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.

pH-Dependent Thermal Stability of Vibrio cholerae L-asparaginase

2019 ◽  
Vol 26 (10) ◽  
pp. 743-750 ◽  
Author(s):  
Remya Radha ◽  
Sathyanarayana N. Gummadi
Keyword(s):  
Vibrio Cholerae ◽  
Conformational Changes ◽  
Kinetic Studies ◽  
Structural Features ◽  
Structure Stability ◽  
Kcal Mole ◽  
Scanning Calorimetry ◽  
Wide Range ◽  
Ph Dependent ◽  
Ph Range

Background:pH is one of the decisive macromolecular properties of proteins that significantly affects enzyme structure, stability and reaction rate. Change in pH may protonate or deprotonate the side group of aminoacid residues in the protein, thereby resulting in changes in chemical and structural features. Hence studies on the kinetics of enzyme deactivation by pH are important for assessing the bio-functionality of industrial enzymes. L-asparaginase is one such important enzyme that has potent applications in cancer therapy and food industry.Objective:The objective of the study is to understand and analyze the influence of pH on deactivation and stability of Vibrio cholerae L-asparaginase.Methods:Kinetic studies were conducted to analyze the effect of pH on stability and deactivation of Vibrio cholerae L-asparaginase. Circular Dichroism (CD) and Differential Scanning Calorimetry (DSC) studies have been carried out to understand the pH-dependent conformational changes in the secondary structure of V. cholerae L-asparaginase.Results:The enzyme was found to be least stable at extreme acidic conditions (pH< 4.5) and exhibited a gradual increase in melting temperature from 40 to 81 °C within pH range of 4.0 to 7.0. Thermodynamic properties of protein were estimated and at pH 7.0 the protein exhibited ΔG37of 26.31 kcal mole-1, ΔH of 204.27 kcal mole-1 and ΔS of 574.06 cal mole-1 K-1.Conclusion:The stability and thermodynamic analysis revealed that V. cholerae L-asparaginase was highly stable over a wide range of pH, with the highest stability in the pH range of 5.0–7.0.

The crystal structure of kalsilite, KAlSiO4

1965 ◽  
Vol 35 (272) ◽  
pp. 588-595 ◽  
Author(s):  
A. J. Perrotta ◽  
J. V. Smith
Keyword(s):  
Crystal Structure ◽  
Oxygen Atom ◽  
Crystal Structures ◽  
Bond Angle ◽  
Three Dimensional ◽  
Full Matrix ◽  
Ideal Position ◽  
Wide Range ◽  
The Ideal

SummaryA full-matrix, three-dimensional refinement of kalsilite, KAlSi04 (hexagonal, a 5·16, c 8.69 Å, P6a), shows that the silicon and aluminium atoms are ordered. The respective tetrahedral distances of 1·61 and 1·74 Å agree with values of 1·61 and 1·75 Å taken to be typical of framework structures. As in nepheline, an oxygen atom is statistically distributed over three sites displaced 0·25 Å from the ideal position on a triad axis. This decreases the bond angle from 180° to 163° in conformity with observations on some other crystal structures. The potassiumoxygen distances of 2·77, 2·93, and 2·99 Å are consistent with the wide range normally found for this weakly bonded atom.

scholarly journals Crystal Structure of the N112A Mutant of the Light-Driven Sodium Pump KR2

Crystals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 496
Author(s):  
Nina Maliar ◽  
Kirill Kovalev ◽  
Christian Baeken ◽  
Taras Balandin ◽  
Roman Astashkin ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ground State ◽  
Rational Design ◽  
Sodium Pump ◽  
Ion Selectivity ◽  
Structural Data ◽  
Functional Variants ◽  
Model Protein ◽  
The Moment ◽  
A Minor

