Analysis of void volumes in proteins and application to stability of the p53 tumour suppressor protein

We have developed a new method for the analysis of voids in proteins (defined as empty cavities not accessible to solvent). This method combines analysis of individual discrete voids with analysis of packing quality. While these are different aspects of the same effect, they have traditionally been analysed using different approaches. The method has been applied to the calculation of total void volume and maximum void size in a non-redundant set of protein domains and has been used to examine correlations between thermal stability and void size. The tumour-suppressor protein p53 has then been compared with the non-redundant data set to determine whether its low thermal stability results from poor packing. We found that p53 has average packing, but the detrimental effects of some previously unexplained mutations to p53 observed in cancer can be explained by the creation of unusually large voids. (C) 2004 Elsevier Ltd. All rights reserved.

Ditopic hexaazamacrocycles containing pyridine: synthesis, protonation and complexation studies

Structural studies of metal complexes of five ditopic hexaazamacrocycles containing two pyridine rings ([n] py(2)N(4) n = 18, 20, 22, 24 and 26) have been carried out. The synthesis of macrocycles [22]- to [26]- py(2)N(4) are also reported. The protonation constants of the last three compounds and the stability constants of their complexes with Ni2+, Cu2+, Zn2+, and Pb2+ were determined at 25 degreesC in 0.10 mol dm(-3) KNO3 in aqueous solution. Our results with [22] py(2)N(4) show significant differences from those described previously, while [24] py(2)N(4) has not been studied before and [ 26] py2N4 is a new compound. Mononuclear and dinuclear complexes of the divalent metal ions studied with [ 22]- to [26]- py(2)N(4) were found in solution. The stability constants for the ML complexes of the three ligands follow the Irving - Williams order: NiL2+ < CuL2+ >> ZnL2+ > PbL2+, however for the dinuclear complexes the values for Pb2+ complexes are higher than the corresponding values for the Ni2+ and the Zn2+ complexes. The X-ray single crystal structures of the supramolecular aggregates [Cu-2([20] py(2)N(4))(H2O)(4)][Cu(H2O)(6)](SO4)(3) . 3H(2)O ( 1) and [Cu-2([20] py(2)N(4))(CH3CN)(4)][Ni([20] py(2)N(4))](2)(ClO4)(8) . H2O (2), which are composed of homodinuclear [Cu-2([20] py(2)N(4)])(H2O)(4)](4+) ( 1a) and [Cu-2([20] py(2)N(4)])(CH3CN))(4)](4+) (2a), and mononuclear species, [Cu(H2O)(6)](2+) (1b) and [Ni([20] py(2)N(4))](2+) ( 2b), respectively, assembled by an extensive network of hydrogen bonds, are also reported. In both homodinuclear complexes the copper centres are located at the end of the macrocycle and display distorted square pyramidal coordination environments with the basal plane defined by three consecutive nitrogen donors and one solvent molecule, water in 1a and acetonitrile in 2a. The macrocycle adopts a concertina-type conformation leading to the formation of macrocyclic cavities with the two copper centres separated by intramolecular distances of 5.526(1) and 5.508(7) Angstrom in 1a and 2a, respectively. The mononuclear complex [Ni([20] py(2)N(4)])](2+) displays a distorted octahedral co-ordination environment with the macrocycle wrapping the metal centre in a helical shape. EPR spectroscopy of the copper complexes indicated the presence of mono- and dinuclear species.

Thallium pi-cation complexation by calix[4]tubes: Tl-205 NMR and X-ray evidence

Thallium cation complexation by calix[4]tubes has been investigated by a combination of (TI)-T-205, H-1 NMR and ES MS demonstrating the solution formation of a dithallium complex in which the cations are held in the calix[4]arene cavities. In addition, the structure of the complex has been determined in the solid state revealing the cations to be held exclusively by pi-cation interactions. Furthermore, this crystal structure has been used as the basis for molecular dynamics simulations to confirm that binding of the smaller K+ cation in the calix[4]tube cryptand like array occurs via the axial route featuring a g-cation intermediate.

