scholarly journals Crystallization, structure and dynamics of the proton-translocating P-type ATPase

2000 ◽  
Vol 203 (1) ◽  
pp. 147-154
Author(s):  
G.A. Scarborough
Keyword(s):  
Conformational Changes ◽  
Crystal Packing ◽  
Membrane Surface ◽  
Transmembrane Helix ◽  
Carbon Films ◽  
Crystallographic Analysis ◽  
Two Dimensional ◽  
Structure And Dynamics ◽  
Sequence Of Events ◽  
Detergent Interactions

Large single three-dimensional crystals of the dodecylmaltoside complex of the Neurospora crassa plasma membrane H(+)-ATPase (H(+) P-ATPase) can be grown in polyethylene-glycol-containing solutions optimized for moderate supersaturation of both the protein surfaces and detergent micellar region. Large two-dimensional H(+) P-ATPase crystals also grow on the surface of such mixtures and on carbon films located at such surfaces. Electron crystallographic analysis of the two-dimensional crystals grown on carbon films has recently elucidated the structure of the H(+) P-ATPase at a resolution of 0.8 nm in the membrane plane. The two-dimensional crystals comprise two offset layers of ring-shaped ATPase hexamers with their exocytoplasmic surfaces face to face. Side-to-side interactions between the cytoplasmic regions of the hexamers in each layer can be seen, and an interaction between identical exocytoplasmic loops in opposing hexamer layers holds the two layers together. Detergent rings around the membrane-embedded region of the hexamers are clearly visible, and detergent-detergent interactions between the rings are also apparent. The crystal packing forces thus comprise both protein-protein and detergent-detergent interactions, supporting the validity of the original crystallization strategy. Ten transmembrane helices in each ATPase monomer are well-defined in the structure map. They are all relatively straight, closely packed, moderately tilted at various angles with respect to a plane normal to the membrane surface and average approximately 3.5 nm in length. The transmembrane helix region is connected in at least three places to the larger cytoplasmic region, which comprises several discrete domains separated by relatively wide, deep clefts. Previous work has shown that the H(+) P-ATPase undergoes substantial conformational changes during its catalytic cycle that are not changes in secondary structure. Importantly, the results of hydrogen/deuterium exchange experiments indicate that these conformational changes are probably rigid-body interdomain movements that lead to cleft closure. When interpreted within the framework of established principles of enzyme catalysis, this information on the structure and dynamics of the H(+) P-ATPase molecule provides the basis of a rational model for the sequence of events that occurs as the ATPase proceeds through its transport cycle. The forces that drive the sequence can also be clearly stipulated. However, an understanding of the molecular mechanism of ion transport catalyzed by the H(+) P-ATPase awaits an atomic resolution structure.

Structural basis for amino-acid recognition and transmembrane signalling by tandem Per–Arnt–Sim (tandem PAS) chemoreceptor sensory domains

2015 ◽  
Vol 71 (10) ◽  
pp. 2127-2136 ◽  
Author(s):  
Yu C. Liu ◽  
Mayra A. Machuca ◽  
Simone A. Beckham ◽  
Menachem J. Gunzburg ◽  
Anna Roujeinikova
Keyword(s):  
Amino Acid ◽  
Ligand Binding ◽  
Conformational Changes ◽  
Transmembrane Helix ◽  
Crystallographic Analysis ◽  
Structural Basis ◽  
Bacterial Populations ◽  
Piston Displacement ◽  
Downward Displacement

Chemotaxis, mediated by methyl-accepting chemotaxis protein (MCP) receptors, plays an important role in the ecology of bacterial populations. This paper presents the first crystallographic analysis of the structure and ligand-induced conformational changes of the periplasmic tandem Per-Arnt-Sim (PAS) sensing domain (PTPSD) of a characterized MCP chemoreceptor. Analysis of the complex of theCampylobacter jejuniTlp3 PTPSD with isoleucine (a chemoattractant) revealed that the PTPSD is a dimer in the crystal. The two ligand-binding sites are located in the membrane-distal PAS domains on the faces opposite to the dimer interface. Mutagenesis experiments show that the five strongly conserved residues that stabilize the main-chain moiety of isoleucine are essential for binding, suggesting that the mechanism by which this family of chemoreceptors recognizes amino acids is highly conserved. Although the fold and mode of ligand binding of the PTPSD are different from the aspartic acid receptor Tar, the structural analysis suggests that the PTPSDs of amino-acid chemoreceptors are also likely to signal by a piston displacement mechanism. The PTPSD fluctuates between piston (C-terminal helix) `up' and piston `down' states. Binding of an attractant to the distal PAS domain locks it in the closed form, weakening its association with the proximal domain and resulting in the transition of the latter into an open form, concomitant with a downward (towards the membrane) 4 Å piston displacement of the C-terminal helix.In vivo, this movement would generate a transmembrane signal by driving a downward displacement of the transmembrane helix 2 towards the cytoplasm.

