scholarly journals Immobilization of a Catalytically Active Rhodium Complex by Electrostatic Interactions of Multiply Charged Phosphine Ligands with a Soluble Polyelectrolyte and Recovery by Ultrafiltration

2001 ◽  
Vol 20 (26) ◽  
pp. 5504-5506 ◽  
Author(s):  
Ernst Schwab ◽  
Stefan Mecking
Keyword(s):  
Electrostatic Interactions ◽  
Phosphine Ligands ◽  
Rhodium Complex ◽  
Multiply Charged ◽  
Catalytically Active

scholarly journals Role of a ribosomal RNA phosphate oxygen during the EF-G–triggered GTP hydrolysis

2015 ◽  
Vol 112 (20) ◽  
pp. E2561-E2568 ◽  
Author(s):  
Miriam Koch ◽  
Sara Flür ◽  
Christoph Kreutz ◽  
Eric Ennifar ◽  
Ronald Micura ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Electrostatic Interactions ◽  
Elongation Factor ◽  
Direct Interaction ◽  
Phosphate Group ◽  
Gtp Hydrolysis ◽  
Elongation Cycle ◽  
Close Proximity ◽  
Catalytically Active ◽  
Gtpase Activation

Elongation factor-catalyzed GTP hydrolysis is a key reaction during the ribosomal elongation cycle. Recent crystal structures of G proteins, such as elongation factor G (EF-G) bound to the ribosome, as well as many biochemical studies, provide evidence that the direct interaction of translational GTPases (trGTPases) with the sarcin-ricin loop (SRL) of ribosomal RNA (rRNA) is pivotal for hydrolysis. However, the precise mechanism remains elusive and is intensively debated. Based on the close proximity of the phosphate oxygen of A2662 of the SRL to the supposedly catalytic histidine of EF-G (His87), we probed this interaction by an atomic mutagenesis approach. We individually replaced either of the two nonbridging phosphate oxygens at A2662 with a methyl group by the introduction of a methylphosphonate instead of the natural phosphate in fully functional, reconstituted bacterial ribosomes. Our major finding was that only one of the two resulting diastereomers, the SP methylphosphonate, was compatible with efficient GTPase activation on EF-G. The same trend was observed for a second trGTPase, namely EF4 (LepA). In addition, we provide evidence that the negative charge of the A2662 phosphate group must be retained for uncompromised activity in GTP hydrolysis. In summary, our data strongly corroborate that the nonbridging proSP phosphate oxygen at the A2662 of the SRL is critically involved in the activation of GTP hydrolysis. A mechanistic scenario is supported in which positioning of the catalytically active, protonated His87 through electrostatic interactions with the A2662 phosphate group and H-bond networks are key features of ribosome-triggered activation of trGTPases.

scholarly journals Activation and selectivity of OTUB-1 and OTUB-2 deubiquitinylases

2020 ◽  
Vol 295 (20) ◽  
pp. 6972-6982
Author(s):  
Dakshinamurthy Sivakumar ◽  
Vikash Kumar ◽  
Michael Naumann ◽  
Matthias Stein
Keyword(s):  
Active Site ◽  
Electrostatic Interactions ◽  
Active Form ◽  
Cysteine Proteases ◽  
Binding Pocket ◽  
Catalytic Triad ◽  
Catalytic Site ◽  
Dynamics Simulation ◽  
Active Site Residues ◽  
Catalytically Active

The ovarian tumor domain (OTU) deubiquitinylating cysteine proteases OTUB1 and OTUB2 (OTU ubiquitin aldehyde binding 1 and 2) are representative members of the OTU subfamily of deubiquitinylases. Deubiquitinylation critically regulates a multitude of important cellular processes, such as apoptosis, cell signaling, and growth. Moreover, elevated OTUB expression has been observed in various cancers, including glioma, endometrial cancer, ovarian cancer, and breast cancer. Here, using molecular dynamics simulation approaches, we found that both OTUB1 and OTUB2 display a catalytic triad characteristic of proteases but differ in their configuration and protonation states. The OTUB1 protein had a prearranged catalytic site, with strong electrostatic interactions between the active-site residues His265 and Asp267. In OTUB2, however, the arrangement of the catalytic triad was different. In the absence of ubiquitin, the neutral states of the catalytic-site residues in OTUB2 were more stable, resulting in larger distances between these residues. Only upon ubiquitin binding did the catalytic triad in OTUB2 rearrange and bring the active site into a catalytically feasible state. An analysis of water access channels revealed only a few diffusion trajectories for the catalytically active form of OTUB1, whereas in OTUB2 the catalytic site was solvent-accessible, and a larger number of water molecules reached and left the binding pocket. Interestingly, in OTUB2, the catalytic residues His224 and Asn226 formed a stable hydrogen bond. We propose that the observed differences in activation kinetics, protonation states, water channels, and active-site accessibility between OTUB1 and OTUB2 may be relevant for the selective design of OTU inhibitors.