The light-driven sodium pump KR2, found in 2013 in the marine bacteria Krokinobacter eikastus, serves as a model protein for the studies of the sodium-pumping microbial rhodopsins (NaRs). KR2 possesses a unique NDQ (N112, D116, and Q123) set of the amino acid residues in the functionally relevant positions, named the NDQ motif. The N112 was shown to determine the Na+/H+ selectivity and pumping efficiency of the protein. Thus, N112A mutation converts KR2 into an outward proton pump. However, no structural data on the functional conversions of the light-driven sodium pumps are available at the moment. Here we present the crystal structure of the N112A mutant of KR2 in the ground state at the resolution of 2.4 Å. The structure revealed a minor deflection in the central part of the helix C and a double conformation of the L74 residue in the mutant. The organization of the retinal Schiff base and neighboring water molecules is preserved in the ground state of KR2-N112A. The presented data provide structural insights into the effects of the alterations of the characteristic NDQ motif of NaRs. Our findings also demonstrate that for the rational design of the KR2 variants with modified ion selectivity for optogenetic applications, the structures of the intermediate states of both the protein and its functional variants are required.

scholarly journals Crystal structures of two furazidin polymorphs revealed by a joint effort of crystal structure prediction and NMR crystallography

2020 ◽  
Vol 76 (3) ◽  
pp. 322-335 ◽  
Author(s):  
Marta K. Dudek ◽  
Piotr Paluch ◽  
Edyta Pindelska
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structure Determination ◽  
Structure Prediction ◽  
Structural Features ◽  
Crystal Structure Determination ◽  
Crystal Structure Prediction ◽  
Crystal Forms ◽  
Space Groups ◽  
Nmr Crystallography

This work presents the crystal structure determination of two elusive polymorphs of furazidin, an antibacterial agent, employing a combination of crystal structure prediction (CSP) calculations and an NMR crystallography approach. Two previously uncharacterized neat crystal forms, one of which has two symmetry-independent molecules (form I), whereas the other one is a Z′ = 1 polymorph (form II), crystallize in P21/c and P 1 space groups, respectively, and both are built by different conformers, displaying different intermolecular interactions. It is demonstrated that the usage of either CSP or NMR crystallography alone is insufficient to successfully elucidate the above-mentioned crystal structures, especially in the case of the Z′ = 2 polymorph. In addition, cases of serendipitous agreement in terms of 1H or 13C NMR data obtained for the CSP-generated crystal structures different from the ones observed in the laboratory (false-positive matches) are analyzed and described. While for the majority of analyzed crystal structures the obtained agreement with the NMR experiment is indicative of some structural features in common with the experimental structure, the mentioned serendipity observed in exceptional cases points to the necessity of caution when using an NMR crystallography approach in crystal structure determination.

Nobiletin: a citrus flavonoid displaying potent physiological activity

2016 ◽  
Vol 72 (2) ◽  
pp. 124-127 ◽  
Author(s):  
Shuji Noguchi ◽  
Haruka Atsumi ◽  
Yasunori Iwao ◽  
Toshiyuki Kan ◽  
Shigeru Itai
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Physiological Activity ◽  
Covalent Bond ◽  
Physiological Properties ◽  
Wide Range ◽  
Methoxy Groups ◽  
Citrus Peels ◽  
Anti Inflammatory ◽  
Chromene Ring

Nobiletin [systematic name: 2-(3,4-dimethoxyphenyl)-5,6,7,8-tetramethoxy-4H-chromen-4-one; C21H22O8] is a flavonoid found in citrus peels, and has been reported to show a wide range of physiological properties, including anti-inflammatory, anticancer and antidementia activities. We have solved the crystal structure of nobiletin, which revealed that the chromene and arene rings of its flavone moiety, as well as the two methoxy groups bound to its arene ring, were coplanar. In contrast, the C atoms of the four methoxy groups bound to the chromene ring are out of the plane, making the molecule conformationally chiral. A comparison of the crystal structures of nobiletin revealed that it could adopt a variety of different conformations through rotation of the covalent bond between the chromene and arene rings, and the orientations of methoxy groups bound to the chromene ring.

scholarly journals Structural Insights into Bak Activation and Oligomerisation

2014 ◽  
Vol 70 (a1) ◽  
pp. C1166-C1166
Author(s):  
Jason Brouwer ◽  
Adeline Robin ◽  
Geoff Thompson ◽  
Ahmad Wardak ◽  
Ruth Kluck ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Cell Death ◽  
Outer Membrane ◽  
Crystal Structures ◽  
Conformational Changes ◽  
Mitochondrial Outer Membrane ◽  
Related Protein ◽  
Mitochondrial Outer Membrane Permeabilisation ◽  
Structural Insights ◽  
Analogous Mechanism

