Inter- and Intra-Chain Attractions in Solutions of Flexible Polyelectrolytes at Nonzero Concentration

Constant temperature molecular dynamics simulations were used to study solutions of flexible polyelectrolyte chains at nonzero concentrations with explicit counterions and unscreened coulombic interactions. Counterion condensation, measured via the self-diffusion coefficient of the counterions, is found to increase with polymer concentration, but contrary to the prediction of Manning theory, the renormalized charge fraction on the chains decreases with increasing Bjerrum length without showing any saturation. Scaling analysis of the radius of gyration shows that the chains are extended at low polymer concentrations and small Bjerrum lengths, while at sufficiently large Bjerrum lengths, the chains shrink to produce compact structures with exponents smaller than a gaussian chain, suggesting the presence of attractive intrachain interactions. A careful study of the radial distribution function of the center-of-mass of the polyelectrolyte chains shows clear evidence that effective interchain attractive interactions also exist in solutions of flexible polyelectrolytes, similar to what has been found for rodlike polyelectrolytes. Our results suggest that the broad maximum observed in scattering experiments is due to clustering of chains.Comment: 12 pages, REVTeX, 15 eps figure

Active Site Structures of CYP11A1 in the Presence of Its Physiological Substrates and Alterations upon Binding of Adrenodoxin

The rate-limiting step in the steroid synthesis pathway is catalyzed by CYP11A1 through three sequential reactions. The first two steps involve hydroxylations at positions 22 and 20, generating 20(R),22(R)-dihydroxycholesterol (20R,22R-DiOHCH), with the third stage leading to a C20–C22 bond cleavage, forming pregnenolone. This work provides detailed information about the active site structure of CYP11A1 in the resting state and substrate-bound ferric forms as well as the CO-ligated adducts. In addition, high-quality resonance Raman spectra are reported for the dioxygen complexes, providing new insight into the status of Fe–O–O fragments encountered during the enzymatic cycle. Results show that the three natural substrates of CYP11A1 have quite different effects on the active site structure, including variations of spin state populations, reorientations of heme peripheral groups, and, most importantly, substrate-mediated distortions of Fe–CO and Fe–O2 fragments, as revealed by telltale shifts of the observed vibrational modes. Specifically, the vibrational mode patterns observed for the Fe–O–O fragments with the first and third substrates are consistent with H-bonding interactions with the terminal oxygen, a structural feature that tends to promote O–O bond cleavage to form the Compound I intermediate. Furthermore, such spectral data are acquired for complexes with the natural redox partner, adrenodoxin (Adx), revealing protein–protein-induced active site structural perturbations. While this work shows that Adx has an only weak effect on ferric and ferrous CO states, it has a relatively stronger impact on the Fe–O–O fragments of the functionally relevant oxy complexes

Multilevel blocking approach to the fermion sign problem in path-integral Monte Carlo simulations

A general algorithm toward the solution of the fermion sign problem in finite-temperature quantum Monte Carlo simulations has been formulated for discretized fermion path integrals with nearest-neighbor interactions in the Trotter direction. This multilevel approach systematically implements a simple blocking strategy in a recursive manner to synthesize the sign cancellations among different fermionic paths throughout the whole configuration space. The practical usefulness of the method is demonstrated for interacting electrons in a quantum dot.Comment: 4 pages RevTeX, incl. two figure

Human P450 CYP17A1: Control of Substrate Preference by Asparagine 202

CYP17A1 is a key steroidogenic enzyme known to conduct several distinct chemical transformations on multiple substrates. In its hydroxylase activity, this enzyme adds a hydroxyl group at the 17α position of both pregnenolone and progesterone at approximately equal rates. However, the subsequent 17,20 carbon–carbon scission reaction displays variable substrate specificity in the numerous CYP17A1 isozymes operating in vertebrates, manifesting as different Kd and kcat values when presented with 17α-hydroxypregnenlone (OHPREG) versus 17α-hydroxyprogesterone (OHPROG). Here we show that the identity of the residue at position 202 in human CYP17A1, thought to form a hydrogen bond with the A-ring alcohol substituent on the pregnene- nucleus, is a key driver of this enzyme’s native preference for OHPREG. Replacement of asparagine 202 with serine completely reverses the preference of CYP17A1, more than doubling the rate of turnover of the OHPROG to androstenedione reaction and substantially decreasing the rate of formation of dehydroepiandrosterone from OHPREG. In a series of resonance Raman experiments, it was observed that, in contrast with the case for the wild-type protein, in the mutant the 17α alcohol of OHPROG tends to form a H-bond with the proximal rather than terminal oxygen of the oxy–ferrous complex. When OHPREG was a substrate, the mutant enzyme was found to have a H-bonding interaction with the proximal oxygen that is substantially weaker than that of the wild type. These results demonstrate that a single-point mutation in the active site pocket of CYP17A1, even when far from the heme, has profound effects on steroidogenic selectivity in androgen biosynthesis

