Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras-GAP proteins as rationalized by ab initio QM/MM simulations

The hydrolysis reaction of guanosine triphosphate (GTP) by p21(ras) (Ras) has been modeled by using the ab initio type quantum mechanical-molecular mechanical simulations. Initial geometry configurations have been prompted by atomic coordinates of the crystal structure (PDBID: 1QRA) corresponding to the prehydrolysis state of Ras in complex with GTP. Multiple searches of minimum energy geometry configurations consistent with the hydrogen bond networks have been performed, resulting in a series of stationary points on the potential energy surface for reaction intermediates and transition states. It is shown that the minimum energy reaction path is consistent with an assumption of a two-step mechanism of GTP hydrolysis. At the first stage, a unified action of the nearest residues of Ras and the nearest water molecules results in a substantial spatial separation of the gamma-phosphate group of GTP from the rest of the molecule (GDP). This phase of hydrolysis process proceeds through the low barrier (16.7 kcal/mol) transition state TS1. At the second stage, the inorganic phosphate is formed in consequence of proton transfers mediated by two water molecules and assisted by the Gln61 residue from Ras. The highest transition state at this segment, TS3, is estimated to have an energy 7.5 kcal/mol above the enzyme-substrate complex. The results of simulations are compared to the previous findings for the GTP hydrolysis in the Ras-GAP (p21(ras)-p120(GAP)) protein complex. Conclusions of the modeling lead to a better understanding of the anticatalytic effect of cancer causing mutation of Gln61 from Ras, which has been debated in recent years.     

Quantum chemical modeling of the GTP hydrolysis by the RAS–GAP protein complex

We present results of the modeling for the hydrolysis reaction of guanosine triphosphate (GTP) in the RAS–GAP protein complex using essentially ab initio quantum chemistry methods. One of the approaches considers a supermolecular cluster composed of 150 atoms at a consistent quantum level. Another is a hybrid QM/MM method based on the effective fragment potential technique, which describes interactions between quantum and molecular mechanical subsystems at the ab initio level of the theory. Our results show that the GTP hydrolysis in the RAS–GAP protein complex can be modeled by a substrate-assisted catalytic mechanism. We can locate a configuration on the top of the barrier corresponding to the transition state of the hydrolysis reaction such that the straightforward descents from this point lead either to reactants GTP+H₂O or to products guanosine diphosphate (GDP)+H₂PO₄^?. However, in all calculations such a single-step process is characterized by an activation barrier that is too high. Another possibility is a two-step reaction consistent with formation of an intermediate. Here the Pγ-O(Pβ) bond is already broken, but the lytic water molecule is still in the pre-reactive state. We present arguments favoring the assumption that the first step of the GTP hydrolysis reaction in the RAS–GAP protein complex may be assigned to the breaking of the Pγ-O(Pβ) bond prior to the creation of the inorganic phosphate.     

Regulation of dynamic polarity switching in bacteria by a Ras‐like G‐protein and its cognate GAP

The rod‐shaped cells of the bacterium Myxococcus xanthus move uni‐directionally and occasionally undergo reversals during which the leading/lagging polarity axis is inverted. Cellular reversals depend on pole‐to‐pole relocation of motility proteins that localize to the cell poles between reversals. We show that MglA is a Ras‐like G‐protein and acts as a nucleotide‐dependent molecular switch to regulate motility and that MglB represents a novel GTPase‐activating protein (GAP) family and is the cognate GAP of MglA. Between reversals, MglA/GTP is restricted to the leading and MglB to the lagging pole defining the leading/lagging polarity axis. For reversals, the Frz chemosensory system induces the relocation of MglA/GTP to the lagging pole causing an inversion of the leading/lagging polarity axis. MglA/GTP stimulates motility by establishing correct polarity of motility proteins between reversals and reversals by inducing their pole‐to‐pole relocation. Thus, the function of Ras‐like G‐proteins and their GAPs in regulating cell polarity is found not only in eukaryotes, but also conserved in bacteria.     

