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 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.

The synthesis, structure, and electrochemical properties of Fe(C≡CC≡N)(dppe)Cp and related compounds

2006 ◽  
Vol 84 (2) ◽  
pp. 154-163 ◽  
Author(s):  
Mark E Smith ◽  
Richard L Cordiner ◽  
David Albesa-Jové ◽  
Dmitri S Yufit ◽  
František Hartl ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Charge Transfer ◽  
Electrochemical Properties ◽  
Key Words ◽  
Ground State ◽  
Structural Data ◽  
Sequential Reaction ◽  
Heterobimetallic Complexes ◽  
Related Compounds ◽  
Degree Of Charge Transfer

The cyanoacetylide complex Fe(C≡CC≡N)(dppe)Cp (3) is readily obtained from sequential reaction of Fe(C≡CSiMe3)(dppe)Cp with methyllithium and phenyl cyanate. Complex 3 is a good metalloligand, and coordination to the metal fragments [RhCl(CO)2], [Ru(PPh3)2Cp]+, and [Ru(dppe)Cp*]+ affords the corresponding cyanoaceylide-bridged heterobimetallic complexes. In the case of the 36-electron complexes [Cp(dppe)Fe-C≡CC≡N-MLn]n+, spectroscopic and structural data are consistent with a degree of charge transfer from the iron centre to the rhodium or ruthenium centre via the C3N bridge, giving rise to a polarized ground state. Electrochemical and spectroelectrochemical methods reveal significant interactions between the metal centres in the oxidized (35 electron) derivatives, [Cp(dppe)Fe-C≡CC≡N-MLn](n+1)+. Key words: cyanide, cyanoacetylide, crystal structure.

scholarly journals Redetermined crystal structure of α-DL-methionine at 340 K

2014 ◽  
Vol 70 (11) ◽  
pp. 337-340 ◽  
Author(s):  
Carl Henrik Görbitz ◽  
Lianglin Qi ◽  
Ngan Thi Kim Mai ◽  
Håvard Kristiansen
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Structural Data ◽  
Side Chain ◽  
Hydrogen Bonding Pattern ◽  
Α Phase ◽  
A Minor ◽  
First Time ◽  
Racemic Amino Acid ◽  
Related Amino Acid

Two forms, α and β, are known for the racemic amino acid DL-methionine, C5H11NO2S. The phase transition between them, taking place around 326 K, is associated with sliding at the central interfaces of the hydrophobic regions in the crystal, leaving the hydrogen-bonding pattern unperturbed. For the high-temperature α phase, only a structure of rather low quality has been available [Rfactor = 0.118, no H-atom coordinates; Taniguchiet al.(1980).Bull. Chem. Soc. Jpn,53, 803–804]. We here present accurate structural data for this polymorph [R(F) = 0.049], which are compared with other related amino acid structures with similar properties. We report for the first time that the side chain of this phase has a minor disorder component [occupancy 0.0491 (18)] with agauche+ rather than agauche− conformation for the N—C—C—C group. In the crystal of the title compound, N—H...O hydrogen bonds link the molecules into (100) sheets.

POLARON IN A QUANTUM DOT UNDER AN ELECTRIC FIELD

2007 ◽  
Vol 21 (24) ◽  
pp. 1635-1642
Author(s):  
MIAN LIU ◽  
WENDONG MA ◽  
ZIJUN LI
Keyword(s):  
Quantum Dot ◽  
Electric Field ◽  
Field Intensity ◽  
Ground State Energy ◽  
Ground State ◽  
Electric Field Intensity ◽  
State Energy ◽  
Theoretical Study ◽  
The Moment ◽  
Transformation Methods

We conducted a theoretical study on the properties of a polaron with electron-LO phonon strong-coupling in a cylindrical quantum dot under an electric field using linear combination operator and unitary transformation methods. The changing relations between the ground state energy of the polaron in the quantum dot and the electric field intensity, restricted intensity, and cylindrical height were derived. The numerical results show that the polar of the quantum dot is enlarged with increasing restricted intensity and decreasing cylindrical height, and with cylindrical height at 0 ~ 5 nm , the polar of the quantum dot is strongest. The ground state energy decreases with increasing electric field intensity, and at the moment of just adding electric field, quantum polarization is strongest.

