Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function

The intrinsic ability of protein structures to exhibit the geometric features required for molecular function in the absence of evolution is examined in the context of three systems: the reference set of real, single domain protein structures, a library of computationally generated, compact homopolypeptides, artificial structures with protein-like secondary structural elements, and quasi-spherical random proteins packed at the same density as proteins but lacking backbone secondary structure and hydrogen bonding. Without any evolutionary selection, the library of artificial structures has similar backbone hydrogen bonding, global shape, surface to volume ratio and statistically significant structural matches to real protein global structures. Moreover, these artificial structures have native like ligand binding cavities, and a tiny subset has interfacial geometries consistent with native-like protein-protein interactions and DNA binding. In contrast, the quasi-spherical random proteins, being devoid of secondary structure, have a lower surface to volume ratio and lack ligand binding pockets and intermolecular interaction interfaces. Surprisingly, these quasi-spherical random proteins exhibit protein like distributions of virtual bond angles and almost all have a statistically significant structural match to real protein structures. This implies that it is local chain stiffness, even without backbone hydrogen bonding, and compactness that give rise to the likely completeness of the library solved single domain protein structures. These studies also suggest that the packing of secondary structural elements generates the requisite geometry for intermolecular binding. Thus, backbone hydrogen bonding plays an important role not only in protein structure but also in protein function. Such ability to bind biological molecules is an inherent feature of protein structure; if combined with appropriate protein sequences, it could provide the non-zero background probability for low-level function that evolution requires for selection to occur. © 2011 the Owner Societies

The Rise and Decline of Car Use in Beijing and Shanghai

Chinese cities have primarily evolved around walking, bicycling and public transport with their dense, linear form and mixed land use. The recent urban growth spurt has involved private motorisation, but because of land constraints and not fearing urban density, as in Anglo-Saxon cities, the same dense urbanism has been maintained. This means that automobiles do not easily fit into this traditional fabric and especially the historic walking fabric. Issues like congestion and air quality have become major constraints to further growth. Using Beijing and Shanghai as case studies, the next phase of urban and transport development now appears to be to reduce car use with the dramatic growth in urban rail as in most developed cities in the twenty-first century. This decoupling of car use from economic growth is consistent with other developed cities but is a first for emerging cities, hence the paper aims to explain this pattern from the cultural, political and especially urban fabric perspectives. The application to other Chinese cities and emerging cities is now possible following Beijing and Shanghai’s lead

Growth of a Giant: A Historical and Current Perspective on the Chinese Automobile Industry

The automobile industry in China has marched into its 5th decade since 1956 and in 2009 surpassed the USA as the giant of global automobile production and consumption. Rapidly increasing motorization in China exerts unprecedented economic, social, and environmental effects at home and abroad. This paper aims to provide a synoptic overview of the Chinese automobile industry, classifying it into four distinct phases, which are characterized by the prevailing institutional environments. These are the Start-up Phase from 1956 to 1978, Growing Phase from 1979 to 2001, Prosperity Phase from 2002 to 2010, and finally the Stationary Phase from 2011 until the present day. It analyses China’s national political, economic, trade, international relations and other factors and how these affected the development of the overall Chinese automobile industry, with a specific emphasis on the formulated and applied automobile industry policies. The dramatic growth in the automobile industry currently faces a potential period of decline as China’s latest industrial policies focus on alleviating the ownership and use of private vehicles, especially in its major cities due to severe congestion and other impacts. Thus, China has entered an era similar to other developed nations and cities, though it has made such economic changes at a speed and scale unparalleled in history

Magnetized black holes and black rings in the higher dimensional dilaton gravity

In this paper we consider magnetized black holes and black rings in the higher dimensional dilaton gravity. Our study is based on exact solutions generated by applying a Harrison transformation to known asymptotically flat black hole and black ring solutions in higher dimensional spacetimes. The explicit solutions include the magnetized version of the higher dimensional Schwarzschild-Tangherlini black holes, Myers-Perry black holes and five dimensional (dipole) black rings. The basic physical quantities of the magnetized objects are calculated. We also discuss some properties of the solutions and their thermodynamics. The ultrarelativistic limits of the magnetized solutions are briefly discussed and an explicit example is given for the $D$-dimensional magnetized Schwarzschild-Tangherlini black holes.Comment: LaTeX, 23 pages; v2 references and comments added, some typos corrected;v3 minor change