Controlling the Active Sites of Sulfur‐Doped Carbon Nanotube–Graphene Nanolobes for Highly Efficient Oxygen Evolution and Reduction Catalysis

Controlling active sites of metal‐free catalysts is an important strategy to enhance activity of the oxygen evolution reaction (OER). Many attempts have been made to develop metal‐free catalysts, but the lack of understanding of active‐sites at the atomic‐level has slowed the design of highly active and stable metal‐free catalysts. A sequential two‐step strategy to dope sulfur into carbon nanotube–graphene nanolobes is developed. This bidoping strategy introduces stable sulfur–carbon active‐sites. Fluorescence emission of the sulfur K‐edge by X‐ray absorption near edge spectroscopy (XANES) and scanning transmission electron microscopy electron energy loss spectroscopy (STEM‐EELS) mapping and spectra confirm that increasing the incorporation of heterocyclic sulfur into the carbon ring of CNTs not only enhances OER activity with an overpotential of 350 mV at a current density of 10 mA cm^?2, but also retains 100% of stability after 75 h. The bidoped sulfur carbon nanotube–graphene nanolobes behave like the state‐of‐the‐art catalysts for OER but outperform those systems in terms of turnover frequency (TOF) which is two orders of magnitude greater than (20% Ir/C) at 400 mV overpotential with very high mass activity 1000 mA cm^?2 at 570 mV. Moreover, the sulfur bidoping strategy shows high catalytic activity for the oxygen reduction reaction (ORR). Stable bifunctional (ORR and OER) catalysts are low cost, and light‐weight bidoped sulfur carbon nanotubes are potential candidates for next‐generation metal‐free regenerative fuel cells.     

Analysis of proton wires in the enzyme active site suggests a mechanism of c‐di‐GMP hydrolysis by the EAL domain phosphodiesterases

We report for the first time a hydrolysis mechanism of the cyclic dimeric guanosine monophosphate (c‐di‐GMP) by the EAL domain phosphodiesterases as revealed by molecular simulations. A model system for the enzyme‐substrate complex was prepared on the base of the crystal structure of the EAL domain from the BlrP1 protein complexed with c‐di‐GMP. The nucleophilic hydroxide generated from the bridging water molecule appeared in a favorable position for attack on the phosphorus atom of c‐di‐GMP. The most difficult task was to find a pathway for a proton transfer to the O3' atom of c‐di‐GMP to promote the O3'? P bond cleavage. We show that the hydrogen bond network extended over the chain of water molecules in the enzyme active site and the Glu359 and Asp303 side chains provides the relevant proton wires. The suggested mechanism is consistent with the structural, mutagenesis, and kinetic experimental studies on the EAL domain phosphodiesterases. Proteins 2016; 84:1670–1680. © 2016 Wiley Periodicals, Inc.     

Differential regulation of the high‐affinity choline transporter by wild‐type and Swedish mutant amyloid precursor protein

The high‐affinity choline transporter (CHT) is responsible for choline uptake into cholinergic neurons, with this being the rate‐limiting step for acetylcholine production. Altering CHT protein disposition directly impacts choline uptake activity and cholinergic neurotransmission. Amyloid precursor protein (APP) interacts with CHT proteins and increases their endocytosis from the cell surface. The goal of this study was to examine regulation of CHT trafficking and activity by wild‐type APP (APP_wt) and determine if this differs with Swedish mutant APP (APP_Swe) in SH‐SY5Y human neuroblastoma cells. APP_Swe differs from APP_wt in its trafficking from the cell surface through endosomes. We report for the first time that CHT interacts significantly less with APP_Swe than with APP_wt. Surprisingly, however, CHT cell surface levels and choline uptake activity are decreased to the same extent and CHT co‐localization to early endosomes increased similarly in cells expressing either APP_wt or APP_Swe. A critical observation is that CHT co‐immunoprecipitates with βCTF from APP_Swe‐expressing cells. We propose that decreased CHT function is mediated differently by APP_wt and APP_Swe; APP_wt interaction with CHT facilitates its endocytosis from the cell surface, whereas the effect of APP_Swe on CHT is mediated indirectly potentially by binding to the βCTF fragment or by Aβ released from cells.