Role of spectrin in membrane fusion and in shape change of human erythrocyte ghost

1978 ◽  
Vol 36 (2) ◽  
pp. 328-329
Author(s):  
Hideo Hayashi ◽  
Yoshikazu Hirai ◽  
John T. Penniston
Keyword(s):  
Conformational Changes ◽  
Human Erythrocyte ◽  
Shape Change ◽  
Membrane Surface ◽  
Slight Modification ◽  
Active Role ◽  
Main Role ◽  
Bank Blood ◽  
Human Erythrocyte Ghost

Spectrin is a membrane associated protein most of which properties have been tentatively elucidated. A main role of the protein has been assumed to give a supporting structure to inside of the membrane. As reported previously, however, the isolated spectrin molecule underwent self assemble to form such as fibrous, meshwork, dispersed or aggregated arrangements depending upon the buffer suspended and was suggested to play an active role in the membrane conformational changes. In this study, the role of spectrin and actin was examined in terms of the molecular arrangements on the erythrocyte membrane surface with correlation to the functional states of the ghosts.Human erythrocyte ghosts were prepared from either freshly drawn or stocked bank blood by the method of Dodge et al with a slight modification as described before. Anti-spectrin antibody was raised against rabbit by injection of purified spectrin and partially purified.

Simulation studies of the interactions between membrane proteins and detergents

2005 ◽  
Vol 33 (5) ◽  
pp. 910-912 ◽  
Author(s):  
P.J. Bond ◽  
J. Cuthbertson ◽  
M.S.P. Sansom
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Self Assembly ◽  
Kinetic Mechanism ◽  
Coarse Grained ◽  
Simulation Studies ◽  
High Resolution Data ◽  
Biologically Relevant ◽  
Structure And Dynamics ◽  
Detergent Interactions

Interactions between membrane proteins and detergents are important in biophysical and structural studies and are also biologically relevant in the context of folding and transport. Despite a paucity of high-resolution data on protein–detergent interactions, novel methods and increased computational power enable simulations to provide a means of understanding such interactions in detail. Simulations have been used to compare the effect of lipid or detergent on the structure and dynamics of membrane proteins. Moreover, some of the longest and most complex simulations to date have been used to observe the spontaneous formation of membrane protein–detergent micelles. Common mechanistic steps in the micelle self-assembly process were identified for both α-helical and β-barrel membrane proteins, and a simple kinetic mechanism was proposed. Recently, simplified (i.e. coarse-grained) models have been utilized to follow long timescale transitions in membrane protein–detergent assemblies.

scholarly journals A structural framework for unidirectional transport by a bacterial ABC exporter

2020 ◽  
Vol 117 (32) ◽  
pp. 19228-19236
Author(s):  
Chengcheng Fan ◽  
Jens T. Kaiser ◽  
Douglas C. Rees
Keyword(s):  
Conformational Changes ◽  
Iron Homeostasis ◽  
Atp Hydrolysis ◽  
Transmembrane Helix ◽  
Reverse Direction ◽  
Conformational States ◽  
X Ray Crystallography ◽  
Binding Domains ◽  
Structural Framework ◽  
Glutathione Derivatives

The ATP-binding cassette (ABC) transporter of mitochondria (Atm1) mediates iron homeostasis in eukaryotes, while the prokaryotic homolog fromNovosphingobium aromaticivorans(NaAtm1) can export glutathione derivatives and confer protection against heavy-metal toxicity. To establish the structural framework underlying theNaAtm1 transport mechanism, we determined eight structures by X-ray crystallography and single-particle cryo-electron microscopy in distinct conformational states, stabilized by individual disulfide crosslinks and nucleotides. AsNaAtm1 progresses through the transport cycle, conformational changes in transmembrane helix 6 (TM6) alter the glutathione-binding site and the associated substrate-binding cavity. Significantly, kinking of TM6 in the post-ATP hydrolysis state stabilized by MgADPVO4eliminates this cavity, precluding uptake of glutathione derivatives. The presence of this cavity during the transition from the inward-facing to outward-facing conformational states, and its absence in the reverse direction, thereby provide an elegant and conceptually simple mechanism for enforcing the export directionality of transport byNaAtm1. One of the disulfide crosslinkedNaAtm1 variants characterized in this work retains significant glutathione transport activity, suggesting that ATP hydrolysis and substrate transport by Atm1 may involve a limited set of conformational states with minimal separation of the nucleotide-binding domains in the inward-facing conformation.

