Chiral interfaces and molecular recognition phenomena are of special interest not only for the understanding of biological recognition processes but also for the potential application in material ...science. Langmuir monolayers at the air-water interface have successfully been used as simple models to mimic biological phenomena. Recent experimental studies revealed that both chirality and molecular recognition processes of amphiphiles are controlling the features of the nano-aggregates at the air/water interface. The objective of experimental studies has been to gain information about the properties of mesoscopic length scale aggregates obtained on the basis of chiral discrimation effects and the formation of supramolecular entities by molecular recognition of non-surface active species dissolved in the aqueous subphase. Differences in the two-dimensional morphology and lattice structures of the nano-aggregates cannot be explained by macroscopic theories and needed information about the detailed orientation and distance dependence of the intermolecular interaction within the aggregates. First new bottom-up studies have been directed toward understanding the driving forces for the aggregation processes of monolayers. Different types of interactions have been successfully considered using semi-empirical quantum chemical methods. The possibilities of Langmuir-Blodgett (LB) patterning to be an alternative paradigm for large-area patterning with mesostructured features are discussed.
Aminoacylation is a vital step of natural biosynthesis of peptide. Correct aminoacylation is a necessary prerequisite for the elimination of noncognate amino acids such as d-amino acids. In the ...present work, we studied the fidelity mechanism of histidine (His) activation (first step of aminoacylation reaction) using a combined quantum mechanical/semiempirical method based on a model of crystal structure of the oligomeric complex of histidyl-tRNA synthetase (HisRS) from Escherichia coli. The study of the variation in the energy during the mutual approach of the His and ATP to form adenylate shows that the surrounding nanospace of synthetase confines the reactants (l-His and ATP) and proximally places in a geometry suitable for the in-line nucleophilic attack. The significantly higher energy of the energy surface of the model containing d-His is due to unfavorable interaction of d-His with ATP and surrounding residues. This indicates that the network of interaction (principally electrostatic) is highly unfavorable when d-amino acid is incorporated. The reorganization of the surrounding nanospace can lower the unfavorable nature of the intermolecular energy surface of d-His and surrounding residues. However, such a rearrangement requires large-scale structural reorganization of the synthetase structure and is unfavorable. The variation in the bond angles and distances in going from the reactant state to the product state via transition state confirms the mechanism of nucleophilic attack and concomitant inversion of oxygen atoms around α-phosphorus (α-P). Calculation of the electrostatic potential indicates that in addition to the Mg2+ the Arg residues in the active site facilitate the nucleophilic attack by reducing the negative charge distributed over the oxygen atoms attached to the α-P of ATP. Arg 259 residue has a role similar to that played by the two Mg2+ cations as this residue is in close proximity of the α-P of ATP. Arg 113 also facilitates the reduction of the negative charge on the other side of the reaction center. The favorable electrostatic interaction of the Arg 259 with ATP and His is also concluded from the calculation of the binding energy. The Arg 259 anchors the carboxylic acid group of His and the oxygen atom of the α-phosphate group during the progress of reaction. Consequently, Arg 259 plays an important catalytic role in the activation step rather than merely reducing the negative charge density over the ATP.
