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1.
Annu Rev Biochem ; 92: 351-384, 2023 06 20.
Artículo en Inglés | MEDLINE | ID: mdl-37068769

RESUMEN

Thiolases are CoA-dependent enzymes that catalyze the thiolytic cleavage of 3-ketoacyl-CoA, as well as its reverse reaction, which is the thioester-dependent Claisen condensation reaction. Thiolases are dimers or tetramers (dimers of dimers). All thiolases have two reactive cysteines: (a) a nucleophilic cysteine, which forms a covalent intermediate, and (b) an acid/base cysteine. The best characterized thiolase is the Zoogloea ramigera thiolase, which is a bacterial biosynthetic thiolase belonging to the CT-thiolase subfamily. The thiolase active site is also characterized by two oxyanion holes, two active site waters, and four catalytic loops with characteristic amino acid sequence fingerprints. Three thiolase subfamilies can be identified, each characterized by a unique sequence fingerprint for one of their catalytic loops, which causes unique active site properties. Recent insights concerning the thiolase reaction mechanism, as obtained from recent structural studies, as well as from classical and recent enzymological studies, are addressed, and open questions are discussed.


Asunto(s)
Coenzima A , Cisteína , Coenzima A/química , Coenzima A/metabolismo , Cisteína/metabolismo , Modelos Moleculares , Acetil-CoA C-Acetiltransferasa/química , Acetil-CoA C-Acetiltransferasa/metabolismo , Dominio Catalítico
2.
J Biol Chem ; 300(7): 107475, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-38879008

RESUMEN

Photosystem II (PSII) is the water-plastoquinone photo-oxidoreductase central to oxygenic photosynthesis. PSII has been extensively studied for its ability to catalyze light-driven water oxidation at a Mn4CaO5 cluster called the oxygen-evolving complex (OEC). Despite these efforts, the complete reaction mechanism for water oxidation by PSII is still heavily debated. Previous mutagenesis studies have investigated the roles of conserved amino acids, but these studies have lacked a direct structural basis that would allow for a more meaningful interpretation. Here, we report a 2.14-Å resolution cryo-EM structure of a PSII complex containing the substitution Asp170Glu on the D1 subunit. This mutation directly perturbs a bridging carboxylate ligand of the OEC, which alters the spectroscopic properties of the OEC without fully abolishing water oxidation. The structure reveals that the mutation shifts the position of the OEC within the active site without markedly distorting the Mn4CaO5 cluster metal-metal geometry, instead shifting the OEC as a rigid body. This shift disturbs the hydrogen-bonding network of structured waters near the OEC, causing disorder in the conserved water channels. This mutation-induced disorder appears consistent with previous FTIR spectroscopic data. We further show using quantum mechanics/molecular mechanics methods that the mutation-induced structural changes can affect the magnetic properties of the OEC by altering the axes of the Jahn-Teller distortion of the Mn(III) ion coordinated to D1-170. These results offer new perspectives on the conserved water channels, the rigid body property of the OEC, and the role of D1-Asp170 in the enzymatic water oxidation mechanism.


Asunto(s)
Dominio Catalítico , Complejo de Proteína del Fotosistema II , Agua , Complejo de Proteína del Fotosistema II/metabolismo , Complejo de Proteína del Fotosistema II/química , Complejo de Proteína del Fotosistema II/genética , Agua/metabolismo , Agua/química , Oxidación-Reducción , Mutación , Microscopía por Crioelectrón , Manganeso/metabolismo , Manganeso/química
3.
Small ; : e2406962, 2024 Oct 06.
Artículo en Inglés | MEDLINE | ID: mdl-39370663

