Structural mobility and transformations in globular proteins

Although globular proteins are endowed with well defined three-dimensional structures, they exhibit substantial mobility within the framework of the given threedimensional structure. The different types of mobility found in proteins by and large correspond to the different levels of organisational hierarchy in protein architecture. They are of considerable structural and functional significance, and can be broadly classified into(a) thermal and conformational fluctuations, (b) segmental mobility, (c) interdomain mobility and (d) intersubunit mobility. Protein crystallographic studies has provided a wealth of information on all of them. The temperature factors derived from X-ray diffraction studies provide a measure of atomic displacements caused by thermal and conformational fluctuations. The variation of displacement along the polypeptide chain have provided functionally significant information on the flexibility of different regions of the molecule in proteins such as myoglobin, lysozyme and prealbumin. Segmental mobility often involves the movement of a region or a segment of a molecule with respect to the rest, as in the transition between the apo and the holo structures of lactate dehydrogenase. It may also involve rigidification of a disordered region of the molecule as in the activation of the zymogens of serine proteases. Transitions between the apo and the holo structures of alcohol dehydrogenase,and between the free and the sugar bound forms of hexokinase, are good examples of interdomain mobility caused by hinge-bending. The capability of different domains to move semi-independently contributes greatly to the versatility of immunoglobulin molecules. Interdomain mobility in citrate synthase appears to be more complex and its study has led to an alternative description of domain closure. The classical and the most thoroughly studied case of intersubunit mobility is that in haemoglobin. The stereochemical mechanism of the action of this allosteric protein clearly brings out the functional subtilities that could be achieved through intersubunit movements. In addition to ligand binding and activation,environmental changes also often cause structural transformations. The reversible transformation between 2 Zn insulin and 4 Zn insulin is caused by changes in the ionic strength of the medium. Adenylate Kinase provides a good example for functionally significant reversible conformational transitions induced by variation in pH. Available evidences indicate that reversible structural transformations in proteins could also be caused by changes in the aqueous environment, including those in the amount of water surrounding protein molecules.

Online_DPI: a web server to calculate the diffraction precision index for a protein structure

An online computing server, Online_DPI (where DPI denotes the diffraction precision index), has been created to calculate the `Cruickshank DPI' value for a given three-dimensional protein or macromolecular structure. It also estimates the atomic coordinate error for all the atoms available in the structure. It is an easy-to-use web server that enables users to visualize the computed values dynamically on the client machine. Users can provide the Protein Data Bank (PDB) identification code or upload the three-dimensional atomic coordinates from the client machine. The computed DPI value for the structure and the atomic coordinate errors for all the atoms are included in the revised PDB file. Further, users can graphically view the atomic coordinate error along with `temperature factors' (i.e. atomic displacement parameters). In addition, the computing engine is interfaced with an up-to-date local copy of the Protein Data Bank. New entries are updated every week, and thus users can access all the structures available in the Protein Data Bank. The computing engine is freely accessible online at http://cluster.physics.iisc.ernet.in/dpi/.

I. The crystal structure of trimesic acid. II. Topics in crystallographic calculations

I. Trimesic acid (1, 3, 5-benzenetricarboxylic acid) crystallizes with a monoclinic unit cell of dimensions a = 26.52 A, b = 16.42 A, c = 26.55 A, and β = 91.53° with 48 molecules /unit cell. Extinctions indicated a space group of Cc or C2/c; a satisfactory structure was obtained in the latter with 6 molecules/asymmetric unit - C₅₄O₃₆H₃₆ with a formula weight of 1261 g. Of approximately 12,000 independent reflections within the CuK_α sphere, intensities of 11,563 were recorded visually from equi-inclination Weissenberg photographs.

The structure was solved by packing considerations aided by molecular transforms and two- and three-dimensional Patterson functions. Hydrogen positions were found on difference maps. A total of 978 parameters were refined by least squares; these included hydrogen parameters and anisotropic temperature factors for the C and O atoms. The final R factor was 0.0675; the final "goodness of fit" was 1.49. All calculations were carried out on the Caltech IBM 7040-7094 computer using the CRYRM Crystallographic Computing System.

