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1.
Machado NF Calheiros R Fiuza SM Borges F Gaspar A Garrido J Marques MP 《Journal of molecular modeling》2007,13(8):865-877
The conformational preferences of several potential anticancer dihydroxycinnamic esters with a variable length alkyl chain
were studied by quantum-mechanical (DFT) calculations (both for the isolated molecule and for aqueous solutions). The orientation
of the hydroxyl ring substituents and of the alkyl ester moiety relative to the carbonyl group showed these to be the most
determinant factors for the overall stability of this type of phenolic systems, strongly dependent on an effective π-electron
delocalization. Compared to the parent caffeic acid (dihydroxycinnamic acid), esterification was found to lead to a higher
conformational freedom, and to affect mainly the energy barrier corresponding to the (O=)C-OR internal rotation. No particular
differences were verified to occur upon lengthening of the ester alkyl chain, except when this is branched instead of linear.
The vibrational spectra of the whole series of compounds were simulated, based on their calculated harmonic vibrational frequencies,
and a preliminary assignment was performed.
Figure Schematic representation of the dihydroxycinnamic esters studied in the present work and of the main internal rotations affecting
the overall stability of the molecules. (R=(CH2)n, n = 0,1,2,3,7,11 for MC, EC, PC, BC, OC and DC, respectively; R=(CHCH3) for IPC. The atom numbering is included, with the exception of the alkyl ester group) 相似文献
2.
Abbandonato G Signore G Nifosì R Voliani V Bizzarri R Beltram F 《European biophysics journal : EBJ》2011,40(11):1205-1214
The photoswitching behaviour of the green fluorescent protein (GFP) chromophore and its analogs opens up exciting horizons
for the engineering and development of molecular devices for high sensitivity in vivo studies. In this work we present the
synthesis and photophysical study of four GFP chromophore analogs belonging to butenolide and pyrrolinone classes. These chromophores
possess an intriguing photoinduced cis–trans isomerization mechanism. Stereochemical structural assignment was unambiguously performed by 1D Nuclear Overhauser Effect
NMR measurements. The spectroscopic properties of both cis and trans isomers were studied, and photoconversion quantum yield for cis–trans isomerization was assessed to be in the 0.1–0.4 range. Finally, the 3JC,H coupling constant in the 13C–C=C–H motif was in excellent agreement with theoretical DFT calculations, thus providing a further confirmation of cis–trans photoisomerization of the structurally analog GFP chromophore. 相似文献
3.
Hossein Hooshyar Karim Zare Naser Modirshahla Salah Khanahmadzadeh 《Journal of molecular modeling》2009,15(3):247-256
The effect of the molecular structure on the properties of C = O…HX (X = F, Cl) bonds was investigated in a set of small cyclic
carbonyl compounds, using vibrational spectroscopy and B3LYP/6–311G** calculations. Two main effects were studied: the size
of the ring and the inclusion of oxygen atoms in the ring. In these complexes the C = O and H–X participating bonds in the
hydrogen–bond are elongated, while others bonds are compressed. The calculated vibrational spectra were interpreted and band
assignments were reported. Surface potential energy calculations are carried out with scanning HCl and HF near oxygen atom. 相似文献
4.
5.
J. B. K. Leonard J. F. Norieka B. Kynard S. D. McCormick 《Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology》1999,169(4-5):287-295
To assess the energetics of migration in an anadromous fish, adult American shad (Alosa sapidissima) were swum in a large respirometer at a range of speeds (1.0–2.3 body lengths (BL) s−1, 13–24 °C). Metabolic rate (MO2) was logarithmically related to swimming speed (Bl s−1; r
2 = 0.41, slope = 0.23 ± 0.037) and tailbeat frequency (beats × min−1; r
2 = 0.52, slope = 0.003 ± 0.0003). Temperature had a significant effect on metabolic rate (r
2 = 0.41) with a Q10 of 2.2. Standard metabolic rate (SMR), determined directly after immobilization with the neuroblocker gallamine triethiodide,
ranged from 2.2–6.2 mmolO2 kg−1 h−1 and scaled with mass (W) such that SMR = 4.0 (±0.03)W0.695(±0.15). Comparison of directly determined and extrapolated SMR suggests that swimming respirometry provides a good estimate of SMR
in this species, given the differences in basal activity monitored by the two methods. Overall, American shad metabolic rates
(MO2 and SMR) were intermediate between salmonids and fast-swimming perciforms, including tunas, and may be a result of evolutionary
adaptation to their active pelagic, schooling life history. This study demonstrates variability in metabolic strategy among
anadromous fishes that may be important to understanding the relative success of different migratory species under varying
environmental conditions.
