Recognition of Interaction Interface Residues in Low-Resolution Structures of Protein Assemblies Solely from the Positions of C alpha Atoms

Background: The number of available structures of large multi-protein assemblies is quite small. Such structures provide phenomenal insights on the organization, mechanism of formation and functional properties of the assembly. Hence detailed analysis of such structures is highly rewarding. However, the common problem in such analyses is the low resolution of these structures. In the recent times a number of attempts that combine low resolution cryo-EM data with higher resolution structures determined using X-ray analysis or NMR or generated using comparative modeling have been reported. Even in such attempts the best result one arrives at is the very course idea about the assembly structure in terms of trace of the C alpha atoms which are modeled with modest accuracy. Methodology/Principal Findings: In this paper first we present an objective approach to identify potentially solvent exposed and buried residues solely from the position of C alpha atoms and amino acid sequence using residue type-dependent thresholds for accessible surface areas of C alpha. We extend the method further to recognize potential protein-protein interface residues. Conclusion/Significance: Our approach to identify buried and exposed residues solely from the positions of C alpha atoms resulted in an accuracy of 84%, sensitivity of 83-89% and specificity of 67-94% while recognition of interfacial residues corresponded to an accuracy of 94%, sensitivity of 70-96% and specificity of 58-94%. Interestingly, detailed analysis of cases of mismatch between recognition of interface residues from C alpha positions and all-atom models suggested that, recognition of interfacial residues using C alpha atoms only correspond better with intuitive notion of what is an interfacial residue. Our method should be useful in the objective analysis of structures of protein assemblies when positions of only C alpha positions are available as, for example, in the cases of integration of cryo-EM data and high resolution structures of the components of the assembly.

The effects of marriage partners' socio-economic positions on the risk of divorce in Finland

Väitöskirjatutkimuksen tavoitteena oli selvittää, miten aviopuolisoiden sosioekonominen asema vaikuttaa avioeroriskiin Suomessa. Tutkimuksessa käytettiin Tilastokeskuksen rekistereistä koottua aineistoa, joka koskee suomalaisten ensimmäisiä avioliittoja vuoden 1990 lopussa ja avioeroja vuosina 1991−93. Väitöskirjaan sisältyy kolme osatutkimusta. Ensimmäinen osatutkimus käsitteli avioeroriskin vaihtelua aviopuolisoiden sosioekonomisen aseman eri osatekijöiden (koulutusaste, sosiaaliryhmä, pääasiallinen toiminta, tulotaso, asunnon omistaminen ja asumisahtaus) mukaan. Kaiken kaikkiaan avioeroriski oli sitä pienempi, mitä paremmassa taloudellisessa ja sosiaalisessa asemassa aviopuolisot olivat. Esimerkiksi miehen ja vaimon korkea koulutusaste, toimihenkilöammatti, työssäkäynti (etenkin verrattuna työttömyyteen) sekä omistusasunnossa asuminen liittyivät pienentyneeseen avioeroriskiin. Vaimon sosioekonomisen aseman yhteys avioeroriskiin oli paljolti samanlainen kuin miehen aseman yhteys. Huomattavin poikkeus tähän oli, että vaimon suuret tulot lisäsivät avioeroriskiä, vaikka miehen suurilla tuloilla oli päinvastainen vaikutus. Lisäksi kotitaloustyötä pääasiallisena toimintanaan tekevillä naisilla (pääasiallisen toiminnan luokka ”muut”) oli vielä pienempi avioeroriski kuin työssäkäyvillä naisilla. Toisessa osatutkimuksessa keskityttiin aviomiehen ja vaimon aseman yhdistettyyn vaikutukseen. Selviä viitteitä siitä, että puolisoiden koulutustasojen erilaisuus lisäisi eroriskiä, ei saatu. Pareilla, joissa molemmilla oli enintään perusasteen koulutus, oli kuitenkin odotettua pienempi avioeroriski. Eroriski oli suhteellisen alhainen pareilla, joissa vaimo oli työssäkäyvä tai kotitaloustyötä tekevä ja aviomies työssäkäyvä. Eroriskiä kasvatti se, että aviomies, vaimo tai molemmat puolisot olivat työttömiä. Vaimon korkea tulotaso lisäsi eroriskiä miehen kaikilla tulotasoilla mutta erityisen voimakkaasti silloin, kun miehen tulotaso oli alhainen. Kolmanneksi selvitettiin, vaikuttaako puolisoiden sosioekonominen asema avioeroriskiin eri tavalla riippuen siitä, kauanko avioliitto on kestänyt. Tällöin havaittiin, että vähän koulutettujen ja työntekijäammateissa toimivien puolisoiden suuri eroriski rajoittuu paljolti nuorimpiin avioliittoihin. Sen sijaan esim. puolisoiden työttömyys, vaimon korkea tulotaso ja vuokra-asunnossa asuminen kasvattivat eroriskiä riippumatta siitä, kuinka kauan avioliitto oli kestänyt. Kaiken kaikkiaan eroriski oli siis sitä pienempi, mitä paremmassa taloudellisessa ja sosiaalisessa asemassa puolisot olivat. Vaimon taloudellisilla ja sosiaalisilla resursseilla näyttää kuitenkin olevan myös joitakin avioeroriskiä lisääviä vaikutuksia.