RESUMEN

Hexaazatrinaphthalene (HATN) has attracted a lot of attention in aqueous proton batteries (APBs). However, its redox potential as an anode is insufficiently negative. The introduction of electron-donating substituent groups, such as hydroxyl groups, is considered as a good approach to reduce the redox potential of HATN. Nevertheless, manufacturing hydroxyl-substituted HATN (HATN-OH) requires either expensive precursors or multi-step process, limiting their research. Herein, a straightforward strategy is proposed to synthesize HATN-OH based on the nucleophilic substitution reaction of halogenated HATN in a molten alkali. The redox potential of 1,2,7,8,13,14-hexahydroxy-5,6,11,12,17,18-hexaazatrinaphthalene (34-HATN-6OH) electrode may be lowered by 0.15 V in comparison to HATN, and exhibits a high specific capacity, low redox potential, remarkable rate capability, and outstanding long-term cycling performance. The electrochemical redox kinetics is significantly enhanced owing to the formation of rapid proton transport channels created by intermolecular hydrogen bond network. The assembled MnO2||34-HATN-6OH full battery delivers a high discharge voltage (1.16 V) and cycling stability (74% capacity retention after 5000 cycles). This study provides a general cost-effective molten alkali approach for the synthesis of hydroxyl-substituted conjugated small molecules from their halogenated counterparts and further enriches the regulation means of electro-chemical performances of organic electrodes for enabling high-capacity and high-voltage APBs.

4.
Angew Chem Int Ed Engl ; 63(34): e202405738, 2024 Aug 19.
Artículo en Inglés | MEDLINE | ID: mdl-38850230

RESUMEN

The anion exchange membrane water electrolysis is widely regarded as the next-generation technology for producing green hydrogen. The OH- conductivity of the anion exchange membrane plays a key role in the practical implementation of this device. Here, we present a series of Z-S-x membranes with dibenzothiophene groups. These membranes contain sulfur-enhanced hydrogen bond networks that link surrounding surface site hopping regions, forming continuous OH- conducting highways. Z-S-20 has a high through-plane OH- conductivity of 182±28 mS cm-1 and ultralong stability of 2650 h in KOH solution at 80 °C. Based on rational design, we achieved a high PGM-free alkaline water electrolysis performance of 7.12 A cm-2 at 2.0 V in a flow cell and demonstrated durability of 650 h at 2 A cm-2 at 40 °C with a cell voltage increase of 0.65 mV/h.

5.
Angew Chem Int Ed Engl ; 63(21): e202316991, 2024 May 21.
Artículo en Inglés | MEDLINE | ID: mdl-38520357

RESUMEN

Conventional strategies for highly efficient and selective CO2 photoreduction focus on the design of catalysts and cocatalysts. In this study, we discover that hydrogen bond network breakdown in reaction system can suppress H2 evolution, thereby improving CO2 photoreduction performance. Photosensitive poly(ionic liquid)s are designed as photocatalysts owing to their strong hydrogen bonding with solvents. The hydrogen bond strength is tuned by solvent composition, thereby effectively regulating H2 evolution (from 0 to 12.6 mmol g-1 h-1). No H2 is detected after hydrogen bond network breakdown with trichloromethane or tetrachloromethane as additives. CO production rate and selectivity increase to 35.4 mmol g-1 h-1 and 98.9 % with trichloromethane, compared with 0.6 mmol g-1 h-1 and 26.2 %, respectively, without trichloromethane. Raman spectroscopy and theoretical calculations confirm that trichloromethane broke the systemic hydrogen bond network and subsequently suppressed H2 evolution. This hydrogen bond network breakdown strategy may be extended to other catalytic reactions involving H2 evolution.

6.
Angew Chem Int Ed Engl ; 63(17): e202319462, 2024 Apr 22.
Artículo en Inglés | MEDLINE | ID: mdl-38286750

RESUMEN

Developing highly active oxygen evolution reaction (OER) catalysts in acidic conditions is a pressing demand for proton-exchange membrane water electrolysis. Manipulating proton character at the electrified interface, as the crux of all proton-coupled electrochemical reactions, is highly desirable but elusive. Herein we present a promising protocol, which reconstructs a connected hydrogen-bond network between the catalyst-electrolyte interface by coupling hydrophilic units to boost acidic OER activity. Modelling on N-doped-carbon-layer clothed Mn-doped-Co3O4 (Mn-Co3O4@CN), we unravel that the hydrogen-bond interaction between CN units and H2O molecule not only drags the free water to enrich the surface of Mn-Co3O4 but also serves as a channel to promote the dehydrogenation process. Meanwhile, the modulated local charge of the Co sites from CN units/Mn dopant lowers the OER barrier. Therefore, Mn-Co3O4@CN surpasses RuO2 at high current density (100 mA cm-2 @ ~538 mV).

