Protein kinases associated with the yeast phosphoproteome

BACKGROUND: Protein phosphorylation is an extremely important mechanism of cellular regulation. A large-scale study of phosphoproteins in a whole-cell lysate of Saccharomyces cerevisiae has previously identified 383 phosphorylation sites in 216 peptide sequences. However, the protein kinases responsible for the phosphorylation of the identified proteins have not previously been assigned. RESULTS: We used Predikin in combination with other bioinformatic tools, to predict which of 116 unique protein kinases in yeast phosphorylates each experimentally determined site in the phosphoproteome. The prediction was based on the match between the phosphorylated 7-residue sequence and the predicted substrate specificity of each kinase, with the highest weight applied to the residues or positions that contribute most to the substrate specificity. We estimated the reliability of the predictions by performing a parallel prediction on phosphopeptides for which the kinase has been experimentally determined. CONCLUSION: The results reveal that the functions of the protein kinases and their predicted phosphoprotein substrates are often correlated, for example in endocytosis, cytokinesis, transcription, replication, carbohydrate metabolism and stress response. The predictions link phosphoproteins of unknown function with protein kinases with known functions and vice versa, suggesting functions for the uncharacterized proteins. The study indicates that the phosphoproteins and the associated protein kinases represented in our dataset have housekeeping cellular roles; certain kinases are not represented because they may only be activated during specific cellular responses. Our results demonstrate the utility of our previously reported protein kinase substrate prediction approach (Predikin) as a tool for establishing links between kinases and phosphoproteins that can subsequently be tested experimentally

Frustration - how it can be measured

A misfit parameter is used to characterize the degree of frustration of ordered and disordered systems. It measures the increase of the ground-state energy due to frustration in comparison with that of a relevant reference state. The misfit parameter is calculated for various spin-glass models. It allows one to compare these models with each other. The extension of this concept to other combinatorial optimization problems with frustration, e.g. p-state Potts glasses, graph-partitioning problems and coloring problems is given.Comment: 10 pages, 1 table, no figures, uses revtex.st

Using the local density approximation and the LYP, BLYP, and B3LYP functionals within Reference--State One--Particle Density--Matrix Theory

For closed-shell systems, the local density approximation (LDA) and the LYP, BLYP, and B3LYP functionals are shown to be compatible with reference-state one-particle density-matrix theory, where this recently introduced formalism is based on Brueckner-orbital theory and an energy functional that includes exact exchange and a non-universal correlation-energy functional. The method is demonstrated to reduce to a density functional theory when the exchange-correlation energy-functional has a simplified form, i.e., its integrand contains only the coordinates of two electron, say r1 and r2, and it has a Dirac delta function -- delta(r1 - r2) -- as a factor. Since Brueckner and Hartree--Fock orbitals are often very similar, any local exchange functional that works well with Hartree--Fock theory is a reasonable approximation with reference-state one-particle density-matrix theory. The LDA approximation is also a reasonable approximation. However, the Colle--Salvetti correlation-energy functional, and the LYP variant, are not ideal for the method, since these are universal functionals. Nevertheless, they appear to provide reasonable approximations. The B3LYP functional is derived using a linear combination of two functionals: One is the BLYP functional; the other uses exact exchange and a correlation-energy functional from the LDA.Comment: 26 Pages, 0 figures, RevTeX 4, Submitted to Mol. Phy

On the Quasiparticle Description of Lattice QCD Thermodynamics

We propose a novel quasiparticle interpretation of the equation of state of deconfined QCD at finite temperature. Using appropriate thermal masses, we introduce a phenomenological parametrization of the onset of confinement in the vicinity of the predicted phase transition. Lattice results of the energy density, the pressure and the interaction measure of pure SU(3) gauge theory are excellently reproduced. We find a relationship between the thermal energy density of the Yang-Mills vacuum and the chromomagnetic condensate _T. Finally, an extension to QCD with dynamical quarks is discussed. Good agreement with lattice data for 2, 2+1 and 3 flavour QCD is obtained. We also present the QCD equation of state for realistic quark masses.Comment: 20 pages, 10 eps figure

Postglacial vegetation and climate change in the Lake Onega region of eastern Fennoscandia derived from a radiocarbon-dated pollen record

