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1.
Yu Wang Douglas C. Goodwin 《Biochimica et Biophysica Acta - Proteins and Proteomics》2013,1834(1):362-371
Catalase–peroxidases (KatGs) have two peroxidase-like domains. The N-terminal domain contains the heme-dependent, bifunctional active site. Though the C-terminal domain lacks the ability to bind heme or directly catalyze any reaction, it has been proposed to serve as a platform to direct the folding of the N-terminal domain. Toward such a purpose, its I′-helix is highly conserved and appears at the interface between the two domains. Single and multiple substitution variants targeting highly conserved residues of the I′-helix were generated for intact KatG as well as the stand-alone C-terminal domain (KatGC). Single variants of intact KatG produced only subtle variations in spectroscopic and catalytic properties of the enzyme. However, the double and quadruple variants showed substantial increases in hexa-coordinate low-spin heme and diminished enzyme activity, similar to that observed for the N-terminal domain on its own (KatGN). The analogous variants of KatGC showed a much more profound loss of function as evaluated by their ability to return KatGN to its active conformation. All of the single variants showed a substantial decrease in the rate and extent of KatGN reactivation, but with two substitutions, KatGC completely lost its capacity for the reactivation of KatGN. These results suggest that the I′-helix is central to direct structural adjustments in the adjacent N-terminal domain and supports the hypothesis that the C-terminal domain serves as a platform to direct N-terminal domain conformation and bifunctionality. 相似文献
2.
We performed longitudinal examinations by neurofeedback in 17 subjects. The subjects were trained for 12 training seßsions (three weeks) to voluntarily increase the intensity of the ß2 frequencies in the frontal EEG electrodes of the right (the D scenario) and the left (the S scenario) hemispheres. All the subjects were divided into three groups depending on the training efficacy: a group of subjects that successfully controlled the ß activity in the frontal electrodes of both hemispheres (nine subjects), a group of subjects that successfully controlled this activity only in the right hemisphere (four subjects), and a group of subjects that failed to train during the specified period (four subjects). Analysis of the obtained data showed that the training efficacy depended on the cognitive activity that was focused on achieving the corresponding EEG effects and on the individual personality characteristics. 相似文献
3.
StressEraser is a commercially marketed biofeedback device designed to enhance heart rate variability. StressEraser makes its internal calculations on beat-to-beat measures of finger pulse intervals. However, the accuracy and precision of StressEraser in quantifying interbeat intervals using finger pulse intervals has not been evaluated against standard laboratory equipment using R-R intervals. Accuracy was assessed by simultaneously recording interbeat intervals using StressEraser and a standard laboratory ECG system. The interbeat intervals were highly correlated between the systems. The average deviation in interbeat interval recordings between the systems was approximately 6 ms. Moreover, correlations approached unity between the systems on estimates of heart period, heart rate, and heart rate variability. Feedback from StressEraser is based on an interbeat time series that provides sufficient information to provide an excellent estimate of the dynamic changes in heart rate and heart rate variability. The slight variations between StressEraser and the laboratory equipment in quantifying heart rate and heart rate variability are due to features related to monitoring heart rate with finger pulse: (1) a lack in precision in the peak of the finger pulse relative to the clearly defined inflection point in the R-wave, and (2) contribution of variations in pulse transit time. 相似文献
4.
Yu. N. Vorobjev 《Molecular Biology》2005,39(5):777-784
Three-dimensional atomic models of complexes between yeast tRNAPhe and 10- or 15-mer oligonucleotides complementary to the 3′-terminal tRNA sequence have been constructed using computer modeling. It has been found that rapidly formed primary complexes appear when an oligonucleotide binds to the coaxial acceptor and T stems of the tRNAPhe along the major groove, which results in the formation of a triplex. Long stems allow the formation of a sufficiently strong complex with the oligonucleotide, which delivers its 3′-terminal nucleotides to the vicinity of the T loop adjoining the stem. These nucleotides destabilize the loop structure and initiate conformational rearrangements involving local tRNAPhe destruction and formation of the final tRNAPhe-oligonucleotide complementary complex. The primary complex formation and the following tRNAPhe destruction constitute the “molecular wedge” mechanism. An effective antisence oligonucleotide should consist of three segments—(1) complex initiator, (2) primary complex stabilizer, and (3) loop destructor—and be complementary to the (free end)/loop-stem-loop tRNA structural element. 相似文献
5.