     

A cell‐based Dkk1 binding assay reveals roles for extracellular domains of LRP5 in Dkk1 interaction and highlights differences between wild‐type and the high bone mass mutant LRP5(G171V)

Dkk1 is a secreted antagonist of the LRP5‐mediated Wnt signaling pathway that plays a pivotal role in bone biology. Because there are no well‐documented LRP5‐based assays of Dkk1 binding, we developed a cell‐based assay of Dkk1/LRP5 binding using radioactive ¹²⁵I‐Dkk1. In contrast to LRP6, transfection of LRP5 alone into 293A cells resulted in a low level of specific binding that was unsuitable for routine assay. However, co‐transfection of LRP5 with the chaperone protein MesD (which itself does not bind Dkk1) or Kremen‐2 (a known Dkk1 receptor), or both, resulted in a marked enhancement of specific binding that was sufficient for evaluation of Dkk1 antagonists. LRP5 fragments comprising the third and fourth β‐propellers plus the ligand binding domain, or the first β‐propeller, each inhibited Dkk1 binding, with mean IC₅₀s of 10 and 196 nM, respectively. The extracellular domain of Kremen‐2 (“soluble Kremen”) was a weaker antagonist (mean IC₅₀ 806 nM). We also found that cells transfected with a high bone mass mutation LRP5(G171V) had a subtly reduced level of Dkk1 binding, compared to wild type LRP5‐transfected cells, and no enhancement of binding by MesD. We conclude that (1) LRP5‐transfected cells do not offer a suitable cell‐based Dkk1 binding assay, unless co‐transfected with either MesD, Kremen‐2, or both; (2) soluble fragments of LRP5 containing either the third and fourth β‐propellers plus the ligand binding domain, or the first β‐propeller, antagonize Dkk1 binding; and (3) a high bone mass mutant LRP5(G171V), has subtly reduced Dkk1 binding, and, in contrast to LRP5, no enhancement of binding with MesD. J. Cell. Biochem. 108: 1066–1075, 2009. © 2009 Wiley‐Liss, Inc.     

Comparison of a Molecular and an Immobilized Gadolinium(III)‐tris[(1R,4S)‐3‐heptafluorobutanoyl‐camphor] as Catalyst in the Asymmetric Danishefsky‐Hetero‐Diels‐Alder‐Reaction

On‐column reaction gas chromatography combines the power of separation and rapid analysis of reactants and reaction products with screening of reactions in a single step. Not only conversions but the reaction rates at various temperatures can be obtained from single measurements, making this approach superior to the time‐consuming measurements typically performed in reaction progress analysis. However, this approach has only been used in the investigation of interconversion processes, rearrangement reactions, and only a few examples of higher‐order reactions are known. Here we present the screening of immobilized gadolinium(III)‐tris[(1R,4S)‐3‐heptafluorobutanoyl‐camphor] in the Danishefsky‐hetero‐Diels‐Alder‐reaction by enantioselective on‐column reaction gas chromatography utilizing cryogenic focusing to achieve catalytic conversions in this higher‐order reaction and subsequent separation of the enantiomeric product mixture to determine the enantiomeric ratio. The results obtained by this approach could be transferred to the conventional batch reaction at a larger scale, demonstrating that on‐column reaction chromatography provides reliable results in the screening of enantioselective reactions. Chirality 26:243–248, 2014. © 2014 Wiley Periodicals, Inc.     