7.
Angew Chem Int Ed Engl ; : e202415447, 2024 Oct 25.
Artículo en Inglés | MEDLINE | ID: mdl-39449645

RESUMEN

Understanding the role of adsorbed intermediates at the polarized catalyst-electrolyte interface on the structure of electrical double layer (EDL) is essential for developing highly efficient electrocatalysts. Here, we prepared a series of unconventional face-centered-cubic (fcc) phase Ru-based catalysts (i.e. fcc-Ru, fcc-RuCr, and fcc-RuCrW) by rational tuning the binding energetics of hydroxyl intermediate to engineer the electrochemical interface and boost the performance of alkaline hydrogen oxidation reaction (HOR). The introduction of oxyphilic metals Cr and W can regulate the orbital occupation of Ru, promote the adsorption of hydroxyl species, resulting in an anomalous behavior that HOR performance under alkaline media exceeds acidic media. Experimental results and theoretical calculations unravel that the modulated adsorption of hydroxyl species on the electrode surface are responsible for the reconstruction of interfacial water structure and dynamic evolution of free water molecules from nearest to the electrode surface to above the gap region in the EDL, thereby leading to significantly increased water connectivity and hydrogen bond network. Our work reveals a new understanding of the surface intermediates in controlling the dynamic process of interfacial water and hydrogen bonding network in HOR electrocatalysis, and will guide rational design of advanced electrocatalysts through electrochemical interfacial engineering.

8.
Photosynth Res ; 156(1): 101-112, 2023 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-36307598

RESUMEN

Protons participate in many reactions. In proteins, protons need paths to move in and out of buried active sites. The vectorial movement of protons coupled to electron transfer reactions establishes the transmembrane electrochemical gradient used for many reactions, including ATP synthesis. Protons move through hydrogen bonded chains of waters and hydroxy side chains via the Grotthuss mechanism and by proton binding and release from acidic and basic residues. MCCE analysis shows that proteins exist in a large number of protonation states. Knowledge of the equilibrium ensemble can provide a rational basis for setting protonation states in simulations that fix them, such as molecular dynamics (MD). The proton path into the QB site in the bacterial reaction centers (RCs) of Rb. sphaeroides is analyzed by MD to provide an example of the benefits of using protonation states found by the MCCE program. A tangled web of side chains and waters link the cytoplasm to QB. MCCE analysis of snapshots from multiple trajectories shows that changing the input protonation state of a residue in MD biases the trajectory shifting the proton affinity of that residue. However, the proton affinity of some residues is more sensitive to the input structure. The proton transfer networks derived from different trajectories are quite robust. There are some changes in connectivity that are largely restricted to the specific residues whose protonation state is changed. Trajectories with QB•- are compared with earlier results obtained with QB [Wei et. al Photosynthesis Research volume 152, pages153-165 (2022)] showing only modest changes. While introducing new methods the study highlights the difficulty of establishing the connections between protein conformation.


Asunto(s)
Proteínas del Complejo del Centro de Reacción Fotosintética , Rhodobacter sphaeroides , Protones , Proteínas del Complejo del Centro de Reacción Fotosintética/metabolismo , Concentración de Iones de Hidrógeno , Transporte de Electrón , Fotosíntesis , Rhodobacter sphaeroides/metabolismo
9.
Bioorg Chem ; 140: 106788, 2023 11.
Artículo en Inglés | MEDLINE | ID: mdl-37598433

RESUMEN

Vibegron is a novel, potent, highly selective ß3-adrenergic receptor agonist for the treatment of overactive bladder with higher therapeutic capacity and lower side effects. Methyl(2S,3R)-2-((tert-butoxycarbonyl)amino)-3-hydroxy-3-phenylpropanoate ((2S,3R)-aminohydroxy ester) is a key chiral intermediate for the synthesis of Vibegron. A novel carbonyl reductase from Exiguobacterium sp. s126 (EaSDR6) was isolated using data mining technology from GenBank database with preferable catalytic activity. Hydrogen bond network regulation was performed using site-directed saturation mutagenesis and combination mutagenesis. The mutant EaSDR6A138L/S193A was obtained with the activity improvement by 4.58 folds compared with the wild type EaSDR6. The Km of EaSDR6A138L/S193A was decreased from 1.57 mM to 0.67 mM, kcat was increased by 2.17 folds, and the overall catalytic efficiency kcat/Km was increased by 5.07 folds. The organic-aqueous biphasic bioreaction system for the asymmetric synthesis of (2S,3R)-aminohydroxy ester was constructed for the first time. Under the substrate concentration of 150 g/L, the yield of (2S,3R)-aminohydroxy ester was > 99.99%, the e.e. was > 99.99%, and the spatiotemporal yield was 1.55 g/(L·h·g DCW) after 12 h reaction. While the substrate concentration was increased to 200 g/L and the reaction lasted for 36 h, the yield of (2S,3R)-aminohydroxy ester was > 99.99%, the e.e. was > 99.99% and the spatiotemporal yield was 1.05 g/(L·h·g DCW). The substrate concentration and spatiotemporal yield were higher than ever reported.