W. W. W. DE JONG 《Nature: New biology》1971,234(49):176-177
STUDIES of adult1 and foetal2 haemoglobin from the chimpanzee (Pan troglodytes) have shown that the amino-acid compositions of tryptic and chymotryptic peptides of the α, β and γ-chains are indistinguishable from those of man. The primary structures of chimpanzee α, β and γ-chains are therefore almost certainly identical to the homologous human chains. The two types of γ-chains found in man3, Gγ and Aγ, with glycine and alanine in position γ136, respectively, are likewise present in the chimpanzee2. 相似文献
6.
Cuthbert Ross N. Diagne Christophe Haubrock Phillip J. Turbelin Anna J. Courchamp Franck 《Biological invasions》2022,24(7):1895-1904
Biological Invasions - Biological invasions are increasing worldwide, damaging ecosystems and socioeconomic sectors. Two decades ago, the “100 of the world’s worst” invasive alien... 相似文献
7.
What is the matter with transcendence? On the place of religion in the new anthropology of ethics★
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Joel Robbins 《The journal of the Royal Anthropological Institute》2016,22(4):767-781
A focus on ordinary or everyday ethics has become perhaps the dominant concern in the rapidly developing anthropology of ethics. In this article, I argue that this focus tends to marginalize the study of the ways in which religion contributes to people's moral lives. After defining religion and transcendence in terms that make them less uncongenial to the study of ethics than many proponents of ordinary ethics suggest, I examine values as one sometimes transcendent cultural form that often informs ethical life. I draw on Victor Turner (along with Durkheim) to develop an account of how rituals often both present people with and allow them to perform transcendent versions of values. These encounters, in turn, shape people's ethical sensibilities, including those they bring to bear in everyday life, in ways we cannot understand unless we accord religion a more central role in the anthropology of ethics than it has played to this point. I illustrate my arguments with material drawn both from Turner's Ndembu ethnography and from my own research on Christianity in Papua New Guinea. 相似文献
8.
9.
The effect of the establishment of Entodinium caudatum on the population of Eudiplodinium maggii was examined in the rumen of three sheep fed a hay/ground barley diet. The cell concentration of E. maggii were 15.9-38.5 and 11.7-12.4 x 10(3) cells per g of the rumen contents in the absence and presence of E. caudatum, respectively. Microscopic analysis showed that starch was the only material engulfed by eudiplodinia irrespective of the time after feeding and the presence or absence of E. caudatum. Up to 82-93% of individuals contained starch grains when E. maggii was the only ciliate species in the rumen; the proportion was 70-77% after entodinia had been established. The largest quantity of starch engulfed by E. maggii ciliates was 12.4-19.0 and 6.7-7.6 mg per 100 mg protozoal dry mass in the absence and presence of entodinia, respectively. No visible engulfment of hay was observed in vivo in spite of the fact that hay particles up to 42 microns in length were dominating in rumen fluid. Ingestion of fresh particles of hay separated from the rumen digesta was found when they were added in the proportion of 1 g per 40 mL suspension of ciliates. No preferential intake of starch was observed when E. maggii ciliates were incubated in vitro with a mixture of hay and barley starch. It is suggested that competition for starch between the two ciliate species was responsible for the drop in the numbers of E. maggii. This could result from a too low concentration of small particles of hay in the rumen fluid. 相似文献
10.