The incidence of oral Gram-negative bacteria in patients with Parkinson's disease

Background: Parkinson's disease is a common neurodegenerative disorder that affects an increasing number of older people every year. Dysphagia is not only a common feature, but one that results in poor nutrition and an increased risk of bronchopneumonia. Previous work has suggested that the oral flora is altered in patients with oral pathology. Methods: Fifty patients were assessed to quantify the incidence of oral Gram-negative bacteria. Results: Sixteen of the patients with Parkinson's disease were found to have six different Gram-negative bacilli in their oral cavities. The 20 different Gram-negative bacteria present were Escherichia coli (n=7), Klebsiella spp. (n=3), Kluyvera spp. (n=3), Serratia spp. (n=3), Proteus spp. (n=2) and Enterobacter spp. (n=2). We found that the oral cavity of 16 (32%) of the patients with Parkinson's disease was abnormally colonised with Gram-negative bacteria and that Gram-negative bacteria were more likely to occur in those patients in whom oromuscular dysfunction was present (88% vs. 21%; p<0.05). Conclusion: Further work is required to determine the association between oral flora and the pathogenic organisms found in aspiration pneumonia as well as work on innovative treatments to reduce oral Gram-negative bacteria in those patients at particular risk of aspiration pneumonia.

A statistical mechanical approach for the computation of the climatic response to general forcings

The climate belongs to the class of non-equilibrium forced and dissipative systems, for which most results of quasi-equilibrium statistical mechanics, including the fluctuation-dissipation theorem, do not apply. In this paper we show for the first time how the Ruelle linear response theory, developed for studying rigorously the impact of perturbations on general observables of non-equilibrium statistical mechanical systems, can be applied with great success to analyze the climatic response to general forcings. The crucial value of the Ruelle theory lies in the fact that it allows to compute the response of the system in terms of expectation values of explicit and computable functions of the phase space averaged over the invariant measure of the unperturbed state. We choose as test bed a classical version of the Lorenz 96 model, which, in spite of its simplicity, has a well-recognized prototypical value as it is a spatially extended one-dimensional model and presents the basic ingredients, such as dissipation, advection and the presence of an external forcing, of the actual atmosphere. We recapitulate the main aspects of the general response theory and propose some new general results. We then analyze the frequency dependence of the response of both local and global observables to perturbations having localized as well as global spatial patterns. We derive analytically several properties of the corresponding susceptibilities, such as asymptotic behavior, validity of Kramers-Kronig relations, and sum rules, whose main ingredient is the causality principle. We show that all the coefficients of the leading asymptotic expansions as well as the integral constraints can be written as linear function of parameters that describe the unperturbed properties of the system, such as its average energy. Some newly obtained empirical closure equations for such parameters allow to define such properties as an explicit function of the unperturbed forcing parameter alone for a general class of chaotic Lorenz 96 models. We then verify the theoretical predictions from the outputs of the simulations up to a high degree of precision. The theory is used to explain differences in the response of local and global observables, to define the intensive properties of the system, which do not depend on the spatial resolution of the Lorenz 96 model, and to generalize the concept of climate sensitivity to all time scales. We also show how to reconstruct the linear Green function, which maps perturbations of general time patterns into changes in the expectation value of the considered observable for finite as well as infinite time. Finally, we propose a simple yet general methodology to study general Climate Change problems on virtually any time scale by resorting to only well selected simulations, and by taking full advantage of ensemble methods. The specific case of globally averaged surface temperature response to a general pattern of change of the CO2 concentration is discussed. We believe that the proposed approach may constitute a mathematically rigorous and practically very effective way to approach the problem of climate sensitivity, climate prediction, and climate change from a radically new perspective.

Arthrobacter nasiphocae sp. nov., from the common seal (Phoca vitulina)

An unknown gram-positive, catalase-positive, strictly aerobic, rod-shaped bacterium was isolated from the nasal cavities of two common seals. Chemical analysis revealed the presence in the bacterium of a hitherto unknown cell-wall murein [type: L-Lys-L-Ala2-Gly(2-3)-L-Ala (Gly)]. Comparative 16S rRNA gene sequencing showed that the unidentified rod was related to the Arthrobacter group of organisms, although sequence divergence values of >3% from established members of this genus indicated that it represents a novel species. On the basis of phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium from seals (Phoca vitulina) be classified as a novel species, Arthrobacter nasiphocae sp. nov. The type strain of Arthrobacter nasiphocae is CCUG 42953T.

Metal-directed assembly of large dinuclear copper(II) dithiocarbamate macrocyclic complexes

The synthesis of a range of dinuclear Cu(II) dithiocarbamate (dtc)-based macrocycles and their characterisation are described. By carefully tuning the size of the aromatic spacer, cavities of different dimensions can be designed. The length and flexibility of the chosen spacer group dictates the intermetallic distance and hence the degree of communication between the two metal centres as evidenced by electrochemical and EPR experiments. This is illustrated by crystallographic evidence that show the macrocycles can host guests (such as CH2Cl2) or can fold and form unexpected Cu(I) dtc clusters.