Asunto(s)
Oxidorreductasas de Alcohol , Pirimidinonas , Enlace de Hidrógeno , Oxidorreductasas de Alcohol/genética , Ésteres
10.
Chem Pharm Bull (Tokyo) ; 71(4): 299-306, 2023 Apr 01.
Artículo en Inglés | MEDLINE | ID: mdl-36724968

RESUMEN

The fragment molecular orbital (FMO) method is a fast quantum-mechanics method that divides systems into pieces of fragments and performs ab initio calculations. The method has been expected to improve the accuracy of describing protein-ligand interactions by incorporating electronic effects. In this article, FMO calculation with solvation methods were applied to the affinity prediction at the ATP-binding site of PDHK4. As the ionized aspartic acid lies at the center and is involved in the complex hydrogen bond networks, this system has turned out to be a difficult target to describe by traditional molecular-mechanics method. In the FMO calculation with the polarizable continuum model (PCM) solvation method, a considerable amount of charge (-0.27e) was transferred from the ionized aspartate to the surrounding residues. We found that using FMO with the PCM solvation method was important to increase the correlation, and by incorporating the ligand deformation energy, the correlation was improved to R = 0.81 for whole twelve compounds and R = 0.91 without one outlier compound.


Asunto(s)
Oxidorreductasas , Teoría Cuántica , Enlace de Hidrógeno , Ligandos , Piruvatos
11.
Molecules ; 28(19)2023 Sep 27.
Artículo en Inglés | MEDLINE | ID: mdl-37836665

RESUMEN

The relationship between structure and reactivity plays a dominant role in water dissociation on the various TiO2 crystallines. To observe the adsorption and dissociation behavior of H2O, the reaction force field (ReaxFF) is used to investigate the dynamic behavior of H2O on rutile (110) and anatase (101) surfaces in an aqueous environment. Simulation results show that there is a direct proton transfer between the adsorbed H2O (H2Oad) and the bridging oxygen (Obr) on the rutile (110) surface. Compared with that on the rutile (110) surface, an indirect proton transfer occurs on the anatase (101) surface along the H-bond network from the second layer of water. This different mechanism of water dissociation is determined by the distance between the 5-fold coordinated Ti (Ti5c) and Obr of the rutile and anatase TiO2 surfaces, resulting in the direct or indirect proton transfer. Additionally, the hydrogen bond (H-bond) network plays a crucial role in the adsorption and dissociation of H2O on the TiO2 surface. To describe interfacial water structures between TiO2 and bulk water, the double-layer model is proposed. The first layer is the dissociated H2O on the rutile (110) and anatase (101) surfaces. The second layer forms an ordered water structure adsorbed to the surface Obr or terminal OH group through strong hydrogen bonding (H-bonding). Affected by the H-bond network, the H2O dissociation on the rutile (110) surface is inhibited but that on the anatase (101) surface is promoted.

12.
Angew Chem Int Ed Engl ; 62(40): e202310577, 2023 Oct 02.
Artículo en Inglés | MEDLINE | ID: mdl-37578644

RESUMEN

Aqueous rechargeable zinc-ion batteries (ARZBs) are impeded by the mutual problems of unstable cathode, electrolyte parasitic reactions, and dendritic growth of zinc (Zn) anode. Herein, a triple-functional strategy by introducing the tetramethylene sulfone (TMS) to form a hydrated eutectic electrolyte is reported to ameliorate these issues. The activity of H2 O is inhibited by reconstructing hydrogen bonds due to the strong interaction between TMS and H2 O. Meanwhile, the preferentially adsorbed TMS on the Zn surface increases the thickness of double electric layer (EDL) structure, which provides a shielding buffer layer to suppress dendrite growth. Interestingly, TMS modulates the primary solvation shell of Zn2+ ultimately to achieve a novel solvent co-intercalation ((Zn-TMS)2+ ) mechanism, and the intercalated TMS works as a "pillar" that provides more zincophilic sites and stabilizes the structure of cathode (NH4 V4 O10 , (NVO)). Consequently, the Zn||NVO battery exhibits a remarkably high specific capacity of 515.6 mAh g-1 at a low current density of 0.2 A g-1 for over 40 days. This multi-functional electrolytes and solvent co-intercalation mechanism will significantly propel the practical development of aqueous batteries.