Abstract
Dark matter search experiments demand a low to ultralow radiation background to operate. It is very important to understand the nature of the radiation background including knowledge about ...the sources contributing to it. Sometimes, evaluation of the background becomes very specific to the site chosen for the experiment, and also to the experimental configuration. A dark matter search experiment is proposed to be set up at the Jaduguda Underground Science Laboratory (JUSL) in India. The laboratory will be located inside an existing mine with 555 m of vertical rock overburden. Neutrons produced from (α,n) reactions, spontaneous fission of natural radioactive impurities in the rocks, and also from cosmic muon-induced reactions are considered as the main background which can affect the sensitivity and outcome of the experiment. In this work, simulations based on GEANT4 are done to understand both the radiogenic neutron background caused by natural radioactivity of the surrounding rock and the cosmogenic neutron background due to interactions of the deeply penetrating cosmic muons with the rock material. The muon flux in the cavern is obtained to be 4.49(±0.25)×10
-7
cm
-2
s
-1
and the fluxes of radiogenic and cosmogenic neutrons above an energy threshold of 1 MeV in the cavern are obtained to be 5.75(±0.69)×10
-6
cm
-2
s
-1
and 7.25(±0.40)× 10
-9
cm
-2
s
-1
respectively. The values obtained are comparable with estimates and measurements from DAMA, WIPP, and dark matter experiments at Boulby mine. The effectiveness of different shielding materials is also investigated to obtain the best possible neutron background reduction for a dark matter search experiment at JUSL. We also estimate the sensitivity of a CsI based detector for Weakly Interacting Massive Particle (WIMP) dark matter search at JUSL considering the estimated neutron background.
The relation between the conservation of active site residues and the molecular mechanism of aminoacylation reaction is an unexplored problem. In the present paper, the influences of the conserved ...active site residues on the reaction mechanism as well as the electrostatic potential near the reaction center are analyzed for Histidyl tRNA synthetase from
Escherichia coli,
Thermus thermophilus and
Staphylococcus aureus. While the primary structures show both convergence as well as divergence, the secondary level structures of the active sites of the three species show considerable conservation in the respective structural organizations. The conserved active site residues near the reaction center, which have a major role in the reaction mechanism and catalysis, retain their specific position and orientation relative to the substrate in the three species. In order to understand the influence of different conserved and nonconserved residues near the reaction center, two different models are considered. First, a large model of active site with the substrates, Mg
2+ ions and water is constructed in which the first shell residues (including both conserved as well as nonconserved) near the reaction center are studied. From the large model, a smaller model is constructed for reaction path modeling individually for three species. Validation of the smaller model is carried out by comparing the energy surfaces of large and small models as a function of reaction coordinates. Further, the electrostatic potential near the reaction center for the large and small model are compared. The transition state structures of the activation step of aminoacylation reaction for
E. coli,
T. thermophilus and
S. aureus are calculated using the combined
ab-initio/semi-empirical calculation. The similarity of the energy profiles as a function of the relevant reaction coordinate and the orientation of the catalytic residue, Arg259, indicate that the reaction mechanisms are identical which are guided by the strikingly similar structural pattern formed by conserved residues for three species. The energy surfaces have close resemblance in three species and present a clear perspective that how the reaction proceeds with the aid of different conserved residues. The study of electrostatic potential confirms this view. The present study provides an understanding of the relationship between the conservation of residues and the efficient reaction mechanism of aminoacylation reaction.
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► A QM/MM study of the aminoacylation reaction in three species is carried out. ► The reaction is observed to follow a common reaction pathway for the three species. ► Conserved structural patterns are noted in aminoacylation reaction. ► The mechanism is dependent on conserved active site residues in close proximity of the reactants.