Nelli Mnatsakanyan Arathianand M. Krishnakumar Toshiharu Suzuki Joachim Weber 《The Journal of biological chemistry》2009,284(17):11336-11345
ATP synthase uses a unique rotational mechanism to convert chemical energy
into mechanical energy and back into chemical energy. The helix-turn-helix
motif, termed “DELSEED-loop,” in the C-terminal domain of the
β subunit was suggested to be involved in coupling between catalysis and
rotation. Here, the role of the DELSEED-loop was investigated by functional
analysis of mutants of Bacillus PS3 ATP synthase that had 3–7
amino acids within the loop deleted. All mutants were able to catalyze ATP
hydrolysis, some at rates several times higher than the wild-type enzyme. In
most cases ATP hydrolysis in membrane vesicles generated a transmembrane
proton gradient, indicating that hydrolysis occurred via the normal rotational
mechanism. Except for two mutants that showed low activity and low abundance
in the membrane preparations, the deletion mutants were able to catalyze ATP
synthesis. In general, the mutants seemed less well coupled than the wild-type
enzyme, to a varying degree. Arrhenius analysis demonstrated that in the
mutants fewer bonds had to be rearranged during the rate-limiting catalytic
step; the extent of this effect was dependent on the size of the deletion. The
results support the idea of a significant involvement of the DELSEED-loop in
mechanochemical coupling in ATP synthase. In addition, for two deletion
mutants it was possible to prepare an
α3β3γ subcomplex and measure nucleotide
binding to the catalytic sites. Interestingly, both mutants showed a severely
reduced affinity for MgATP at the high affinity site.F1F0-ATP synthase catalyzes the final step of
oxidative phosphorylation and photophosphorylation, the synthesis of ATP from
ADP and inorganic phosphate. F1F0-ATP synthase consists
of the membrane-embedded F0 subcomplex, with, in most bacteria, a
subunit composition of ab2c10, and the peripheral
F1 subcomplex, with a subunit composition of
α3β3γδε. The energy
necessary for ATP synthesis is derived from an electrochemical transmembrane
proton (or, in some organisms, a sodium ion) gradient. Proton flow down the
gradient through F0 is coupled to ATP synthesis on F1 by
a unique rotary mechanism. The protons flow through (half) channels at the
interface of the a and c subunits, which drives rotation of the ring of c
subunits. The c10 ring, together with F1 subunits
γ and ε, forms the rotor. Rotation of γ leads to
conformational changes in the catalytic nucleotide binding sites on the β
subunits, where ADP and Pi are bound. The conformational changes
result in the formation and release of ATP. Thus, ATP synthase converts
electrochemical energy, the proton gradient, into mechanical energy in the
form of subunit rotation and back into chemical energy as ATP. In bacteria,
under certain physiological conditions, the process runs in reverse. ATP is
hydrolyzed to generate a transmembrane proton gradient, which the bacterium
requires for such functions as nutrient import and locomotion (for reviews,
see Refs.
1–6).F1 (or F1-ATPase) has three catalytic nucleotide
binding sites located on the β subunits at the interface to the adjacent
α subunit. The catalytic sites have pronounced differences in their
nucleotide binding affinity. During rotational catalysis, the sites switch
their affinities in a synchronized manner; the position of γ determines
which catalytic site is the high affinity site
(Kd1 in the nanomolar range), which site is the
medium affinity site (Kd2 ≈ 1
μm), and which site is the low affinity site
(Kd3 ≈ 30–100 μm; see
Refs. 7 and
8). In the original crystal
structure of bovine mitochondrial F1
(9), one of the three catalytic
sites, was filled with the ATP analog
AMP-PNP,2 a second was
filled with ADP (plus azide) (see Ref.
10), and the third site was
empty. Hence, the β subunits are referred to as βTP,
βDP, and βE. The occupied β subunits,
βTP and βDP, were in a closed conformation,
and the empty βE subunit was in an open conformation. The main
difference between these two conformations is found in the C-terminal domain.
Here, the “DELSEED-loop,” a helix-turn-helix structure containing
the conserved DELSEED motif, is in an “up” position when the
catalytic site on the respective β subunit is filled with nucleotide and
in a “down” position when the site is empty
(Fig. 1A). When all
three catalytic sites are occupied by nucleotide, the previously open
βE subunit assumes an intermediate, half-closed
(βHC) conformation. It cannot close completely because of
steric clashes with γ
(11).Open in a separate windowFIGURE 1.The βDELSEED-loop. A, interaction of the
βTP and βE subunits with theγ
subunit.β subunits are shown in yellow andγ in
blue. The DELSEED-loop (shown in orange, with the DELSEED
motif itself in green)of βTP interacts with the
C-terminal helixγ and the short helix that runs nearly perpendicular to
the rotation axis. The DELSEED-loop of βE makes contact with
the convex portion of γ, formed mainly by the N-terminal helix. A
nucleotide molecule (shown in stick representation) occupies the catalytic
site of βTP, and the subunit is in the closed conformation.