scholarly journals Fullerene ion chemistry: a journey of discovery and achievement

2016 ◽  
Vol 374 (2076) ◽  
pp. 20150321 ◽  
Author(s):  
Diethard K. Böhme
Keyword(s):  
Electrostatic Interactions ◽  
Coulomb Repulsion ◽  
Reaction Rates ◽  
Chemistry Laboratory ◽  
Carbon Surface ◽  
Reaction Products ◽  
Ion Chemistry ◽  
Ion Formation ◽  
Multiply Charged ◽  
Buckminster Fullerene

An account is provided of the extraordinary features of buckminster fullerene cations and their chemistry that we discovered in our Ion Chemistry Laboratory at York University (Canada) during a ‘golden’ period of research in the early 1990s, just after C 60 powder became available. We identified new chemical ways of C 60 ionization and tracked novel chemistry of C 60 n + as a function of charge state ( n =1–3) with some 50 different reagent molecules. We found that multiple charges enhance reaction rates and diversify reaction products and mechanisms. Strong electrostatic interactions with reagent molecules were seen to reduce barriers to carbon surface bonding and charge-separation reactions, while intramolecular Coulomb repulsion appeared to localize charge on the surface or the substituent and so influence higher order chemistry, including ‘spindle’, ‘star’, ‘fuzzy ball’, ‘ball-and-chain’ and dimer ion formation. We introduced the notion of ‘apparent’ gas-phase acidity with measurements of proton-transfer reactions of multiply charged fullerene cations. We also explored the attachment of atomic metal cations to C 60 and their subsequent reactions. All these findings were applied to the possible chemistry of fullerene cations in the interstellar medium with a focus on multiply charged fullerene ion formation and the intervention of fullerene cations in fullerene derivatization and molecular synthesis, with a view to their possible future detection. This article is part of the themed issue ‘Fullerenes: past, present and future, celebrating the 30th anniversary of Buckminster Fullerene’.

scholarly journals Aldolase A Ins(1,4,5)P3-binding domains as determined by site-directed mutagenesis

1999 ◽  
Vol 341 (3) ◽  
pp. 805-812 ◽  
Author(s):  
Carl B. BARON ◽  
Dean R. TOLAN ◽  
Kyung H. CHOI ◽  
Ronald F. COBURN
Keyword(s):  
Catalytic Activity ◽  
Active Site ◽  
Electrostatic Interactions ◽  
Bond Cleavage ◽  
Site Directed Mutagenesis ◽  
Binding Domains ◽  
Carbon Carbon Bond ◽  
Catalytically Active ◽  
Aldolase Activity ◽  
Aldolase A

We substituted neutral amino acids for some positively charged residues (R42, K107, K146, R148 and K229) that line the active site of aldolase A in an effort to determine binding sites for inositol 1,4,5-trisphosphate. In addition, D33 (involved in carbon-carbon bond cleavage) was mutated. K229A and D33S aldolases showed almost no catalytic activity, but Ins(1,4,5)P3 binding was similar to that determined with the use of wild-type aldolase A. R42A, K107A, K146R and R148A had markedly decreased affinities for Ins(1,4,5)P3 binding, increased EC50 values for Fru(1,6)P2-evoked release of bound Ins(1,4,5)P3 and increased Ki values for Ins(1,4,5)P3-evoked inhibition of aldolase activity. K146Q (positive charge removal) had essentially no catalytic activity and could not bind Ins(1,4,5)P3. Computer-simulated docking of Ins(1,4,5)P3 in the aldolase A structure was consistent with electrostatic binding of Ins(1,4,5)P3 to K107, K146, R148, R42, R303 and backbone nitrogens, as has been reported for Fru(1,6)P2 binding. Results indicate that Ins(1,4,5)P3 binding occurs at the active site and is not dependent on having a catalytically active enzyme; they also suggest that there is competition between Ins(1,4,5)P3 and Fru(1,6)P2 for binding. Although Ins(1,4,5)P3 binding to aldolase involved electrostatic interactions, the aldolase A Ins(1,4,5)P3-binding domain did not show other similarities to pleckstrin homology domains or phosphotyrosine-binding domains known to bind Ins(1,4,5)P3 in other proteins.