Accepted: 3 March 1999 相似文献
6.
Xiaodong Li Myong Jong Yi Yowhan Son Pil Sun Park Kyeong Hak Lee Yeong Mo Son Rae Hyun Kim Mi Jeong Jeong 《Journal of Plant Biology》2010,53(6):381-386
Biomass expansion factors, which convert the timber volume (or dry weight) to biomass, are used to estimate the forest biomass
and account for the carbon budget at the national or regional level. This study estimated the biomass conversion and expansion
factors (BCEF), root to shoot ratio (R), biomass expansion factors (BEF) of natural Japanese Red Pine (Pinus densiflora Sieb. et Zucc.) forests based on direct field measurements and publications in Korea. This study attempted to fit the non-linear
relationships between the biomass expansion factors (BCEF and BEF) and main stand factors [stand age, tree height, and diameter
at breast height (DBH)]. The relationship between BEF and each main stand factor was expressed as a simple logarithmical equation.
The BCEF was also expressed as a logarithmical equation of the tree height, DBH, and stand volume, whereas there was no significant
relationship between BCEF and stand age. The mean value for BCEF, BEF, and R was 0.5821 Mg m−3 (n = 22, SD = 0.1196), 1.4465 (n = 22, SD = 0.2905), and 0.2220 (n = 17, SD = 0.0687), respectively. The values of the biomass expansion factors in this study may indicate much representativeness
to estimate forest biomass in natural Japanese Red Pine forests of Korea than the default values given by the IPCC (2003, 2006). 相似文献
7.
Under intracellular recording, we studied the effect of ATP on nerve cells of the rat intact nodose ganglion. The resting
membrane potential of the examined neurons was, on average, –60.3 ± 1.4 mV (n = 84); among such units, 88% were classified as C cells. Local application of 2 mM ATP to the surface of the ganglion using
a modified laminar flow system led to depolarization of neurons by 7.1 ± 0.9 mV, on average (n = 19). A blocker of P2X receptors, PPADS (100 μM), suppressed these depolarization responses, decreasing their amplitude,
on average, to 16 ± 3% (n = 3) of the initial value. The obtained data indicate that an overwhelming majority of neurons of the intact nodose ganglion
possess functional P2X receptors on their membranes. The absence of the corresponding responses in a considerable part of
neurons of intact spinal ganglia [13-15] was, apparently, determined by the fact that P2X receptors in the course of the described experiments had enough time to
desensitize before ATP reached the effective concentration. 相似文献
8.
Lughaidh Ó Néill Tijmen Veldhuizen Addy de Jongh John Rochford 《European Journal of Wildlife Research》2009,55(4):363-370
We examined the spatial structure and socio-biology of a native wild population of Eurasian otters (Lutra lutra) on mesotrophic rivers in a mild temperate climate. Radio-tracking of 20 individuals revealed exclusive intra-sexual adult
home-ranges. Adult female home-ranges (7.5 km, SD = 1.5 km, n = 7) were inversely related to river width (, F
6 = 13.5, P = 0.014) and so appeared to be based on food resources. The aquatic area within adult male home-ranges (30.2 ha, SD = 9.5 ha,
n = 5) was greater than that within adult female’s (16.8 ha, SD = 7.0 ha) (t
10 = 2.437, P = 0.035), though this result is inconclusive because some males were tracked on oligotrophic rivers. One adult male expanded
its range from 10.2 km to 19.3 km within 5 days of the death of the neighbouring male, suggesting that male home-ranges were
heavily influenced by conspecifics. 相似文献
9.
Transient expression and stable transformation of soybean using the jellyfish green fluorescent protein 总被引:13,自引:6,他引:7
Embryogenic soybean [Glycine max (L.) Merrill.] suspension cultures were bombarded with five different gene constructions encoding the jellyfish (Aequorea victoria) green fluorescent protein (GFP). These constructions had altered codon usage compared to the native GFP gene and mutations
that increased the solubility of the protein and/or altered the native chromophore. All of the constructions produced green
fluorescence in soybean cultures upon blue light excitation, although a soluble modified red-shifted GFP (smRS-GFP) was the
easiest to detect based on the brightness and number of foci produced. Expression of smRS-GFP was visible as early as 1.5 h
after bombardment, with peak expression at approximately 6.5 h. Large numbers of smRS-GFP-expressing areas were visible for
48 h postbombardment and declined rapidly thereafter. Stably transformed cultures and plants exhibited variation in the intensity
and location of GFP expression. PCR and Southern hybridization analyses confirmed the presence of introduced GFP genes in
stably transformed cultures.