Characterization of esterases involved in the stereoselective hydrolysis of ester‐type prodrugs of propranolol in rat liver and plasma

An inhibition study showed that the stereoselective hydrolysis of butyryl propranolol (butyryl PL) in rat liver microsomes and plasma involves carboxylesterase. The hydrolysis of (S)‐butyryl PL in plasma was specifically inhibited by eserine and bis‐nitrophenyl phosphate (BNPP), compared to the (R)‐isomer, despite the non‐stereoselective hydrolysis of butyryl PL in plasma. In addition, inhibition of hydroloysis by eserine and BNPP showed little stereoselectivity for butyryl PL in liver, although liver microsomes showed an (S)‐preferential hydrolysis for butyryl PL (R/S ratio of Vmax/Km: 2.1 ± 0.2). The hydrolysis of butyryl PL was not inhibited by a polyclonal antibody against a high affinity carboxylesterase (hydrolase A, RH1). Moreover, the high Km value and the high IC₅₀ for phenylmethylsulfonyl fluoride (PMSF) against the hydrolysis of butyryl PL in rat liver microsomes suggest that a low affinity carboxylesterase (perhaps hydrolase B) might be involved in this hydrolysis in rat liver. Chirality 11:10–13, 1999. © 1999 Wiley‐Liss, Inc.     

Wnt signaling loss accelerates the appearance of neuropathological hallmarks of Alzheimer's disease in J20‐APP transgenic and wild‐type mice

Alzheimer's disease (AD ) is a neurodegenerative pathology characterized by aggregates of amyloid‐β (Aβ) and phosphorylated tau protein, synaptic dysfunction, and spatial memory impairment. The Wnt signaling pathway has several key functions in the adult brain and has been associated with AD , mainly as a neuroprotective factor against Aβ toxicity and tau phosphorylation. However, dysfunction of Wnt/β‐catenin signaling might also play a role in the onset and development of the disease. J20 APP swInd transgenic (Tg) mouse model of AD was treated i.p. with various Wnt signaling inhibitors for 10 weeks during pre‐symptomatic stages. Then, cognitive, biochemical and histochemical analyses were performed. Wnt signaling inhibitors induced severe changes in the hippocampus, including alterations in Wnt pathway components and loss of Wnt signaling function, severe cognitive deficits, increased tau phosphorylation and Aβ_1–42 peptide levels, decreased Aβ42/Aβ40 ratio and Aβ_1–42 concentration in the cerebral spinal fluid, and high levels of soluble Aβ species and synaptotoxic oligomers in the hippocampus, together with changes in the amount and size of senile plaques. More important, we also observed severe alterations in treated wild‐type (WT ) mice, including behavioral impairment, tau phosphorylation, increased Aβ_1–42 in the hippocampus, decreased Aβ_1–42 in the cerebral spinal fluid, and hippocampal dysfunction. Wnt inhibition accelerated the development of the pathology in a Tg AD mouse model and contributed to the development of Alzheimer's‐like changes in WT mice. These results indicate that Wnt signaling plays important roles in the structure and function of the adult hippocampus and suggest that inhibition of the Wnt signaling pathway is an important factor in the pathogenesis of AD .

Read the Editorial Highlight for this article on page 356 .

     

Preparation and characterization of a new open‐tubular capillary column for enantioseparation by capillary electrochromatography

In order to use the enantioseparation capability of cationic cyclodextrin and to combine the advantages of capillary electrochromatography (CEC) with open‐tubular (OT) column, in this study, a new OT‐CEC, coated with cationic cyclodextrin (1‐allylimidazolium‐β‐cyclodextrin [AI‐β‐CD]) as chiral stationary phase (CSP), was prepared and applied for enantioseparation. Synthesized AI‐β‐CD was characterized by infrared (IR) spectrometry and mass spectrometry (MS). The preparation conditions for the AI‐β‐CD‐coated column were optimized with the orthogonal experiment design L₉(3⁴). The column prepared was characterized by scanning electron microscopy (SEM) and elemental analysis (EA). The results showed that the thickness of stationary phase in the inner surface of the AI‐β‐CD‐coated columns was about 0.2 to 0.5 μm. The AI‐β‐CD content in stationary phase based on the EA was approximately 2.77 mmol·m^?2. The AI‐β‐CD‐coated columns could separate all 14 chiral compounds (histidine, lysine, arginine, glutamate, aspartic acid, cysteine, serine, valine, isoleucine, phenylalanine, salbutamol, atenolol, ibuprofen, and napropamide) successfully in the study and exhibit excellent reproducibility and stability. We propose that the column, coated with AI‐β‐CD, has a great potential for enantioseparation in OT‐CEC.     

