82 research outputs found
Localization Properties of Electronic States in Polaron Model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers
We numerically investigate localization properties of electronic states in a
static model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers with
realistic parameters obtained by quantum-chemical calculation. The randomness
in the on-site energies caused by the electron-phonon coupling are completely
correlated to the off-diagonal parts. In the single electron model, the effect
of the hydrogen-bond stretchings, the twist angles between the base pairs and
the finite system size effects on the energy dependence of the localization
length and on the Lyapunov exponent are given. The localization length is
reduced by the influence of the fluctuations in the hydrogen bond stretchings.
It is also shown that the helical twist angle affects the localization length
in the poly(dG)-poly(dC) DNA polymer more strongly than in the
poly(dA)-poly(dT) one. Furthermore, we show resonance structures in the energy
dependence of the localization length when the system size is relatively small.Comment: 6 pages, 6 figure
Dynamical transition, hydrophobic interface, and the temperature dependence of electrostatic fluctuations in proteins
Molecular dynamics simulations have revealed a dramatic increase, with
increasing temperature, of the amplitude of electrostatic fluctuations caused
by water at the active site of metalloprotein plastocyanin. The increased
breadth of electrostatic fluctuations, expressed in terms of the reorganization
energy of changing the redox state of the protein, is related to the formation
of the hydrophobic protein/water interface allowing large-amplitude collective
fluctuations of the water density in the protein's first solvation shell. On
the top of the monotonic increase of the reorganization energy with increasing
temperature, we have observed a spike at 220 K also accompanied by a
significant slowing of the exponential collective Stokes shift dynamics. In
contrast to the local density fluctuations of the hydration-shell waters, these
spikes might be related to the global property of the water solvent crossing
the Widom line.Comment: 9 pages, 8 figure
Redox Entropy of Plastocyanin: Developing a Microscopic View of Mesoscopic Polar Solvation
We report applications of analytical formalisms and Molecular Dynamics (MD)
simulations to the calculation of redox entropy of plastocyanin metalloprotein
in aqueous solution. The goal of our analysis is to establish critical
components of the theory required to describe polar solvation at the mesoscopic
scale. The analytical techniques include a microscopic formalism based on
structure factors of the solvent dipolar orientations and density and continuum
dielectric theories. The microscopic theory employs the atomistic structure of
the protein with force-field atomic charges and solvent structure factors
obtained from separate MD simulations of the homogeneous solvent. The MD
simulations provide linear response solvation free energies and reorganization
energies of electron transfer in the temperature range 280--310 K. We found
that continuum models universally underestimate solvation entropies, and a more
favorable agreement is reported between the microscopic calculations and MD
simulations. The analysis of simulations also suggests that difficulties of
extending standard formalisms to protein solvation are related to the
inhomogeneous structure of the solvation shell at the protein-water interface
combining islands of highly structured water around ionized residues along with
partial dewetting of hydrophobic patches. Quantitative theories of
electrostatic protein hydration need to incorporate realistic density profile
of water at the protein-water interface.Comment: 17 pages, 12 figure
Mathematical literacy in Plant Physiology undergraduates: results of interventions aimed at improving students' performance
The importance of mathematical literacy in any scientific career is widely recognized. However, various studies report lack of numeracy and mathematical literacy in students from various countries. In the present work we present a detailed study of the mathematical literacy of Spanish undergraduate students of Biology enrolled in a Plant Physiology course. We have performed individual analyses of results obtained during the period 2000-2011, for questions in the examinations requiring and not requiring mathematical skills. Additionally, we present the outcome of two interventions introduced with the aim of helping students improve their prospects for success in the course. Our results confirm previous research showing students' deficiencies in mathematical skills. However, the scores obtained for mathematical questions in the examinations are good predictors of the final grades attained in Plant Physiology, as there are strong correlations at the individual level between results for questions requiring and not requiring mathematical skills. The introduction of a laboratory session devoted to strengthening the application of students' previously acquired mathematical knowledge did not change significantly the results obtained for mathematical questions. Since mathematical abilities of students entering university have declined in recent years, this intervention may have helped to maintain students' performance to a level comparable to that of previous years. The outcome of self-assessment online tests indicates that though Mathematics anxiety is lower than during examinations, the poor results obtained for questions requiring mathematical skills are, at least in part, due to a lack of self-efficacy
Experimental evidence of the ferroelectric phase transition near the point in liquid water
We studied dielectric properties of nano-sized liquid water samples confined
in polymerized silicates MCM-41 characterized by the porous sizes \sim 3-10nm.