The six independent molecules fall into two groups of three nearly parallel molecules. All molecules are connected by carboxylto- carboxyl hydrogen bond pairs to form a continuous array of sixmolecule rings with a chicken-wire appearance. These arrays bend to assume two orientations, forming pleated sheets. Arrays in different orientations interpenetrate - three molecules in one orientation passing through the holes of three parallel arrays in the alternate orientation - to produce a completely interlocking network. One third of the carboxyl hydrogen atoms were found to be disordered.

II. Optical transforms as related to x-ray diffraction patterns are discussed with reference to the theory of Fraunhofer diffraction.

The use of a systems approach in crystallographic computing is discussed with special emphasis on the way in which this has been done at the California Institute of Technology.

An efficient manner of calculating Fourier and Patterson maps on a digital computer is presented. Expressions for the calculation of to-scale maps for standard sections and for general-plane sections are developed; space-group-specific expressions in a form suitable for computers are given for all space groups except the hexagonal ones.

Expressions for the calculation of settings for an Eulerian-cradle diffractometer are developed for both the general triclinic case and the orthogonal case.

Photographic materials on pp. 4, 6, 10, and 20 are essential and will not reproduce clearly on Xerox copies. Photographic copies should be ordered.

Determination by MAD-DM of the structure of the DNA duplex d[ACGTACG(5-BrU)]2 at 1.46 Å and 100 K

A four-wavelength MAD experiment on a new brominated octanucleotide is reported here. d[ACGTACG(5-BrU)], C77H81BrN30O32P7, (DNA) = 2235, tetragonal, P43212 (No. 96), a = 43.597, c = 26.268 Å, V = 49927.5 Å3, Z = 8, T = 100 K, R = 10.91% for 4312 reflections between 15.0 and 1.46 Å resolution. The self-complementary brominated octanucleotide d[ACGTACG(5-BrU)]2 has been crystallized and data measured to 1.45 Å at both 293 K and a second crystal flash frozen at 100 K. The latter data collection was carried out to the same resolution at the four wavelengths 0.9344, 0.9216, 0.9208 and 0.9003 Å, around the Br K edge at 0.92 Å and the structure determined from a map derived from a MAD data analysis using pseudo-MIR methodology, as implemented in the program MLPHARE. This is one of the first successful MAD phasing experiments carried out at Sincrotrone Elettra in Trieste, Italy. The structure was refined using the data measured at 0.9003 Å, anisotropic temperature factors and the restrained least-squares refinement implemented in the program SHELX96, and the helical parameters are compared with those previously determined for the isomorphous d(ACGTACGT)2 analogue. The asymmetric unit consists of a single strand of octamer with 96 water molecules. No countercations were located. The A-DNA helix geometry obtained has been analysed using the CURVES program.

The ecology of lizard reproductive output

Aim  We provide a new quantitative analysis of lizard reproductive ecology. Comparative studies of lizard reproduction to date have usually considered life-history components separately. Instead, we examine the rate of production (productivity hereafter) calculated as the total mass of offspring produced in a year. We test whether productivity is influenced by proxies of adult mortality rates such as insularity and fossorial habits, by measures of temperature such as environmental and body temperatures, mode of reproduction and activity times, and by environmental productivity and diet. We further examine whether low productivity is linked to high extinction risk. Location  World-wide. Methods  We assembled a database containing 551 lizard species, their phylogenetic relationships and multiple life history and ecological variables from the literature. We use phylogenetically informed statistical models to estimate the factors related to lizard productivity. Results  Some, but not all, predictions of metabolic and life-history theories are supported. When analysed separately, clutch size, relative clutch mass and brood frequency are poorly correlated with body mass, but their product – productivity – is well correlated with mass. The allometry of productivity scales similarly to metabolic rate, suggesting that a constant fraction of assimilated energy is allocated to production irrespective of body size. Island species were less productive than continental species. Mass-specific productivity was positively correlated with environmental temperature, but not with body temperature. Viviparous lizards were less productive than egg-laying species. Diet and primary productivity were not associated with productivity in any model. Other effects, including lower productivity of fossorial, nocturnal and active foraging species were confounded with phylogeny. Productivity was not lower in species at risk of extinction. Main conclusions  Our analyses show the value of focusing on the rate of annual biomass production (productivity), and generally supported associations between productivity and environmental temperature, factors that affect mortality and the number of broods a lizard can produce in a year, but not with measures of body temperature, environmental productivity or diet.