Castration reduces motoneuron soma size but not dendritic length in the spinal nucleus of the bulbocavernosus of wild‐type and BCL‐2 overexpressing mice

Motoneurons in the spinal nucleus of the bulbocavernosus (SNB) and their target muscles, bulbocavernosus and levator ani (BC/LA), constitute an androgen‐sensitive neuromuscular system. Testosterone regulates SNB soma size, SNB dendritic length, and BC/LA muscle mass in adult male rats. Recent evidence indicates that the cell death‐regulatory protein, Bcl‐2, may also play a role in adult neural plasticity. The present study examined whether gonadal hormones and/or the Bcl‐2 protein influence the morphology of the SNB neuromuscular system in adult B6D2F1 mice. In Experiment 1, adult wild‐type and Bcl‐2 overexpressing males were castrated and implanted with silastic capsules containing testosterone or left blank. Six weeks after castration, cholera toxin‐horseradish peroxidase was injected into the BC muscle to label SNB dendrites. Animals were killed 48 h later, and BC/LA muscle mass, SNB soma size, and SNB dendritic arbors were examined. In Experiment 2, wild‐type and Bcl‐2 overexpressing males were castrated or sham castrated, implanted with testosterone‐filled or blank capsules, and examined 12 weeks later. In both experiments, BC/LA muscle mass and SNB soma size were significantly reduced in castrates receiving blank capsules. Surprisingly, however, there was no effect of hormone manipulation on any of several measures of dendritic length. Thus, the dendritic morphology of SNB motoneurons appears to be relatively insensitive to circulating androgen levels in B6D2F1 mice. Bcl‐2 overexpression did not influence BC/LA muscle mass, SNB soma size, or SNB dendritic length, indicating that the morphology of this neuromuscular system and the response to castration are not altered by forced expression of the Bcl‐2 protein. © 2002 Wiley Periodicals, Inc. J Neurobiol 53: 403–412, 2002     

Replacement of Ca by Ni in a Perovskite Titanate to Yield a Novel Perovskite Exsolution Architecture for Oxygen‐Evolution Reactions

For efficient catalysis and electrocatalysis well‐designed, high‐surface‐area support architectures covered with highly dispersed metal nanoparticles with good catalyst‐support interactions are required. In situ grown Ni nanoparticles on perovskites have been recently reported to enhance catalytic activities in high‐temperature systems such as solid oxide cells (SOCs). However, the micrometer‐scale primary particles prepared by conventional solid‐state reactions have limited surface area and tend to retain much of the active catalytic element within the bulk, limiting efficacy of such exsolution processes in low‐temperature systems. Here, a new, highly efficient, solvothermal route is demonstrated to exsolution from smaller scale primary particles. Furthermore, unlike previous reports of B‐site exsolution, it seems that the metal nanoparticles are exsolved from the A‐site of these perovskites. The catalysts show large active site areas and strong metal‐support interaction (SMSI), leading to ≈26% higher geometric activity (25 times higher mass activity with 1.4 V of E_on‐set) and stability for oxygen‐evolution reaction (OER) with only 0.72 µg base metal contents compared to typical 20 wt% Ni/C and even commercial 20 wt% Ir/C. The findings obtained here demonstrate the potential design and development of heterogeneous catalysts in various low‐temperature electrochemical systems including alkaline fuel cells and metal–air batteries.     

