Dynamics of Co-translational Membrane Protein Integration and Translocation via the Sec Translocon

An important aspect of cellular function is the correct targeting and delivery of newly synthesized proteins. Central to this task is the machinery of the Sec translocon, a transmembrane channel that is involved in both the translocation of nascent proteins across cell membranes and the integration of proteins into the membrane. Considerable experimental and computational effort has focused on the Sec translocon and its role in nascent protein biosynthesis, including the correct folding and expression of integral membrane proteins. However, the use of molecular simulation methods to explore Sec-facilitated protein biosynthesis is hindered by the large system sizes and long (i.e., minute) timescales involved. In this work, we describe the development and application of a coarse-grained simulation approach that addresses these challenges and allows for direct comparison with both in vivo and in vitro experiments. The method reproduces a wide range of experimental observations, providing new insights into the underlying molecular mechanisms, predictions for new experiments, and a strategy for the rational enhancement of membrane protein expression levels

A Two-Coordinate Nickel Imido Complex That Effects C−H Amination

An exceptionally low coordinate nickel imido complex, (IPr*)Ni═N(dmp) (2) (dmp = 2,6-dimesitylphenyl), has been prepared by the elimination of N_2 from a bulky aryl azide in its reaction with (IPr*)Ni(η^6-C_7H_8) (1). The solid-state structure of 2 features two-coordinate nickel with a linear C−Ni−N core and a short Ni−N distance, both indicative of multiple-bond character. Computational studies using density functional theory showed a Ni═N bond dominated by Ni(dπ)−N(pπ) interactions, resulting in two nearly degenerate singly occupied molecular orbitals (SOMOs) that are Ni−N π* in character. Reaction of 2 with CO resulted in nitrene-group transfer to form (dmp)NCO and (IPr*)Ni(CO)_3 (3). Net C−H insertion was observed in the reaction of 2 with ethene, forming the vinylamine (dmp)NH(CH═CH_2) (5) via an azanickelacyclobutane intermediate, (IPr*)Ni{N,C:κ^2-N(dmp)CH_2CH_2} (4)

The niche party concept and its measurement

The concept of the niche party has become increasingly popular in analyses of party competition. Yet, existing approaches vary in their definitions and their measurement approaches. We propose using a minimal definition that allows us to compare political parties in terms of their ‘nicheness’. We argue that the conceptual core of the niche party concept is based on issue emphasis and that a niche party emphasizes policy areas neglected by its rivals. Based on this definition, we propose a continuous measure that allows for more fine-grained measurement of a party’s ‘nicheness’ than the dominant, dichotomous approaches and thereby limits the risk of measurement error. Drawing on data collected by the Comparative Manifesto Project, we show that (1) our measure has high face validity and (2) exposes differences among parties that are not captured by alternative, static or dichotomous measures

Bias Analysis in Entropy Estimation

We consider the problem of finite sample corrections for entropy estimation. New estimates of the Shannon entropy are proposed and their systematic error (the bias) is computed analytically. We find that our results cover correction formulas of current entropy estimates recently discussed in literature. The trade-off between bias reduction and the increase of the corresponding statistical error is analyzed.Comment: 5 pages, 3 figure

Identification of two Mycobacterium tuberculosis H37Rv ORFs involved in resistance to killing by human macrophages

BACKGROUND: The ability of Mycobacterium tuberculosis to survive and replicate in macrophages is crucial for the mycobacterium's ability to infect the host and cause tuberculosis. To identify Mycobacterium tuberculosis genes involved in survival in macrophages, a library of non-pathogenic Mycobacterium smegmatis bacteria, each carrying an individual integrated cosmid containing M. tuberculosis H37Rv genomic DNA, was passed through THP-1 human macrophages three times. RESULTS: Two of the clones recovered from this enrichment process, sur2 and sur3, exhibited significantly increased survival relative to wild-type bacteria. In coinfection experiments, the ratio of sur2 colonies to wild-type colonies was 1:1 at 0 hours but increased to 20:1 at 24 hours post phagocytosis. The ratio of sur3 colonies to wild-type colonies was 1:1 at 0 hours and 5:1 at 24 hours. The M. tuberculosis ORFs responsible for increased survival were shown to be Rv0365c for the sur2 clone and Rv2235 for the sur3 clone. These ORFs encode proteins with as-of-yet unknown functions. CONCLUSIONS: We identified two M. tuberculosis ORFs which may be involved in the ability of tubercle bacilli to survive in macrophages