Received: 23 September 1998 / Revision received: 4 January 1999 / Accepted: 15 January 1999 相似文献
10.
The molecular geometries, vibrational properties, and thermodynamic properties of the clusters (Br2GaN3)
n
(n = 1–4) were studied at the B3LYP/6-311+G* level. The optimized clusters (Br2GaN3)
n
(n = 2–4) were all found to possess a cyclic structure consisting of Ga atoms bridged by the α-nitrogen of the azide groups.
A discussion of the relationships between the geometrical parameters and the degree of oligomerization n is provided. Features in the IR spectra were assigned by vibrational analysis. Trends in thermodynamic properties with temperature
and degree of oligomerization n are discussed. Thermodynamic analysis of the gas-phase reaction showed that the formation of the clusters (Br2GaN3)
n
(n = 2–4) is thermodynamically favorable considering the enthalpies at 298.2 K. The calculated results for the Gibbs free energies
were negative, which indicates that the oligomerizations can occur spontaneously at 298.2 K. 相似文献
11.
12.
Zheng Zhao Karel Kuijvenhoven Walter M. van Gulik Joseph J. Heijnen Wouter A. van Winden Peter J. T. Verheijen 《Applied microbiology and biotechnology》2011,89(1):63-72
The in vivo flux through the oxidative branch of the pentose phosphate pathway (oxPPP) in Penicillium chrysogenum was determined during growth in glucose/ethanol carbon-limited chemostat cultures, at the same growth rate. Non-stationary
13C flux analysis was used to measure the oxPPP flux. A nearly constant oxPPP flux was found for all glucose/ethanol ratios
studied. This indicates that the cytosolic NADPH supply is independent of the amount of assimilated ethanol. The cofactor
assignment in the model of van Gulik et al. (Biotechnol Bioeng 68(6):602–618, 2000) was supported using the published genome annotation of P. chrysogenum. Metabolic flux analysis showed that NADPH requirements in the cytosol remain nearly the same in these experiments due to
constant biomass growth. Based on the cytosolic NADPH balance, it is known that the cytosolic aldehyde dehydrogenase in P. chrysogenum is NAD + dependent. Metabolic modeling shows that changing the NAD + -aldehyde dehydrogenase to NADP + -aldehyde dehydrogenase can increase the penicillin yield on substrate. 相似文献
13.
Amin O. Elzupir Mohammed A. Suliman Ibrahim A. Ibrahim M. Himmat Fadul Abdelrahim M. Elhussein 《Mycotoxin Research》2010,26(2):69-73
Vegetable oil (n = 81) for human consumption from Khartoum State in Sudan were analyzed for aflatoxins (AFs), using high-performance liquid
chromatography (HPLC) with fluorescence detection following extraction with methanol:water (80:20) and clean-up using petroleum
ether. Sampling included sesame oil (n = 14), peanut oil (n = 21), and sunflower oil (n = 19) purchased from retail shops, and mixed oil produced by two local manufacturers (factory A, n = 15; factory B, n = 12). AF contamination was found in 80/81 (98.8%) samples, with total AF levels ( AFB1 + AFB2 + AFG1 + AFG2 ) \left( {{\hbox{AF}}{{\hbox{B}}_{\rm{1}}} + {\hbox{AF}}{{\hbox{B}}_{\rm{2}}} + {\hbox{AF}}{{\hbox{G}}_{\rm{1}}} + {\hbox{AF}}{{\hbox{G}}_{\rm{2}}}} \right) of 0.43–339.9 μg/kg and mean level of 57.5 μg/kg. All sesame oils had total AF levels that were much higher than the United
States Food and Drug Administration acceptable limit of 20 μg/kg. The percentage of samples with total AF values <20 μg/kg
in other oils varied and was 57.14% in peanut oil, 36.8% in sunflower oil, 66.7% (mixed oil from factory A), and 91.7% (mixed
oil from factory B). In conclusion, the levels of total AFs in edible oil as available in Khartoum State are quite alarming.
To reduce the health hazards for the consumers, an intervention strategy to manage AFs in food commodities from Sudan is urgently
required. 相似文献
14.
Kimotsuki T Niwa N Hicks MN Dunne M Cobbe SM Watanabe MA 《Journal of biological physics》2010,36(3):299-315
Roughly speaking, restitution is the dependence of recovery time of cardiac electrical activity on heart rate. Increased restitution
slope is theorized to be predictive of sudden death after heart injury such as from coronary artery occlusion (ischemia).
Adrenaline analogs are known to increase restitution slope in normal hearts, but their effects in failing hearts are unknown.
