Systematic study on crystal-contact engineering of diphthine synthase: influence of mutations at crystal-packing regions on X-ray diffraction quality

It is well known that protein crystallizability can be influenced by site-directed mutagenesis of residues on the molecular surface of proteins, indicating that the intermolecular interactions in crystal-packing regions may play a crucial role in the structural regularity at atomic resolution of protein crystals. Here, a systematic examination was made of the improvement in the diffraction resolution of protein crystals on introducing a single mutation of a crystal-packing residue in order to provide more favourable packing interactions, using diphthine synthase from Pyrococcus horikoshii OT3 as a model system. All of a total of 21 designed mutants at 13 different crystal-packing residues yielded almost isomorphous crystals from the same crystallization conditions as those used for the wild-type crystals, which diffracted X-rays to 2.1 angstrom resolution. Of the 21 mutants, eight provided crystals with an improved resolution of 1.8 angstrom or better. Thus, it has been clarified that crystal quality can be improved by introducing a suitable single mutation of a crystal-packing residue. In the improved crystals, more intimate crystal-packing interactions than those in the wild-type crystal are observed. Notably, the mutants K49R and T146R yielded crystals with outstandingly improved resolutions of 1.5 and 1.6 angstrom, respectively, in which a large-scale rearrangement of packing interactions was unexpectedly observed despite the retention of the same isomorphous crystal form. In contrast, the mutants that provided results that were in good agreement with the designed putative structures tended to achieve only moderate improvements in resolution of up to 1.75 angstrom. These results suggest a difficulty in the rational prediction of highly effective mutations in crystal engineering.

Theory of the unusual doping and temperature dependence of photoemission spectra in manganites

A recent, major, puzzle in the core-level photoemission spectra of doped manganites is the observation of a 1–2 eV wide shoulder with intensity varying with temperature T as the square of the magnetization over a T scale of order 200 K, an order of magnitude less than electronic energies. This is addressed and resolved here, by extending a recently proposed two-fluid polaron–mobile electron model for these systems to include core-hole effects. The position of the shoulder is found to be determined by Coulomb and Jahn-Teller energies, while its spectral weight is determined by the mobile electron energetics which is strongly T and doping dependent, due to annealed disorder scattering from the polarons and the t2g core spins. Our theory accounts quantitatively for the observed T dependence of the difference spectra, and furthermore, explains the observed correspondence between spectral changes due to increasing doping and decreasing T.

Self-regularized pseudo time-marching schemes for structural system identification with static measurements

We explore the application of pseudo time marching schemes, involving either deterministic integration or stochastic filtering, to solve the inverse problem of parameter identification of large dimensional structural systems from partial and noisy measurements of strictly static response. Solutions of such non-linear inverse problems could provide useful local stiffness variations and do not have to confront modeling uncertainties in damping, an important, yet inadequately understood, aspect in dynamic system identification problems. The usual method of least-square solution is through a regularized Gauss-Newton method (GNM) whose results are known to be sensitively dependent on the regularization parameter and data noise intensity. Finite time,recursive integration of the pseudo-dynamical GNM (PD-GNM) update equation addresses the major numerical difficulty associated with the near-zero singular values of the linearized operator and gives results that are not sensitive to the time step of integration. Therefore, we also propose a pseudo-dynamic stochastic filtering approach for the same problem using a parsimonious representation of states and specifically solve the linearized filtering equations through a pseudo-dynamic ensemble Kalman filter (PD-EnKF). For multiple sets of measurements involving various load cases, we expedite the speed of thePD-EnKF by proposing an inner iteration within every time step. Results using the pseudo-dynamic strategy obtained through PD-EnKF and recursive integration are compared with those from the conventional GNM, which prove that the PD-EnKF is the best performer showing little sensitivity to process noise covariance and yielding reconstructions with less artifacts even when the ensemble size is small.