Hybrid peptide hairpins containing alpha- and omega-amino acids: Conformational analysis of decapeptides with unsubstituted beta-, gamma-, and delta-residues at positions 3 and 8

The effects of inserting unsubstituted omega-amino acids into the strand segments of model beta-hairpin peptides was investigated by using four synthetic decapeptides, Boc-Lcu-Val-Xxx-Val-D-Pro-Gly-Leu-Xxx-Val-Val- OMe: pepticle 1 (Xxx=Gly), pepticle 2 (Xxx=beta Gly=beta hGly=homoglycine, beta-glycine), pepticle 3 (Xxx=gamma Abu=gamma-aminobutyric acid), pepticle 4 (Xxx= delta Ava=delta-aminovaleric acid). H-1 NMR studies (500 MHz, methanol) reveal several critical cross-strand NOEs, providing evidence for P-hairpin conformations in peptides 2-4. In peptide 3, the NMR results support the formation of the nucleating turn, however, evidence for cross-strand registry is not detected. Single-crystal X-ray diffraction studies of peptide 3 reveal a beta-hairpin conformation for both molecules in the crystallographic asymmetric unit, stabilized by four cross-strand hydrogen bonds, with the gamma Abu residues accommodated within the strands. The D-Pro-Gly segment in both molecules (A,B) adopts a type II' beta-turn conformation. The circular dichroism spectrum for peptide 3 is characterized by a negative CD band at 229 rim, whereas for peptides 2 and 4, the negative band is centered at 225 nm, suggesting a correlation between the orientation of the amide units in the strand segments and the observed CD pattern.

An Empirical Investigation of Value-at-Risk in Long and Short Trading Positions

This paper uses the Value-at-Risk approach to define the risk in both long and short trading positions. The investigation is done on some major market indices(Japanese, UK, German and US). The performance of models that takes into account skewness and fat-tails are compared to symmetric models in relation to both the specific model for estimating the variance, and the distribution of the variance estimate used as input in the VaR estimation. The results indicate that more flexible models not necessarily perform better in predicting the VaR forecast; the reason for this is most probably the complexity of these models. A general result is that different methods for estimating the variance are needed for different confidence levels of the VaR, and for the different indices. Also, different models are to be used for the left respectively the right tail of the distribution.

On methods of calculating successive positions of a shock front

In this paper we have discussed limits of the validity of Whitham's characteristic rule for finding successive positions of a shock in one space dimension. We start with an example for which the exact solution is known and show that the characteristic rule gives correct result only if the state behind the shock is uniform. Then we take the gas dynamic equations in two cases: one of a shock propagating through a stratified layer and other down a nonuniform tube and derive exact equations for the evolution of the shock amplitude along a shock path. These exact results are then compared with the results obtained by the characteristic rule. The characteristic rule not only incorrectly accounts for the deviation of the state behind the shock from a uniform state but also gives a coefficient in the equation which differ significantly from the exact coefficients for a wide range of values of the shock strength.

Probing the role of highly conserved residues in triosephosphate isomerase-analysis of site specific mutants at positions 64 and 75 in the Plasmodial enzyme

Highly conserved residues in enzymes are often found to be clustered close to active sites, suggesting that functional constraints dictate the nature of amino acid residues accommodated at these sites. Using the Plasmodiumfalciparum triosephosphate isomerase (PfTIM) enzyme () as a template, we have examined the effects of mutations at positions 64 and 75, which are not directly involved in the proton transfer cycle. Thr (T) occurring at position 75 is completely conserved, whereas only Gln (Q) and Glu (E) are accommodated at position 64. Biophysical and kinetic data are reported for four T75 (T75S/V/C/N) and two Q64 (Q64N/E) mutants. The dimeric structure is weakened in the Q64E and Q64N mutants, whereas dimer integrity is unimpaired in all four T75 mutants. Measurement of the concentration dependence of enzyme activity permits an estimate of K-d values for dimer dissociation (Q64N=73.79.2nm and Q64E=44.6 +/- 8.4nm). The T75S/V/C mutants have activities comparable to the wild-type enzyme, whereas a fourfold drop is observed for T75N. All four T75 mutants show a dramatic fall in activity between 35 degrees C and 45 degrees C. Crystal structure determination of the T75S/V/N mutants provides insights into the variations in local interactions, with the T75N mutant showing the largest changes. Hydrogen-bond interactions determine dimer stability restricting the choice of residues at position 64 to Gln (Q) and Glu (E). At position 75, the overwhelming preference for Thr (T) may be dictated by the imperative of maintaining temperature stability of enzyme activity.