Aminoacylation is a vital step in natural biosynthesis process of peptide and is the key step in correlating the realm of protein with the RNA world. Incorrect aminoacylation might lead to ...misacylation of
d-amino acid in the tRNA which might cause synthesis of a hetero-peptide rather than natural homopeptide leading to the altered functionality of the peptide. However, the accuracy of this process is remarkable and leads to the attachment of the correct enantiomer of the amino acid with their cognate tRNA. Thus, the chiral discrimination is stringent. In the present work, we presented a combined ONIOM (
ab initio/semi-empirical) study of the chiral discrimination in the first step of aminoacylation reaction based on a model of crystal structure of the oligomeric complex of histidyl-tRNA synthetase (HisRS) from
Escherichia coli complexed with ATP and histidinol and histidyl-adenylate. The study reveals that the molecular mechanism of the chiral discrimination involves the amino acid, ATP as well as surrounding residues of the synthetase. Several factors are noted to be responsible for discrimination and explain the high level of stereospecificity of the process. The chirality of the amino acid of the substrate and its (principally) electrostatic interaction with the ATP is important for discrimination. The distance and orientational changes involved in the approach of the
d-His towards the ATP is energetically unfavorable. The charge distributions on the His and ATP are important for the discrimination. Removal of the charges in the model drastically reduces the discrimination. Restricted nature of the mutual orientation within the cavity of the active site where the His and ATP are located during the change in orientation for the approach to form the adenylate makes the resultant interaction profile as different for
l-His and
d-His also influences chiral discrimination. The analysis of the transition state structure revealed that alteration of the chirality of the His destabilize the transition state by removing the favorable electrostatic interaction between the Glu-83 and NH
3
+ group of the His substrate. The proximity of the surrounding residues as present in the active site of the synthetase with the His and ATP (the separation is of nanometer range) has influence of discrimination. The study provides a molecular mechanism of the retention of biological homochirality.
At low temperatures (T ≤ 10 °C), the surface pressure−area (π−A) isotherms of some amphiphilic amides reveal a striking second critical point indicating the existence of a second phase transition ...between two condensed phases. Studies of 3-hydroxy-N-tridecyl propanoic acid amide (HTPA) monolayers have shown that this phase transition between two condensed phases is accompanied by an abrupt change of important 2D lattice parameters. Thorough grazing incidence X-ray diffraction (GIXD) studies have revealed a new phenomenon. The cross-sectional area (A 0) of the alkyl chain of HTPA jumps from a smaller value in the phase at the lower surface pressure to a larger value in the phase existing at higher pressure. The opposite behavior should be expected and is usually noted in the lattice structures of Langmuir monolayers. The phase diagram of the HTPA monolayers is constructed on the basis of the equilibrium π−A isotherms. The fact that two condensed monolayer phases exist and the phase observed above the fluid/condensed transition at higher temperature has a structure similar to that observed at high pressure and low temperatures, as observed by the GIXD experiments, can be thermodynamically explained by the generalized equation of state for Langmuir monolayers for the existence of two condensed phases. The IRRA spectra did not show a substantial change in the band positions below and above the phase transition between the two condensed states, but differences in the dichroic ratio indicate changes in the hydrogen bonding system. The computational studies, using the ab initio level of theory for the headgroup and the molecular mechanical theory for the alkyl chain part, provide a reasonable explanation for the unexpected, novel finding that the cross-sectional area of the alkyl chains jumps to larger values at the phase transition on increasing pressure. It is shown that shortening of the hydrogen bond separation at higher pressure in the headgroup region obviously drives the increase in separation between the alkyl chains, in reasonable agreement with the GIXD results.
Rare presentation of a common disease D, Sahu; S, Dutta; S, Banik
Journal of the Association of Physicians of India,
01/2016, Letnik:
64, Številka:
1
Journal Article
The influence of polyfunctional monomers—tripropyleneglycol diacrylate (TPGDA), trimethylolpropane triacrylate (TMPTA), trimethylolpropane trimetbacrylate (TMPTMA), tetramethylolmethane tetracrylate ...(TMMT) and triallyl cyanurate (TAC)—on the structural changes of fluorocarbon terpolymer (F content 68%, H 1.4%) in the presence of an electron beam has been investigated with the help of IR spectroscopy (in the ATR mode) and sol-gel analysis. The absorbances at 1397, 1021, 672 and 504 cm
−1 due to the C-F group, decrease on irradiation of the mixtures of fluoroelastomer and TMPTA, indicating dehydrofluorination and scission. The concentration of the double bond decreases both in the polyfunctional monomer and its blends with the polymer as a result of grafting and crosslinking. The concentration of the carbonyl group increases with radiation dose in the fluoroelastomer due to aerial oxidation. The effect of trimethylolpropane triacrylate (TMPTA) is to lower the amount of oxidation, especially at relatively higher levels. At a particular radiation dose, the behaviours of TPGDA, TMPTMA, TMMT and TAC based systems are similar to that of the TMPTA based one. The gel content increases with radiation dose. The influence of polyfunctional monomer on gel fraction is more prominent at higher concentrations, where distinct changes are observed at lower doses. At a particular level of multifunctional monomer, the gel fraction is lower for systems based on TPGDA. The ratio of chain scission to crosslinks calculated using the Charlesby-Pinner equation indicates a much higher crosslinking efficiency with polyfunctional monomer-fluorocarbon rubber matrix as compared to the control rubber.