Prediction of protein B-factor profiles

The polypeptide backbones and side chains of proteins are constantly moving due to thermal motion and the kinetic energy of the atoms. The B-factors of protein crystal structures reflect the fluctuation of atoms about their average positions and provide important information about protein dynamics. Computational approaches to predict thermal motion are useful for analyzing the dynamic properties of proteins with unknown structures. In this article, we utilize a novel support vector regression (SVR) approach to predict the B-factor distribution (B-factor profile) of a protein from its sequence. We explore schemes for encoding sequences and various settings for the parameters used in SVR. Based on a large dataset of high-resolution proteins, our method predicts the B-factor distribution with a Pearson correlation coefficient (CC) of 0.53. In addition, our method predicts the B-factor profile with a CC of at least 0.56 for more than half of the proteins. Our method also performs well for classifying residues (rigid vs. flexible). For almost all predicted B-factor thresholds, prediction accuracies (percent of correctly predicted residues) are greater than 70%. These results exceed the best results of other sequence-based prediction methods. (C) 2005 Wiley-Liss, Inc.

Avaliação da incerteza de medição no Setor Médico-hospitalar

This study aims to evaluate the uncertainty associated with measurements made by aneroid sphygmomanometer, neonatal electronic balance and electrocautery. Therefore, were performing repeatability tests on all devices for the subsequent execution of normality tests using Shapiro-Wilk; identification of influencing factors that affect the measurement result of each measurement; proposition of mathematical models to calculate the measurement uncertainty associated with measuring evaluated for all equipament and calibration for neonatal electronic balance; evaluation of the measurement uncertainty; and development of a computer program in Java language to systematize the calibration uncertainty of estimates and measurement uncertainty. It was proposed and carried out 23 factorial design for aneroid sphygmomanometer order to investigate the effect of temperature factors, patient and operator and another 32 planning for electrocautery, where it investigated the effects of temperature factors and output electrical power. The expanded uncertainty associated with the measurement of blood pressure significantly reduced the extent of the patient classification tracks. In turn, the expanded uncertainty associated with the mass measurement with neonatal balance indicated a variation of about 1% in the dosage of medication to neonates. Analysis of variance (ANOVA) and the Turkey test indicated significant and indirectly proportional effects of temperature factor in cutting power values and clotting indicated by electrocautery and no significant effect of factors investigated for aneroid sphygmomanometer.

Hydrobiology of Colombo (Beira) Lake, 1. Diurnal variations in temperature, hydrochemical factors and zooplankton

An extensive study of the hydrobiology of the Colombo Lake was initiated by the authors in May 1969 as a contribution to the International Biological Program (Productivity of freshwater communities) by the Department of Zoology, Vidyalankara University of Ceylon, Kelaniya. The Colombo Lake often referred to as the Beira Lake covers an area of approximately 160 acres. The water is usually very turbid with a greenish blue appearance due to the presence of large quantities of blue green algae.

Design factors for a transition temperature Pockels tube.

"Supported in part by contract number U.S. AEC AT(11-1) 1469."