Twenty-six rabbits underwent coronary ligation (n = 15) or sham surgery (n = 11) and implantation of a lead in the heart for recording electrocardiograms. Eight weeks later, unanesthetized rabbits
were given 0.25–2.0 ml of 1 μmol/L isoprenaline intravenously, which increased heart rate. Heart rate was quantified by time
between QRS peaks (RR) and heart activity duration by R to T peak time (QTp). Ligated rabbits (n = 6) had lower ejection fraction than sham rabbits (n = 7, p < 0.0001) indicative of heart failure, but similar baseline RR (269 ± 15 vs 292 ± 23 ms, p = 0.07), QTp (104 ± 17 vs 91 ± 9 ms, p = 0.1), and isoprenaline-induced minimum RR (204 ± 11 vs 208 ± 6 ms, p = 0.4). The trajectory of QTp vs TQ plots displayed hysteresis and regions of negative slope. The slope of the positive slope
region was >1 in ligated rabbits (1.27 ± 0.66) and <1 in sham rabbits (0.35 ± 0.14, p = 0.004). The absolute value of the negative slope was greater in ligated rabbits (− 0.81 ± 0.52 vs − 0.35 ± 0.14, p = 0.04). Isoprenaline increased heart rate and slopes of restitution trajectory in failing hearts. The dynamics of restitution
trajectory may hold clues for sudden death in heart failure patients. 相似文献
15.
Lee JY Doddareddy MR Cho YS Choo H Koh HY Kang JH No KT Pae AN 《Journal of molecular modeling》2007,13(5):543-558
Comparative quantitative structure–activity relationship (QSAR) analyses of peptide deformylase (PDF) inhibitors were performed
with a series of previously published (British Biotech Pharmaceuticals, Oxford, UK) reverse hydroxamate derivatives having
antibacterial activity against Escherichia coli PDF, using 2D and 3D QSAR methods, comparative molecular field analysis (CoMFA), comparative molecular similarity indices
analysis (CoMSIA), and hologram QSAR (HQSAR). Statistically reliable models with good predictive power were generated from
all three methods (CoMFA r
2 = 0.957, q
2 = 0.569; CoMSIA r
2 = 0.924, q
2 = 0.520; HQSAR r
2 = 0.860, q
2 = 0.578). The predictive capability of these models was validated by a set of compounds that were not included in the training
set. The models based on CoMFA and CoMSIA gave satisfactory predictive r
2 values of 0.687 and 0.505, respectively. The model derived from the HQSAR method showed a low predictability of 0.178 for
the test set. In this study, 3D prediction models showed better predictive power than 2D models for the test set. This might
be because 3D information is more important in the case of datasets containing compounds with similar skeletons. Superimposition
of CoMFA contour maps in the active site of the PDF crystal structure showed a meaningful correlation between receptor–ligand
binding and biological activity. The final QSAR models, along with information gathered from 3D contour and 2D contribution
maps, could be useful for the design of novel active inhibitors of PDF.
Figure Superimposition of comparative molecular field analysis (CoMFA) contour plot in the active site of peptide deformylase (PDF) 相似文献
16.
Colin R. Andrew Jane Han Tanneke den Blaauwen Gertie van Pouderoyen Erik Vijgenboom Gerard W. Canters Thomas M. Loehr J. Sanders-Loehr 《Journal of biological inorganic chemistry》1997,2(1):98-107
In the redox center of azurin, the Cu(II) is strongly coordinated to one thiolate S from Cys 112 and two imidazole Ns from
His 46 and 117. This site yields a complex resonance Raman (RR) spectrum with >20 vibrational modes between 200 and 1500 cm–1. We have investigated the effects of ligand-selective isotope replacements on the RR spectrum of Pseudomonas aeruginosa azurin to determine the relative spectral contribution from each of the copper ligands. Growth on 34S-sulfate labels the cysteine ligand and allows the identification of a cluster of bands with Cu–S(Cys) stretching character
between 370 and 430 cm–1 whose frequencies are consistent with the trigonal or distorted tetrahedral coordination in type 1 sites. In type 2 copper-cysteinate
sites, the lower ν (Cu–S) frequencies between 260 and 320 cm–1 are consistent with square-planar coordination. Addition of exogenous
15N-labeled imidazole or histidine to the His117Gly mutant generates type 1 or type 2 sites, respectively. Because neither the
above nor the His46Gly mutant reconstituted with 15N-imidazole exhibits significant isotope dependence, the histidine ligands can be ruled out as important contributors to the
RR spectrum. Instead, a variety of evidence, including extensive isotope shifts upon global substitution with 15N, suggests that the multiple RR modes of azurin are due principally to vibrations of the cysteine ligand. These are resonance-enhanced
through kinematic coupling with the Cu–S stretch in the ground state or through an excited-state A-term mechanism involving
a Cu-cysteinate chromophore that extends into the peptide backbone.