The catalytic site on βE is empty, and the subunit is in the
open conformation. This figure is based on Protein Data Bank file 1e79
(32). B, deletions in
the βDELSEED-loop. The loop was “mutated” in silico
to represent the PS3 ATP synthase. The 3–4-residue segments that are
removed in the deletion mutants are color-coded as follows:
380LQDI383, pink;
384IAIL387, green;
388GMDE391, yellow;
392LSD394, cyan;
395EDKL398, orange;
399VVHR402, blue. Residues that are the most
involved in contacts with γ are labeled. All figures were generated
using the program PyMOL (DeLano Scientific, San Carlos, CA).The DELSEED-loop of each of the three β subunits makes contact with
the γ subunit. In some cases, these contacts consist of hydrogen bonds
or salt bridges between the negatively charged residues of the DELSEED motif
and positively charged residues on γ. The interactions of the
DELSEED-loop with γ, its movement during catalysis, the conservation of
the DELSEED motif (see 12–14).
Thus, the finding that an AALSAAA mutant in the
α3β3γ complex of ATP synthase from the
thermophilic Bacillus PS3, where several hydrogen bonds/salt bridges
to γ are removed simultaneously, could drive rotation of γ with
the same torque as the wild-type enzyme
(14) came as a surprise. On
the other hand, it seems possible that it is the bulk of the DELSEED-loop,
more so than individual interactions, that drives rotation of γ.
According to a model favored by several authors
(6,
15,
16) (see also Refs.
17–19),
binding of ATP (or, more precisely, MgATP) to the low affinity catalytic site
on βE and the subsequent closure of this site, accompanied by
its conversion into the high affinity site, are responsible for driving the
large (80–90°) rotation substep during ATP hydrolysis, with the
DELSEED-loop acting as a “pushrod.” A recent molecular dynamics
(20) study supports this model
and implicates mainly the region around several hydrophobic residues upstream
of the DELSEED motif (specifically βI386 and
βL387)3 as being
responsible for making contact with γ during the large rotation
substep.
TABLE 1
Conservation of residues in the DELSEED-loop Amino acids found in selected species in the turn region of the DELSEED-loop. Listed are all positions subjected to deletions in the present study. Residue numbers refer to the PS3 enzyme. Consensus annotation: p, polar residue; s, small residue; h, hydrophobic residue; –, negatively charged residue; +, positively charged residue.Open in a separate windowIn the present study, we investigated the function of the DELSEED-loop using an approach less focused on individual residues, by deleting stretches of 3–7 amino acids between positions β380 and β402 of ATP synthase from the thermophilic Bacillus PS3. We analyzed the functional properties of the deletion mutants after expression in Escherichia coli. The mutants showed ATPase activities, which were in some cases surprisingly high, severalfold higher than the activity of the wild-type control. On the other hand, in all cases where ATP synthesis could be measured, the rates where below or equal to those of the wild-type enzyme. In Arrhenius plots, the hydrolysis rates of the mutants were less temperature-dependent than those of wild-type ATP synthase. In those cases where nucleotide binding to the catalytic sites could be tested, the deletion mutants had a much reduced affinity for MgATP at high affinity site 1. The functional role of the DELSEED-loop will be discussed in light of the new information. 相似文献11.