Brief normothermic machine perfusion is increasingly used to assess and recondition grafts before transplant. During normothermic machine perfusion, metabolic activity is typically maintained using ...red blood cell (RBC)-based solutions. However, the utilization of RBCs creates important logistical constraints. This study explored the feasibility of human kidney normothermic perfusion using William's E-based perfusate with no additional oxygen carrier.
Sixteen human kidneys declined for transplant were perfused with a perfusion solution containing packed RBCs or William's E medium only for 6 h using a pressure-controlled system. The temperature was set at 37 °C. Renal artery resistance, oxygen extraction, metabolic activity, energy metabolism, and histological features were evaluated.
Baseline donor demographics were similar in both groups. Throughout perfusion, kidneys perfused with William's E exhibited improved renal flow (
= 0.041) but similar arterial resistance. Lactic acid levels remained higher in kidneys perfused with RBCs during the first 3 h of perfusion but were similar thereafter (
= 0.95 at 6 h). Throughout perfusion, kidneys from both groups exhibited comparable behavior regarding oxygen consumption (
= 0.41) and reconstitution of ATP tissue concentration (
= 0.55). Similarly, nicotinamide adenine dinucleotide levels were preserved during perfusion. There was no evidence of histological damage caused by either perfusate.
In human kidneys, William's E medium provides a logistically convenient, off-the-shelf alternative to packed RBCs for up to 6 h of normothermic machine perfusion.
Dark matter search experiments demand low to ultralow radiation background to operate. It is very important to understand the nature of the radiation background including knowledge about the sources ...contributing to it. Sometimes, evaluation of the background becomes very specific to the site chosen for the experiment, and also to the experimental configuration. A dark matter search experiment is proposed to be set up at the Jaduguda Underground Science Laboratory (JUSL) in India. The laboratory will be located inside an existing mine with 555 m of vertical rock overburden. Neutrons produced from \((\alpha,n)\) reactions, spontaneous fission of natural radioactive impurities in the rocks, and also from cosmic muon induced reactions are considered as the main background which can affect the sensitivity and outcome of the experiment. In this work, simulations based on GEANT4 are done to understand both the radiogenic neutron background caused by natural radioactivity of the surrounding rock and the cosmogenic neutron background due to interaction of the deeply penetrating cosmic muons with the rock. The muon flux in the cavern is obtained to be \(4.49(\pm0.25)\times10^{-7} \)cm\(^{-2}\)s\(^{-1}\) and the fluxes of radiogenic and cosmogenic neutrons above an energy threshold of 1 MeV in the cavern are obtained to be \(5.75(\pm0.58)\times10^{-6}\)cm\(^{-2}\)s\(^{-1}\) and \(7.25(\pm0.65)\times 10^{-9}\) cm\(^{-2}\)s\(^{-1}\) respectively. The values obtained are comparable with estimates and measurements done for DAMA, WIPP and dark matter experiments at Boulby mine. The effectiveness of different shielding materials are also investigated to obtain the best possible neutron background reduction for a dark matter search experiment at JUSL. We also estimate the sensitivity of a CsI based detector for Weakly Interacting Massive Particle (WIMP) dark matter search at JUSL considering the estimated neutron background.
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