Received: 29 July 1996 / Accepted: 9 November 1996 相似文献
17.
Structure of nematogenic p-n-Alkoxy cinnamic acids (nOCAC) with various alkyl chain carbon atoms (n = 2, 4, 6, 8) has been optimized using density functional B3LYP with 6-31+G (d) basis set using crystallographic geometry
as input. Using the optimized geometry, electronic structure of the molecules has been evaluated using the semiempirical methods
and DFT calculations. Molecular charge distribution and phase stability of these systems have been analyzed based on Mulliken
and L?wdin population analysis. The electronic absorption spectra of nOCAC molecules have been simulated by employing DFT method, semiempirical CNDO/S and INDO/S parameterizations. Two types of
calculations have been performed for model systems containing single and double molecules of nOCAC. UV-Visible spectra have been calculated for all single molecules. The UV stability of the molecules has been discussed
in light of the electronic transition oscillator strength (f). The dimer complexes of higher homologues (n = 6, 8) have also been reported to enable the comparison between single and double molecules. 相似文献
18.
Microsomal prostaglandin E2 synthase (mPGES-1) has been identified recently as a novel target for treating pain and inflammation. The aim of this study
is to understand the binding affinities of reported inhibitors for mPGES-1 and further to design potential new mPGES-1 inhibitors.
3D-QSAR-CoMFA (comparative molecular field analysis) and CoMSIA (comparative molecular similarity indices analysis) - techniques
were employed on a series of indole derivatives that act as selective mPGES-1 inhibitors. The lowest energy conformer of the
most active compound obtained from systematic conformational search was used as a template for the alignment of 32 compounds.
The models obtained were used to predict the activities of the test set of eight compounds, and the predicted values were
in good agreement with the experimental results. The 3D-QSAR models derived from the training set of 24 compounds were all
statistically significant (CoMFA; q
2 = 0.89, r
2 = 0.95, , and CoMSIA; q
2 = 0.84, r
2 = 0.93, , ). Contour plots generated for the CoMFA and CoMSIA models reveal useful clues for improving the activity of mPGES-1 inhibitors.
In particular, substitutions of an electronegative fluorine atom or a bulky hydrophilic phenoxy group at the meta or para positions of the biphenyl rings might improve inhibitory activity. A plausible binding mode between the ligands and mPGES-1
is also proposed. 相似文献
19.
20.
Borzyszkowska J Stanislawska-Sachadyn A Wirtwein M Sobiczewski W Ciecwierz D Targonski R Gruchala M Rynkiewicz A Limon J 《Journal of applied genetics》2012,53(2):175-182
This study examines whether renin-angiotensin-aldosterone system gene polymorphisms: ACE (encoding for angiotensin converting enzyme) c.2306-117_404 I/D, AGTR1 (encoding for angiotensin II type-1 receptor) c.1080*86A>C and CYP11B2 (encoding for aldosterone synthase) c.-344C>T are associated with the extension of coronary atherosclerosis in a group of
647 patients who underwent elective coronary angiography. The extension of CAD was evaluated using the Gensini score. The
polymorphisms were determined by PCR and RFLP assays. The associations between genotypes and the extent of coronary atherosclerosis
were tested by the Kruskal-Wallis test, followed by pairwise comparisons using Wilcoxon test. The population has been divided
into groups defined by: sex, smoking habit, past myocardial infarction, BMI (>, ≤ 25), age (>, ≤ 55), diabetes mellitus, level
of total cholesterol (>, ≤ 200 mg/dl), LDL cholesterol (>, ≤ 130 mg/dl), HDL cholesterol (>, ≤ 40 mg/dl), triglycerides (>,
≤ 150 mg/dl). Significant associations between the ACE c.2306-117_404 I/D polymorphism and the Gensini score in men with high total cholesterol levels (PKruskal-Wallis = 0.008; Padjusted = 0.009), high level of LDL cholesterol (PKruskal-Wallis = 0.016; Padjusted = 0.028) and low level of HDL cholesterol (PKruskal-Wallis = 0.04; Padjusted = 0.055) have been found. No association between the AGTR1 c.1080*86A>C and CYP11B2 c.-344C>T and the Gensini score has been found. These results suggest that men who carry ACE c.2306-117_404 DD genotype and have high total cholesterol, high LDL cholesterol and low HDL cholesterol levels may be predisposed
to the development of more severe CAD. 相似文献