A comprehensive basis for determining the allocation of urban street space

There are many competing demands for the use of urban street space, but very little comprehensive research or guidance on how to allocate space between these various street user groups. Most guidance focuses on transport and is mode-specific (e.g. cycling, loading), with very little consideration being given to on-street activities (e.g. sitting or socialising), and space allocations are usually determined on the basis of political priorities (e.g. the needs of buses or cyclists have priority). The objective of this paper is to set out a more comprehensive framework for determining street user needs, taking into account both the Link/Movement and Place functions of urban streets. It considers some of the ways in which these can be met in different contexts, how competing demands might be reconciled and sets out different bases upon which decisions over final space allocations might be taken. It draws on several research projects and includes examples from different English cites

The nucleotide-free state of the multidrug resistance ABC transporter LmrA: Sulfhydryl cross-linking supports a constant contact, head-to-tail configuration of the nucleotide-binding domains

© 2015 Jones, George. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABC transporters are integral membrane pumps that are responsible for the import or export of a diverse range of molecules across cell membranes. ABC transporters have been implicated in many phenomena of medical importance, including cystic fibrosis and multidrug resistance in humans. The molecular architecture of ABC transporters comprises two transmembrane domains and two ATP-binding cassettes, or nucleotide-binding domains (NBDs), which are highly conserved and contain motifs that are crucial to ATP binding and hydrolysis. Despite the improved clarity of recent structural, biophysical, and biochemical data, the seemingly simple process of ATP binding and hydrolysis remains controversial, with a major unresolved issue being whether the NBD protomers separate during the catalytic cycle. Here chemical cross-linking data is presented for the bacterial ABC multidrug resistance (MDR) transporter LmrA. These indicate that in the absence of nucleotide or substrate, the NBDs come into contact to a significant extent, even at 4°C, where ATPase activity is abrogated. The data are clearly not in accord with an inward-closed conformation akin to that observed in a crystal structure of V. cholerae MsbA. Rather, they suggest a head-to-tail configuration 'sandwich' dimer similar to that observed in crystal structures of nucleotide-bound ABC NBDs. We argue the data are more readily reconciled with the notion that the NBDs are in proximity while undergoing intra-domain motions, than with an NBD 'Switch' mechanism in which the NBD monomers separate in between ATP hydrolysis cycles

An Asymmetric Post-Hydrolysis State of the ABC Transporter ATPase Dimer

ABC transporters are a superfamily of enzyme pumps that hydrolyse ATP in exchange for translocation of substrates across cellular membranes. Architecturally, ABC transporters are a dimer of transmembrane domains coupled to a dimer of nucleotide binding domains (NBDs): the NBD dimer contains two ATP-binding sites at the intersubunit interface. A current controversy is whether the protomers of the NBD dimer separate during ATP hydrolysis cycling, or remain in constant contact. In order to investigate the ABC ATPase catalytic mechanism, MD simulations using the recent structure of the ADP+Pi-bound MJ0796 isolated NBD dimer were performed. In three independent simulations of the ADP+Pi/apo state, comprising a total of >0.5 μs, significant opening of the apo (empty) active site was observed; occurring by way of intrasubunit rotations between the core and helical subdomains within both NBD monomers. In contrast, in three equivalent simulations of the ATP/apo state, the NBD dimer remained close to the crystal structure, and no opening of either active site occurred. The results thus showed allosteric coupling between the active sites, mediated by intrasubunit conformational changes. Opening of the apo site is exquisitely tuned to the nature of the ligand, and thus to the stage of the reaction cycle, in the opposite site. In addition to this, in also showing how one active site can open, sufficient to bind nucleotide, while the opposite site remains occluded and bound to the hydrolysis products ADP+Pi, the results are consistent with a Constant Contact Model. Conversely, they show how there may be no requirement for the NBD protomers to separate to complete the catalytic cycle. © 2013 Jones, George

The effectiveness of changes in street layout and design for reducing barriers to walking

This study analyses the effectiveness of two types of interventions to reduce built environment barriers to walking: changing the layout of the local street network (by increasing the density and connectivity of the links available to pedestrians) and redesigning a busy road (by adding crossing facilities, reducing speed limit, or reallocating road space to pedestrians). The analysis focuses on a residential neighbourhood in London which is being extensively redeveloped. The anticipated effects of the interventions are assessed in terms of the distance, delay, safety, and environmental quality of walking trips from residences to public transport nodes. The study also addresses methodological issues, by modelling the off-street space available to pedestrians and considering alternative hypotheses for pedestrian route choice. The results show that changes to the street layout always reduce delay and improve the pedestrian environment, although they may increase trip distances and collision risk. Adding crossing facilities reduces risk but do not decrease delay, while reducing the number of vehicle lanes reduces distance and delay but may increase risk. All types of intervention improve the pedestrian environment, even in the cases of routes chosen to minimize delay or exposure to traffic

Street Mobility Project: Video surveys

The Street Mobility toolkit provides a set of tools that can be used by practitioners, local communities, and others, to assess and value the costs of the 'barrier effect' of roads. This document describes how to use video surveys to who uses busy roads, when, and how. The comparison of the actual pedestrian flows along different roads with what might be expected from walkability models can give an indication of places that pedestrians avoid. These may indicate where action is needed to improve the conditions for pedestrians and to facilitate more walking for travel in the area. The data collected can also be used to identify particular problems faced by pedestrians at different times of the day, which may be related to variations in the levels or types of motor traffic

Computational analysis of the MCoTI-II plant defence knottin reveals a novel intermediate conformation that facilitates trypsin binding

MCoTI-I and II are plant defence proteins, potent trypsin inhibitors from the bitter gourd Momordica cochinchinensis. They are members of the Knottin Family, which display exceptional stability due to unique topology comprising three interlocked disulfide bridges. Knottins show promise as scaffolds for new drug development. A crystal structure of trypsin-bound MCoTI-II suggested that loop 1, which engages the trypsin active site, would show decreased dynamics in the bound state, an inference at odds with an NMR analysis of MCoTI-I, which revealed increased dynamics of loop 1 in the presence of trypsin. To investigate this question, we performed unrestrained MD simulations of trypsin-bound and free MCoTI-II. This analysis found that loop 1 of MCoTI-II is not more dynamic in the trypsin-bound state than in the free state. However, it revealed an intermediate conformation, transitional between the free and bound MCoTI-II states. The data suggest that MCoTI-II binding involves a process in which initial interaction with trypsin induces transitions between the free and intermediate conformations, and fluctuations between these states account for the increase in dynamics of loop 1 observed for trypsin-bound MCoTI-I. The MD analysis thus revealed new aspects of the inhibitors dynamics that may be of utility in drug design