Optimization of positions and currents of tokamak poloidal field coils using genetic algorithms

Plasma equilibrium geometry has a great influence on the confinement and magnetohydrodynamic stability in tokamaks. The poloidal field (PF) system of a tokamak should be optimized to support the prescribed plasma equilibrium geometry. In this paper, a genetic algorithm-based method is applied to solve the optimization of the positions and currents of tokamak PF coils. To achieve this goal, we first describe the free-boundary code EQT Based on the EQT code, a genetic algorithm-based method is introduced to the optimization. We apply this new method to the PF system design of the fusion-driven subcritical system and plasma equilibrium geometry optimization of the Experimental Advanced Superconducting Tokamak (EAST). The results indicate that the optimization of the plasma equilibrium geometry can be improved by using this method.

Part I. Efforts directed towards the total synthesis of shionone. Part II. Conversion of estrone to androst-4-EN-3-ONE: a new method for activating the C-9 and C-10 positions of estrogenic steroids for substitution

Part I: An approach to the total synthesis of the triterpene shionone is described, which proceeds through the tetracyclic ketone i. The shionone side chain has been attached to this key intermediate in 5 steps, affording the olefin 2 in 29% yield. A method for the stereo-specific introduction of the angular methyl group at C-5 of shionone has been developed on a model system. The attempted utilization of this method to convert olefin 2 into shionone is described.

Part II: A method has been developed for activating the C-9 and C-10 positions of estrogenic steroids for substitution. Estrone has been converted to 4β,5β-epoxy-10β-hydroxyestr-3-one; cleavage of this epoxyketone using an Eschenmoser procedure, and subsequent modification of the product afforded 4-seco-9-estren-3,5-dione 3-ethylene acetal. This versatile intermediate, suitable for substitution at the 9 and/or 10 position, was converted to androst-4-ene-3-one by known procedures.

Contrasting abundance and residency patterns of two sympatric populations of transient killer whales (Orcinus orca) in the northern Gulf of Alaska

Two sympatric populations of “transient” (mammal-eating) killer whales were photo-identified over 27 years (1984–2010) in Prince William Sound and Kenai Fjords, coastal waters of the northern Gulf of Alaska (GOA). A total of 88 individuals were identified during 203 encounters with “AT1” transients (22 individuals) and 91 encounters with “GOA” transients (66 individuals). The median number of individuals identified annually was similar for both populations (AT1=7; GOA=8), but mark-recapture estimates showed the AT1 whales to have much higher fidelity to the study area, whereas the GOA whales had a higher exchange of individuals. Apparent survival estimates were generally high for both populations, but there was a significant reduction in the survival of AT1 transients after the Exxon Valdez oil spill in 1989, with an abrupt decline in estimated abundance from a high of 22 in 1989 to a low of seven whales at the end of 2010. There was no detectable decline in GOA population abundance or survival over the same period, but abundance ranged from just 6 to 18 whales annually. Resighting data from adjacent coastal waters and movement tracks from satellite tags further indicated that the GOA whales are part of a larger population with a more extensive range, whereas AT1 whales are resident to the study area.

Home range and seasonal movements of Black Sea Bass (Centropristis striata) during their inshore residency at a reef in the mid-Atlantic Bight

Black Sea Bass (Centropristis striata) in the mid-Atlantic Bight undertake seasonal cross-shelf movements to occupy inshore rocky reefs and hardbottom habitats between spring and fall. Shelf-wide migrations of this stock are well documented, but movements and home ranges of fish during their inshore residency period have not been described. We tagged 122 Black Sea Bass with acoustic transmitters at a mid-Atlantic reef to estimate home-range size and factors that influence movements (>400 m) at a 46.1-km2 study site between May and November 2003. Activity of Black Sea Bass was greatest and most consistent during summer but declined rapidly in September as water temperatures at the bottom of the seafloor increased on the inner shelf. Black Sea Bass maintained relatively large home ranges that were fish-size invariant but highly variable (13.7–736.4 ha), underscoring the importance of large sample sizes in examination of population-level characteristics of mobile species with complex social interactions. On the basis of observed variations in movement patterns and the size of home ranges, we postulate the existence of groups of conspecifics that exhibit similar space-use behaviors. The group of males released earlier in the tagging period used larger home ranges than the group of males released later in our study. In addition, mean activity levels and the probability of movement among acoustic stations varied among groups of fish in a complex manner that depended on sex. These differences in movement behaviors may increase the vulnerability of male fish to passive fishing gears, further exacerbating variation in exploitation rates for this species among reefs.

Some effects of Earth's surface on winter jet stream positions in the Northern Hemisphere and rainfall patterns in northern and central California

EXTRACT (SEE PDF FOR FULL ABSTRACT): This report shows that the mean wintertime polar-front jet stream structure consists of three long waves. Prominent ridges in the jet stream flow occur near the longitudes of India, eastern Pacific/west coast of North America, and eastern Atlantic/British Isles; prominent troughs occur near the longitudes of the Middle East, western Pacific, and western Atlantic/east coast of North America. ... One of the climatological ridges occurs along the west coast of North America ... just off the central Oregon coast. The position of the jet stream at this location appears to be the main reason most Pacific storms pass to the north of California. Sustained rainfall in northern and central California occurs only when the storm track is displaced southward of this climatological position.