Haruo Ogawa ◽  
Kanna Motoyama ◽  
Bente Vilsen ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Conformational Changes ◽  
Ground State ◽  
Sodium Pump ◽  
Structural Features ◽  
Animal Cells ◽  
Inhibitory Potency ◽  
New Members ◽  
Wide Range

The sodium pump (Na+, K+-ATPase, NKA) is vital for animal cells, as it actively maintains Na+ and K+ electrochemical gradients across the cell membrane. It is a target of cardiotonic steroids (CTSs) such as ouabain and digoxin. As CTSs are almost unique strong inhibitors specific to NKA, a wide range of derivatives has been developed for potential therapeutic use. Several crystal structures have been published for NKA-CTS complexes, but they fail to explain the largely different inhibitory properties of the various CTSs. For instance, although CTSs are thought to inhibit ATPase activity by binding to NKA in the E2P state, we do not know if large conformational changes accompany binding, as no crystal structure is available for the E2P state free of CTS. Here, we describe crystal structures of the BeF3− complex of NKA representing the E2P ground state and then eight crystal structures of seven CTSs, including rostafuroxin and istaroxime, two new members under clinical trials, in complex with NKA in the E2P state. The conformations of NKA are virtually identical in all complexes with and without CTSs, showing that CTSs bind to a preformed cavity in NKA. By comparing the inhibitory potency of the CTSs measured under four different conditions, we elucidate how different structural features of the CTSs result in different inhibitory properties. The crystal structures also explain K+-antagonism and suggest a route to isoform specific CTSs.

scholarly journals Recognition of an α-helical hairpin in P22 large terminase by a synthetic antibody fragment

2020 ◽  
Vol 76 (9) ◽  
pp. 876-888
Author(s):  
Ravi K. Lokareddy ◽  
Ying-Hui Ko ◽  
Nathaniel Hong ◽  
Steven G. Doll ◽  
Marcin Paduch ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Recombinant Antibody ◽  
Antibody Fragment ◽  
Genome Packaging ◽  
Synthetic Antibody ◽  
High Affinity ◽  
N Terminus ◽  
Helical Hairpin ◽  
Accessible Surface

The genome-packaging motor of tailed bacteriophages and herpesviruses is a multisubunit protein complex formed by several copies of a large (TerL) and a small (TerS) terminase subunit. The motor assembles transiently at the portal protein vertex of an empty precursor capsid to power the energy-dependent packaging of viral DNA. Both the ATPase and nuclease activities associated with genome packaging reside in TerL. Structural studies of TerL from bacteriophage P22 have been hindered by the conformational flexibility of this enzyme and its susceptibility to proteolysis. Here, an unbiased, synthetic phage-display Fab library was screened and a panel of high-affinity Fabs against P22 TerL were identified. This led to the discovery of a recombinant antibody fragment, Fab4, that binds a 33-amino-acid α-helical hairpin at the N-terminus of TerL with an equilibrium dissociation constant K d of 71.5 nM. A 1.51 Å resolution crystal structure of Fab4 bound to the TerL epitope (TLE) together with a 1.15 Å resolution crystal structure of the unliganded Fab4, which is the highest resolution ever achieved for a Fab, elucidate the principles governing the recognition of this novel helical epitope. TLE adopts two different conformations in the asymmetric unit and buries as much as 1250 Å2 of solvent-accessible surface in Fab4. TLE recognition is primarily mediated by conformational changes in the third complementarity-determining region of the Fab4 heavy chain (CDR H3) that take place upon epitope binding. It is demonstrated that TLE can be introduced genetically at the N-terminus of a target protein, where it retains high-affinity binding to Fab4.

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