Rational design and crystal structure prediction of ring-fused double-PDI compounds as n-channel organic semiconductors: a DFT study

2021 ◽  
Author(s):  
Suryakanti Debata ◽  
Smruti R. Sahoo ◽  
Rudranarayan Khatua ◽  
Sridhar Sahu
Keyword(s):  
Crystal Structure ◽  
Charge Transport ◽  
Organic Semiconductors ◽  
Structure Prediction ◽  
Rational Design ◽  
Molecular Design ◽  
Design Strategy ◽  
Dft Study ◽  
Crystal Structure Prediction ◽  
Model Compounds

In this study, we present an effective molecular design strategy to develop the n-type charge transport characteristics in organic semiconductors, using ring-fused double perylene diimides (DPDIs) as the model compounds.

scholarly journals Next Step in Gene Delivery: Modern Approaches and Further Perspectives of AAV Tropism Modification

Pharmaceutics ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 750
Author(s):  
Maxim A. Korneyenkov ◽  
Andrey A. Zamyatnin
Keyword(s):  
Gene Therapy ◽  
Genome Organization ◽  
Rational Design ◽  
Structural Data ◽  
Rational Approach ◽  
Tissue Tropism ◽  
Adeno Associated Virus ◽  
Chemical Conjugation ◽  
The Usa ◽  
Therapy Delivery

Today, adeno-associated virus (AAV) is an extremely popular choice for gene therapy delivery. The safety profile and simplicity of the genome organization are the decisive advantages which allow us to claim that AAV is currently among the most promising vectors. Several drugs based on AAV have been approved in the USA and Europe, but AAV serotypes’ unspecific tissue tropism is still a serious limitation. In recent decades, several techniques have been developed to overcome this barrier, such as the rational design, directed evolution and chemical conjugation of targeting molecules with a capsid. Today, all of the abovementioned approaches confer the possibility to produce AAV capsids with tailored tropism, but recent data indicate that a better understanding of AAV biology and the growth of structural data may theoretically constitute a rational approach to most effectively produce highly selective and targeted AAV capsids. However, while we are still far from this goal, other approaches are still in play, despite their drawbacks and limitations.

scholarly journals Crystal structure of Pistol, a class of self-cleaving ribozyme

2017 ◽  
Vol 114 (5) ◽  
pp. 1021-1026 ◽  
Author(s):  
Laura A. Nguyen ◽  
Jimin Wang ◽  
Thomas A. Steitz
Keyword(s):  
Crystal Structure ◽  
Rna Structure ◽  
Tertiary Structure ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Nonbridging Oxygen ◽  
Close Proximity ◽  
Domains Of Life ◽  
Guanine Base ◽  
A Minor

Small self-cleaving ribozymes have been discovered in all evolutionary domains of life. They can catalyze site-specific RNA cleavage, and as a result, they have relevance in gene regulation. Comparative genomic analysis has led to the discovery of a new class of small self-cleaving ribozymes named Pistol. We report the crystal structure of Pistol at 2.97-Å resolution. Our results suggest that the Pistol ribozyme self-cleavage mechanism likely uses a guanine base in the active site pocket to carry out the phosphoester transfer reaction. The guanine G40 is in close proximity to serve as the general base for activating the nucleophile by deprotonating the 2′-hydroxyl to initiate the reaction (phosphoester transfer). Furthermore, G40 can also establish hydrogen bonding interactions with the nonbridging oxygen of the scissile phosphate. The proximity of G32 to the O5′ leaving group suggests that G32 may putatively serve as the general acid. The RNA structure of Pistol also contains A-minor interactions, which seem to be important to maintain its tertiary structure and compact fold. Our findings expand the repertoire of ribozyme structures and highlight the conserved evolutionary mechanism used by ribozymes for catalysis.

Crystal structure of the wild-type and D30A mutant thioredoxin h of Chlamydomonas reinhardtii and implications for the catalytic mechanism

2001 ◽  
Vol 359 (1) ◽  
pp. 65-75 ◽  
Author(s):  
Valeria MENCHISE ◽  
Catherine CORBIER ◽  
Claude DIDIERJEAN ◽  
Michele SAVIANO ◽  
Ettore BENEDETTI ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Proton Transfer ◽  
Chlamydomonas Reinhardtii ◽  
Catalytic Mechanism ◽  
Structural Data ◽  
Careful Analysis ◽  
Wild Type ◽  
Thioredoxin H ◽  
Dynamics Simulations