Intra- and inter-ion-pair protonic-hydridic bonding in polyhydridobis(phosphine)rhenates

2001 ◽  
Vol 79 (5-6) ◽  
pp. 964-976 ◽  
Author(s):  
Kamaluddin Abdur-Rashid ◽  
Alan J Lough ◽  
Robert H Morris
Keyword(s):  
Self Assembly ◽  
Electrostatic Interactions ◽  
Ion Pairs ◽  
Low Frequency ◽  
Chain Structure ◽  
Ion Pair ◽  
Proton Donor ◽  
Phosphine Ligands ◽  
Zigzag Chain ◽  
One Dimensional

The hexahydridobis(phosphine)rhenate anions, [ReH6(PR3)2]- (PR3 = PCy3, P-i-Pr3, PPh3, PMe3) were generated by potassium hydride deprotonation of the neutral heptahydride conjugate acids (ReH7(PR3)2), isolated as their [K(18-crown-6)]+ and [K(1,10-diaza-18-crown-6)]+ salts, and characterized by NMR and IR spectroscopy and elemental analyses. Structures from single crystal X-ray diffraction were obtained for the [K(1,10-diaza-18-crown-6)]+salts and these indicate the presence of short protonic—hydridic bonds involving the hydrides of the anions and the proton donor NH moieties of the cations. The structure of [K(1,10-diaza-18-crown-6)][ReH6(P-i-Pr3)2] adopts a one-dimensional zigzag chain with alternating cations and anions connected and held together by inter-ion N-H···Hx-Re interactions (x = 1 or 2). Short distances between the NH protons of the cations and hydrides of the anion ranging from 1.6 to 1.9 Å are estimated for this complex. A different kind of chain structure is observed for [K(1,10-diaza-18-crown-6)][ReH6(PMe3)2] in which the combined effects of inter-ion protonic—hydridic bonding (N-H···Hx-Re) and inter-ion electrostatic interactions (ReH-x···K+···H-xRe), result in one-dimensional networks of alternating cations and anions, with the metals and hydrides occupying the interior and the organic moieties of the phosphine ligands and crown ether lining the exterior of cylindrical supramolecular assemblies. A combination of intra- and inter-ion protonic-hydridic and intra-ion-pair electrostatic interactions in [K(1,10-diaza-18-crown-6)][ReH6(PPh3)2] result in the formation of discrete two-dimensional {[K(1,10-diaza-18-crown-6)][ReH6(PPh3)2]}4 tetramers. The PCy3 salt is disordered but appears to consist of isolated 1:1 ion pairs containing strong intra-ion-pair NH···HRe bonding. The solid-state IR spectra of the [K(1,10-diaza-18-crown-6)]+ salts show low-frequency shifts for the NH bands relative to [K(1,10-diaza-18-crown-6)][BPh4], and perturbed Re-H bands relative to those in the [K(18-crown-6)]+ salts. The magnitude of ΔνNH is related to the basicity of the anion as indicated by the pKαTHF of the conjugate acid form (ReH7(PR3)2), which increases as PPh3 < < PMe3 < P-i-Pr3 < PCy3. Solution 1H NMR, NOE, and T1 relaxation measurements of [K(1,10-diaza-18-crown-6)][ReH6(PPh3)2] indicate that these interactions also persist in toluene solutions of this compound.Key words: rhenium, hydride, phosphine, hydrogen bonding, self-assembly.

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