scholarly journals Understanding the structure and dynamics of hydrogenases by ultrafast and two-dimensional infrared spectroscopy

2019 ◽  
Vol 10 (39) ◽  
pp. 8981-8989 ◽  
Author(s):  
Marius Horch ◽  
Janna Schoknecht ◽  
Solomon L. D. Wrathall ◽  
Gregory M. Greetham ◽  
Oliver Lenz ◽  
...  
Keyword(s):  
Infrared Spectroscopy ◽  
Two Dimensional ◽  
Proof Of Concept ◽  
Concept Study ◽  
Structure And Dynamics ◽  
Two Dimensional Infrared Spectroscopy

A proof-of-concept study on a catalytic [NiFe] intermediate reveals structural and dynamical details of hydrogenases by ultrafast and two-dimensional infrared spectroscopies.

Ethylammonium saccharinate

2006 ◽  
Vol 62 (5) ◽  
pp. o1800-o1801
Author(s):  
Zi-Liang Wang ◽  
Lin-Heng Wei ◽  
Ming-Xue Li ◽  
Jing-Ping Wang
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Crystal Packing ◽  
Two Dimensional ◽  
Asymmetric Unit ◽  
Framework Structure ◽  
Compound C

The asymmetric unit of the title compound, C2H8N+·C7H4NO3S−, contains a saccharinate anion and a protonated ethylamine cation. Intermolecular N—H...O hydrogen bonds link these ions into a two-dimensional framework structure. The crystal packing is further stabilized by weak intermolecular C—H...O hydrogen bonds

scholarly journals Synthesis and crystal structures of a bis(3-hydroxy-cyclohex-2-en-1-one) and two hexahydroquinoline derivatives

2020 ◽  
Vol 76 (2) ◽  
pp. 125-131
Author(s):  
Scott A. Steiger ◽  
Chun Li ◽  
Christina Gates ◽  
Nicholas R. Natale
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Crystal Packing ◽  
Structural Features ◽  
Boat Conformation ◽  
Two Dimensional ◽  
Aryl Group ◽  
Dimensional Network ◽  
A Chain ◽  
Intramolecular Hydrogen

The title compound I, 2,2′-[(2-nitrophenyl)methylene]bis(3-hydroxy-5,5-dimethylcyclohex-2-enone), C23H27NO6, features a 1,3-ketone–enol conformation which is stabilized by two intramolecular hydrogen bonds. The most prominent intermolecular interactions in compound I are C—H...O hydrogen bonds, which link molecules into a two-dimensional network parallel to the (001) plane and a chain perpendicular to (1\overline{1}1). Both title compounds II, ethyl 4-(4-hydroxy-3,5-dimethoxyphenyl)-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, C23H29NO6, and III, ethyl 4-(anthracen-9-yl)-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, C29H29NO3, share the same structural features, such as a shallow boat conformation of the dihydropyridine group and an orthogonal aryl group attached to the dihydropyridine. Intermolecular N—H...O bonding is present in the crystal packing of both compound II and III.

scholarly journals Kinetic analysis of ASIC1a delineates conformational signaling from proton-sensing domains to the channel gate

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Sabrina Vullo ◽  
Nicolas Ambrosio ◽  
Jan P Kucera ◽  
Olivier Bignucolo ◽  
Stephan Kellenberger
Keyword(s):  
Ion Channels ◽  
Kinetic Analysis ◽  
Conformational Changes ◽  
Transmembrane Helix ◽  
Activation Mechanism ◽  
Pain Sensation ◽  
Channel Activation ◽  
Channel Pore ◽  
Acid Sensing Ion Channels ◽  
Channel Gate

Acid-sensing ion channels (ASICs) are neuronal Na+ channels that are activated by a drop in pH. Their established physiological and pathological roles, involving fear behaviors, learning, pain sensation and neurodegeneration after stroke, make them promising targets for future drugs. Currently, the ASIC activation mechanism is not understood. Here we used voltage-clamp fluorometry (VCF) combined with fluorophore-quencher pairing to determine the kinetics and direction of movements. We show that conformational changes with the speed of channel activation occur close to the gate and in more distant extracellular sites, where they may be driven by local protonation events. Further, we provide evidence for fast conformational changes in a pathway linking protonation sites to the channel pore, in which an extracellular interdomain loop interacts via aromatic residue interactions with the upper end of a transmembrane helix and would thereby open the gate.

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