Self-regularized pseudo time-marching schemes for structural system identification with static measurements

We explore the application of pseudo time marching schemes, involving either deterministic integration or stochastic filtering, to solve the inverse problem of parameter identification of large dimensional structural systems from partial and noisy measurements of strictly static response. Solutions of such non-linear inverse problems could provide useful local stiffness variations and do not have to confront modeling uncertainties in damping, an important, yet inadequately understood, aspect in dynamic system identification problems. The usual method of least-square solution is through a regularized Gauss-Newton method (GNM) whose results are known to be sensitively dependent on the regularization parameter and data noise intensity. Finite time, recursive integration of the pseudo-dynamical GNM (PD-GNM) update equation addresses the major numerical difficulty associated with the near-zero singular values of the linearized operator and gives results that are not sensitive to the time step of integration. Therefore, we also propose a pseudo-dynamic stochastic filtering approach for the same problem using a parsimonious representation of states and specifically solve the linearized filtering equations through apseudo-dynamic ensemble Kalman filter (PD-EnKF). For multiple sets ofmeasurements involving various load cases, we expedite the speed of the PD-EnKF by proposing an inner iteration within every time step. Results using the pseudo-dynamic strategy obtained through PD-EnKF and recursive integration are compared with those from the conventional GNM, which prove that the PD-EnKF is the best performer showing little sensitivity to process noise covariance and yielding reconstructions with less artifacts even when the ensemble size is small. Copyright (C) 2009 John Wiley & Sons, Ltd.

Truthful and Quality Conscious Query Incentive Networks

Query incentive networks capture the role of incentives in extracting information from decentralized information networks such as a social network. Several game theoretic tilt:Kids of query incentive networks have been proposed in the literature to study and characterize the dependence, of the monetary reward required to extract the answer for a query, on various factors such as the structure of the network, the level of difficulty of the query, and the required success probability.None of the existing models, however, captures the practical andimportant factor of quality of answers. In this paper, we develop a complete mechanism design based framework to incorporate the quality of answers, in the monetization of query incentive networks. First, we extend the model of Kleinberg and Raghavan [2] to allow the nodes to modulate the incentive on the basis of the quality of the answer they receive. For this qualify conscious model. we show are existence of a unique Nash equilibrium and study the impact of quality of answers on the growth rate of the initial reward, with respect to the branching factor of the network. Next, we present two mechanisms; the direct comparison mechanism and the peer prediction mechanism, for truthful elicitation of quality from the agents. These mechanisms are based on scoring rules and cover different; scenarios which may arise in query incentive networks. We show that the proposed quality elicitation mechanisms are incentive compatible and ex-ante budget balanced. We also derive conditions under which ex-post budget balance can beachieved by these mechanisms.

Micellar size and shape in solutions of calcium stearate in cetane from optical depolarization data

Observations at a series of temperatures of the changes in viscosities and depolarization factors of 1% and 18% solutions of calcium stearate in cetane to which varying amounts of water have been added can be interpreted in terms of the existence of anisometric micelles. In general, changes in the size of the micelles inferred from values of ρh agree with those deduced from the viscosity data. The correlation between anisometry of micelles from rheological and optical observations is much poorer in the case of ρν, presumably because of the difficulty in differentiating the contribution of anisometry and anisotropy to ρν.

Triangular Ising antiferromagnet in a staggered field

We study the equilibrium properties of the nearest-neighbor Ising antiferromagnet on a triangular lattice in the presence of a staggered field conjugate to one of the degenerate ground states. Using a mapping of the ground states of the model without the staggered field to dimer coverings on the dual lattice, we classify the ground states into sectors specified by the number of "strings." We show that the effect of the staggered field is to generate long-range interactions between strings. In the limiting case of the antiferromagnetic coupling constant J becoming infinitely large, we prove the existence of a phase transition in this system and obtain a finite lower bound for the transition temperature. For finite J, we study the equilibrium properties of the system using Monte Carlo simulations with three different dynamics. We find that in all the three cases, equilibration times for low-field values increase rapidly with system size at low temperatures. Due to this difficulty in equilibrating sufficiently large systems at low temperatures, our finite-size scaling analysis of the numerical results does not permit a definite conclusion about the existence of st phase transition for finite values of J. A surprising feature in the system is the fact that unlike usual glassy systems; a zero-temperature quench almost always leads to the ground state, while a slow cooling does not.

High-yield bacterial expression and structural characterization of recombinant human insulin-like growth factor binding protein-2