Apoptotic stimuli activate and oligomerise the pro-apoptotic proteins Bak and Bax resulting in mitochondrial outer membrane permeabilisation and subsequent cell death. This activation can occur when certain BH3-only proteins directly interact with Bak and Bax. A recent crystal structure by Czabotar et al. (2013) revealed a novel conformational change for Bax upon activation by BH3-only peptides. Distinguishing characteristics of BH3-only proteins capable of directly activating Bax were also elucidated. Here we describe complementary studies on the related protein Bak. We identify specific BH3-only peptides capable of inducing Bak dimerisation and describe crystal structures that provide key insights into Bak activation and oligomerisation. These structures demonstrate that Bak undergoes similar conformational changes upon activation to those observed with Bax. Altogether our results confirm an analogous mechanism for activation and dimerization of Bak and Bax in response to BH3-only peptides.

scholarly journals The genome of a Bacteroidetes inhabitant of the human gut encodes a structurally distinct enoyl-acyl carrier protein reductase (FabI)

2020 ◽  
Vol 295 (22) ◽  
pp. 7635-7652
Author(s):  
Christopher D. Radka ◽  
Matthew W. Frank ◽  
Jiangwei Yao ◽  
Jayaraman Seetharaman ◽  
Darcie J. Miller ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Change ◽  
Conformational Changes ◽  
Active Site ◽  
Acyl Carrier Protein ◽  
Acid Synthesis ◽  
Binding Pocket ◽  
Structural Features ◽  
Antibacterial Drug ◽  
Carrier Protein

Enoyl-acyl carrier protein reductase (FabI) catalyzes a rate-controlling step in bacterial fatty-acid synthesis and is a target for antibacterial drug development. A phylogenetic analysis shows that FabIs fall into four divergent clades. Members of clades 1–3 have been structurally and biochemically characterized, but the fourth clade, found in members of phylum Bacteroidetes, is uncharacterized. Here, we identified the unique structure and conformational changes that distinguish clade 4 FabIs. Alistipes finegoldii is a prototypical Bacteroidetes inhabitant of the gut microbiome. We found that A. finegoldii FabI (AfFabI) displays cooperative kinetics and uses NADH as a cofactor, and its crystal structure at 1.72 Å resolution showed that it adopts a Rossmann fold as do other characterized FabIs. It also disclosed a carboxyl-terminal extension that forms a helix–helix interaction that links the protomers as a unique feature of AfFabI. An AfFabI·NADH crystal structure at 1.86 Å resolution revealed that this feature undergoes a large conformational change to participate in covering the NADH-binding pocket and establishing the water channels that connect the active site to the central water well. Progressive deletion of these interactions led to catalytically compromised proteins that fail to bind NADH. This unique conformational change imparted a distinct shape to the AfFabI active site that renders it refractory to a FabI drug that targets clade 1 and 3 pathogens. We conclude that the clade 4 FabI, found in the Bacteroidetes inhabitants of the gut, have several structural features and conformational transitions that distinguish them from other bacterial FabIs.

Octachalcogen Cations Te82+, Se82+, and Mixed (Te8-xSex)82+ Stabilized by Chlorometallates of Bi, Zr, and Hf: Synthesis and Crystal Structures of Se8[Bi4Cl14] and E8[MCl6] (E = Se, Te; M = Zr, Hf)

1999 ◽  
Vol 54 (10) ◽  
pp. 1253-1259 ◽  
Author(s):  
A. Baumann ◽  
J. Beck ◽  
T. Hilbert
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Two Dimensional ◽  
Metal Halides ◽  
Bond Lengths ◽  
Wide Range ◽  
Polymeric Anion

