CCBuilder:An interactive web-based tool for building, designing and assessing coiled-coil protein assemblies

Motivation: The ability to accurately model protein structures at the atomistic level underpins efforts to understand protein folding, to engineer natural proteins predictably and to design proteins de novo . Homology-based methods are well established and produce impressive results. However, these are limited to structures presented by and resolved for natural proteins. Addressing this problem more widely and deriving truly ab initio models requires mathematical descriptions for protein folds; the means to decorate these with natural, engineered or de novo sequences; and methods to score the resulting models. Results: We present CCBuilder, a web-based application that tackles the problem for a defined but large class of protein structure, the α-helical coiled coils. CCBuilder generates coiled-coil backbones, builds side chains onto these frameworks and provides a range of metrics to measure the quality of the models. Its straightforward graphical user interface provides broad functionality that allows users to build and assess models, in which helix geometry, coiled-coil architecture and topology and protein sequence can be varied rapidly. We demonstrate the utility of CCBuilder by assembling models for 653 coiled-coil structures from the PDB, which cover >96% of the known coiled-coil types, and by generating models for rarer and de novo coiled-coil structures. Availability and implementation: CCBuilder is freely available, without registration, at http://coiledcoils.chm.bris.ac.uk/app/cc_builder

Interpretation of heart rate variability via detrended fluctuation analysis and alpha-beta filter

Detrended fluctuation analysis (DFA), suitable for the analysis of nonstationary time series, has confirmed the existence of persistent long-range correlations in healthy heart rate variability data. In this paper, we present the incorporation of the alpha-beta filter to DFA to determine patterns in the power-law behaviour that can be found in these correlations. Well-known simulated scenarios and real data involving normal and pathological circumstances were used to evaluate this process. The results presented here suggest the existence of evolving patterns, not always following a uniform power-law behaviour, that cannot be described by scaling exponents estimated using a linear procedure over two predefined ranges. Instead, the power law is observed to have a continuous variation with segment length. We also show that the study of these patterns, avoiding initial assumptions about the nature of the data, may confer advantages to DFA by revealing more clearly abnormal physiological conditions detected in congestive heart failure patients related to the existence of dominant characteristic scales.Comment: 18 pages, 14 figure

Modular Design of Self-Assembling Peptide-Based Nanotubes.

An ability to design peptide-based nanotubes (PNTs) rationally with defined and mutable internal channels would advance understanding of peptide self-assembly, and present new biomaterials for nanotechnology and medicine. PNTs have been made from Fmoc dipeptides, cyclic peptides, and lock-washer helical bundles. Here we show that blunt-ended α-helical barrels, that is, preassembled bundles of α-helices with central channels, can be used as building blocks for PNTs. This approach is general and systematic, and uses a set of de novo helical bundles as standards. One of these bundles, a hexameric α-helical barrel, assembles into highly ordered PNTs, for which we have determined a structure by combining cryo-transmission electron microscopy, X-ray fiber diffraction, and model building. The structure reveals that the overall symmetry of the peptide module plays a critical role in ripening and ordering of the supramolecular assembly. PNTs based on pentameric, hexameric, and heptameric α-helical barrels sequester hydrophobic dye within their lumens.N.C.B. thanks the EPSRC-funded Bristol Centre for Functional Nanomaterials Centre for Doctoral Training for a postgraduate scholarship (EP/G036780/1). F.T. and D.N.W. thank the Leverhulme Trust for funding (RPG-2012-536). D.N.W. holds a Royal Society Wolfson Research Merit Award.This is the author accepted manuscript. The final version is available from the American Chemical Society via http://dx.doi.org/10.1021/jacs.5b0397

Attractiveness of periodic orbits in parametrically forced systemswith time-increasing friction

We consider dissipative one-dimensional systems subject to a periodic force and study numerically how a time-varying friction affects the dynamics. As a model system, particularly suited for numerical analysis, we investigate the driven cubic oscillator in the presence of friction. We find that, if the damping coefficient increases in time up to a final constant value, then the basins of attraction of the leading resonances are larger than they would have been if the coefficient had been fixed at that value since the beginning. From a quantitative point of view, the scenario depends both on the final value and the growth rate of the damping coefficient. The relevance of the results for the spin-orbit model are discussed in some detail.Comment: 30 pages, 6 figure

The moral discourses of ‘post-crisis’ neoliberalism: a case study of Lithuania’s Labour Code reform

This article problematizes the neoliberal reconfiguration of labour rights in Lithuania, a newer European Union member state, in which the impacts of the global economic and financial crisis were particularly severe and where radical austerity measures were subsequently imposed. Now, after six years, in an attempt to resolve the exhaustion of previous austerity-based solutions for economic recovery, a new Labour Code is being introduced which will further weaken labour protections and labour rights. This article analyses conflicting positions in current debates over Labour Code reform. It attempts to map the mobilization of strategic discursive resources in an unfolding dialogical ‘moral’ politics of Labour Code reform in the current conjuncture of ‘post- crisis’. Theoretically, this article draws upon the seminal work of the early Soviet Marxist scholar V. N. Voloshinov in proposing a dialogical method which foregrounds the interconnections of language, class and ideology

A monodisperse transmembrane α-helical peptide barrel

The fabrication of monodisperse transmembrane barrels formed from short synthetic peptides has not been demonstrated previously. This is in part because of the complexity of the interactions between peptides and lipids within the hydrophobic environment of a membrane. Here we report the formation of a transmembrane pore through the self-assembly of 35 amino acid α-helical peptides. The design of the peptides is based on the C-terminal D4 domain of the Escherichia coli polysaccharide transporter Wza. By using single-channel current recording, we define discrete assembly intermediates and show that the pore is most probably a helix barrel that contains eight D4 peptides arranged in parallel. We also show that the peptide pore is functional and capable of conducting ions and binding blockers. Such α-helix barrels engineered from peptides could find applications in nanopore technologies such as single-molecule sensing and nucleic-acid sequencing

Making or Breaking Metal- Dependent Catalytic Activity: The Role of Stammers in Designed Three- Stranded Coiled Coils

While many life- critical reactions would be infeasibly slow without metal cofactors, a detailed understanding of how protein structure can influence catalytic activity remains elusive. Using de novo designed three- stranded coiled coils (TRI and Grand peptides formed using a heptad repeat approach), we examine how the insertion of a three residue discontinuity, known as a stammer insert, directly adjacent to a (His)3 metal binding site alters catalytic activity. The stammer, which locally alters the twist of the helix, significantly increases copper- catalyzed nitrite reductase activity (CuNiR). In contrast, the well- established zinc- catalyzed carbonic anhydrase activity (p- nitrophenyl acetate, pNPA) is effectively ablated. This study illustrates how the perturbation of the protein sequence using non- coordinating and non- acid base residues in the helical core can perturb metalloenzyme activity through the simple expedient of modifying the helical pitch adjacent to the catalytic center.The addition of a stammer discontinuity within a de novo designed three- stranded coiled coil containing a symmetric (His)3 metal binding site enhances copper nitrite reductase activity and ablates zinc esterase activity. These results suggest catalytic activity of designed α- helical systems can be modulated by inclusion of discontinuity insertions and deletions.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/163477/3/ange202008356_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/163477/2/ange202008356-sup-0001-misc_information.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/163477/1/ange202008356.pd