We report the direct measurements of the dielectric constant by the dielectric
spectroscopy method at frequencies 25Hz-1MHz and demonstrate clear signatures
of the second-order phase transition of ferroelectric nature at temperatures
next to the \lambda- point in the bulk supercooled water. The presented results
support the previously developed polar liquid phenomenology and hence establish
its applicability to model actual phenomena in liquid water.Comment: 4 pages, single figur
General Anesthetics Predicted to Block the GLIC Pore with Micromolar Affinity
Although general anesthetics are known to modulate the activity of ligand-gated ion channels in the Cys-loop superfamily, there is at present neither consensus on the underlying mechanisms, nor predictive models of this modulation. Viable models need to offer quantitative assessment of the relative importance of several identified anesthetic binding sites. However, to date, precise affinity data for individual sites has been challenging to obtain by biophysical means. Here, the likely role of pore block inhibition by the general anesthetics isoflurane and propofol of the prokaryotic pentameric channel GLIC is investigated by molecular simulations. Microscopic affinities are calculated for both single and double occupancy binding of isoflurane and propofol to the GLIC pore. Computations are carried out for an open-pore conformation in which the pore is restrained to crystallographic radius, and a closed-pore conformation that results from unrestrained molecular dynamics equilibration of the structure. The GLIC pore is predicted to be blocked at the micromolar concentrations for which inhibition by isofluorane and propofol is observed experimentally. Calculated affinities suggest that pore block by propofol occurs at signifcantly lower concentrations than those for which inhibition is observed: we argue that this discrepancy may result from binding of propofol to an allosteric site recently identified by X-ray crystallography, which may cause a competing gain-of-function effect. Affinities of isoflurane and propofol to the allosteric site are also calculated, and shown to be 3 mM for isoflurane and for propofol; both anesthetics have a lower affinity for the allosteric site than for the unoccupied pore
Reorganization Energy for Internal Electron Transfer in Multicopper Oxidases.
We have calculated the reorganization energy for the intramolecular electron transfer between the reduced type 1 copper site and the peroxy intermediate of the trinuclear cluster in the multicopper oxidase CueO. The calculations are performed at the combined quantum mechanics and molecular mechanics (QM/MM) level, based on molecular dynamics simulations with tailored potentials for the two copper sites. We obtain a reorganization energy of 91-133 kJ/mol, depending on the theoretical treatment. The two Cu sites contribute by 12 and 22 kJ/mol to this energy, whereas the solvent contribution is 34 kJ/mol. The rest comes from the protein, involving small contributions from many residues. We have also estimated the energy difference between the two electron-transfer states and show that the reduction of the peroxy intermediate is exergonic by 43-87 kJ/mol, depending on the theoretical method. Both the solvent and the protein contribute to this energy difference, especially charged residues close to the two Cu sites. We compare these estimates with energies obtained from QM/MM optimizations and QM calculations in a vacuum and discuss differences between the results obtained at various levels of theory
ANG II AT(1) and AT(2) receptors in developing kidney of normal microswine
To identify an appropriate model of human renin-angiotensin system (RAS) involvement in fetal origins of adult disease, we quantitated renal ANG II AT(1) and AT(2) receptors (AT1R and AT2R, respectively) in fetal (90-day gestation, n = 14), neonatal (3-wk, n = 5), and adult (6-mo, n = 8) microswine by autoradiography ((125)I-labeled [Sar(1)Ile(8)]ANG II+cold CGP-42112 for AT1R, (125)I-CGP-42112 for AT2R) and by whole kidney radioligand binding. The developmental pattern of renal AT1R in microswine, like many species, exhibited a 10-fold increase postnatally (P \u3c 0.001), with maximal postnatal density in glomeruli and lower density AT1R in extraglomerular cortical and outer medullary sites. With aging, postnatal AT1R glomerular profiles increased in size (P \u3c 0.001) and fractional area occupied (P \u3c 0.04), with no change in the number per unit area. Cortical levels of AT2R by autoradiography fell with age from congruent with 5,000 fmol/g in fetal kidneys to congruent with 60 and 20% of fetal levels in neonatal and adult cortex, respectively (P \u3c 0.0001). The pattern of AT2R binding in postnatal pig kidney mimicked that described in human and simian, but not rodent, species: dense AT2R confined to discrete cortical structures, including pre- and juxtaglomerular, but not intraglomerular, vasculature. Our results provide a quantitative assessment of ANG II receptors in developing pig kidney and document the concordance of pigs and primates in developmental regulation of renal AT1R and AT2R
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