The diverse biological activities of the insulin-like growth factors (IGF-1 and IGF-2) are mediated by the IGF-1 receptor (IGF-1R). These actions are modulated by a family of six IGF-binding proteins (ICFBP-1-6; 22-31 kDa) that via high affinity binding to the IGFs (K-D similar to 300-700 pM) both protect the IGFs in the circulation and attenuate IGF action by blocking their receptor access In recent years, IGFBPs have been implicated in a variety of cancers However, the structural basis of their interaction with IGFs and/or other proteins is not completely understood A critical challenge in the structural characterization of full-length IGFBPs has been the difficulty in expressing these proteins at levels suitable for NMR/X-ray crystallography analysis Here we describe the high-yield expression of full-length recombinant human IGFBP-2 (rhIGFBP-2) in Eschericha coli Using a single step purification protocol, rhIGFBP-2 was obtained with >95% purity and structurally characterized using NMR spectroscopy. The protein was found to exist as a monomer at the high concentrations required for structural studies and to exist in a single conformation exhibiting a unique intra-molecular disulfide-bonding pattern The protein retained full biologic activity. This study represents the first high-yield expression of wild-type recombinant human IGFBP-2 in E coli and first structural characterization of a full-length IGFBP (C) 2010 Elsevier Inc. All rights reserved

Crystal Chemistry of the Noncentrosymmetric Eulytites: A(3)Bi(XO4)(3) (X = V, A = Pb; X = P, A = Ca, Cd, Sr, Pb)

Eulytite compounds, A(3)Bi(XO4)(3) (X = P, A = Ca, Cd, Sr, Pb), belong to the noncentrosymmetric space group l (4) over bar 3d (No. 220) as determined by single-crystal X-ray diffraction studies. The crystals were grown from the melt-cool technique with considerable difficulty as the compounds melt incongruently at their melting temperature, except for the compound Pb3Bi(PO4)(3). The unit cell parameter a is 9.984(5), 9.8611(3), 10.2035(3), and 10.3722(2) angstrom for Ca3Bi(PO4)(3), Cd3Bi(PO4)(3), Sr3Bi(PO4)(3), and Pb3Bi(PO4)(3) respectively, and there are four formula units in the unit cell. The structure of Pb3Bi(VO4)(3), a unique eulytite with vanadium substitution, is compared with all these phosphorus substituted eulytites. The A(2+) and Bi3+ cations occupy the special position (16c) while the O anions occupy the general Wyckoff position (48e) in the crystal structure. Only one O position has been identified for Pb3Bi(PO4)(3) and Pb3Bi(VO4)(3), whereas two O atom sites were identified for Ca3Bi(PO4)(3), Cd3Bi(PO4)(3), and Sr3Bi(PO4)(3). The UV-vis diffuse reflectance spectra indicate large band gaps for all the phosphate eulytites while a lower band gap is observed for the vanadate eulytite. The feasibility of the use of these compounds in optoelectronic devices has been tested by measuring the second-harmonic generation (SHG) values which have been found to be of a magnitude equivalent to the commercially used KDP (KH2PO4).

Sociobiology in turmoil again

Altruism is defined as any behaviour that lowers the Darwinian fitness of the actor while increasing that of the recipient. Such altruism (especially in the form of lifetime sterility exhibited by sterile workers in eusocial insects such as ants, bees, wasps and termites) has long been considered a major difficulty for the theory of natural selection. In the 1960s W. D. Hamilton potentially solved this problem by defining a new measure of fitness that he called inclusive fitness, which also included the effect of an individual's action on the fitness of genetic relatives. This has come to be known as inclusive fitness theory, Hamilton's rule or kin selection. E. O. Wilson almost single-handedly popularized this new approach in the 1970s and thus helped create a large body of new empirical research and a large community of behavioural ecologists and kin selectionists. Adding thrill and drama to our otherwise sombre lives, Wilson is now leading a frontal attack on Hamilton's approach, claiming that the inclusive fitness theory is not as mathematically general as the standard natural selection theory, has led to no additional biological insights and should therefore be abandoned. The world cannot but sit up and take notice.

Optimal explicit terminal guidance for a launch vehicle

It is observed that general explicit guidance schemes exhibit numerical instability close to the injection point. This difficulty is normally attributed to the demand for exact injection which, in turn, calls for finite corrections to be enforced in a relatively short time. The deviations in vehicle state which need corrective maneuvers are caused by the off-nominal operating conditions. Hence, the onset of terminal instability depends on the type of off-nominal conditions encountered. The proposed separate terminal guidance scheme overcomes the above difficulty by minimizing a quadratic penalty on injection errors rather than demanding an exact injection. There is also a special requirement in the terminal phase for the faster guidance computations. The faster guidance computations facilitate a more frequent guidance update enabling an accurate terminal thrust cutoff. The objective of faster computations is realized in the terminal guidance scheme by employing realistic assumptions that are accurate enough for a short terminal trajectory. It is observed from simulations that one of the guidance parameters (P) related to the thrust steering angular rates can indicate the onset of terminal instability due to different off-nominal operating conditions. Therefore, the terminal guidance scheme can be dynamically invoked based on monitoring of deviations in the lone parameter P.