The title compounds were obtained by the reaction of elemental chalcogens E (E = Se, Te) with the respective tetrachlorides ECl4 and the Lewis acidic metal halides ZrCl4, HfCl4, and BiCl3. An alternative way, particularly for the preparation of mixed Se/Te-species, is the enlargement of smaller cationic rings in E4MCl6] (M = Zr, Hf) by adding the respective complementary chalcogen. All reactions were carried out in sealed, evacuated glass ampoules at temperatures between 120 °C and 220 °C, and yielded black crystals of Se8[Bi4Cl14], (Te5.0Se3.0)[HfCl6], (Te5.3 Se2.7)[ZrCl6], (Te6.5Se1.5)[ZrCl6] and Te8[HfCl6], which have been identified by crystal structure analyses. All five compounds contain eight-membered chalcogen rings in an endo-exo-conformation which are isostructural to the known octachalcogen dications E82+ (E = S, Se, Te). While in (Te5 .0Se3.0)[HfCl6], (Te5.3Se2 .7 )[ZrCl6], (Te6 .5Se1.5 )[ZrCl6] and Te8[HfCl6] the molecular polycations are surrounded by discrete, octahedral [MCl6]2- counterions, Se4[Bi4Cl14] contains a two-dimensional polymeric anion ([Bi4Cl14]2-)n built of a variety of vertex and edge-sharing BiClx-polyhedra (x = 6, 7). The Bi-Cl bond lengths are spread over a wide range between 250 and 350 pm.

scholarly journals Crystal structure of the cyan fluorescent protein Cerulean-S175G

2016 ◽  
Vol 72 (7) ◽  
pp. 516-522 ◽  
Author(s):  
Sang-wook Park ◽  
Sunghyun Kang ◽  
Tae-Sung Yoon
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Conformational Changes ◽  
Fluorescent Protein ◽  
Detailed Comparison ◽  
Cyan Fluorescent Protein ◽  
Double Mutation ◽  
Aequorea Victoria ◽  
Green Fluorescent ◽  
Enhanced Cyan Fluorescent Protein

Enhanced cyan fluorescent protein (ECFP) was derived fromAequorea victoriagreen fluorescent protein (avGFP), notably with S65T/Y66W mutations. Its chromophore consists of a tripeptide comprised of Thr65, Trp66 and Gly67 (TWG) residues, while that ofavGFP consists of a Ser65, Tyr66 and Gly67 (SYG) tripeptide. Cerulean and SCFP3A were derived from ECFP-S72A/H148D (a double mutation) with additional Y145A and S175G mutations, respectively, while Cerulean-S175G has both mutations (Y145A and S175G). The crystal structures of these ECFP variants at neutral pH were reported to adopt two distinct major conformations calledECFPandCerulean. In this study, Cerulean-S175G was revealed to adopt only theCeruleanconformation, while Cerulean has been reported to adopt both theECFPand theCeruleanconformations in its crystal structures. Sharing the same S175G mutation with SCFP3A, Cerulean-S175G showed a slightly increased quantum yield, like SCFP3A, but did not adopt theECFPconformation adopted by SCFP3A. Detailed comparison of Cerulean-S175G and other ECFP variants revealed that the notable conformational changes in ECFP variants can be understood mainly in terms of the interaction between the Trp66 residue of the chromophore and residues 145–148 of β-strand 7.

scholarly journals Crystallography365 and Crystals in the City: IYCr 2014 activities in Australia

2014 ◽  
Vol 70 (a1) ◽  
pp. C1308-C1308
Author(s):  
Helen Maynard-Casely ◽  
Neeraj Sharma
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Early Career ◽  
Public Display ◽  
Crystallographic Groups ◽  
The Public ◽  
South Wales ◽  
Wide Range ◽  
Australian Science ◽  
The City

Reflecting the strong heritage of crystallographic research in Australia, we wish to present two of the public outreach projects that are underway down-under to celebrate International year of crystallography 2014. A project that is already up and running is Crystallography365 - Blogging a crystal structure a day at http://crystallography365.wordpress.com/. Gathering a group of, principally students and early career researchers based in Australia, each day during 2014 a different crystal structure will be presented and described. The goals of the project is to present the wide range of uses crystal structures have to a broad spectrum of sciences, and to provide an outlet for this group of scientists to engage with International Year of Crystallography. The other (hopefully bigger) project is Crystals in the city will run 9th-30 August 2014 (coinciding with National Science Week in Australia). A partnership between ANSTO and University of New South Wales, it will bring a public display of 10-15 person-size crystal structure models exhibited in cities around Australia. The goal is that the crystal structures will `reflect' their surroundings and instil pride among the public in the crystallographic achievements of Australian science. Accompanying the exhibition will be website, where the public can find more about each of the structures and students can learn of studying opportunities. The project will also unite a host of supporters and sponsors; universities, museums and crystallographic groups.

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