13.
Angew Chem Int Ed Engl ; 62(38): e202309601, 2023 Sep 18.
Artículo en Inglés | MEDLINE | ID: mdl-37548132

RESUMEN

High-voltage aqueous rechargeable energy storage devices with safety and high specific energy are hopeful candidates for the future energy storage system. However, the electrochemical stability window of aqueous electrolytes is a great challenge. Herein, inspired by density functional theory (DFT), polyethylene glycol (PEG) can interact strongly with water molecules, effectively reconstructing the hydrogen bond network. In addition, N, N-dimethylformamide (DMF) can coordinate with Zn2+ , assisting in the rapid desolvation of Zn2+ and stable plating/stripping process. Remarkably, by introducing PEG400 and DMF as co-solvents into the electrolyte, a wide electrochemical window of 4.27 V can be achieved. The shift in spectra indicate the transformation in the number and strength of hydrogen bonds, verifying the reconstruction of hydrogen bond network, which can largely inhibit the activity of water molecule, according well with the molecular dynamics simulations (MD) and online electrochemical mass spectroscopy (OEMS). Based on this electrolyte, symmetric Zn cells survived up to 5000 h at 1 mA cm-2 , and high voltage aqueous zinc ion supercapacitors assembled with Zn anode and activated carbon cathode achieved 800 cycles at 0.1 A g-1 . This work provides a feasible approach for constructing high-voltage alkali metal ion supercapacitors through reconstruction strategy of hydrogen bond network.

14.
Angew Chem Int Ed Engl ; 62(27): e202304413, 2023 Jul 03.
Artículo en Inglés | MEDLINE | ID: mdl-37160619

RESUMEN

Designing highly efficient and stable electrode-electrolyte interface for hydrogen peroxide (H2 O2 ) electrosynthesis remains challenging. Inhibiting the competitive side reaction, 4 e- oxygen reduction to H2 O, is essential for highly selective H2 O2 electrosynthesis. Instead of hindering excessive hydrogenation of H2 O2 via catalyst modification, we discover that adding a hydrogen-bond acceptor, dimethyl sulfoxide (DMSO), to the KOH electrolyte enables simultaneous improvement of the selectivity and activity of H2 O2 electrosynthesis. Spectral characterization and molecular simulation confirm that the formation of hydrogen bonds between DMSO and water molecules at the electrode-electrolyte interface can reduce the activity of water dissociation into active H* species. The suitable H* supply environment hinders excessive hydrogenation of the oxygen reduction reaction (ORR), thus improving the selectivity of 2 e- ORR and achieving over 90 % selectivity of H2 O2 . This work highlights the importance of regulating the interfacial hydrogen-bond environment by organic molecules as a means of boosting electrochemical performance in aqueous electrosynthesis and beyond.

15.
Photosynth Res ; 152(2): 167-175, 2022 May.
Artículo en Inglés | MEDLINE | ID: mdl-35322325

RESUMEN

The oxygen-evolving complex (OEC) of photosystem II (PSII) cycles through redox intermediate states Si (i = 0-4) during the photochemical oxidation of water. The S2 state involves an equilibrium of two isomers including the low-spin S2 (LS-S2) state with its characteristic electron paramagnetic resonance (EPR) multiline signal centered at g = 2.0, and a high-spin S2 (HS-S2) state with its g = 4.1 EPR signal. The relative intensities of the two EPR signals change under experimental conditions that shift the HS-S2/LS-S2 state equilibrium. Here, we analyze the effect of glycerol on the relative stability of the LS-S2 and HS-S2 states when bound at the narrow channel of PSII, as reported in an X-ray crystal structure of cyanobacterial PSII. Our quantum mechanics/molecular mechanics (QM/MM) hybrid models of cyanobacterial PSII show that the glycerol molecule perturbs the hydrogen-bond network in the narrow channel, increasing the pKa of D1-Asp61 and stabilizing the LS-S2 state relative to the HS-S2 state. The reported results are consistent with the absence of the HS-S2 state EPR signal in native cyanobacterial PSII EPR spectra and suggest that the narrow water channel hydrogen-bond network regulates the relative stability of OEC catalytic intermediates during water oxidation.