Stochastic Cutoff Method for Long-Range Interacting Systems

A new Monte-Carlo method for long-range interacting systems is presented. This method consists of eliminating interactions stochastically with the detailed balance condition satisfied. When a pairwise interaction $V_{ij}$ of a $N$-particle system decreases with the distance as $r_{ij}^{-\alpha}$, computational time per one Monte Carlo step is ${\cal O}(N)$ for $\alpha \ge d$ and ${\cal O}(N^{2-\alpha/d})$ for $\alpha < d$, where $d$ is the spatial dimension. We apply the method to a two-dimensional magnetic dipolar system. The method enables us to treat a huge system of $256^2$ spins with reasonable computational time, and reproduces a circular order originated from long-range dipolar interactions.Comment: 18 pages, 9 figures, 1 figure and 1 reference are adde

Resonance Raman Spectroscopy Reveals that Substrate Structure Selectively Impacts the Heme-Bound Diatomic Ligands of CYP17

An important function of steroidogenic cytochromes P450 is the transformation of cholesterol to produce androgens, estrogens, and the corticosteroids. The activities of cytochrome P450c17 (CYP17) are essential in sex hormone biosynthesis, with severe developmental defects being a consequence of deficiency or mutations. The first reaction catalyzed by this multifunctional P450 is the 17α-hydroxylation of pregnenolone (PREG) to 17α-hydroxypregnenolone (17-OH PREG) and progesterone (PROG) to 17α-hydroxyprogesterone (17-OH PROG). The hydroxylated products then either are used for production of corticoids or undergo a second CYP17 catalyzed transformation, representing the first committed step of androgen formation. While the hydroxylation reactions are catalyzed by the well-known Compound I intermediate, the lyase reaction is believed to involve nucleophilic attack of the earlier peroxo- intermediate on the C20-carbonyl. Herein, resonance Raman (rR) spectroscopy reveals that substrate structure does not impact heme structure for this set of physiologically important substrates. On the other hand, rR spectra obtained here for the ferrous CO adducts with these four substrates show that substrates do interact differently with the Fe-C-O fragment, with large differences between the spectra obtained for the samples containing 17-OH PROG and 17-OH PREG, the latter providing evidence for the presence of two Fe-C-O conformers. Collectively, these results demonstrate that individual substrates can differentially impact the disposition of a heme-bound ligand, including dioxygen, altering the reactivity patterns in such a way as to promote preferred chemical conversions, thereby avoiding the profound functional consequences of unwanted side reactions

Relativistic Compact Objects in Isotropic Coordinates

We present a matrix method for obtaining new classes of exact solutions for Einstein's equations representing static perfect fluid spheres. By means of a matrix transformation, we reduce Einstein's equations to two independent Riccati type differential equations for which three classes of solutions are obtained. One class of the solutions corresponding to the linear barotropic type fluid with an equation of state $p=\gamma \rho$ is discussed in detail.Comment: 9 pages, no figures, accepted for publication in Pramana-Journal of Physic

Causal Bulk Viscous Dissipative Isotropic Cosmologies with Variable Gravitational and Cosmological Constants

We consider the evolution of a flat Friedmann-Robertson-Walker Universe, filled with a causal bulk viscous cosmological fluid, in the presence of variable gravitational and cosmological constants. The basic equation for the Hubble parameter, generalizing the evolution equation in the case of constant gravitational coupling and cosmological term, is derived, under the supplementary assumption that the total energy of the Universe is conserved. By assuming that the cosmological constant is proportional to the square of the Hubble parameter and a power law dependence of the bulk viscosity coefficient, temperature and relaxation time on the energy density of the cosmological fluid, two classes of exact solutions of the field equations are obtained. In the first class of solutions the Universe ends in an inflationary era, while in the second class of solutions the expansion of the Universe is non-inflationary for all times. In both models the cosmological "constant" is a decreasing function of time, while the gravitational "constant" increases in the early period of evolution of the Universe, tending in the large time limit to a constant value.Comment: 14 pages, 15 figure