Thioredoxins are ubiquitous proteins which catalyse the reduction of disulphide bridges on target proteins. The catalytic mechanism proceeds via a mixed disulphide intermediate whose breakdown should be enhanced by the involvement of a conserved buried residue, Asp-30, as a base catalyst towards residue Cys-39. We report here the crystal structure of wild-type and D30A mutant thioredoxin h from Chlamydomonas reinhardtii, which constitutes the first crystal structure of a cytosolic thioredoxin isolated from a eukaryotic plant organism. The role of residue Asp-30 in catalysis has been revisited since the distance between the carboxylate OD1 of Asp-30 and the sulphur SG of Cys-39 is too great to support the hypothesis of direct proton transfer. A careful analysis of all available crystal structures reveals that the relative positioning of residues Asp-30 and Cys-39 as well as hydrophobic contacts in the vicinity of residue Asp-30 do not allow a conformational change sufficient to bring the two residues close enough for a direct proton transfer. This suggests that protonation/deprotonation of Cys-39 should be mediated by a water molecule. Molecular-dynamics simulations, carried out either in vacuo or in water, as well as proton-inventory experiments, support this hypothesis. The results are discussed with respect to biochemical and structural data.

Structural Studies on N-(2,4,6-Trimethylphenyl)-methyl/ chloro-acetamides, 2,4,6-(CH3)3C6H2NH-CO-CH3–yXy (X = CH3 or Cl and y = 0, 1, 2)

2006 ◽  
Vol 61 (10-11) ◽  
pp. 588-594 ◽  
Author(s):  
Basavalinganadoddy Thimme Gowda ◽  
Jozef Kožíšek ◽  
Hartmut Fuess
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structural Data ◽  
The Other ◽  
Side Chain ◽  
Structural Studies ◽  
Asymmetric Unit ◽  
Lattice Constants ◽  
Peptide Linkage ◽  
The Mean

TMPAThe effect of substitutions in the ring and in the side chain on the crystal structure of N- (2,4,6-trimethylphenyl)-methyl/chloro-acetamides of the configuration 2,4,6-(CH3)3C6H2NH-COCH3− yXy (X = CH3 or Cl and y = 0,1, 2) has been studied by determining the crystal structures of N-(2,4,6-trimethylphenyl)-acetamide, 2,4,6-(CH3)3C6H2NH-CO-CH3 (); N-(2,4,6- trimethylphenyl)-2-methylacetamide, 2,4,6-(CH3)3C6H2NH-CO-CH2-CH3 (TMPMA); N-(2,4,6- trimethylphenyl)-2,2-dimethylacetamide, 2,4,6-(CH3)3C6H2NH-CO-CH(CH3)2 (TMPDMA) and N-(2,4,6-trimethylphenyl)-2,2-dichloroacetamide, 2,4,6-(CH3)3C6H2NH-CO-CHCl2 (TMPDCA). The crystallographic system, space group, formula units and lattice constants in Å are: TMPA: monoclinic, Pn, Z = 2, a = 8.142(3), b = 8.469(3), c = 8.223(3), β = 113.61(2)◦; TMPMA: monoclinic, P21/n, Z = 8, a = 9.103(1), b = 15.812(2), c = 16.4787(19), α = 89.974(10)◦, β = 96.951(10)◦, γ =89.967(10)◦; TMPDMA: monoclinic, P21/c, Z = 4, a =4.757(1), b= 24.644(4), c =10.785(2), β = 99.647(17)◦; TMPDCA: triclinic, P¯1, Z = 2, a = 4.652(1), b = 11.006(1), c = 12.369(1), α = 82.521(7)◦, β = 83.09(1)◦, γ = 79.84(1)◦. The results are analyzed along with the structural data of N-phenylacetamide, C6H5NH-CO-CH3; N-(2,4,6-trimethylphenyl)-2-chloroacetamide, 2,4,6-(CH3)3C6H2NH-CO-CH2Cl; N-(2,4,6-trichlorophenyl)-acetamide, 2,4,6-Cl3C6H2NH-COCH3; N-(2,4,6-trichlorophenyl)-2-chloroacetamide, 2,4,6-Cl3C6H2NH-CO-CH2Cl; N-(2,4,6-trichlorophenyl)- 2,2-dichloroacetamide, 2,4,6-Cl3C6H2NH-CO-CHCl2 and N-(2,4,6-trichlorophenyl)- 2,2,2-trichloroacetamide, 2,4,6-Cl3C6H2NH-CO-CCl3. TMPA, TMPMA and TMPDCA have one molecule each in their asymmetric units, while TMPDMA has two molecules in its asymmetric unit. Changes in the mean ring distances are smaller on substitution as the effect has to be transmitted through the peptide linkage. The comparison of the other bond parameters reveal that there are significant changes in them on substitution.

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