Analyses of the folding properties of ferredoxin‐like fold proteins by means of a coarse‐grained Gō model: Relationship between the free energy profiles and folding cores

The folding mechanisms of proteins with multi‐state transitions, the role of the intermediate states, and the precise mechanism how each transition occurs are significant on‐going research issues. In this study, we investigate ferredoxin‐like fold proteins which have a simple topology and multi‐state transitions. We analyze the folding processes by means of a coarse‐grained Gō model. We are able to reproduce the differences in the folding mechanisms between U1A, which has a high‐free‐energy intermediate state, and ADA2h and S6, which fold into the native structure through two‐state transitions. The folding pathways of U1A, ADA2h, S6, and the S6 circular permutant, S6_p54‐55, are reproduced and compared with experimental observations. We show that the ferredoxin‐like fold contains two common regions consisting folding cores as predicted in other studies and that U1A produces an intermediate state due to the distinct cooperative folding of each core. However, because one of the cores of S6 loses its cooperativity and the two cores of ADA2h are tightly coupled, these proteins fold into the native structure through a two‐state mechanism. Proteins 2014; 82:954–965. © 2013 Wiley Periodicals, Inc.     

Mechanism for verification of mismatched and homoduplex DNAs by nucleotides‐bound MutS analyzed by molecular dynamics simulations

In order to understand how MutS recognizes mismatched DNA and induces the reaction of DNA repair using ATP, the dynamics of the complexes of MutS (bound to the ADP and ATP nucleotides, or not) and DNA (with mismatched and matched base‐pairs) were investigated using molecular dynamics simulations. As for DNA, the structure of the base‐pairs of the homoduplex DNA which interacted with the DNA recognition site of MutS was intermittently disturbed, indicating that the homoduplex DNA was unstable. As for MutS, the disordered loops in the ATPase domains, which are considered to be necessary for the induction of DNA repair, were close to (away from) the nucleotide‐binding sites in the ATPase domains when the nucleotides were (not) bound to MutS. This indicates that the ATPase domains changed their structural stability upon ATP binding using the disordered loop. Conformational analysis by principal component analysis showed that the nucleotide binding changed modes which have structurally solid ATPase domains and the large bending motion of the DNA from higher to lower frequencies. In the MutS–mismatched DNA complex bound to two nucleotides, the bending motion of the DNA at low frequency modes may play a role in triggering the formation of the sliding clamp for the following DNA‐repair reaction step. Moreover, MM‐PBSA/GBSA showed that the MutS–homoduplex DNA complex bound to two nucleotides was unstable because of the unfavorable interactions between MutS and DNA. This would trigger the ATP hydrolysis or separation of MutS and DNA to continue searching for mismatch base‐pairs. Proteins 2016; 84:1287–1303. © 2016 Wiley Periodicals, Inc.     

Graphitic‐Shell Encapsulation of Metal Electrocatalysts for Oxygen Evolution,Oxygen Reduction,and Hydrogen Evolution in Alkaline Solution

Developing highly efficient, cost effective, and environmentally friendly electrocatalysts for the oxygen evolution reaction (OER), oxygen reduction reaction (ORR), and hydrogen evolution reaction (HER) is of interest for sustainable and clean energy technologies, including metal–air batteries and fuel cells. In this work, the screening of electrocatalytic activities of a series of single metallic iron, cobalt, and nickel nanoparticles and their binary and ternary alloys encapsulated in a graphitic carbon shell toward the OER, ORR, and HER in alkaline media is reported. Synthesis of these compounds proceeds by a two‐step sol–gel and carbothermal reduction procedure. Various ex situ characterizations show that with harsh electrochemical activation, the graphitic shell undergoes an electrochemical exfoliation. The modified electronic properties of the remaining graphene layers prevent their exfoliation, protect the bulk of the metallic cores, and participate in the electrocatalysis. The amount of near‐surface, higher‐oxidation‐state metals in the as‐prepared samples increases with electrochemical cycling, indicating that some metallic nanoparticles are not adequately encased within the graphite shell. Such surface oxide species provide secondary active sites for the electrocatalytic activities. The Ni–Fe binary system gives the most promising results for the OER, and the Co–Fe binary system shows the most promise for the ORR and HER.