Quantifying chaos: a tale of two maps

In many applications, there is a desire to determine if the dynamics of interest are chaotic or not. Since positive Lyapunov exponents are a signature for chaos, they are often used to determine this. Reliable estimates of Lyapunov exponents should demonstrate evidence of convergence; but literature abounds in which this evidence lacks. This paper presents two maps through which it highlights the importance of providing evidence of convergence of Lyapunov exponent estimates. The results suggest cautious conclusions when confronted with real data. Moreover, the maps are interesting in their own right.

Guanine specific binding at a DNA junction formed by d[CG(5-BrU)ACG]2 with a topoisomerase poison in the presence of Co2+Ions†,‡

The structure of the duplex d[CG(5-BrU)ACG]2 bound to 9-bromophenazine-4-carboxamide has been solved through MAD phasing at 2.0 Å resolution. It shows an unexpected and previously unreported intercalation cavity stabilized by the drug and novel binding modes of Co2+ ions at certain guanine N7 sites. For the intercalation cavity the terminal cytosine is rotated to pair with the guanine of a symmetry-related duplex to create a pseudo-Holliday junction geometry, with two such cavities linked through the minor groove interactions of the N2/N3 guanine sites at an angle of 40°, creating a quadruplex-like structure. The mode of binding of the drug is shown to be disordered, with the major conformations showing the side chain bound to the N7 position of adjacent guanines. The other end of the duplex exhibits a terminal base fraying in the presence of Co2+ ions linking symmetry-related guanines, causing the helices to intertwine through the minor groove. The stabilization of the structure by the intercalating drug shows that this class of compound may bind to DNA junctions as well as duplex DNA or to strand-nicked DNA (‘hemi-intercalated'), as in the cleavable complex. This suggests a structural basis for the dual poisoning of topoisomerase I and II enzymes by this family of drugs.

Frontiers and borderlands in Imperial perspectives: exploring Rome’s Egyptian frontier

Archaeological research has addressed imperial frontiers for more than a century. Romanists, in particular, have engaged in exploring frontiers from economic, militaristic, political, and (more recently) social vantages. This article suggests that we also consider the dialogue between space and social perception to understand imperial borderland developments. In addition to formulating new theoretical approaches to frontiers, this contribution represents the first comprehensive overview of both the documentary sources and the archaeological material found in Egypt's Great Oasis during the Roman period (ca. 30 B.C.E. to the sixth century C.E.). A holistic analysis of these sources reveals that Egypt's Great Oasis, which consisted of two separate but linked oases, served as a conceptual, physical, and human buffer zone for the Roman empire. This buffer zone protected the "ordered" Nile Valley inhabitants from the "chaotic" desert nomads, who lived just beyond the oases. This conclusion suggests that nomads required specific imperial frontier policies and that these policies may have been ideological as well as economic and militaristic.

Response theory for equilibrium and non-equilibrium statistical mechanics: causality and generalized Kramers-Kronig relations

We consider the general response theory recently proposed by Ruelle for describing the impact of small perturbations to the non-equilibrium steady states resulting from Axiom A dynamical systems. We show that the causality of the response functions entails the possibility of writing a set of Kramers-Kronig (K-K) relations for the corresponding susceptibilities at all orders of nonlinearity. Nonetheless, only a special class of directly observable susceptibilities obey K-K relations. Specific results are provided for the case of arbitrary order harmonic response, which allows for a very comprehensive K-K analysis and the establishment of sum rules connecting the asymptotic behavior of the harmonic generation susceptibility to the short-time response of the perturbed system. These results set in a more general theoretical framework previous findings obtained for optical systems and simple mechanical models, and shed light on the very general impact of considering the principle of causality for testing self-consistency: the described dispersion relations constitute unavoidable benchmarks that any experimental and model generated dataset must obey. The theory exposed in the present paper is dual to the time-dependent theory of perturbations to equilibrium states and to non-equilibrium steady states, and has in principle similar range of applicability and limitations. In order to connect the equilibrium and the non equilibrium steady state case, we show how to rewrite the classical response theory by Kubo so that response functions formally identical to those proposed by Ruelle, apart from the measure involved in the phase space integration, are obtained. These results, taking into account the chaotic hypothesis by Gallavotti and Cohen, might be relevant in several fields, including climate research. In particular, whereas the fluctuation-dissipation theorem does not work for non-equilibrium systems, because of the non-equivalence between internal and external fluctuations, K-K relations might be robust tools for the definition of a self-consistent theory of climate change.