Factors influencing the temperature sensitivity of PMMA based optical fiber Bragg gratings

The Bragg wavelength of a PMMA based fiber grating is determined by the effective core index and the grating pitch, which, in temperature sensing, depend on the thermo-optic and thermal expansion coefficients of PMMA. These two coefficients are a function of surrounding temperature and humidity. Amorphous polymers including PMMA exhibit a certain degree of anisotropic thermal expansion. The anisotropic nature of expansion mainly depends on the polymer processing history. The expansion coefficient is believed to be lower in the direction of the molecular orientation than in the direction perpendicular to the draw direction. Such anisotropic behavior of polymers can be expected in drawn PMMA based optical fiber, and will lead to a reduced thermal expansion coefficient and larger temperature sensitivity than would be the case were the fiber to be isotropic. Extensive work has been carried out to identify these factors. The temperature responses of gratings have been measured at different relative humidity. Gratings fabricated on annealed and non-annealed PMMA optical fibers are used to compare the sensitivity performance as annealing is considered to be able to mitigate the anisotropic effect in PMMA optical fiber. Furthermore an experiment has been designed to eliminate the thermal expansion contribution to the grating wavelength change, leading to increased temperature sensitivity and improved response linearity. © 2014 Copyright SPIE.

Factors influencing the radiative surface temperature of grey seal (Halichoerus grypus) pups during early and late lactation

The aim of this study was to examine the variation in body surface temperature of grey seal (Halichoerus grypus) pups throughout lactation in response to different environmental conditions. Radiative surface temperatures (T r, °C) of pups were measured on the Isle of May (56°11′N, 02°33′W), southeast Scotland from 29 October to 25 November 2003. Records were obtained from a total of 60 pups (32 female and 28 male) from three different pupping sites during early and late lactation. Pups were sheltered from high wind speeds but air temperature, humidity and solar radiation at pupping sites were similar to general meteorological conditions. The mean T r of all pups was 15.8°C (range 7.7–29.7°C) at an average air temperature of 10.2°C (range 6.5–13.8°C). There was no difference in the mean T r of pups between early and late lactation. However, the T r varied between different regions of the body with hind flippers on average 2–6°C warmer than all other areas measured. There was no difference in mean T r of male and female pups and pup body mass did not account for the variation in T r during early or late lactation. Throughout the day there was an increase in the T r of pups and this explained 20–28% of the variation in T r depending on stage of lactation. There was no difference in the mean T r of pups between pupping sites or associated with different substrate types. Wind speed and substrate temperature had no effect on the T r of pups. However, solar radiation, air temperature and relative humidity accounted for 48% of the variation in mean T r of pups during early lactation. During late lactation air temperature and solar radiation alone accounted for 43% of the variation in T r. These results indicate that environmental conditions explain only some of the variation in T r of grey seal pups in natural conditions. Differences in T r however indicate that the cost of thermoregulation for pups will vary throughout lactation. Further studies examining intrinsic factors such as blubber thickness and activity levels are necessary before developing reliable biophysical models for grey seals.

Temperature-averaged and total free-free Gaunt factors for κ and Maxwellian distributions of electrons

Aims. Optically thin plasmas may deviate from thermal equilibrium and thus, electrons (and ions) are no longer described by the Maxwellian distribution. Instead they can be described by κ-distributions. The free-free spectrum and radiative losses depend on the temperature-averaged (over the electrons distribution) and total Gaunt factors, respectively. Thus, there is a need to calculate and make available these factors to be used by any software that deals with plasma emission. Methods. We recalculated the free-free Gaunt factor for a wide range of energies and frequencies using hypergeometric functions of complex arguments and the Clenshaw recurrence formula technique combined with approximations whenever the difference between the initial and final electron energies is smaller than 10−10 in units of z2Ry. We used double and quadruple precisions. The temperature- averaged and total Gaunt factors calculations make use of the Gauss-Laguerre integration with 128 nodes. Results. The temperature-averaged and total Gaunt factors depend on the κ parameter, which shows increasing deviations (with respect to the results obtained with the use of the Maxwellian distribution) with decreasing κ. Tables of these Gaunt factors are provided.