Asunto(s)
Cianobacterias , Complejo de Proteína del Fotosistema II , Espectroscopía de Resonancia por Spin del Electrón , Glicerol , Hidrógeno , Oxidación-Reducción , Oxígeno , Agua
16.
Chemphyschem ; 23(21): e202200446, 2022 11 04.
Artículo en Inglés | MEDLINE | ID: mdl-35851985

RESUMEN

Recent studies have reported manifold industrial applications of aqueous choline chloride (ChCl) solution as an alternative to deep eutectic solvent. ChCl also serves as a protecting co-solvent for proteins by restricting urea to approach the protein surface and thereby maintaining the water structure around the protein. However, a detailed molecular-level picture of the ChCl and water, even in the absence of urea around a representative hydrophobe is largely lacking. This motivates us to probe the effect of varying wt % of ChCl on the occupancy and orientations of the constituents around a representative solute like methane using computer simulations. Accumulation of water molecules and preferential exclusion of ChCl from the surface of methane perturb the tetrahedral geometry of water around it. We find a tangential alignment of the polar part of the ChCl molecules that interact with water, whereas its hydrophobic part is preferentially facing the methane. With an increase in ChCl wt %, a disruption in the tetrahedrality is evident for water molecules accompanied by a reduction in hydrogen bonds between water pairs in the solution. In short, ChCl induces crowding and modifies the microscopic arrangement and hydrogen bonding structure of the water around the methane and beyond.


Asunto(s)
Colina , Agua , Agua/química , Colina/química , Metano/química , Simulación de Dinámica Molecular , Solventes/química , Urea/química
17.
Molecules ; 26(15)2021 Jul 31.
Artículo en Inglés | MEDLINE | ID: mdl-34361809

RESUMEN

The increase in conductivity with temperature in 1H-pyrazol-2-ium 2,6-dicarboxybenzoate monohydrate was analyzed, and the influence of the mobility of the water was discussed in this study. The electric properties of the salt were studied using the impedance spectroscopy method. WB97XD/6-311++G(d,p) calculations were performed, and the quantum theory of atoms in molecules (QTAiM) approach and the Hirshfeld surface method were applied to analyze the hydrogen bond interaction. It was found that temperature influences the spectroscopic properties of pyrazolium salt, particularly the carbonyl and hydroxyl frequencies. The influence of water molecules, connected by three-center hydrogen bonds with co-planar tetrameters, on the formation of structural defects is also discussed in this report.

18.
J Struct Biol ; 212(3): 107634, 2020 12 01.
Artículo en Inglés | MEDLINE | ID: mdl-33007367

RESUMEN

Protein and protein-water hydrogen bonds shape the conformational energy landscape of G Protein-Coupled Receptors, GPCRs. As numerous static structures of GPCRs have been solved, the important question arises whether GPCR structures and GPCR conformational dynamics could be described in terms of conserved hydrogen-bond networks, and alterations of these hydrogen-bond networks along the reaction coordinate of the GPCR. To enable efficient analyses of the hydrogen-bond networks of GPCRs we implemented graph-based algorithms, and applied these algorithms to static GPCR structures from structural biology, and from molecular dynamics simulations of two opioid receptors. We find that static GPCR structures tend to have a conserved, core hydrogen-bond network which, when protein and water dynamics are included with simulations, extends to comprise most of the interior of an inactive receptor. In an active receptor, the dynamic protein-water hydrogen-bond network spans the entire receptor, bridging all functional motifs. Such an extensive, dynamic hydrogen-bond network might contribute to the activation mechanism of the GPCR.