Evidence of dispersion relations for the nonlinear response of the Lorenz 63 system

Along the lines of the nonlinear response theory developed by Ruelle, in a previous paper we have proved under rather general conditions that Kramers-Kronig dispersion relations and sum rules apply for a class of susceptibilities describing at any order of perturbation the response of Axiom A non equilibrium steady state systems to weak monochromatic forcings. We present here the first evidence of the validity of these integral relations for the linear and the second harmonic response for the perturbed Lorenz 63 system, by showing that numerical simulations agree up to high degree of accuracy with the theoretical predictions. Some new theoretical results, showing how to derive asymptotic behaviors and how to obtain recursively harmonic generation susceptibilities for general observables, are also presented. Our findings confirm the conceptual validity of the nonlinear response theory, suggest that the theory can be extended for more general non equilibrium steady state systems, and shed new light on the applicability of very general tools, based only upon the principle of causality, for diagnosing the behavior of perturbed chaotic systems and reconstructing their output signals, in situations where the fluctuation-dissipation relation is not of great help.

Stochastic perturbations to dynamical systems: a response theory approach

Using the formalism of the Ruelle response theory, we study how the invariant measure of an Axiom A dynamical system changes as a result of adding noise, and describe how the stochastic perturbation can be used to explore the properties of the underlying deterministic dynamics. We first find the expression for the change in the expectation value of a general observable when a white noise forcing is introduced in the system, both in the additive and in the multiplicative case. We also show that the difference between the expectation value of the power spectrum of an observable in the stochastically perturbed case and of the same observable in the unperturbed case is equal to the variance of the noise times the square of the modulus of the linear susceptibility describing the frequency-dependent response of the system to perturbations with the same spatial patterns as the considered stochastic forcing. This provides a conceptual bridge between the change in the fluctuation properties of the system due to the presence of noise and the response of the unperturbed system to deterministic forcings. Using Kramers-Kronig theory, it is then possible to derive the real and imaginary part of the susceptibility and thus deduce the Green function of the system for any desired observable. We then extend our results to rather general patterns of random forcing, from the case of several white noise forcings, to noise terms with memory, up to the case of a space-time random field. Explicit formulas are provided for each relevant case analysed. As a general result, we find, using an argument of positive-definiteness, that the power spectrum of the stochastically perturbed system is larger at all frequencies than the power spectrum of the unperturbed system. We provide an example of application of our results by considering the spatially extended chaotic Lorenz 96 model. These results clarify the property of stochastic stability of SRB measures in Axiom A flows, provide tools for analysing stochastic parameterisations and related closure ansatz to be implemented in modelling studies, and introduce new ways to study the response of a system to external perturbations. Taking into account the chaotic hypothesis, we expect that our results have practical relevance for a more general class of system than those belonging to Axiom A.

Chaos in high performance digital robot controllers

Active robot force control requires some form of dynamic inner loop control for stability. The author considers the implementation of position-based inner loop control on an industrial robot fitted with encoders only. It is shown that high gain velocity feedback for such a robot, which is effectively stationary when in contact with a stiff environment, involves problems beyond the usual caveats on the effects of unknown environment stiffness. It is shown that it is possible for the controlled joint to become chaotic at very low velocities if encoder edge timing data are used for velocity measurement. The results obtained indicate that there is a lower limit on controlled velocity when encoders are the only means of joint measurement. This lower limit to speed is determined by the desired amount of loop gain, which is itself determined by the severity of the nonlinearities present in the drive system.

Probabilistic evaluation of time series models : a comparison of several approaches

Several methods are examined which allow to produce forecasts for time series in the form of probability assignments. The necessary concepts are presented, addressing questions such as how to assess the performance of a probabilistic forecast. A particular class of models, cluster weighted models (CWMs), is given particular attention. CWMs, originally proposed for deterministic forecasts, can be employed for probabilistic forecasting with little modification. Two examples are presented. The first involves estimating the state of (numerically simulated) dynamical systems from noise corrupted measurements, a problem also known as filtering. There is an optimal solution to this problem, called the optimal filter, to which the considered time series models are compared. (The optimal filter requires the dynamical equations to be known.) In the second example, we aim at forecasting the chaotic oscillations of an experimental bronze spring system. Both examples demonstrate that the considered time series models, and especially the CWMs, provide useful probabilistic information about the underlying dynamical relations. In particular, they provide more than just an approximation to the conditional mean.