The Madras Triple Helix:Origins and Current Status

Madras triple helix’ was the name assigned by the scientific community in the West, to the molecular model proposed for the fibrous protein collagen, by G N Ramachandran’s group at the University of Madras. As mentioned jocularly in a recent retrospective of this work by Sasisekharan and Yathindra [1], the term was possibly coined due to the difficulty of Western scientists in pronouncing the Indian names of Ramachandran and his associates. The unravelling of the precise nature of collagen structure indeed makes for a fascinating story and as succinctly put by Dickerson [2]: “... to trace the evolution of the structure of collagen is to trace the evolution of fibrous protein crystallography in miniature”. This article is a brief review highlighting the pioneering contributions made by G N Ramachandran in elucidating the correct structure of this important molecule and is a sincere tribute by the author to her mentor, doctoral thesis supervisor and major source of inspiration for embarking on a career in biophysics

A possible origin of viscosity in Keplerian accretion disks due to secondary perturbation: Turbulent transport without magnetic fields

The origin of hydrodynamic turbulence in rotating shear flow is a long standing puzzle. Resolving it is especially important in astrophysics when the flow's angular momentum profile is Keplerian which forms an accretion disk having negligible molecular viscosity. Hence, any viscosity in such systems must be due to turbulence, arguably governed by magnetorotational instability, especially when temperature T greater than or similar to 10(5). However, such disks around quiescent cataclysmic variables, protoplanetary and star-forming disks, and the outer regions of disks in active galactic nuclei are practically neutral in charge because of their low temperature, and thus are not expected to be coupled with magnetic fields enough to generate any transport due to the magnetorotational instability. This flow is similar to plane Couette flow including the Coriolis force, at least locally. What drives their turbulence and then transport, when such flows do not exhibit any unstable mode under linear hydrodynamic perturbation? We demonstrate that the three-dimensional secondary disturbance to the primarily perturbed flow that triggers elliptical instability may generate significant turbulent viscosity in the range 0.0001 less than or similar to nu(t) less than or similar to 0.1, which can explain transport in accretion flows.

Assortative mating and the adaptive landscape

The ability of a population to shift from one adaptive peak to another was examined for a two-locus model with different degrees of assortative mating, selection, and linkage. As expected, if the proportion of the population that mates assortatively increases, so does its ability to shift to a new peak. Assortative mating affects this process by allowing the mean fitness of a population to increase monotonically as it passes through intermediate gene frequencies on the way to a new, higher, homozygotic peak. Similarly, if the height of the new peak increases or selection against intermediates becomes less severe, the population becomes more likely to shift to a new peak. Close linkage also helps the shift to a new adaptive peak and acts similarly to assortative mating, but it is not necessary for such a shift as was previously thought. When a population shifts to a new peak, the number of generations required is significantly less than that needed to return to the original peak when that happens. The short period of time required may be an explanation for rapid changes in the geological record. Under extremely high degrees of assortative mating, the shift takes longer, presumably because of the difficulty of breaking up less favored allelic combinations.

Unsteady three-dimensional boundary layer flow due to a stretching surface

In this numerical study, the unsteady laminar incompressible boundary-layer flow over a continuously stretching surface has been investigated when the velocity of the stretching surface varies arbitrarily with time. Both the nodal and the saddle point regions of flow have been considered for the analysis. Also, constant wall temperature/concentration and constant heat/mass flux at the stretching surface have been taken into account. The quasilinearisation method with an implicit finite-difference scheme is used in the nodal point region (0 less-than-or-equal-to c less-than-or-equal-to 1) where c denotes the stretching ratio. This method fails in the saddle point region (-1 less-than-or-equal-to c less-than-or-equal-to 0) due to the occurrence of reverse flow in the y-component of velocity. In order to overcome this difficulty, the method of parametric differentiation with an implicit finite-difference scheme is used, where the values at c = 0 are taken as starting values. Results have been obtained for the stretching velocities which are accelerating and decelerating with time. Results show that the skin friction, the heat transfer and the mass transfer parameters respond significantly to the time dependent stretching velocities. Suction (A > 0) is found to be an important parameter in obtaining convergent solution in the case of the saddle point region of flow. The Prandtl number and the Schmidt number strongly affect the heat and mass transfer of the diffusing species, respectively.