Asunto(s)
Receptores Acoplados a Proteínas G/química , Agua/química , Enlace de Hidrógeno , Unión Proteica/fisiología , Relación Estructura-Actividad
19.
Retrovirology ; 17(1): 13, 2020 05 19.
Artículo en Inglés | MEDLINE | ID: mdl-32430025

RESUMEN

BACKGROUND: HIV-1 can develop resistance to antiretroviral drugs, mainly through mutations within the target regions of the drugs. In HIV-1 protease, a majority of resistance-associated mutations that develop in response to therapy with protease inhibitors are found in the protease's active site that serves also as a binding pocket for the protease inhibitors, thus directly impacting the protease-inhibitor interactions. Some resistance-associated mutations, however, are found in more distant regions, and the exact mechanisms how these mutations affect protease-inhibitor interactions are unclear. Furthermore, some of these mutations, e.g. N88S and L76V, do not only induce resistance to the currently administered drugs, but contrarily induce sensitivity towards other drugs. In this study, mutations N88S and L76V, along with three other resistance-associated mutations, M46I, I50L, and I84V, are analysed by means of molecular dynamics simulations to investigate their role in complexes of the protease with different inhibitors and in different background sequence contexts. RESULTS: Using these simulations for alchemical calculations to estimate the effects of mutations M46I, I50L, I84V, N88S, and L76V on binding free energies shows they are in general in line with the mutations' effect on [Formula: see text] values. For the primary mutation L76V, however, the presence of a background mutation M46I in our analysis influences whether the unfavourable effect of L76V on inhibitor binding is sufficient to outweigh the accompanying reduction in catalytic activity of the protease. Finally, we show that L76V and N88S changes the hydrogen bond stability of these residues with residues D30/K45 and D30/T31/T74, respectively. CONCLUSIONS: We demonstrate that estimating the effect of both binding pocket and distant mutations on inhibitor binding free energy using alchemical calculations can reproduce their effect on the experimentally measured [Formula: see text] values. We show that distant site mutations L76V and N88S affect the hydrogen bond network in the protease's active site, which offers an explanation for the indirect effect of these mutations on inhibitor binding. This work thus provides valuable insights on interplay between primary and background mutations and mechanisms how they affect inhibitor binding.


Asunto(s)
Farmacorresistencia Viral/genética , Inhibidores de la Proteasa del VIH/farmacología , Proteasa del VIH/metabolismo , VIH-1/efectos de los fármacos , VIH-1/genética , Mutación , Sitios de Unión , Dominio Catalítico , Humanos , Enlace de Hidrógeno , Concentración 50 Inhibidora , Simulación de Dinámica Molecular
20.
Photosynth Res ; 146(1-3): 41-54, 2020 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-32342261

RESUMEN

PsbV (cytochrome c550) is one of the three extrinsic proteins of photosystem II (PSII) and functions to maintain the stability and activity of the Mn4CaO5 cluster, the catalytic center for water oxidation. PsbV-Y137 is the C-terminal residue of PsbV and is located at the exit of a hydrogen-bond network mediated by the D1-Y161-H190 residue pair. In order to examine the function of PsbV-Y137, four mutants, PsbV-Y137A, PsbV-Y137F, PsbV-Y137G, and PsbV-Y137W, were generated with Thermosynechococcus vulcanus (T. vulcanus). These mutants showed growth rates similar to that of the wild-type strain (WT); however, their oxygen-evolving activities were different. At pH 6.5, the oxygen evolution rates of Y137F and Y137W were almost identical to that of WT, whereas the oxygen evolution rates of the Y137A, Y137G mutants were 64% and 61% of WT, respectively. However, the oxygen evolution in the latter two mutants decreased less at higher pHs, suggesting that higher pHs facilitated oxygen evolution probably by facilitating proton egress in these two mutants. Furthermore, thylakoid membranes isolated from the PsbV-Y137A, PsbV-Y137G mutants exhibited much lower levels of oxygen-evolving activity than that of WT, which was found to be caused by the release of PsbV. In addition, PSII complexes purified from the PsbV-Y137A and PsbV-Y137G mutants lost all of the three extrinsic proteins but instead bind Psb27, an assembly cofactor of PSII. These results demonstrate that the PsbV-Tyr137 residue is required for the stable binding of PsbV to PSII, and the hydrogen-bond network mediated by D1-Y161-H190 is likely to function in proton egress during water oxidation.


Asunto(s)
Complejo de Proteína del Fotosistema II/metabolismo , Enlace de Hidrógeno , Modelos Moleculares , Mutagénesis Sitio-Dirigida , Oxidación-Reducción , Oxígeno/metabolismo , Complejo de Proteína del Fotosistema II/genética , Protones , Thermosynechococcus/genética , Thermosynechococcus/metabolismo , Agua/metabolismo
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