Intracellular β-Carbonic Anhydrase of the Unicellular Green
Alga Coccomyxa
: Cloning of the cDNA and Characterization of the Functional
Enzyme Overexpressed in Escherichia coli
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Thomas Hiltonen Harry Bj?rkbacka Cecilia Forsman Adrian K. Clarke G?ran Samuelsson 《Plant physiology》1998,117(4):1341-1349
Carbonic anhydrase (CA) (EC 4.2.1.1) enzymes catalyze the reversible hydration of CO2, a reaction that is important in many physiological processes. We have cloned and sequenced a full-length cDNA encoding an intracellular β-CA from the unicellular green alga Coccomyxa. Nucleotide sequence data show that the isolated cDNA contains an open reading frame encoding a polypeptide of 227 amino acids. The predicted polypeptide is similar to β-type CAs from Escherichia coli and higher plants, with an identity of 26% to 30%. The Coccomyxa cDNA was overexpressed in E. coli, and the enzyme was purified and biochemically characterized. The mature protein is a homotetramer with an estimated molecular mass of 100 kD. The CO2-hydration activity of the Coccomyxa enzyme is comparable with that of the pea homolog. However, the activity of Coccomyxa CA is largely insensitive to oxidative conditions, in contrast to similar enzymes from most higher plants. Fractionation studies further showed that Coccomyxa CA is extrachloroplastic. 相似文献
12.
S. I. Bakholdina E. V. Sidorin V. A. Khomenko M. P. Isaeva N. Yu. Kim E. P. Bystritskaya E. A. Pimenova T. F. Solov’eva 《Russian Journal of Bioorganic Chemistry》2018,44(2):178-187
The effect of the concentration of an inducer (IPTG) and the time of induction at 37°С on the heterologous synthesis of the mature membrane protein phospholipase А1 (PldA) from Yersinia pseudotuberculosis in the form of inclusion bodies (IBs) and on the physicochemical and structural characteristics of IBs has been studied. The sizes, shape, stability (solubility in urea and detergents, resistance against proteolysis), the secondary structure of the protein of IBs, and the presence of amyloid structures have been determined by electron microscopy, dynamic light scattering, and optical spectroscopy. It was found that IBs have a shape close to spherical and a rough surface and are cleaved by proteinase K. The protein contained in IBs has an ordered secondary structure with a high content of β-structure. As the inducer concentration and the time of expression increase, the conformation of the recombinant protein in IBs undergoes changes, as indicated by an increase in the stability of IBs and a decrease in the enzymatic activity of the protein. When IBs are dissolved in 0.06% SDS and 5 M urea, the recombinant protein retains the secondary structure in a partially modified form, and the addition of a zwitterionic detergent at a micellar concentration does not transform the protein conformation into the native one. 相似文献
13.
A comparative evaluation of the level of extracellular peroxidase activity and light-emission intensity of the mycelium of the luminescent basidiomycete Neonothopanus nambi in the presence of β-glucosidase was performed. The enzyme activity damages the hyphae of the fungus leading to osmotic imbalance, partial degradation of the mycelium, and release of extracellular peroxidases into the incubation medium. The presence of β-glucosidase reduces the time necessary to reach the maximum luminescence. Putative biochemical mechanisms that underlie the stimulation of reactive oxygen species formation (first and foremost, of hydrogen peroxide) in the N. nambi mycelium in the presence of β-glucosidase are proposed. 相似文献
14.
15.
The Phorusrhacidae, a group of large terrestrial carnivorous birds mostly known from the Cenozoic of South America, are often placed in a superfamily, for which the taxon name Phororhacoidea Patterson, 1941 is frequently used. However, according to the International Code of Zoological Nomenclature, Phororhacoidea is not valid. The proper taxon name at the superfamily level is Phorusrhacoidea Ameghino, 1889. 相似文献
16.
Aimed at achieving a good understanding of the 3-dimensional structures of human α1A-adrenoceptor (α1A-AR), we have successfully developed its homology model based on the crystal structure of β2-AR. Subsequent structural refinements were performed to mimic the receptor’s natural membrane environment by using molecular
mechanics (MM) and molecular dynamics (MD) simulations in the GBSW implicit membrane model. Through molecular docking and
further simulations, possible binding modes of subtype-selective α1A-AR antagonists, Silodosin, RWJ-69736 and (+)SNAP-7915, were examined. Results of the modeling and docking studies are qualitatively
consistent with available experimental data from mutagenesis studies. The homology model built should be very useful for designing
more potent subtype-selective α1A-AR antagonists and for guiding further mutagenesis studies.
Figure The superposition of β2-AR crystal structure (gold ribbons) and α1A-AR homology model (blue ribbons) 相似文献
17.
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18.
19.