With its numerous environmental archives stored in lake and peat sediments and relatively low human pressure, the Lake Onega region in eastern Fennoscandia is regarded as a particularly promising area for studying past changes in vegetation and climate since the Lateglacial period. The 885-cm-long sediment core RZ19 (62°27′53″N, 34°26′4″E) was collected from Razlomnoe Peat on the northern shore of Lake Onega in 2019, radiocarbon-dated and analysed for pollen and cryptogam spores. The age-depth model suggests continuous sedimentation since ca. 11,800 a BP (all ages given in years (a) or kiloyears (ka) before present (BP) with BP referring to 1950 CE). The results of pollen analysis and pollen-based biome reconstruction show rapid afforestation of the area in the Early Holocene, although the scores of the tundra biome remain relatively high prior to ca. 11,450 a BP, suggesting that the vegetation was likely more open than today. Between 8300 and 8000 a BP, Betula sect. Albae shows a marked increase in pollen percentage, while Pinus sylvestris experiences a marked decrease. These changes coinciding with the 8.2 ka BP cooling event indicate less favourable conditions for Scots pine while being beneficial for fast-growing birch. The transition from the Early to Middle Holocene (i.e. from Greenlandian to Northgrippian) is marked by an increase in pollen productivity, spread of Picea and further afforestation of the area. The decrease in arboreal and Picea pollen percentages and the abrupt increase in landscape openness after ca. 4000 a BP mark the onset of the Late Holocene (i.e. Northgrippian-Meghalayan transition) and likely reflect the combined effect of insolation-induced temperature decrease and associated paludification and forest retreat rather than a decrease in atmospheric precipitation and/or spread of Late Neolithic agriculture

Strong time operators associated with generalized Hamiltonians

Let the pair of operators, $(H, T)$, satisfy the weak Weyl relation: $Te^{-itH} = e^{-itH}(T + t)$, where $H$ is self-adjoint and $T$ is closed symmetric. Suppose that g is a realvalued Lebesgue measurable function on \RR such that $g \in C^2(R K)$ for some closed subset K \subset \RR with Lebesgue measure zero. Then we can construct a closed symmetric operator $D$ such that $(g(H), D)$ also obeys the weak Weyl relation.Comment: 10 page

Time decay of the remanent magnetization in the ±J\pm J spin glass model at T=0

Using the zero-temperature Metropolis dynamics, the time decay of the remanent magnetization in the $\pm J$ Edward-Anderson spin glass model with a uniform random distribution of ferromagnetic and antiferromagnetic interactions has been investigated. Starting from the saturation, the magnetization per spin $m$ reveals a slow decrease with time, which can be approximated by a power law:$m(t)=m_{\infty}+ ({t\over a_{0}})^{a_{1}}$, $a_{1} < 0$. Moreover, its relaxation does not lead it into one of the ground states, and therefore the system is trapped in metastable isoenergetic microstates remaining magnetized. Such behaviour is discussed in terms of a random walk the system performs on its available configuration space.Comment: 9 pages, 3 figure

Predicting Protein Kinase Specificity: Predikin Update and Performance in the DREAM4 Challenge

Predikin is a system for making predictions about protein kinase specificity. It was declared the “best performer” in the protein kinase section of the Peptide Recognition Domain specificity prediction category of the recent DREAM4 challenge (an independent test using unpublished data). In this article we discuss some recent improvements to the Predikin web server — including a more streamlined approach to substrate-to-kinase predictions and whole-proteome predictions — and give an analysis of Predikin's performance in the DREAM4 challenge. We also evaluate these improvements using a data set of yeast kinases that have been experimentally characterised, and we discuss the usefulness of Frobenius distance in assessing the predictive power of position weight matrices

Effects of growth rate, size, and light availability on tree survival across life stages: a demographic analysis accounting for missing values and small sample sizes.

The data set supporting the results of this article is available in the Dryad repository, http://dx.doi.org/10.5061/dryad.6f4qs. Moustakas, A. and Evans, M. R. (2015) Effects of growth rate, size, and light availability on tree survival across life stages: a demographic analysis accounting for missing values.Plant survival is a key factor in forest dynamics and survival probabilities often vary across life stages. Studies specifically aimed at assessing tree survival are unusual and so data initially designed for other purposes often need to be used; such data are more likely to contain errors than data collected for this specific purpose

Time in Quantum Mechanics and Quantum Field Theory

W. Pauli pointed out that the existence of a self-adjoint time operator is incompatible with the semibounded character of the Hamiltonian spectrum. As a result, people have been arguing a lot about the time-energy uncertainty relation and other related issues. In this article, we show in details that Pauli's definition of time operator is erroneous in several respects.Comment: 20 page